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Sample records for biochemical analysis suggests

  1. Probabilistic sensitivity analysis of biochemical reaction systems.

    Science.gov (United States)

    Zhang, Hong-Xuan; Dempsey, William P; Goutsias, John

    2009-09-07

    Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical.

  2. Thermodynamic analysis of biochemical systems

    International Nuclear Information System (INIS)

    Yuan, Y.; Fan, L.T.; Shieh, J.H.

    1989-01-01

    Introduction of the concepts of the availability (or exergy), datum level materials, and the dead state has been regarded as some of the most significant recent developments in classical thermodynamics. Not only the available energy balance but also the material and energy balances of a biological system may be established in reference to the datum level materials in the dead state or environment. In this paper these concepts are illustrated with two examples of fermentation and are shown to be useful in identifying sources of thermodynamic inefficiency, thereby leading naturally to the rational definition of thermodynamic efficiency of a biochemical process

  3. Applied spectrophotometry: analysis of a biochemical mixture.

    Science.gov (United States)

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. Copyright © 2013 Wiley Periodicals, Inc.

  4. Skin biochemical composition analysis by Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Patricia Karen; Tosato, Maira Gaspar; Alves, Rani de Souza; Martin, Airton Abrahao; Favero, Priscila Pereira; Raniero, Leandro, E-mail: amartin@univap.br [Laboratorio de Espectroscopia Vibracional Biomedica, Instituto de Pesquisa e Desenvolvimento - IP e D, Universidade do Vale do Paraiba - UniVap, Sao Jose dos Campos, SP (Brazil)

    2012-09-15

    Skin aging is characterized by cellular and molecular alterations. In this context, Confocal Raman spectroscopy was used in vivo to measure these biochemical changes as function of the skin depth. In this study we have tried to correlate spectra from pure amino acids to in vivo spectra from volunteers with different ages. This study was performed on 32 volunteers: 11 from Group A (20-23 years), 11 from Group B (39-42 years) and 10 from Group C (59-62 years). For each group, the Raman spectra were measured on the surface (0 mm), 30 +- 3 mm and 60 +- 3 {mu}m below the surface. The results from intergroup comparisons showed that the oldest group had a prevalence of the tyrosine band, but it also presented a decrease in the band centered at 875 cm{sup -1} of pyrrolidone acid. The amide I band centered at 1637 cm{sup -1} that is attributed to collagen, as well as other proteins and lipid, showed a smaller amount of these biomolecules for Group C, which can be explained by the decrease in collagen concentration as a function of age. (author)

  5. Interferon-β treatment associated with a biochemical profile suggestive of acromegaly. A case report of a patient treated for multiple sclerosis

    DEFF Research Database (Denmark)

    Andreassen, Mikkel; Frystyk, Jan; Miller, Karen K

    2010-01-01

    We describe a 34-year-old female treated with IFN-ß for 8 years with a biochemical profile suggestive of acromegaly. The patient presented with elevated serum insulin-like growth factor-I (IGF-I) and insufficient suppression of growth hormone (GH) during oral glucose tolerance test (OGTT). There ......-I. In conclusion, IFN-ß treatment mimicked acromegaly biochemically. The changes were partially reversible....

  6. Interferon-β treatment associated with a biochemical profile suggestive of acromegaly. A case report of a patient treated for multiple sclerosis

    DEFF Research Database (Denmark)

    Andreassen, Mikkel; Frystyk, Jan; Miller, Karen K

    2010-01-01

    We describe a 34-year-old female treated with IFN-β for 8 years with a biochemical profile suggestive of acromegaly. The patient presented with elevated serum insulin-like growth factor-I (IGF-I) and insufficient suppression of growth hormone (GH) during oral glucose tolerance test (OGTT). There ......-I. In conclusion, IFN-β treatment mimicked acromegaly biochemically. The changes were partially reversible....

  7. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    admin

    Biochemical analysis of aroma was performed with the 1.7% KOH solution and molecular analysis of aroma was carried out with microsatellite markers present on chromosome 8 (BAD2, BADEX7-5, SCUSSR1) to determine the extent of association between trait, marker and chromosome 8. Among these markers, BAD2 ...

  8. Biochemical and cytological analysis of five cultivars of Cicer ...

    African Journals Online (AJOL)

    SAM

    2014-03-12

    Mar 12, 2014 ... variability and relatedness, seed storage protein analysis represents a valid alternative to ... Indian Institute of Pulse Research, Kanpur (U.P.) India. During the present study, five accessions were used for biochemical and cytological analysis. The details of five ... using pestle and mortar. 500 ml of protein ...

  9. Leigh-Like Syndrome Due to Homoplasmic m.8993T>G Variant with Hypocitrullinemia and Unusual Biochemical Features Suggestive of Multiple Carboxylase Deficiency (MCD).

    Science.gov (United States)

    Balasubramaniam, Shanti; Lewis, B; Mock, D M; Said, H M; Tarailo-Graovac, M; Mattman, A; van Karnebeek, C D; Thorburn, D R; Rodenburg, R J; Christodoulou, J

    2017-01-01

    Leigh syndrome (LS), or subacute necrotizing encephalomyelopathy, is a genetically heterogeneous, relentlessly progressive, devastating neurodegenerative disorder that usually presents in infancy or early childhood. A diagnosis of Leigh-like syndrome may be considered in individuals who do not fulfil the stringent diagnostic criteria but have features resembling Leigh syndrome.We describe a unique presentation of Leigh-like syndrome in a 3-year-old boy with elevated 3-hydroxyisovalerylcarnitine (C5-OH) on newborn screening (NBS). Subsequent persistent plasma elevations of C5-OH and propionylcarnitine (C3) as well as fluctuating urinary markers were suggestive of multiple carboxylase deficiency (MCD). Normal enzymology and mutational analysis of genes encoding holocarboxylase synthetase (HLCS) and biotinidase (BTD) excluded MCD. Biotin uptake studies were normal excluding biotin transporter deficiency. His clinical features at 13 months of age comprised psychomotor delay, central hypotonia, myopathy, failure to thrive, hypocitrullinemia, recurrent episodes of decompensation with metabolic keto-lactic acidosis and an episode of hyperammonemia. Biotin treatment from 13 months of age was associated with increased patient activity, alertness, and attainment of new developmental milestones, despite lack of biochemical improvements. Whole exome sequencing (WES) analysis failed to identify any other variants which could likely contribute to the observed phenotype, apart from the homoplasmic (100%) m.8993T>G variant initially detected by mitochondrial DNA (mtDNA) sequencing.Hypocitrullinemia has been reported in patients with the m.8993T>G variant and other mitochondrial disorders. However, persistent plasma elevations of C3 and C5-OH have previously only been reported in one other patient with this homoplasmic mutation. We suggest considering the m.8993T>G variant early in the diagnostic evaluation of MCD-like biochemical disturbances, particularly when associated with

  10. Applied Spectrophotometry: Analysis of a Biochemical Mixture

    Science.gov (United States)

    Trumbo, Toni A.; Schultz, Emeric; Borland, Michael G.; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the…

  11. Study on color difference estimation method of medicine biochemical analysis

    Science.gov (United States)

    Wang, Chunhong; Zhou, Yue; Zhao, Hongxia; Sun, Jiashi; Zhou, Fengkun

    2006-01-01

    The biochemical analysis in medicine is an important inspection and diagnosis method in hospital clinic. The biochemical analysis of urine is one important item. The Urine test paper shows corresponding color with different detection project or different illness degree. The color difference between the standard threshold and the test paper color of urine can be used to judge the illness degree, so that further analysis and diagnosis to urine is gotten. The color is a three-dimensional physical variable concerning psychology, while reflectance is one-dimensional variable; therefore, the estimation method of color difference in urine test can have better precision and facility than the conventional test method with one-dimensional reflectance, it can make an accurate diagnose. The digital camera is easy to take an image of urine test paper and is used to carry out the urine biochemical analysis conveniently. On the experiment, the color image of urine test paper is taken by popular color digital camera and saved in the computer which installs a simple color space conversion (RGB -> XYZ -> L *a *b *)and the calculation software. Test sample is graded according to intelligent detection of quantitative color. The images taken every time were saved in computer, and the whole illness process will be monitored. This method can also use in other medicine biochemical analyses that have relation with color. Experiment result shows that this test method is quick and accurate; it can be used in hospital, calibrating organization and family, so its application prospect is extensive.

  12. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    For molecular and biochemical analysis of aroma, a mapping population comprising 208 recombinant inbred lines (RILs) derived from a diverse cross between CSR10 and Taraori Basmati through Single seed descent (SSD) method was used. RILs are among the best mapping populations, which provide a novel material ...

  13. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-11-01

    Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

  14. Interferon-beta treatment associated with a biochemical profile suggestive of acromegaly. A case report of a patient treated for multiple sclerosis

    DEFF Research Database (Denmark)

    Andreassen, Mikkel; Frystyk, Jan; Miller, K.K.

    2010-01-01

    We describe a 34-year-old female treated with IFN-beta for 8 years with a biochemical profile suggestive of acromegaly. The patient presented with elevated serum insulin-like growth factor-I (IGF-I) and insufficient suppression of growth hormone (GH) during oral glucose tolerance test (OGTT......). There were no clinical features of acromegaly. A 5-day profile showed higher GH levels on the 3 days following IFN-beta injections. Total and bioactive IGF-I were also elevated but did not fluctuate. Four weeks off IFN-beta normalized suppression of GH during OGTT but did not reduce serum IGF-I or bioactive...... IGF-I. In conclusion, IFN-beta treatment mimicked acromegaly biochemically. The changes were partially reversible...

  15. Genomic analysis suggests higher susceptibility of children to air pollution

    DEFF Research Database (Denmark)

    van Leeuwen, Danitsja M; Pedersen, Marie; Hendriksen, Peter J M

    2008-01-01

    modulated gene expressions. In addition, gene expressions in both children and adults were investigated for associations with micronuclei frequencies. Both analysis approaches returned considerably more genes or gene groups and pathways that significantly differed between children from both regions than......Differences in biological responses to exposure to hazardous airborne substances between children and adults have been reported, suggesting children to be more susceptible. Aim of this study was to improve our understanding of differences in susceptibility in cancer risk associated with air...... pollution by comparing genome-wide gene expression profiles in peripheral blood of children and their parents. Gene expression analysis was performed in blood from children and parents living in two different regions in the Czech Republic with different levels of air pollution. Data were analyzed by two...

  16. Biochemical analysis of force-sensitive responses using a large-scale cell stretch device.

    Science.gov (United States)

    Renner, Derrick J; Ewald, Makena L; Kim, Timothy; Yamada, Soichiro

    2017-09-03

    Physical force has emerged as a key regulator of tissue homeostasis, and plays an important role in embryogenesis, tissue regeneration, and disease progression. Currently, the details of protein interactions under elevated physical stress are largely missing, therefore, preventing the fundamental, molecular understanding of mechano-transduction. This is in part due to the difficulty isolating large quantities of cell lysates exposed to force-bearing conditions for biochemical analysis. We designed a simple, easy-to-fabricate, large-scale cell stretch device for the analysis of force-sensitive cell responses. Using proximal biotinylation (BioID) analysis or phospho-specific antibodies, we detected force-sensitive biochemical changes in cells exposed to prolonged cyclic substrate stretch. For example, using promiscuous biotin ligase BirA* tagged α-catenin, the biotinylation of myosin IIA increased with stretch, suggesting the close proximity of myosin IIA to α-catenin under a force bearing condition. Furthermore, using phospho-specific antibodies, Akt phosphorylation was reduced upon stretch while Src phosphorylation was unchanged. Interestingly, phosphorylation of GSK3β, a downstream effector of Akt pathway, was also reduced with stretch, while the phosphorylation of other Akt effectors was unchanged. These data suggest that the Akt-GSK3β pathway is force-sensitive. This simple cell stretch device enables biochemical analysis of force-sensitive responses and has potential to uncover molecules underlying mechano-transduction.

  17. Faecal analysis suggests generalist diets in three species of ...

    African Journals Online (AJOL)

    The overlap in other arthropod taxa ingested was low across species and seasons, suggesting an opportunistic component to their foraging behaviour. We distinguished plant matter in faecal samples of all species in all seasons, reflecting either voluntary or accidental ingestion. The results of this study suggest that the ...

  18. Analysis of existing risk assessments, and list of suggestions

    CERN Document Server

    Heimsch, Laura

    2016-01-01

    The scope of this project was to analyse risk assessments made at CERN and extracting some crucial information about the different methodologies used, profiles of people who make the risk assessments, and gathering information of whether the risk matrix was used and if the acceptable level of risk was defined. Second step of the project was to trigger discussion inside HSE about risk assessment by suggesting a risk matrix and a risk assessment template.

  19. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions

    DEFF Research Database (Denmark)

    Pendle, Alison F; Clark, Gillian P; Boon, Reinier

    2005-01-01

    The eukaryotic nucleolus is involved in ribosome biogenesis and a wide range of other RNA metabolism and cellular functions. An important step in the functional analysis of the nucleolus is to determine the complement of proteins of this nuclear compartment. Here, we describe the first proteomic ...

  20. Infants' brain responses to speech suggest analysis by synthesis.

    Science.gov (United States)

    Kuhl, Patricia K; Ramírez, Rey R; Bosseler, Alexis; Lin, Jo-Fu Lotus; Imada, Toshiaki

    2014-08-05

    Historic theories of speech perception (Motor Theory and Analysis by Synthesis) invoked listeners' knowledge of speech production to explain speech perception. Neuroimaging data show that adult listeners activate motor brain areas during speech perception. In two experiments using magnetoencephalography (MEG), we investigated motor brain activation, as well as auditory brain activation, during discrimination of native and nonnative syllables in infants at two ages that straddle the developmental transition from language-universal to language-specific speech perception. Adults are also tested in Exp. 1. MEG data revealed that 7-mo-old infants activate auditory (superior temporal) as well as motor brain areas (Broca's area, cerebellum) in response to speech, and equivalently for native and nonnative syllables. However, in 11- and 12-mo-old infants, native speech activates auditory brain areas to a greater degree than nonnative, whereas nonnative speech activates motor brain areas to a greater degree than native speech. This double dissociation in 11- to 12-mo-old infants matches the pattern of results obtained in adult listeners. Our infant data are consistent with Analysis by Synthesis: auditory analysis of speech is coupled with synthesis of the motor plans necessary to produce the speech signal. The findings have implications for: (i) perception-action theories of speech perception, (ii) the impact of "motherese" on early language learning, and (iii) the "social-gating" hypothesis and humans' development of social understanding.

  1. Biochemical analysis of CTLA-4 immunoreactive material from human blood

    Directory of Open Access Journals (Sweden)

    Dennert Kate

    2009-09-01

    Full Text Available Abstract Background CTLA-4 was initially described as a membrane-bound molecule that inhibited lymphocyte activation by interacting with B7.1 and B7.2 molecules on antigen presenting cells. Alternative splicing of mRNA encoding the CTLA-4 receptor leads to the production of a molecule (sCTLA-4 that lacks a membrane anchor and is therefore secreted into the extracellular space. Despite studies finding that people with autoimmune disease more frequently express high levels of sCTLA-4 in their blood than apparently healthy people, the significance of these findings is unclear. Methods Molecules isolated from blood using CTLA-4 specific antibodies were analyzed with ligand binding assays, mass spectroscopy, and biochemical fractionation in an effort to increase our understanding of CTLA-4 immunoreactive material. Results Mass spectroscopy analysis of the molecules recognized by multiple CTLA-4-specific antibodies failed to identify any CTLA-4 protein. Even though these molecules bind to the CTLA-4 receptors B7.1 and B7.2, they also exhibit properties common to immunoglobulins. Conclusion We have identified molecules in blood that are recognized by CTLA-4 specific antibodies but also exhibit properties of immunoglobulins. Our data indicates that what has been called sCTLA-4 is not a direct product of the CTLA-4 gene, and that the CTLA-4 protein is not part of this molecule. These results may explain why the relationship of sCTLA-4 to immune system activity has been difficult to elucidate.

  2. Imminent Cardiac Risk Assessment via Optical Intravascular Biochemical Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wetzel, D.; Wetzel, L; Wetzel, M; Lodder, R

    2009-01-01

    Heart disease is by far the biggest killer in the United States, and type II diabetes, which affects 8% of the U.S. population, is on the rise. In many cases, the acute coronary syndrome and/or sudden cardiac death occurs without warning. Atherosclerosis has known behavioral, genetic and dietary risk factors. However, our laboratory studies with animal models and human post-mortem tissue using FT-IR microspectroscopy reveal the chemical microstructure within arteries and in the arterial walls themselves. These include spectra obtained from the aortas of ApoE-/- knockout mice on sucrose and normal diets showing lipid deposition in the former case. Also pre-aneurysm chemical images of knockout mouse aorta walls, and spectra of plaque excised from a living human patient are shown for comparison. In keeping with the theme of the SPEC 2008 conference Spectroscopic Diagnosis of Disease this paper describes the background and potential value of a new catheter-based system to provide in vivo biochemical analysis of plaque in human coronary arteries. We report the following: (1) results of FT-IR microspectroscopy on animal models of vascular disease to illustrate the localized chemical distinctions between pathological and normal tissue, (2) current diagnostic techniques used for risk assessment of patients with potential unstable coronary syndromes, and (3) the advantages and limitations of each of these techniques illustrated with patent care histories, related in the first person, by the physician coauthors. Note that the physician comments clarify the contribution of each diagnostic technique to imminent cardiac risk assessment in a clinical setting, leading to the appreciation of what localized intravascular chemical analysis can contribute as an add-on diagnostic tool. The quality of medical imaging has improved dramatically since the turn of the century. Among clinical non-invasive diagnostic tools, laboratory tests of body fluids, EKG, and physical examination are

  3. Energy analysis of biochemical conversion processes of biomass to bioethanol

    Energy Technology Data Exchange (ETDEWEB)

    Bakari, M.; Ngadi, M.; Bergthorson, T. [McGill Univ., Ste-Anne-de-Bellevue, PQ (Canada). Dept. of Bioresource Engineering

    2010-07-01

    Bioethanol is among the most promising of biofuels that can be produced from different biomass such as agricultural products, waste and byproducts. This paper reported on a study that examined the energy conversion of different groups of biomass to bioethanol, including lignocelluloses, starches and sugar. Biochemical conversion generally involves the breakdown of biomass to simple sugars using different pretreatment methods. The energy needed for the conversion steps was calculated in order to obtain mass and energy efficiencies for the conversions. Mass conversion ratios of corn, molasses and rice straw were calculated as 0.3396, 0.2300 and 0.2296 kg of bioethanol per kg of biomass, respectively. The energy efficiency of biochemical conversion of corn, molasses and rice straw was calculated as 28.57, 28.21 and 31.33 per cent, respectively. The results demonstrated that lignocelluloses can be efficiently converted with specific microorganisms such as Mucor indicus, Rhizopus oryzae using the Simultaneous Saccharification and Fermentation (SSF) methods.

  4. Fourier transform infrared microspectroscopy for the analysis of the biochemical composition of C. elegans worms.

    Science.gov (United States)

    Sheng, Ming; Gorzsás, András; Tuck, Simon

    2016-01-01

    Changes in intermediary metabolism have profound effects on many aspects of C. elegans biology including growth, development and behavior. However, many traditional biochemical techniques for analyzing chemical composition require relatively large amounts of starting material precluding the analysis of mutants that cannot be grown in large amounts as homozygotes. Here we describe a technique for detecting changes in the chemical compositions of C. elegans worms by Fourier transform infrared microspectroscopy. We demonstrate that the technique can be used to detect changes in the relative levels of carbohydrates, proteins and lipids in one and the same worm. We suggest that Fourier transform infrared microspectroscopy represents a useful addition to the arsenal of techniques for metabolic studies of C. elegans worms.

  5. Crystallographic and biochemical analysis of the mouse poly(ADP-ribose glycohydrolase.

    Directory of Open Access Journals (Sweden)

    Zhizhi Wang

    Full Text Available Protein poly(ADP-ribosylation (PARylation regulates a number of important cellular processes. Poly(ADP-ribose glycohydrolase (PARG is the primary enzyme responsible for hydrolyzing the poly(ADP-ribose (PAR polymer in vivo. Here we report crystal structures of the mouse PARG (mPARG catalytic domain, its complexes with ADP-ribose (ADPr and a PARG inhibitor ADP-HPD, as well as four PARG catalytic residues mutants. With these structures and biochemical analysis of 20 mPARG mutants, we provide a structural basis for understanding how the PAR polymer is recognized and hydrolyzed by mPARG. The structures and activity complementation experiment also suggest how the N-terminal flexible peptide preceding the PARG catalytic domain may regulate the enzymatic activity of PARG. This study contributes to our understanding of PARG catalytic and regulatory mechanisms as well as the rational design of PARG inhibitors.

  6. Loss of Niemann-Pick C1 or C2 protein results in similar biochemical changes suggesting that these proteins function in a common lysosomal pathway.

    Directory of Open Access Journals (Sweden)

    Sayali S Dixit

    Full Text Available Niemann-Pick Type C (NPC disease is a lysosomal storage disorder characterized by accumulation of unesterified cholesterol and other lipids in the endolysosomal system. NPC disease results from a defect in either of two distinct cholesterol-binding proteins: a transmembrane protein, NPC1, and a small soluble protein, NPC2. NPC1 and NPC2 are thought to function closely in the export of lysosomal cholesterol with both proteins binding cholesterol in vitro but they may have unrelated lysosomal roles. To investigate this possibility, we compared biochemical consequences of the loss of either protein. Analyses of lysosome-enriched subcellular fractions from brain and liver revealed similar decreases in buoyant densities of lysosomes from NPC1 or NPC2 deficient mice compared to controls. The subcellular distribution of both proteins was similar and paralleled a lysosomal marker. In liver, absence of either NPC1 or NPC2 resulted in similar alterations in the carbohydrate processing of the lysosomal protease, tripeptidyl peptidase I. These results highlight biochemical alterations in the lysosomal system of the NPC-mutant mice that appear secondary to lipid storage. In addition, the similarity in biochemical phenotypes resulting from either NPC1 or NPC2 deficiency supports models in which the function of these two proteins within lysosomes are linked closely.

  7. Ultraviolet inactivation of avian sarcoma virus: biological and biochemical analysis

    International Nuclear Information System (INIS)

    Owada, M.; Ihara, S.; Toyoshima, K.; Kozai, Y.; Sugino, Y.

    1976-01-01

    The rate of inactivation by ultraviolet light of the focus-forming capacity of avian sarcoma virus was almost the same as that of the virus-producing capacity, measured as plaque formation. In addition, no significant difference was observed in inactivation of the transforming capacity assayed on C/BE chick embryo fibroblasts (CEF), which carry endogenous avian tumor virus DNA, and on duck embryo fibroblasts (DEF), which are known to be devoid of this DNA. All foci induced by nonirradiated virus produced infectious sarcoma virus, but some of the foci induced by uv-irradiated virus did not produce infectious virus of either transforming or transformation-defective type. The proportion of nonproducer foci was 3.4 times more in DEF than in gs - chf - CEF. RNAs extracted from uv-irradiated virions by sodium dodecyl sulfate (SDS) treatment were found to be composed of 60--70 S and 4 S RNAs by analysis in a sucrose gradient containing 0.5 percent SDS. The large RNA, however, became hydrophobic after irradiation and was sedimented with SDS by addition of one drop of saturated potassium chloride solution. This RNA was not dissociated into 30--40S components by heating at 100 0 for 45 sec, unlike 60--70 S RNA from uv-irradiated virions. After SDS--Pronase treatment, the 60--70 S RNA from uv-irradiated virions no longer had these altered characteristics. Reverse transcriptase activity with the endogenous template decreased in parallel with increase in the uv dose. The reduction rate was similar to that assayed with exogenous template or in the presence of actinomycin D. These data strongly suggest that RNA damage is not the only cause of virus inactivation by uv light

  8. A modular microfluidic architecture for integrated biochemical analysis.

    Science.gov (United States)

    Shaikh, Kashan A; Ryu, Kee Suk; Goluch, Edgar D; Nam, Jwa-Min; Liu, Juewen; Thaxton, C Shad; Chiesl, Thomas N; Barron, Annelise E; Lu, Yi; Mirkin, Chad A; Liu, Chang

    2005-07-12

    Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb(2+) (lead) at a sensitivity of 500 nM in <1 nl of solution.

  9. Validation of EIA sampling methods - bacterial and biochemical analysis

    Digital Repository Service at National Institute of Oceanography (India)

    Sheelu, G.; LokaBharathi, P.A.; Nair, S.; Raghukumar, C.; Mohandass, C.

    to temporal factors. Paired T-test between pre- and post-disturbance samples suggested that the above methods of sampling and variables like TC, protein and TOC could be used for monitoring disturbance....

  10. Integration of electrochemistry in micro-total analysis systems for biochemical assays: recent developments.

    Science.gov (United States)

    Xu, Xiaoli; Zhang, Song; Chen, Hui; Kong, Jilie

    2009-11-15

    Micro-total analysis systems (microTAS) integrate different analytical operations like sample preparation, separation and detection into a single microfabricated device. With the outstanding advantages of low cost, satisfactory analytical efficiency and flexibility in design, highly integrated and miniaturized devices from the concept of microTAS have gained widespread applications, especially in biochemical assays. Electrochemistry is shown to be quite compatible with microanalytical systems for biochemical assays, because of its attractive merits such as simplicity, rapidity, high sensitivity, reduced power consumption, and sample/reagent economy. This review presents recent developments in the integration of electrochemistry in microdevices for biochemical assays. Ingenious microelectrode design and fabrication methods, and versatility of electrochemical techniques are involved. Practical applications of such integrated microsystem in biochemical assays are focused on in situ analysis, point-of-care testing and portable devices. Electrochemical techniques are apparently suited to microsystems, since easy microfabrication of electrochemical elements and a high degree of integration with multi-analytical functions can be achieved at low cost. Such integrated microsystems will play an increasingly important role for analysis of small volume biochemical samples. Work is in progress toward new microdevice design and applications.

  11. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory

    Directory of Open Access Journals (Sweden)

    Qian Hong

    2008-05-01

    Full Text Available Abstract Background: Several approaches, including metabolic control analysis (MCA, flux balance analysis (FBA, correlation metric construction (CMC, and biochemical circuit theory (BCT, have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results: In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RT BS and ST BS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion: One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA.

  12. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  13. Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans

    NARCIS (Netherlands)

    Kruse, T.; Pas, van de B.A.; Atteia, A.; Krab, K.; Hagen, W.R.; Goodwin, L.; Chain, P.; Boeren, S.; Maphosa, F.; Schraa, G.; Vos, de W.M.; Oost, van der J.; Smidt, H.; Stams, A.J.M.

    2015-01-01

    Desulfitobacterium dehalogenans is able to grow by organohalide respiration using 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) as an electron acceptor. We used a combination of genome sequencing, biochemical analysis of redox active components and shotgun proteomics to study elements of the

  14. Biochemical Cardiovascular Risk Factors After Hypertensive Pregnancy Disorders: A Systematic Review and Meta-analysis

    NARCIS (Netherlands)

    Hermes, W.; Ket, J.C.; Pampus, M.G. van; Franx, A.; Veenendaal, M.V.; Kolster, C.; Tamsma, J.T.; Bloemenkamp, K.W.; Ponjee, G.; van der Hout, E.; Ten Horn, H.; Loix, S.; Mol, B.W.; Groot, C.J. de

    2012-01-01

    The objective of this study was to perform a systematic review and meta-analysis of studies assessing biochemical cardiovascular risk factors in women with previous hypertensive pregnancy disorders and women with previous normotensive pregnancies. Data were collected from PubMed and EMBASE (from

  15. Biochemical Cardiovascular Risk Factors After Hypertensive Pregnancy Disorders : A Systematic Review and Meta-analysis

    NARCIS (Netherlands)

    Hermes, Wietske; Ket, Johannes C. F.; van Pampus, Maria G.; Franx, Arie; Veenendaal, Marjolein V. E.; Kolster, Clara; Tamsma, Jouke T.; Bloemenkamp, Kitty W. M.; Ponjee, Gabrielle; van der Hout, Evelien; ten Horn, Hilde; Loix, Stephanie; Mol, Ben Willem; de Groot, Christianne J. M.

    2012-01-01

    The objective of this study was to perform a systematic review and meta-analysis of studies assessing biochemical cardiovascular risk factors in women with previous hypertensive pregnancy disorders and women with previous normotensive pregnancies. Data were collected from PubMed and EMBASE (from

  16. Molecular and Biochemical Analysis of Chalcone Synthase from Freesia hybrid in flavonoid biosynthetic pathway.

    Directory of Open Access Journals (Sweden)

    Wei Sun

    Full Text Available Chalcone synthase (CHS catalyzes the first committed step in the flavonoid biosynthetic pathway. In this study, the cDNA (FhCHS1 encoding CHS from Freesia hybrida was successfully isolated and analyzed. Multiple sequence alignments showed that both the conserved CHS active site residues and CHS signature sequence were found in the deduced amino acid sequence of FhCHS1. Meanwhile, crystallographic analysis revealed that protein structure of FhCHS1 is highly similar to that of alfalfa CHS2, and the biochemical analysis results indicated that it has an enzymatic role in naringenin biosynthesis. Moreover, quantitative real-time PCR was performed to detect the transcript levels of FhCHS1 in flowers and different tissues, and patterns of FhCHS1 expression in flowers showed significant correlation to the accumulation patterns of anthocyanin during flower development. To further characterize the functionality of FhCHS1, its ectopic expression in Arabidopsis thaliana tt4 mutants and Petunia hybrida was performed. The results showed that overexpression of FhCHS1 in tt4 mutants fully restored the pigmentation phenotype of the seed coats, cotyledons and hypocotyls, while transgenic petunia expressing FhCHS1 showed flower color alteration from white to pink. In summary, these results suggest that FhCHS1 plays an essential role in the biosynthesis of flavonoid in Freesia hybrida and may be used to modify the components of flavonoids in other plants.

  17. Sucrose accumulation in watermelon fruits: genetic variation and biochemical analysis.

    Science.gov (United States)

    Yativ, Merav; Harary, Idan; Wolf, Shmuel

    2010-05-15

    Sugar accumulation, the key process determining fruit quality, is controlled by both the translocation of sugars and their metabolism in developing fruits. Sugar composition in watermelon, as in all cucurbit fruits, includes sucrose, fructose and glucose. The proportions of these three sugars are determined primarily by three enzyme families: invertases, sucrose synthases (SuSys) and sucrose phosphate synthases (SPSs). The goal of the present research was to explore the process of sugar metabolism in watermelon fruits. Crosses between the domestic watermelon (Citrullus lanatus) and three wild species provided a wide germplasm to explore genetic variability in sugar composition and metabolism. This survey demonstrated great genetic variability in sugar content and in the proportions of sucrose, glucose and fructose in mature fruits. Genotypes accumulating high and low percentage of sucrose provided an experimental system to study sugar metabolism in developing fruits. Insoluble invertase activity was high and constant throughout fruit development in control lines and in genotypes accumulating low levels of sucrose, while in genotypes accumulating high levels of sucrose, activity declined sharply 4 weeks after pollination. Soluble acid invertase activity was significantly lower in genotypes accumulating high levels of sucrose than in low-sucrose-accumulating genotypes. Conversely, activities of SuSy and SPS were higher in the high-sucrose-accumulating genotypes. The present results establish that, within the genus Citrullus, there are genotypes that accumulate a high percentage of sucrose in the fruit, while others accumulate high percentages of glucose and fructose. The significant negative correlation between insoluble invertase activity and fruit sucrose level suggests that sucrose accumulation is affected by both phloem unloading and sugar metabolism. (c) 2009 Elsevier GmbH. All rights reserved.

  18. Modelling and Analysis of Biochemical Signalling Pathway Cross-talk

    Directory of Open Access Journals (Sweden)

    Robin Donaldson

    2010-02-01

    Full Text Available Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising parallel composition of instances of generic modules (with internal and external labels. Pathways are then composed by (synchronising parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways.

  19. Molecular and biochemical analysis of symbiotic plant receptor kinase complexes

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Douglas R; Riely, Brendan K

    2010-09-01

    -localize (i.e., the flotillin FLOT4) with symbiotic receptor-like proteins. As controls for TAP tag analysis we have generated protein isoforms that carry fluorescent domains (translational fusions to GFP) and these have been used to establish the subcellular location and dynamics of two symbiotic receptors, LYK3 and DMI2. Both proteins localize to membrane microdomains, or putative lipid rafts, and display dynamic behavior following elicitation with the Nod factor ligand. Finally, mass spectrometry of interacting proteins is yielding lists of candidate proteins that we are poised to test using semi-high throughput RNAi technology and Tnt1 knockout collections in Medicago truncatula.

  20. Biochemical and genetic analysis of the Drk SH2/SH3 adaptor protein of Drosophila.

    Science.gov (United States)

    Raabe, T; Olivier, J P; Dickson, B; Liu, X; Gish, G D; Pawson, T; Hafen, E

    1995-06-01

    The Drk SH3-SH2-SH3 adaptor protein has been genetically identified in a screen for rate-limiting components acting downstream of the Sevenless (Sev) receptor tyrosine kinase in the developing eye of Drosophila. It provides a link between the activated Sev receptor and Sos, a guanine nucleotide release factor that activates Ras1. We have used a combined biochemical and genetic approach to study the interactions between Sev, Drk and Sos. We show that Tyr2546 in the cytoplasmic tail of Sev is required for Drk binding, probably because it provides a recognition site for the Drk SH2 domain. Interestingly, a mutation at this site does not completely block Sev function in vivo. This may suggest that Sev can signal in a Drk-independent, parallel pathway or that Drk can also bind to an intermediate docking protein. Analysis of the Drk-Sos interaction has identified a high affinity binding site for Drk SH3 domains in the Sos tail. We show that the N-terminal Drk SH3 domain is primarily responsible for binding to the tail of Sos in vitro, and for signalling to Ras in vivo.

  1. Meta-analysis of the relationship of mycotoxins with biochemical and hematological parameters in broilers.

    Science.gov (United States)

    Andretta, I; Kipper, M; Lehnen, C R; Lovatto, P A

    2012-02-01

    A meta-analysis was carried out to study the association of mycotoxins with hematological and biochemical profiles in broilers. Ninety-eight articles published between 1980 and 2009 were used in the database, totaling 37,371 broilers. The information was selected from the Materials and Methods and Results sections in the selected articles and then tabulated in a database. Meta-analysis followed 3 sequential analyses: graphic, correlation, and variance-covariance. Mycotoxins reduced (P Mycotoxins also altered (P effect was observed on the relationship between the concentration of aflatoxin in diets and the serum concentration of alkaline phosphatase, γ-glutamyl transferase, alanine aminotransferase, and aspartate aminotransferase. The total protein concentration in blood was 18% lower (P mycotoxin and without the additive. The meta-analysis performed in this study allowed us to address and quantify systematically the relationship of mycotoxins with alterations in hematologic and biochemical profiles in broilers.

  2. Discrete response patterns in the upper range of hypnotic suggestibility: A latent profile analysis.

    Science.gov (United States)

    Terhune, Devin Blair

    2015-05-01

    High hypnotic suggestibility is a heterogeneous condition and there is accumulating evidence that highly suggestible individuals may be comprised of discrete subtypes with dissimilar cognitive and phenomenological profiles. This study applied latent profile analysis to response patterns on a diverse battery of difficult hypnotic suggestions in a sample of individuals in the upper range of hypnotic suggestibility. Comparisons among models indicated that a four-class model was optimal. One class was comprised of very highly suggestible (virtuoso) participants, two classes included highly suggestible participants who were alternately more responsive to inhibitory cognitive suggestions or posthypnotic amnesia suggestions, and the fourth class consisted primarily of medium suggestible participants. These results indicate that there are discrete response profiles in high hypnotic suggestibility. They further provide a number of insights regarding the optimization of hypnotic suggestibility measurement and have implications for the instrumental use of hypnosis for the modeling of different psychological conditions. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Biochemical and ultrastructural studies suggest that the effects of thapsigargin on human platelets are mediated by changes in intracellular calcium but not by intracellular histamine

    DEFF Research Database (Denmark)

    Saxena, S P; McNicol, A; Becker, A B

    1992-01-01

    of DPPE on Tg-induced aggregation were not reversed by the addition of histamine to saponin-permeabilized platelets suggesting non-histamine mediated effects of DPPE on Tg-induced aggregation. Tg stimulated an increase in the cytosolic free calcium concentration which was unaffected by DPPE indicating...

  4. Biofuel and Biochemical Analysis of Amphora coffeaeformis RR03, a Novel Marine Diatom, Cultivated in an Open Raceway Pond

    Directory of Open Access Journals (Sweden)

    Muthu Ganesan Rajaram

    2018-05-01

    Full Text Available (1 Background: To increase the biochemical productivity and to reduce the production cost of microalgal biodiesel, this study aimed to investigate the effects of CO2 on biomass, fatty acids, carbon-hydrogen, and biochemical accumulation of the marine diatom, Amphora coffeaeformis RR03 (A. coffeaeformis RR03. (2 Methods: Fatty acid composition of the dry biomass of A. coffeaeformis RR03 was analysed using Gas chromatography-mass spectrometry (GC-MS. (3 Results: The results showed that A. coffeaeformis RR03 contained high biomass productivity and biochemical composition in different cultivation conditions. A. coffeaeformis RR03 showed maximum growth of 5.2 × 106/mL on 21st day cultivation under CO2 supply. The bio-crude oil production from A. coffeaeformis RR03 was 36.19 megajoule (MJ. GC-MS analysis found that the dry biomass of A. coffeaeformis RR03 contained maximum of 47.72% fatty acids of 16-octadecanoic acid methyl ester (10:12 and 19.58% pentadecanoic acid, 13-methyl-, and methyl ester (9.24. (4 Conclusion: The results of this study may suggest that a novel diatom of A. coffeaeformis RR03 could be a suitable candidate for biocrude production in order to meet the future demand of energy.

  5. A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems

    Directory of Open Access Journals (Sweden)

    Goutsias John

    2010-05-01

    Full Text Available Abstract Background Sensitivity analysis is an indispensable tool for the analysis of complex systems. In a recent paper, we have introduced a thermodynamically consistent variance-based sensitivity analysis approach for studying the robustness and fragility properties of biochemical reaction systems under uncertainty in the standard chemical potentials of the activated complexes of the reactions and the standard chemical potentials of the molecular species. In that approach, key sensitivity indices were estimated by Monte Carlo sampling, which is computationally very demanding and impractical for large biochemical reaction systems. Computationally efficient algorithms are needed to make variance-based sensitivity analysis applicable to realistic cellular networks, modeled by biochemical reaction systems that consist of a large number of reactions and molecular species. Results We present four techniques, derivative approximation (DA, polynomial approximation (PA, Gauss-Hermite integration (GHI, and orthonormal Hermite approximation (OHA, for analytically approximating the variance-based sensitivity indices associated with a biochemical reaction system. By using a well-known model of the mitogen-activated protein kinase signaling cascade as a case study, we numerically compare the approximation quality of these techniques against traditional Monte Carlo sampling. Our results indicate that, although DA is computationally the most attractive technique, special care should be exercised when using it for sensitivity analysis, since it may only be accurate at low levels of uncertainty. On the other hand, PA, GHI, and OHA are computationally more demanding than DA but can work well at high levels of uncertainty. GHI results in a slightly better accuracy than PA, but it is more difficult to implement. OHA produces the most accurate approximation results and can be implemented in a straightforward manner. It turns out that the computational cost of the

  6. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

  7. Biochemical and phyto chemical analysis of dipterygium glaucum collected from Cholistan desert

    International Nuclear Information System (INIS)

    Mehmood, K.; Mehmood, S.; Ramzan, M.

    2010-01-01

    The present study evaluates the Biochemical and phyto chemical analysis of Dipterygium Glaucum from Cholistan desert. Ash contents, carbohydrates, crude fibers, crude fats, were carried out along with the estimation of minerals. Determination of biochemical constituents indicate the presence of total carbohydrates 0.156% (0.174 reducing sugars and O.041 % non reducing),starch contents 0.053%, crude fibers 26.83%, crude fats 13.30% and nitrogen contents 0.0 14%. Concentration of sodium was 3.3%,Potassium 37.6%, lithium 0.1 %, Calcium 0.01 %, Magnesium 0.022%, nickel 0.764%, copper 2.372%, manganese 0.003%, sulphur 0.8%, Phosphorous 1.60%. Moisture and ash contents were 5.60% and 4.75% respectively. alkaloids, glycoside, cardiac glycoside, bound anthraquinones and saponins were present while flavonoids and unbound anthraquinones were absent. no anti bacterial activity was found in this plant extract. (author)

  8. Ixodes ricinus tick lipocalins: identification, cloning, phylogenetic analysis and biochemical characterization.

    Directory of Open Access Journals (Sweden)

    Jérôme Beaufays

    Full Text Available BACKGROUND: During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. METHODOLOGY/PRINCIPAL FINDINGS: Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for "Lipocalin from I. ricinus" and numbered from 1 to 14 (LIR1 to LIR14. According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50-70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. CONCLUSIONS/SIGNIFICANCE: This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C

  9. Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination.

    Science.gov (United States)

    Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E; Evans, David J

    2016-08-19

    Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3' non-coding region we have further developed a cell-based assay (the 3'CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Biochemical Analysis of Synovial Fluid, Cerebrospinal Fluid and Vitreous Humor at Early Postmortem Intervals in Donkeys

    Directory of Open Access Journals (Sweden)

    Doha Yahia

    2014-01-01

    Full Text Available Biochemical analysis of body fluids after death is a helpful tool in veterinary forensic medicine. Synovial fluid, cerebrospinal fluid (CSF and vitreous humor are easily accessible and well preserved from contamination. Five donkeys (Equus africanus asinus aged 1 - 2 years old were subjected to the study. Samples (Synovial fluid, CSF and vitreous humor were collected before death (antimortem and then at 2, 4, 6, 8, 10 and 12 hours postmortem. Samples were analyzed for glucose, chloride, sodium, magnesium, potassium, enzymes and total protein. Synovial fluid analysis showed that glucose concentration started to decrease at 6 hours postmortem, while magnesium level increased with time. Other parameters were more stable. CSF analysis showed several changes related to time after death as the decrease in glucose and sodium levels, and the increased levels of potassium, magnesium, calcium and total protein. Vitreous analysis revealed a reduction in glucose level and increased potassium and magnesium concentrations. The present study concluded that biochemical analysis of synovial fluid, vitreous humor and CSF can help in determination of time since death in donkeys. This study recommend using CSF for determination of early post-mortem intervals.

  11. Intelligence, previous convictions and interrogative suggestibility: a path analysis of alleged false-confession cases.

    Science.gov (United States)

    Sharrock, R; Gudjonsson, G H

    1993-05-01

    The main purpose of this study was to investigate the relationship between interrogative suggestibility and previous convictions among 108 defendants in criminal trials, using a path analysis technique. It was hypothesized that previous convictions, which may provide defendants with interrogative experiences, would correlate negatively with 'shift' as measured by the Gudjonsson Suggestibility Scale (Gudjonsson, 1984a), after intelligence and memory had been controlled for. The hypothesis was partially confirmed and the theoretical and practical implications of the findings are discussed.

  12. Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities.

    Science.gov (United States)

    Bhosle, Amrisha; Chandra, Nagasuma

    2016-03-01

    Antifolates are competitive inhibitors of dihydrofolate reductase (DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the 'supersite' and classified supersites of DHFRs from 56 species into 16 'site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates. © 2016 Federation of European Biochemical Societies.

  13. Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

    Science.gov (United States)

    Bowsher, Clive G

    2011-02-15

    Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

  14. The Comparative Analysis of Biochemical Parameters in Patients with Pleural Effusions: A Prospective Study

    Directory of Open Access Journals (Sweden)

    Ali Kutluk

    2016-09-01

    Full Text Available Aim: The differentiation of exudative from transudative effusion is important to lead the clinician in making further biochemical analysis for possible etiology and in choosing the appropriate treatment strategy. The aim of the study is to evaluate the diagnostic value of biochemical parameters together with Light%u2019s criteria to differentiate exudative from transudative effusions. Material and Method: The LDH, total protein, albumin, adenosine deaminase (ADA, apolipoprotein A1, apolipoprotein B, Lipoprotein-A, total cholesterol, HDL-cholesterol, VLDL-cholesterol, LDL-cholesterol, and triglyceride levels of patients with unknown etiology were measured both in plasma and pleural fluid. Mann-Whitney U was used to compare the groups and p < 0.05 was accepted as statistical significance. Sensitivity, specificity, and accuracy were calculated for each biochemical parameter. The ROC analysis was used to estimate the optimum cut-off value for the highest sensitivity and specificity.Results: Pleural LDH (p=0.001, total protein (p=0.001, albumin (p=0.001, triglyceride (p=0.001, total cholesterol (p=0.001, HDL-cholesterol (p=0.042, VLDL-cholesterol (p=0.001, LDL-cholesterol (p=0.001, apolipoprotein A1 (p=0.021, and HDL-cholesterol/LDL-cholesterol ratio (p=0.048 were found significant in differentiating exudative from transudative effusions. Discussion: The study showed that the use of pleural LDH, total cholesterol, and HDL-cholesterol levels together is more significant than Light%u2019s criteria. The sensitivity, specificity, and accuracy of this test were 99%, 94.1%, and 96.2% respectively.

  15. Comparative study of human blood Raman spectra and biochemical analysis of patients with cancer

    Science.gov (United States)

    Shamina, Lyudmila A.; Bratchenko, Ivan A.; Artemyev, Dmitry N.; Myakinin, Oleg O.; Moryatov, Alexander A.; Orlov, Andrey E.; Kozlov, Sergey V.; Zakharov, Valery P.

    2018-04-01

    In this study we measured spectral features of blood by Raman spectroscopy. Correlation of the obtained spectral data and biochemical studies results is investigated. Analysis of specific spectra allows for identification of informative spectral bands proportional to components whose content is associated with body fluids homeostasis changes at various pathological conditions. Regression analysis of the obtained spectral data allows for discriminating the lung cancer from other tumors with a posteriori probability of 88.3%. The potentiality of applying surface-enhanced Raman spectroscopy with utilized experimental setup for further studies of the body fluids component composition was estimated. The greatest signal amplification was achieved for the gold substrate with a surface roughness of 1 μm. In general, the developed approach of body fluids analysis provides the basis of a useful and minimally invasive method of pathologies screening.

  16. A moment-convergence method for stochastic analysis of biochemical reaction networks.

    Science.gov (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  17. A moment-convergence method for stochastic analysis of biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jiajun [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Nie, Qing [Department of Mathematics, University of California at Irvine, Irvine, California 92697 (United States); Zhou, Tianshou, E-mail: mcszhtsh@mail.sysu.edu.cn [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China); Guangdong Province Key Laboratory of Computational Science and School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China)

    2016-05-21

    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  18. Analysis of postoperative biochemical values and clinical outcomes after adrenalectomy for primary aldosteronism.

    Science.gov (United States)

    Swearingen, Andrew J; Kahramangil, Bora; Monteiro, Rosebel; Krishnamurthy, Vikram; Jin, Judy; Shin, Joyce; Siperstein, Allan; Berber, Eren

    2018-04-01

    Primary aldosteronism causes hypertension and hypokalemia and is often surgically treatable. Diagnosis includes elevated plasma aldosterone, suppressed plasma renin activity, and elevated aldosterone renin ratio. Adrenalectomy improves hypertension and hypokalemia. Postoperative plasma aldosterone and plasma renin activity may be useful in documenting cure or failure. A retrospective analysis of patients who underwent adrenalectomy for primary aldosteronism from 2010 to 2016 was performed, analyzing preoperative and postoperative plasma aldosterone, plasma renin activity, hypertension, and hypokalemia. The utility of postoperative testing was assessed. Clinical cure was defined as improved hypertension control and resolution of potassium loss. Biochemical cure was defined as aldosterone renin ratio reduction to <23.6. Forty-four patients were included; 20 had plasma aldosterone and plasma renin activity checked on postoperative day 1. In the study, 40/44 (91%) were clinically cured. All clinical failures had of biochemical failure at follow-up. Postoperative day 1aldosterone renin ratio <23.6 had PPV of 95% for clinical cure. Cured patients had mean plasma aldosterone drop of 33.1 ng/dL on postoperative day 1; noncured patient experienced 3.9 ng/dL increase. A cutoff of plasma aldosterone decrease of 10 ng/dL had high positive predictive value for clinical cure. Changes in plasma aldosterone and plasma renin activity after adrenalectomy correlate with improved hypertension and hypokalemia. The biochemical impact of adrenalectomy manifests as early as postoperative day 1. We propose a plasma aldosterone decrease of 10 ng/dL as a criterion to predict clinical cure. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Principal component analysis of tomato genotypes based on some morphological and biochemical quality indicators

    Directory of Open Access Journals (Sweden)

    Glogovac Svetlana

    2012-01-01

    Full Text Available This study investigates variability of tomato genotypes based on morphological and biochemical fruit traits. Experimental material is a part of tomato genetic collection from Institute of Filed and Vegetable Crops in Novi Sad, Serbia. Genotypes were analyzed for fruit mass, locule number, index of fruit shape, fruit colour, dry matter content, total sugars, total acidity, lycopene and vitamin C. Minimum, maximum and average values and main indicators of variability (CV and σ were calculated. Principal component analysis was performed to determinate variability source structure. Four principal components, which contribute 93.75% of the total variability, were selected for analysis. The first principal component is defined by vitamin C, locule number and index of fruit shape. The second component is determined by dry matter content, and total acidity, the third by lycopene, fruit mass and fruit colour. Total sugars had the greatest part in the fourth component.

  20. Ultrastructural and biochemical analysis of epidermal xanthophores and dermal chromatophores of the teleost Sparus aurata.

    Science.gov (United States)

    Ferrer, C; Solano, F; Zuasti, A

    1999-04-01

    We have studied the pigmentary system of the teleost Sparus aurata skin by electron microscopy and chromatographic analysis. Under electron microscopy, we found the dermis to contain the three major types of recognized chromatophores: melanophores, xanthophores and iridophores. Melanophores were more abundant in the dorsal region, whereas the iridophores were more abundant in the ventral region. The most important discovery was that of epidermal xanthophores. Epidermal xanthophores were the only chromatophores in the epidermis, something only found in S aurata and in a teleost species living in the Antartic sea. In contrast, the biochemical analysis did not establish any special characteristics: we found pteridine and flavin pigments located mostly in the pigmented dorsal region. Riboflavin and pterin were two of the most abundant coloured pigment types, but other colourless pigments such as xanthopterin and isoxanthopterin were also detected.

  1. Cluster analysis of the biochemical composition in 53 Sichuan EGCG3"Me tea resources

    Science.gov (United States)

    Li, J. H.; Chen, S. X.; Zhu, M. Z.; Meng, X. L.

    2017-09-01

    The EGCG3"Me contents in the young tea leaves of 102 tea resources in sichuan were analyzed accurately using HPLC-DAD. The results revealed that there was a wide variation in EGCG3"Me levels among different tea resources. The EGCG3"Me content in different tea resources was in a range from 0 to 11.04 mg/g, mean was 2.33 mg/g.53 tea resources contained EGCG3"Me, accounting for 51.96% of the total number of resources survey. Shucha5, Jinguanyin, Chengxi11, Fenghuang-dancong, Chongpi 71-1 were found to contain higher EGCG3"Me content (>10mg/g).Cluster analysis showed that: 53 Sichuan EGCG3"Me tea resources were divided into six groups and the difference was obvious between their biochemical composition; tea resources rich in EGCG3"Me were mainly distributed in Sichuan, Chongqing and Fujian Province, mostly were shrub and mid-leaf, mainly existed in tea resources which were suitable to make green tea, oolong tea. The morphological and biochemical distribution provided a good theoretical basis for selecting and utilizing higher EGCG3"Me resources.

  2. Analysis of some biochemical and haematological parameters for Mucuna pruriens (DC) seed powder in male rats.

    Science.gov (United States)

    Chukwudi, Ndukwe Henry; Simeon, Omale; Chinyere, Aguiyi John

    2011-10-01

    The biochemical and haematological effects of the seed powder of Mucuna pruriens in male rats were evaluated to establish some biological properties of this potential biopesticide currently undergoing investigation. The result showed that Mucuna pruriens seed extract produced a significant (p<0.05) increase in white blood cell (WBC) count, as well as in bilirubin concentrations, alkaline phosphatase (ALP), protein and creatinine levels measured. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were significantly reduced (P<0.05) in comparison with the experimental control. PCV, Hb, albumin level and WBC differential counts gave no significant difference between treated and control groups. The results revealed metabolic imbalance in the rats which suggests a mild cholestasis effect of the extract.

  3. Cluster analysis of Helicobacter pylori genomic DNA fingerprints suggests gastroduodenal disease-specific associations.

    Science.gov (United States)

    Go, M F; Chan, K Y; Versalovic, J; Koeuth, T; Graham, D Y; Lupski, J R

    1995-07-01

    Helicobacter pylori infection is now accepted as the most common cause of chronic active gastritis and peptic ulcer disease. The etiologies of many infectious diseases have been attributed to specific or clonal strains of bacterial pathogens. Polymerase chain reaction (PCR) amplification of DNA between repetitive DNA sequences, REP elements (REP-PCR), has been utilized to generate DNA fingerprints to examine similarity among strains within a bacterial species. Genomic DNA from H. pylori isolates obtained from 70 individuals (39 duodenal ulcers and 31 simple gastritis) was PCR-amplified using consensus probes to repetitive DNA elements. The H. pylori DNA fingerprints were analyzed for similarity and correlated with disease presentation using the NTSYS-pc computer program. Each H. pylori strain had a distinct DNA fingerprint except for two pairs. Single-colony DNA fingerprints of H. pylori from the same patient were identical, suggesting that each patient harbors a single strain. Computer-assisted cluster analysis of the REP-PCR DNA fingerprints showed two large clusters of isolates, one associated with simple gastritis and the other with duodenal ulcer disease. Cluster analysis of REP-PCR DNA fingerprints of H. pylori strains suggests that duodenal ulcer isolates, as a group, are more similar to one another and different from gastritis isolates. These results suggest that disease-specific strains may exist.

  4. In silico analysis suggests interaction between Ebola virus and the extracellular matrix

    Directory of Open Access Journals (Sweden)

    Veljko eVeljkovic

    2015-02-01

    Full Text Available The worst Ebola virus (EV outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trendlines in this crisis are grave, and now represents global public health threat concern. Limited therapeutic and/or prophylactic options which are available for humans suffering from Ebola virus disease (EVD further complicate situation. Previous studies suggested that the EV glycoprotein (GP is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM, a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs are involved in interaction between GP and ECM. This finding could contribute to better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.

  5. Genetic Analysis of East Asian Grape Cultivars Suggests Hybridization with Wild Vitis.

    Science.gov (United States)

    Goto-Yamamoto, Nami; Sawler, Jason; Myles, Sean

    2015-01-01

    Koshu is a grape cultivar native to Japan and is one of the country's most important cultivars for wine making. Koshu and other oriental grape cultivars are widely believed to belong to the European domesticated grape species Vitis vinifera. To verify the domesticated origin of Koshu and four other cultivars widely grown in China and Japan, we genotyped 48 ancestry informative single nucleotide polymorphisms (SNPs) and estimated wild and domesticated ancestry proportions. Our principal components analysis (PCA) based ancestry estimation revealed that Koshu is 70% V. vinifera, and that the remaining 30% of its ancestry is most likely derived from wild East Asian Vitis species. Partial sequencing of chloroplast DNA suggests that Koshu's maternal line is derived from the Chinese wild species V. davidii or a closely related species. Our results suggest that many traditional East Asian grape cultivars such as Koshu were generated from hybridization events with wild grape species.

  6. Genetic Analysis of East Asian Grape Cultivars Suggests Hybridization with Wild Vitis.

    Directory of Open Access Journals (Sweden)

    Nami Goto-Yamamoto

    Full Text Available Koshu is a grape cultivar native to Japan and is one of the country's most important cultivars for wine making. Koshu and other oriental grape cultivars are widely believed to belong to the European domesticated grape species Vitis vinifera. To verify the domesticated origin of Koshu and four other cultivars widely grown in China and Japan, we genotyped 48 ancestry informative single nucleotide polymorphisms (SNPs and estimated wild and domesticated ancestry proportions. Our principal components analysis (PCA based ancestry estimation revealed that Koshu is 70% V. vinifera, and that the remaining 30% of its ancestry is most likely derived from wild East Asian Vitis species. Partial sequencing of chloroplast DNA suggests that Koshu's maternal line is derived from the Chinese wild species V. davidii or a closely related species. Our results suggest that many traditional East Asian grape cultivars such as Koshu were generated from hybridization events with wild grape species.

  7. Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals.

    Science.gov (United States)

    Su, Fei; Xu, Ping

    2014-01-29

    Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species.

  8. Kaizen practice in healthcare: a qualitative analysis of hospital employees' suggestions for improvement.

    Science.gov (United States)

    Mazzocato, Pamela; Stenfors-Hayes, Terese; von Thiele Schwarz, Ulrica; Hasson, Henna; Nyström, Monica Elisabeth

    2016-07-29

    Kaizen, or continuous improvement, lies at the core of lean. Kaizen is implemented through practices that enable employees to propose ideas for improvement and solve problems. The aim of this study is to describe the types of issues and improvement suggestions that hospital employees feel empowered to address through kaizen practices in order to understand when and how kaizen is used in healthcare. We analysed 186 structured kaizen documents containing improvement suggestions that were produced by 165 employees at a Swedish hospital. Directed content analysis was used to categorise the suggestions into following categories: type of situation (proactive or reactive) triggering an action; type of process addressed (technical/administrative, support and clinical); complexity level (simple or complex); and type of outcomes aimed for (operational or sociotechnical). Compliance to the kaizen template was calculated. 72% of the improvement suggestions were reactions to a perceived problem. Support, technical and administrative, and primary clinical processes were involved in 47%, 38% and 16% of the suggestions, respectively. The majority of the kaizen documents addressed simple situations and focused on operational outcomes. The degree of compliance to the kaizen template was high for several items concerning the identification of problems and the proposed solutions, and low for items related to the test and implementation of solutions. There is a need to combine kaizen practices with improvement and innovation practices that help staff and managers to address complex issues, such as the improvement of clinical care processes. The limited focus on sociotechnical aspects and the partial compliance to kaizen templates may indicate a limited understanding of the entire kaizen process and of how it relates to the overall organisational goals. This in turn can hamper the sustainability of kaizen practices and results. Published by the BMJ Publishing Group Limited. For

  9. Kaizen practice in healthcare: a qualitative analysis of hospital employees' suggestions for improvement

    Science.gov (United States)

    Mazzocato, Pamela; Stenfors-Hayes, Terese; von Thiele Schwarz, Ulrica; Hasson, Henna

    2016-01-01

    Objectives Kaizen, or continuous improvement, lies at the core of lean. Kaizen is implemented through practices that enable employees to propose ideas for improvement and solve problems. The aim of this study is to describe the types of issues and improvement suggestions that hospital employees feel empowered to address through kaizen practices in order to understand when and how kaizen is used in healthcare. Methods We analysed 186 structured kaizen documents containing improvement suggestions that were produced by 165 employees at a Swedish hospital. Directed content analysis was used to categorise the suggestions into following categories: type of situation (proactive or reactive) triggering an action; type of process addressed (technical/administrative, support and clinical); complexity level (simple or complex); and type of outcomes aimed for (operational or sociotechnical). Compliance to the kaizen template was calculated. Results 72% of the improvement suggestions were reactions to a perceived problem. Support, technical and administrative, and primary clinical processes were involved in 47%, 38% and 16% of the suggestions, respectively. The majority of the kaizen documents addressed simple situations and focused on operational outcomes. The degree of compliance to the kaizen template was high for several items concerning the identification of problems and the proposed solutions, and low for items related to the test and implementation of solutions. Conclusions There is a need to combine kaizen practices with improvement and innovation practices that help staff and managers to address complex issues, such as the improvement of clinical care processes. The limited focus on sociotechnical aspects and the partial compliance to kaizen templates may indicate a limited understanding of the entire kaizen process and of how it relates to the overall organisational goals. This in turn can hamper the sustainability of kaizen practices and results. PMID:27473953

  10. Analysis of gingival pocket microflora and biochemical blood parameters in dogs suffering from periodontal disease.

    Science.gov (United States)

    Polkowska, Izabela; Sobczyńska-Rak, Aleksandra; Gołyńska, Magdalena

    2014-01-01

    Periodontal diseases in dogs are caused by bacteria colonising the oral cavity. The presence of plaque comprising accumulations of aerobic and anaerobic bacteria leads to the development of periodontitis. Due to the fact that in a large percentage of cases periodontal diseases remain undiagnosed, and consequently untreated, they tend to acquire a chronic character, lead to bacteraemia and negatively impact the health of internal organs. The aim of the present study was to perform a qualitative microbiological analysis of gingival pockets and determine the correlations between selected morphological and biochemical blood parameters and the extent periodontal diseases. Twenty-one dogs treated for periodontal diseases were qualified for the study and subsequently divided into two groups: with 3rd and 4th stage of periodontal disease. Swabs from the patients' gingival pockets were taken for bacteriological testing. Blood was tested for parameters including erythrocyte count, haemoglobin concentration, haematocrit values and leukocyte count. Blood serum was analyzed with respect to the concentrations of alanine transaminase (ALT), aspartate transaminase (AspAT/AST) and urea. The microbiological analysis of gingival pockets indicated the presence of numerous pathogens with a growth tendency in bacterial cultures observed in dogs with advanced-stage periodontal disease. The concentration of biochemical blood markers was significantly higher in dogs with 4th stage of periodontal disease, to compared to the 3rd-stage group. Morphological parameters were not significantly different with the exception of haemoglobin concentration, which was lower in dogs with 4th stage disease. In both groups, elevated leukocyte counts were observed. By conducting a detailed microbiological examination, it is possible to provide a better prognosis, plan adequate treatment and monitor dogs treated for peridontopathy. Copyright © 2014 International Institute of Anticancer Research (Dr. John G

  11. Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.

    Science.gov (United States)

    Pantazis, Yannis; Katsoulakis, Markos A; Vlachos, Dionisios G

    2013-10-22

    Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks. Typically, such mathematical models involve networks of coupled jump stochastic processes with a large number of parameters that need to be suitably calibrated against experimental data. In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, existing sensitivity analysis approaches such as variants of the finite difference method can have an overwhelming computational cost in models with a high-dimensional parameter space. We develop a sensitivity analysis methodology suitable for complex stochastic reaction networks with a large number of parameters. The proposed approach is based on Information Theory methods and relies on the quantification of information loss due to parameter perturbations between time-series distributions. For this reason, we need to work on path-space, i.e., the set consisting of all stochastic trajectories, hence the proposed approach is referred to as "pathwise". The pathwise sensitivity analysis method is realized by employing the rigorously-derived Relative Entropy Rate, which is directly computable from the propensity functions. A key aspect of the method is that an associated pathwise Fisher Information Matrix (FIM) is defined, which in turn constitutes a gradient-free approach to quantifying parameter sensitivities. The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks. As a gradient-free method, the proposed sensitivity analysis provides a significant advantage when dealing with complex stochastic systems with a large number of parameters. In addition, the knowledge of the structure of the FIM can allow to efficiently address

  12. A new family of phosphoinositide phosphatases in microorganisms: identification and biochemical analysis

    Directory of Open Access Journals (Sweden)

    Bennett Hayley J

    2010-08-01

    Full Text Available Abstract Background Phosphoinositide metabolism is essential to membrane dynamics and impinges on many cellular processes, including phagocytosis. Modulation of phosphoinositide metabolism is important for pathogenicity and virulence of many human pathogens, allowing them to survive and replicate in the host cells. Phosphoinositide phosphatases from bacterial pathogens are therefore key players in this modulation and constitute attractive targets for chemotherapy. MptpB, a virulence factor from Mycobacterium tuberculosis, has phosphoinositide phosphatase activity and a distinct active site P-loop signature HCXXGKDR that shares characteristics with eukaryotic lipid phosphatases and protein tyrosine phosphatases. We used this P-loop signature as a "diagnostic motif" to identify related putative phosphatases with phosphoinositide activity in other organisms. Results We found more than 200 uncharacterised putative phosphatase sequences with the conserved signature in bacteria, with some related examples in fungi and protozoa. Many of the sequences identified belong to recognised human pathogens. Interestingly, no homologues were found in any other organisms including Archaea, plants, or animals. Phylogenetic analysis revealed that these proteins are unrelated to classic eukaryotic lipid phosphatases. However, biochemical characterisation of those from Listeria monocytogenes and Leishmania major, demonstrated that, like MptpB, they have phosphatase activity towards phosphoinositides. Mutagenesis studies established that the conserved Asp and Lys in the P-loop signature (HCXXGKDR are important in catalysis and substrate binding respectively. Furthermore, we provide experimental evidence that the number of basic residues in the P-loop is critical in determining activity towards poly-phosphoinositides. Conclusion This new family of enzymes in microorganisms shows distinct sequence and biochemical characteristics to classic eukaryotic lipid phosphatases

  13. A new family of phosphoinositide phosphatases in microorganisms: identification and biochemical analysis.

    Science.gov (United States)

    Beresford, Nicola J; Saville, Charis; Bennett, Hayley J; Roberts, Ian S; Tabernero, Lydia

    2010-08-02

    Phosphoinositide metabolism is essential to membrane dynamics and impinges on many cellular processes, including phagocytosis. Modulation of phosphoinositide metabolism is important for pathogenicity and virulence of many human pathogens, allowing them to survive and replicate in the host cells. Phosphoinositide phosphatases from bacterial pathogens are therefore key players in this modulation and constitute attractive targets for chemotherapy. MptpB, a virulence factor from Mycobacterium tuberculosis, has phosphoinositide phosphatase activity and a distinct active site P-loop signature HCXXGKDR that shares characteristics with eukaryotic lipid phosphatases and protein tyrosine phosphatases. We used this P-loop signature as a "diagnostic motif" to identify related putative phosphatases with phosphoinositide activity in other organisms. We found more than 200 uncharacterised putative phosphatase sequences with the conserved signature in bacteria, with some related examples in fungi and protozoa. Many of the sequences identified belong to recognised human pathogens. Interestingly, no homologues were found in any other organisms including Archaea, plants, or animals. Phylogenetic analysis revealed that these proteins are unrelated to classic eukaryotic lipid phosphatases. However, biochemical characterisation of those from Listeria monocytogenes and Leishmania major, demonstrated that, like MptpB, they have phosphatase activity towards phosphoinositides. Mutagenesis studies established that the conserved Asp and Lys in the P-loop signature (HCXXGKDR) are important in catalysis and substrate binding respectively. Furthermore, we provide experimental evidence that the number of basic residues in the P-loop is critical in determining activity towards poly-phosphoinositides. This new family of enzymes in microorganisms shows distinct sequence and biochemical characteristics to classic eukaryotic lipid phosphatases and they have no homologues in humans. This study provides

  14. Cause analysis and suggestion of urea consumption in denitrification system of coal-fired power plant

    Science.gov (United States)

    Zhang, Xueying; Dong, Ruifeng; Guo, Yang; Wang, Fangfang; Yang, Shuo

    2018-02-01

    In the daily operation of many power plants, the urea consumption of denitration system is much more than normal. Therefore, the process of site testing and laboratory analysis are carried out. Several suggestions are given out. (1) The position of sampling hole on the exit flue of denitrification system should be redesigned. (2) The denitrification optimization and adjustment should be carried out based on the technical specifications for the operation system. (3) The flue gas CEMS system for single point sampling should be transformed into two or three point sampling mode. (4) When the coal - fired unit is shutting down, examine the ammonia injection and nozzle branch, in order to improve the operation reliability of denitration system.

  15. Association Analysis Suggests SOD2 as a Newly Identified Candidate Gene Associated With Leprosy Susceptibility.

    Science.gov (United States)

    Ramos, Geovana Brotto; Salomão, Heloisa; Francio, Angela Schneider; Fava, Vinícius Medeiros; Werneck, Renata Iani; Mira, Marcelo Távora

    2016-08-01

    Genetic studies have identified several genes and genomic regions contributing to the control of host susceptibility to leprosy. Here, we test variants of the positional and functional candidate gene SOD2 for association with leprosy in 2 independent population samples. Family-based analysis revealed an association between leprosy and allele G of marker rs295340 (P = .042) and borderline evidence of an association between leprosy and alleles C and A of markers rs4880 (P = .077) and rs5746136 (P = .071), respectively. Findings were validated in an independent case-control sample for markers rs295340 (P = .049) and rs4880 (P = .038). These results suggest SOD2 as a newly identified gene conferring susceptibility to leprosy. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  16. Factors to consider in monitoring programs suggested by statistical analysis of available data

    International Nuclear Information System (INIS)

    Thomas, J.M.

    1977-01-01

    Based on experience gained in the statistical analysis of data collected during monitoring programs at three nuclear power plants, as well as on other studies in the area of impact assessment, I have attempted to outline what has been done and what I believe can be done in assessing environmental changes. Procedural changes that I suggest include the implementation of a stopping rule so field studies are terminated after a negotiated period of time and the commitment of all resources to studies of one or two species. Simulation models are suggested as a useful tool in an iterative process where results of field studies are routinely incorporated until a negotiated stopping time is reached or until acceptable results are attained. Finally, I describe the statistical analyses we have used and their limitations, and I give some sample-size estimates needed to detect changes of specified sizes in population numbers. To detect changes in population numbers of the size we have encountered, calculated sample sizes are found to be much larger than in current use

  17. Metabolomics analysis and modeling suggest a lysophosphocholines-PAF receptor interaction in fibromyalgia.

    Directory of Open Access Journals (Sweden)

    Pierluigi Caboni

    Full Text Available Fibromyalgia Syndrome (FMS is a chronic disease characterized by widespread pain, and difficult to diagnose and treat. We analyzed the plasma metabolic profile of patients with FMS by using a metabolomics approach combining Liquid Chromatography-Quadrupole-Time Of Flight/Mass Spectrometry (LC-Q-TOF/MS with multivariate statistical analysis, aiming to discriminate patients and controls. LC-Q-TOF/MS analysis of plasma (FMS patients: n = 22 and controls: n = 21 identified many lipid compounds, mainly lysophosphocholines (lysoPCs, phosphocholines and ceramides. Multivariate statistical analysis was performed to identify the discriminating metabolites. A protein docking and molecular dynamic (MD study was then performed, using the most discriminating lysoPCs, to validate the binding to Platelet Activating Factor (1-alkyl-2-acetyl-sn-glycero-3-phosphocholine, PAF Receptor (PAFr. Discriminating metabolites between FMS patients and controls were identified as 1-tetradecanoyl-sn-glycero-3-phosphocholine [PC(14:0/0:0] and 1-hexadecanoyl-sn-glycero-3-phosphocholine [PC(16:0/0:0]. MD and docking indicate that the ligands investigated have similar potentialities to activate the PAFr receptor. The application of a metabolomic approach discriminated FMS patients from controls, with an over-representation of PC(14:0/0:0 and PC(16:0/0:0 compounds in the metabolic profiles. These results and the modeling of metabolite-PAFr interaction, allowed us to hypothesize that lipids oxidative fragmentation might generate lysoPCs in abundance, that in turn will act as PAF-like bioactivators. Overall results suggest disease biomarkers and potential therapeutical targets for FMS.

  18. Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe

    NARCIS (Netherlands)

    Slawiak, M.; Beckhoven, van J.R.C.M.; Speksnijder, A.G.C.L.; Czajkowski, R.L.; Grabe, G.; Wolf, van der J.M.

    2009-01-01

    Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing

  19. Retrospective analysis of necropsy reports suggestive of abuse in dogs and cats.

    Science.gov (United States)

    Almeida, Daniel C; Torres, Sheila M F; Wuenschmann, Arno

    2018-02-15

    OBJECTIVE To identify historical and necropsy findings suggestive of neglect or abuse of dogs and cats by retrospective analysis of necropsy reports from a veterinary diagnostic laboratory. DESIGN Retrospective cohort study. SAMPLE 119 necropsy reports of dogs and cats. PROCEDURES Necropsy reports from February 2001 to May 2012 were electronically searched to identify potential animal abuse or neglect cases. Cases were selected and categorized according to a previously proposed method for classification of animal abuse. Inclusion criteria included signs of neglect, nonaccidental injury (NAI; blunt-force or sharp-force trauma, gunshot, burns, drowning, asphyxiation, and suspicious intoxications), and sexual abuse. Poor preservation of cadavers, age abuse cases, determined on the basis of all necropsies performed in the study period, was 73 of 8,417 (0.87%) in dogs and 46 of 4,905 (0.94%) in cats. Neglect and NAI were commonly identified in cats; NAI was most commonly found in dogs. Gunshot and blunt-force trauma were the most common NAIs in dogs and cats, respectively. Pit bull-type dogs (29/73 [40%]) were overrepresented in several abuse categories. Most cats (29/46 [63%]) were domestic shorthair, but no breed association was found. Most (41/71 [58%]) affected animals with age data available were ≤ 2 years old. CONCLUSIONS AND CLINICAL RELEVANCE Approximately 1% of dogs and cats necropsied in the study period had signs suggestive of abuse. Medical findings alone are not necessarily indicative of abuse, but some findings can increase the index of suspicion.

  20. Genomic survey, gene expression analysis and structural modeling suggest diverse roles of DNA methyltransferases in legumes.

    Directory of Open Access Journals (Sweden)

    Rohini Garg

    Full Text Available DNA methylation plays a crucial role in development through inheritable gene silencing. Plants possess three types of DNA methyltransferases (MTases, namely Methyltransferase (MET, Chromomethylase (CMT and Domains Rearranged Methyltransferase (DRM, which maintain methylation at CG, CHG and CHH sites. DNA MTases have not been studied in legumes so far. Here, we report the identification and analysis of putative DNA MTases in five legumes, including chickpea, soybean, pigeonpea, Medicago and Lotus. MTases in legumes could be classified in known MET, CMT, DRM and DNA nucleotide methyltransferases (DNMT2 subfamilies based on their domain organization. First three MTases represent DNA MTases, whereas DNMT2 represents a transfer RNA (tRNA MTase. Structural comparison of all the MTases in plants with known MTases in mammalian and plant systems have been reported to assign structural features in context of biological functions of these proteins. The structure analysis clearly specified regions crucial for protein-protein interactions and regions important for nucleosome binding in various domains of CMT and MET proteins. In addition, structural model of DRM suggested that circular permutation of motifs does not have any effect on overall structure of DNA methyltransferase domain. These results provide valuable insights into role of various domains in molecular recognition and should facilitate mechanistic understanding of their function in mediating specific methylation patterns. Further, the comprehensive gene expression analyses of MTases in legumes provided evidence of their role in various developmental processes throughout the plant life cycle and response to various abiotic stresses. Overall, our study will be very helpful in establishing the specific functions of DNA MTases in legumes.

  1. Molecular Analysis, Biochemical Characterization, Antimicrobial Activity, and Immunological Analysis of Proteus mirabilis Isolated from Broilers.

    Science.gov (United States)

    Yeh, Hung-Yueh; Line, John E; Hinton, Arthur

    2018-03-01

    Proteus mirabilis, a Gram-negative bacterium, is ubiquitous in the environment and is considered as the normal microflora in the human gastrointestinal tract. However, this bacterium is an opportunistic pathogen in humans, often causing urinary tract infections. Moreover, Proteus has been frequently isolated from food animals, including poultry. Whether this bacterium contributes to the foodborne illness in humans is unclear. In this report, P. mirabilis isolates recovered from broilers during housing in the units were characterized, their antimicrobial activity was assayed, and broiler immune response to the soluble proteins was determined. Cecal contents and fecal droppings were treated according to the standard protocol for isolation. Speciation based on biochemical reactions and the antimicrobial activity of the isolates were carried out using commercial kits. Immunoblot was assayed to determine immune status of broilers against P. mirabilis. A total of 10 isolates of P. mirabilis were selected for further characterization. These isolates could grow in pH 6.0 and 1% NaCl conditions. They were resistant to sodium lactate, troleandomycin, rifamycin SV, vancomycin, but sensitive to nalidixic acid, cefotaxime and novobiocin. Moreover, the CTX, ACC, CMY-1, BIC, NDM, VEB, qnrB and qnrD genes were detected by PCR amplification in all isolates. Sera from broilers harboring this bacterium reacted to the P. mirabilis soluble proteins, but not from litter- and age-matched P. mirabilis negative and SPF chickens, indicating that this bacterium infected chickens that could have humoral immune response against P. mirabilis. This study provides a rationale for further monitoring P. mirabilis during poultry production to determine whether this bacterium poses potential threats to public health. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

  2. Assessing earthworm and sewage sludge impacts on microbiological and biochemical soil quality using multivariate analysis

    Directory of Open Access Journals (Sweden)

    Hanye Jafari Vafa

    2017-06-01

    Full Text Available Introduction: Land application of organic wastes and biosolids such as municipal sewage sludge has been an important and attractive practice for improving different properties of agricultural soils with low organic matter content in semi-arid regions, due to an increase of soil organic matter level and fertility. However, application of this organic waste may directly or indirectly affect soil bio-indicators such as microbial and enzymatic activities through a change in the activity of other soil organisms such as earthworms. Earthworms are the most important soil saprophagous fauna and much of the faunal biomass is attributed to the presence of these organisms in the soil. Therefore, it is crucial to evaluate the effect of earthworm activity on soil microbial and biochemical attributes, in particularly when soils are amended with urban sewage sludge. The purpose of this study was to evaluate the earthworm effects on biochemical and microbiological properties of a calcareous soil amended with municipal sewage sludge using Factor Analysis (FA. Materials and Methods: In the present study, the experimental treatments were sewage sludge (without and with 1.5% sewage sludge as the first factor and earthworm (no earthworm, Eiseniafoetida from epigeic group, Allolobophracaliginosa from endogeic group and a mixture of the two species as the second factor. The study was setup as 2×4 full factorial experiment arranged in a completely randomized design with three replications for each treatment under greenhouse conditions over 90 days. A calcareous soil from the 0-30 cm layer with clay loam texture was obtained from a farmland field under fallow without cultivation history for ten years. The soil was air-dried and passed through a 2-mm sieve for the experiment. Sewage sludge as the soil organic amendment was collected from Wastewater Treatment Plant in Shahrekord. Sewage sludge was air-dried and grounded to pass through a 1-mm sieve for a uniform mixture

  3. Integrative Analysis of Desert Dust Size and Abundance Suggests Less Dust Climate Cooling

    Science.gov (United States)

    Kok, Jasper F.; Ridley, David A.; Zhou, Qing; Miller, Ron L.; Zhao, Chun; Heald, Colette L.; Ward, Daniel S.; Albani, Samuel; Haustein, Karsten

    2017-01-01

    Desert dust aerosols affect Earths global energy balance through interactions with radiation, clouds, and ecosystems. But the magnitudes of these effects are so uncertain that it remains unclear whether atmospheric dust has a net warming or cooling effect on global climate. Consequently, it is still uncertain whether large changes in atmospheric dust loading over the past century have slowed or accelerated anthropogenic climate change, and the climate impact of possible future alterations in dust loading is similarly disputed. Here we use an integrative analysis of dust aerosol sizes and abundance to constrain the climatic impact of dust through direct interactions with radiation. Using a combination of observational, experimental, and model data, we find that atmospheric dust is substantially coarser than represented in current climate models. Since coarse dust warms global climate, the dust direct radiative effect (DRE) is likely less cooling than the 0.4 W m superscript 2 estimated by models in a current ensemble. We constrain the dust DRE to -0.20 (-0.48 to +0.20) W m superscript 2, which suggests that the dust DRE produces only about half the cooling that current models estimate, and raises the possibility that dust DRE is actually net warming the planet.

  4. Analysis of the Convention on Nuclear Safety and Suggestions for Improvement

    International Nuclear Information System (INIS)

    Choi, K. S.; Viet, Phuong Nguyen

    2013-01-01

    The innovative approach of the Convention, which is based on incentive after than legal binding, had been considered successful in strengthening the nuclear safety worldwide. However, the nuclear accident at the Fukushima Dai-ichi Nuclear Power Plant (Japan) in March 2011 has exposed a number of weaknesses of the Convention. Given that context, this paper will analyse the characteristics of the CNS in order to understand the advantages and disadvantages of the Convention, and finally to suggest some possible improvements. The analysis in this paper shows that the incentive approach of the CNS has succeeded in facilitating the active roles of its Contracting Parties in making the National Reports and participating in the peer review of these reports. However, the incoherent quality of the National Reports, the different level of participation in the peer review process by different Contracting Parties, and the lack of transparency of the peer review have undermined the effectiveness of the Convention in strengthening the international safety regime as well as preventing serious regulatory errors that had happened in Japan before the Fukushima accident. Therefore, the peer review process should be reformed into a more transparent and independent direction, while an advisory group of regulators within the CNS might also be useful in improving the effectiveness of the Convention as already proven by the good practice in the European Union. Only with such effective change, the CNS can maintain its pivotal role in the international safety regime

  5. A Meta-Analysis Suggests Different Neural Correlates for Implicit and Explicit Learning.

    Science.gov (United States)

    Loonis, Roman F; Brincat, Scott L; Antzoulatos, Evan G; Miller, Earl K

    2017-10-11

    A meta-analysis of non-human primates performing three different tasks (Object-Match, Category-Match, and Category-Saccade associations) revealed signatures of explicit and implicit learning. Performance improved equally following correct and error trials in the Match (explicit) tasks, but it improved more after correct trials in the Saccade (implicit) task, a signature of explicit versus implicit learning. Likewise, error-related negativity, a marker for error processing, was greater in the Match (explicit) tasks. All tasks showed an increase in alpha/beta (10-30 Hz) synchrony after correct choices. However, only the implicit task showed an increase in theta (3-7 Hz) synchrony after correct choices that decreased with learning. In contrast, in the explicit tasks, alpha/beta synchrony increased with learning and decreased thereafter. Our results suggest that explicit versus implicit learning engages different neural mechanisms that rely on different patterns of oscillatory synchrony. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Meta-analysis suggests choosy females get sexy sons more than "good genes".

    Science.gov (United States)

    Prokop, Zofia M; Michalczyk, Łukasz; Drobniak, Szymon M; Herdegen, Magdalena; Radwan, Jacek

    2012-09-01

    Female preferences for specific male phenotypes have been documented across a wide range of animal taxa, including numerous species where males contribute only gametes to offspring production. Yet, selective pressures maintaining such preferences are among the major unknowns of evolutionary biology. Theoretical studies suggest that preferences can evolve if they confer genetic benefits in terms of increased attractiveness of sons ("Fisherian" models) or overall fitness of offspring ("good genes" models). These two types of models predict, respectively, that male attractiveness is heritable and genetically correlated with fitness. In this meta-analysis, we draw general conclusions from over two decades worth of empirical studies testing these predictions (90 studies on 55 species in total). We found evidence for heritability of male attractiveness. However, attractiveness showed no association with traits directly associated with fitness (life-history traits). Interestingly, it did show a positive correlation with physiological traits, which include immunocompetence and condition. In conclusion, our results support "Fisherian" models of preference evolution, while providing equivocal evidence for "good genes." We pinpoint research directions that should stimulate progress in our understanding of the evolution of female choice. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  7. A New Data Analysis System to Quantify Associations between Biochemical Parameters of Chronic Kidney Disease-Mineral Bone Disease.

    Directory of Open Access Journals (Sweden)

    Mariano Rodriguez

    Full Text Available In hemodialysis patients, deviations from KDIGO recommended values of individual parameters, phosphate, calcium or parathyroid hormone (PTH, are associated with increased mortality. However, it is widely accepted that these parameters are not regulated independently of each other and that therapy aimed to correct one parameter often modifies the others. The aim of the present study is to quantify the degree of association between parameters of chronic kidney disease and mineral bone disease (CKD-MBD.Data was extracted from a cohort of 1758 adult HD patients between January 2000 and June 2013 obtaining a total of 46.141 records (10 year follow-up. We used an advanced data analysis system called Random Forest (RF which is based on self-learning procedure with similar axioms to those utilized for the development of artificial intelligence. This new approach is particularly useful when the variables analyzed are closely dependent to each other.The analysis revealed a strong association between PTH and phosphate that was superior to that of PTH and Calcium. The classical linear regression analysis between PTH and phosphate shows a correlation coefficient is 0.27, p<0.001, the possibility to predict PTH changes from phosphate modification is marginal. Alternatively, RF assumes that changes in phosphate will cause modifications in other associated variables (calcium and others that may also affect PTH values. Using RF the correlation coefficient between changes in serum PTH and phosphate is 0.77, p<0.001; thus, the power of prediction is markedly increased. The effect of therapy on biochemical variables was also analyzed using this RF.Our results suggest that the analysis of the complex interactions between mineral metabolism parameters in CKD-MBD may demand a more advanced data analysis system such as RF.

  8. Mosquito salivary gland protein preservation in the field for immunological and biochemical analysis

    Directory of Open Access Journals (Sweden)

    Almeras L

    2011-03-01

    Full Text Available Abstract Mosquito salivary proteins are involved in several biological processes that facilitate their blood feeding and have also been reported to elicit an IgG response in vertebrates. A growing number of studies have focused on this immunological response for its potential use as a biological marker of exposure to arthropod bites. As mosquito saliva collection is extremely laborious and inefficient, most research groups prefer to work on mosquito salivary glands (SGs. Thus, SG protein integrity is a critical factor in obtaining meaningful data from immunological and biochemical analysis. Current methodologies rely on an immediate freezing of SGs after their collection. However, the maintenance of samples in a frozen environment can be hard to achieve in field conditions. In this study, SG proteins from two mosquito species (Aedes aegypti and Anopheles gambiae s.s. stored in different media for 5 days at either +4°C or room temperature (RT were evaluated at the quantitative (i.e., ELISA and qualitative (i.e., SDS-PAGE and immunoblotting levels. Our results indicated that PBS medium supplemented with an anti-protease cocktail seems to be the best buffer to preserve SG antigens for 5 days at +4°C for ELISA analysis. Conversely, cell-lysis buffer (Urea-Thiourea-CHAPS-Tris was best at preventing protein degradation both at +4°C and RT for further qualitative analysis. These convenient storage methods provide an alternative to freezing and are expected to be applicable to other biological samples collected in the field.

  9. Biochemical and Molecular Analysis of the Hb Lepore Boston Washington in a Syrian Homozygous Child

    Directory of Open Access Journals (Sweden)

    Monica Pirastru

    2017-01-01

    Full Text Available Hemoglobin (Hb Lepore is composed of two normal α chains and two δβ fusion globins that arise from unequal crossover events between the δ- and β-globin genes. The Hb Lepore is widespread all over the world and in many ethnic groups. It includes some of the few clinically significant Hb variants that are associated with a β-thalassemia phenotype. Here, we describe the first occurrence of Hb Lepore Boston Washington in a Syrian individual. The patient, a 10-year-old child, shows severe anemia with a Hb level of 6.85 g/dL and typical thalassemic red cell indices. The diagnostic procedure implies hematological, biochemical, and molecular analysis, including multiplex ligation-dependent probe amplification (MLPA assay, GAP-PCR, and DNA sequencing. This latter allowed us to define the correct structure of the hybrid δβ-globin gene. The knowledge of the spectrum of mutations associated with different geographical areas is the prerequisite to set up large-scale screening programs and be able to offer genetic counseling to couples at risk.

  10. Seed Biochemical Analysis Based Profiling of Diverse Wheat Genetic Resource from Pakistan

    Science.gov (United States)

    Khalid, Anam; Hameed, Amjad

    2017-01-01

    Wheat is the major nutrient source worldwide. In Pakistan, it has a crucial place in agriculture as well as in national economy. For seed biochemical compositional analysis, wheat germplasm (77 genotypes) was collected from different agro-climatic zones of Pakistan. Significant variation (p sugar was found in Saleem-2000 (29.86 mg/g s. wt.), reducing sugars in Punjab-96 (12.68 mg/g s. wt.), non-reducing sugars in Saleem-2000 (27.33 mg/g s. wt.). However, highest albumins was identified in TC-4928 (352.89 mg/g s. wt.) and globulins in MEXI PAK (252.67 mg/g s. wt.), salt soluble proteins in Faisalabad-2008 (162.44 mg/g s. wt.), and total soluble proteins in Punjab-96 (487.33 mg/g s. wt.) indicating good quality of wheat genotypes as well as good nutritional status. Genotypes which have been ranked high in respective parameter can be employed in breeding to enhance the nutritional quality of wheat. PMID:28775731

  11. Biochemical analysis of the Hormoconis resinae fungal mycelium in the corrosion of aeronautical aluminium alloys

    International Nuclear Information System (INIS)

    Araya, R.; Bobadilla, C.; Vera, R.; Rosales, B. M.

    2007-01-01

    Biochemical analyses of the Hormoconis resinae fungal mycelium would explain behaviour differences of corrosive and non-corrosive strains of Al and its aeronautical alloys. In previous works its aggressiveness had been studied through SEM-EDX surface analysis, electrochemical techniques and immersion testing. In this paper separation of the proteins of the mycelium produced by a non-corrosive strain and its culture along three generations was performed. cultures were prepared in batch in the presence and absence of pure Al and AA 2024, AA 7005 and AA 7075 alloys. The mycelia grown throughout the three generations increasingly recovered usual characteristics at the third replication, included their corrosiveness on Al and its alloys previously shown by all out strains. Among the bio-molecule fractions isolated and analysed during this preliminary study only the proteins revealed changes with the generation grown. When this fungal strain was cultured in the presence of alloy metal sheets electrophoresis of the protean fraction was correlative with the distinct mycelia behaviour observed, including corrosiveness on Al and its alloys. (Author) 30 refs

  12. Attention-deficit hyperactivity disorder in adults: A systematic review and meta-analysis of genetic, pharmacogenetic and biochemical studies

    Science.gov (United States)

    Bonvicini, C; Faraone, S V; Scassellati, C

    2016-01-01

    The adult form of attention-deficit/hyperactivity disorder has a prevalence of up to 5% and is the most severe long-term outcome of this common disorder. Family studies in clinical samples as well as twin studies suggest a familial liability and consequently different genes were investigated in association studies. Pharmacotherapy with methylphenidate (MPH) seems to be the first-line treatment of choice in adults with attention-deficit hyperactive disorder (ADHD) and some studies were conducted on the genes influencing the response to this drug. Finally some peripheral biomarkers were identified in ADHD adult patients. We believe this work is the first systematic review and meta-analysis of candidate gene association studies, pharmacogenetic and biochemical (metabolomics) studies performed in adults with ADHD to identify potential genetic, predictive and peripheral markers linked specifically to ADHD in adults. After screening 5129 records, we selected 87 studies of which 61 were available for candidate gene association studies, 5 for pharmacogenetics and 21 for biochemical studies. Of these, 15 genetic, 2 pharmacogenetic and 6 biochemical studies were included in the meta-analyses. We obtained an association between adult ADHD and the gene BAIAP2 (brain-specific angiogenesis inhibitor 1-associated protein 2), even after Bonferroni correction, with any heterogeneity in effect size and no publication bias. If we did not apply the Bonferroni correction, a trend was found for the carriers allele 9R of dopamine transporter SLC6A3 40 bp variable tandem repeat polymorphism (VNTR) and for 6/6 homozygotes of SLC6A3 30 bp VNTR. Negative results were obtained for the 9-6 haplotype, the dopamine receptor DRD4 48 bp VNTR, and the enzyme COMT SNP rs4680. Concerning pharmacogenetic studies, no association was found for the SLC6A3 40 bp and response to MPH with only two studies selected. For the metabolomics studies, no differences between ADHD adults and controls were

  13. Geomicrobiology of Hydrothermal Vents in Yellowstone Lake: Phylogenetic and Functional Analysis suggest Importance of Geochemistry (Invited)

    Science.gov (United States)

    Inskeep, W. P.; Macur, R.; Jay, Z.; Clingenpeel, S.; Tenney, A.; Lavalvo, D.; Shanks, W. C.; McDermott, T.; Kan, J.; Gorby, Y.; Morgan, L. A.; Yooseph, S.; Varley, J.; Nealson, K.

    2010-12-01

    outflow channels of YNP. Analysis of functional genes present in the consensus metagenome sequence representing these populations indicate metabolic potential for oxidation of reduced sulfur and hydrogen, both of which are present at high concentrations in these vent ecosystems. Metagenome sequence of biomass associated with sediments from hydrothermal vents at Mary Bay (50 m depth) suggest greater archaeal and bacterial diversity in this environment, which may be due to higher concentrations of hydrogen, iron, and manganese measured in these environments. Results from metagenome sequence and modest 16S rRNA gene surveys from hydrothermal vent biomass indicate that several groups of novel thermophilic archaea inhabit these sites, and in many cases, are represented by organisms not found in YNP terrestrial geothermal environments that have been characterized to date. The hydrothermal vents from Inflated Plain and West Thumb indicate a linkage between various geochemical attributes (sulfide, hydrogen) and the metabolic potential associated with dominant Aquificales populations present in these communities.

  14. A Novel Quantitative Computed Tomographic Analysis Suggests How Sirolimus Stabilizes Progressive Air Trapping in Lymphangioleiomyomatosis.

    Science.gov (United States)

    Argula, Rahul G; Kokosi, Maria; Lo, Pechin; Kim, Hyun J; Ravenel, James G; Meyer, Cristopher; Goldin, Jonathan; Lee, Hye-Seung; Strange, Charlie; McCormack, Francis X

    2016-03-01

    The Multicenter International Lymphangioleiomyomatosis Efficacy and Safety of Sirolimus (MILES) trial demonstrated that sirolimus stabilized lung function and improved measures of functional performance and quality of life in patients with lymphangioleiomyomatosis. The physiologic mechanisms of these beneficial actions of sirolimus are incompletely understood. To prospectively determine the longitudinal computed tomographic lung imaging correlates of lung function change in MILES patients treated with placebo or sirolimus. We determined the baseline to 12-month change in computed tomographic image-derived lung volumes and the volume of the lung occupied by cysts in the 31 MILES participants (17 in sirolimus group, 14 in placebo group) with baseline and 12-month scans. There was a trend toward an increase in median expiratory cyst volume percentage in the placebo group and a reduction in the sirolimus group (+2.68% vs. +0.97%, respectively; P = 0.10). The computed tomographic image-derived residual volume and the ratio of residual volume to total lung capacity increased more in the placebo group than in the sirolimus group (+214.4 ml vs. +2.9 ml [P = 0.054] and +0.05 ml vs. -0.01 ml [P = 0.0498], respectively). A Markov transition chain analysis of respiratory cycle cyst volume changes revealed greater dynamic variation in the sirolimus group than in the placebo group at the 12-month time point. Collectively, these data suggest that sirolimus attenuates progressive gas trapping in lymphangioleiomyomatosis, consistent with a beneficial effect of the drug on airflow obstruction. We speculate that a reduction in lymphangioleiomyomatosis cell burden around small airways and cyst walls alleviates progressive airflow limitation and facilitates cyst emptying.

  15. Psychometric Analysis of the Barber Suggestibility Scale in a Clinical Population.

    Science.gov (United States)

    Pellicer Asensio, Xavier; Fusté Escolano, Adela; Ruiz Rodríguez, José

    2018-04-01

    The aim of the study was to administer the Barber suggestibility scale to a clinical population in Spain and to examine its psychometric properties therein. The reliability and factor structure of the adapted scale was compared with that of the original (American) scale and with data from two other versions (British and Puerto Rican samples). Sex differences in suggestibility were also analyzed. The Barber suggestibility scale was administered (without preliminaries) to a sample of 283 patients (130 women, 153 men) with a range of diagnoses: anxiety disorder (33.9%), substance-related and addictive disorder (25.8%), mood disorder (12.7%), somatic symptom disorder (4.6%), trauma- and stress-related disorder (3.5%), and other disorders (19.5%). Results indicated a higher degree of suggestibility among women, with the effect size being low (d = 0.26) for the objective subscale and moderate (d = 0.55) for the subjective subscale. Therefore, normative scores were reported by sex for both subscales. As a whole, the present clinical sample showed higher suggestibility than has been reported previously for nonclinical populations (p suggestibility scale showed a three-factor structure for the objective subscale and a more complex structure for the subjective subscale. These results suggest that the Barber suggestibility scale is a suitable instrument for assessing the degree of suggestibility in persons with a clinical disorder.

  16. Time from first detectable PSA following radical prostatectomy to biochemical recurrence: A competing risk analysis

    Science.gov (United States)

    de Boo, Leonora; Pintilie, Melania; Yip, Paul; Baniel, Jack; Fleshner, Neil; Margel, David

    2015-01-01

    Introduction: In this study, we estimated the time from first detectable prostate-specific antigen (PSA) following radical prostatectomy (RP) to commonly used definitions of biochemical recurrence (BCR). We also identified the predictors of time to BCR. Methods: We identified subjects who underwent a RP and had an undetectable PSA after surgery followed by at least 1 detectable PSA between 2000 and 2011. The primary outcome was time to BCR (PSA ≥0.2 and successive PSA ≥0.2) and prediction of the rate of PSA rise. Outcomes were calculated using a competing risk analysis, with univariable and multivariable Fine and Grey models. We employed a mixed effect model to test clinical predictors that are associated with the rate of PSA rise. Results: The cohort included 376 patients. The median follow-up from surgery was 60.5 months (interquartile range [IQR] 40.8–91.5) and from detectable PSA was 18 months (IQR 11–32). Only 45.74% (n = 172) had PSA values ≥0.2 ng/mL, while 15.16% (n = 57) reached the PSA level of ≥0.4 ng/mL and rising. On multivariable analysis, the values of the first detectable PSA and pathologic Gleason grade 8 or higher were consistently independent predictors of time to BCR. In the mixed effect model rate, the PSA rise was associated with time from surgery to first detectable PSA, Gleason score, and prostate volume. The main limitation of this study is the large proportion of patients that received treatment without reaching BCR. It is plausible that shorter estimated median times would occur at a centre that does not use salvage therapy at such an early state. Conclusion: The time from first detectable PSA to BCR may be lengthy. Our analyses of the predictors of the rate of PSA rise can help determine a personalized approach for patients with a detectable PSA after surgery. PMID:25624961

  17. Breastmilk donations: Bacteriological assessment, analysis of causes of non-compliance and suggestions for improvement.

    Science.gov (United States)

    Mullié, C; Obin, O; Outurquin, G; Grognet, S; Léké, A; Adjidé, C

    2018-05-01

    A total of 1099 breastmilk donations received by the milk bank at the Amiens University Hospital from January to June 2016 were assessed for bacteriological contamination according to French regulations. This consisted in enumerating the total aerobic flora before and after heat treatment as well as the specific enumeration of coagulase-positive staphylococci. Results above the mandatory limits for at least one of these parameters were found in 25.9% of the donations, resulting in the destruction of approximately one-quarter of the volume of the donations (∼195L). This is a huge loss in both economic and health-related terms for neonates, especially for pre-terms. To identify ways to improve the bacteriological assessment results and reduce the percentage of discarded milk, an analysis of the causes was conducted. The two main causes of non-compliance were the detection of a cultivable aerobic flora after heat treatment and the presence of coagulase-positive staphylococci above the mandatory limit (11.7% and 11.2% of the tested donations, respectively). Bacillus spp. were the leading cause of post-heat-treatment non-compliance. Therefore, the implementation of better environmental control could help reduce this kind of contamination. As for samples harboring coagulase-positive staphylococci, a further detection of toxins using molecular biology techniques could help discriminate actual health-hazardous donations that have to be destroyed while enabling the use of toxin-negative donations. Nevertheless, the economic viability of this proposal needs to be further assessed because these techniques are costly. Finally, a change in breastmilk dilutions used to enumerate the total aerobic flora to better reflect the actual level of these bacteria in the milk was proposed. Indeed, the comparison of various combinations of milk dilutions led to the conclusion that the association of the 1/10 and 1/100 dilutions was the best compromise between technical ease of

  18. Transcriptome and biochemical analysis of a flower color polymorphism in Silene littorea (Caryophyllaceae

    Directory of Open Access Journals (Sweden)

    Inés eCasimiro-Soriguer

    2016-02-01

    Full Text Available Flower color polymorphisms are widely used as model traits from genetics to ecology, yet determining the biochemical and molecular basis can be challenging. Anthocyanin-based flower color variations can be caused by at least 12 structural and three regulatory genes in the anthocyanin biosynthetic pathway. We use mRNA-Seq to simultaneously sequence and estimate expression of these candidate genes in nine samples of Silene littorea representing three color morphs (dark pink, light pink and white across three developmental stages in hopes of identifying the cause of flower color variation. We identified 29 putative paralogues for the 15 candidate genes in the anthocyanin biosynthetic pathway. We assembled complete coding sequences for 16 structural loci and nine of ten regulatory loci. Among these 29 putative paralogues, we identified 622 SNPs, yet only nine synonymous SNPs in Ans had allele frequencies that differentiated pigmented petals (dark pink and light pink from white petals. These Ans allele frequency differences were further investigated with an expanded sequencing survey of 38 individuals, yet no SNPs consistently differentiated the color morphs. We also found one locus, F3h1, with strong differential expression between pigmented and white samples (>42x. This may be caused by decreased expression of Myb1a in white petal buds. Myb1a in S. littorea is a regulatory locus closely related to Subgroup 7 Mybs known to regulate F3h and other loci in the first half of the ABP in model species. We then compare the mRNA-Seq results with petal biochemistry which revealed cyanidin as the primary anthocyanin and five flavonoid intermediates. Concentrations of three of the flavonoid intermediates were significantly lower in white petals than in pigmented petals (rutin, quercetin and isovitexin. The biochemistry results for rutin, quercetin, luteolin and apigenin are consistent with the transcriptome results suggesting a blockage at F3h, possibly caused

  19. Analysis of the reasons of recently some radioactive source accidents and suggestions for management countermeasures

    International Nuclear Information System (INIS)

    Su Yongjie; Feng Youcai; Song Chenxiu; Gao Huibin; Xing Jinsong; Pang Xinxin; Wang Xiaoqing; Wei Hong

    2007-01-01

    The article introduces recently some radioactive source accidents in China, and analyses the reasons of the accidents. Some important issues existed in the process of implementing new regulation were summarized, and some suggestions for managing radioactive sources are made. (authors)

  20. Kaizen practice in healthcare: a qualitative analysis of hospital employees' suggestions for improvement

    OpenAIRE

    Mazzocato, Pamela; Stenfors-Hayes, Terese; von Thiele Schwarz, Ulrica; Hasson, Henna; Nystr?m, Monica Elisabeth

    2016-01-01

    OBJECTIVES: Kaizen, or continuous improvement, lies at the core of lean. Kaizen is implemented through practices that enable employees to propose ideas for improvement and solve problems. The aim of this study is to describe the types of issues and improvement suggestions that hospital employees feel empowered to address through kaizen practices in order to understand when and how kaizen is used in healthcare. METHODS: We analysed 186 structured kaizen documents containing improvement suggest...

  1. An approach to standardization of urine sediment analysis via suggestion of a common manual protocol.

    Science.gov (United States)

    Ko, Dae-Hyun; Ji, Misuk; Kim, Sollip; Cho, Eun-Jung; Lee, Woochang; Yun, Yeo-Min; Chun, Sail; Min, Won-Ki

    2016-01-01

    The results of urine sediment analysis have been reported semiquantitatively. However, as recent guidelines recommend quantitative reporting of urine sediment, and with the development of automated urine sediment analyzers, there is an increasing need for quantitative analysis of urine sediment. Here, we developed a protocol for urine sediment analysis and quantified the results. Based on questionnaires, various reports, guidelines, and experimental results, we developed a protocol for urine sediment analysis. The results of this new protocol were compared with those obtained with a standardized chamber and an automated sediment analyzer. Reference intervals were also estimated using new protocol. We developed a protocol with centrifugation at 400 g for 5 min, with the average concentration factor of 30. The correlation between quantitative results of urine sediment analysis, the standardized chamber, and the automated sediment analyzer were generally good. The conversion factor derived from the new protocol showed a better fit with the results of manual count than the default conversion factor in the automated sediment analyzer. We developed a protocol for manual urine sediment analysis to quantitatively report the results. This protocol may provide a mean for standardization of urine sediment analysis.

  2. Analysis of accidents in uranium mines and suggestions on safety in production

    International Nuclear Information System (INIS)

    Xue Shiqian.

    1989-01-01

    The serious and fatal accidents happening in the uranium mines in China are descibed and analysed based on the classification, cause, age of the dead and economic losses brought by the accidents. The suggestions on safety in production are also presented

  3. Phylogenetic analysis suggests that sociality is associated with reduced effectiveness of selection

    DEFF Research Database (Denmark)

    Settepani, Virginia; Bechsgaard, Jesper Smærup; Bilde, Trine

    2016-01-01

    significantly between the social inbreeding and outcrossing species, but suggest a tendency for lower codon usage bias and higher dN/dS ratios in the social inbreeding species compared with their outcrossing congeners. The differences in dN/dS ratio and codon usage bias between social and subsocial species...

  4. Diagnosing and quantification of acute alcohol intoxication. Comparison of dual-energy CT with biochemical analysis. Initial experience

    International Nuclear Information System (INIS)

    Korkusuz, H.; Abbas Raschidi, B.; Keese, D.; Kromen, W.; Bauer, R.W.; Vogl, T.J.; Namgaladze, D.

    2012-01-01

    Purpose: To quantify the correlation between fat content of an acute alcohol intoxication and the difference of computer tomography attenuation value in dual-energy CT in comparison to biochemical triglyceride analysis and to evaluate qualitatively the value of DECT in the diagnosis of fatty liver caused by ethanol-dosage in rats. Materials and Methods: DECT at 140 kV and 80 kV was performed on 20 rats before and two days after the administration of 3 ml of 50 % ethanol. The CT attenuation value in the livers at 140 kV, 80 kV and the differences between them in Hounsfield units (ΔH) were collected. Parts of the liver (100 mg) were measured in biochemical triglyceride analysis as the reference standard. A blood sample was also taken to measure specific liver enzymes. Results: Linear correlation between biochemical triglyceride analysis and CT density of ΔH was found (r = 0.949). 140 kV attenuation data were between 44 HU and 61.3 HU, 80 kV attenuation data were between 58.4 HU and 64.7 HU, and ΔH data were between 3.4 HU and 14.4 HU (p ≤ 0.037). The biochemical triglyceride analysis data were between 7.1 mg/g and 41.1 mg/g. The hepatic enzymes serum aspartate (ASAT) aminotransferase and alanine aminotransferase (ALAT) were elevated in all rats. ASAT correlated directly with ΔHU (r = -0.86). Conclusion: DECT provides a non-invasive method to determine and evaluate hepatic fat content after acute alcohol intoxication. It provides the possibility to detect and quantify the hepatic fat content of liver graft. (orig.)

  5. Post-Foundational Discourse Analysis: A Suggestion for a Research Program

    Directory of Open Access Journals (Sweden)

    Tomas Marttila

    2015-08-01

    Full Text Available Post-foundational discourse analysis, also labeled as Essex School in Discourse Analysis, has been observed to suffer from a considerable methodological deficit that limits its applicability in empirical research. The principal aim of this article is to overcome this methodological deficit by constructing the research program of the post-foundational discourse analysis that facilitates its operationalization in empirical research. In accordance with Imre LAKATOS (1970 and David HOWARTH (2004a, a research program is referred to an internally consistent and openly scrutinizable system of theoretical, methodological and phenomenal concepts that opens up the possibility to distinguish between the "negative" and the "positive" heuristics of empirical research. The first three sections develop the positive heuristics of the post-foundational discourse analysis by elucidating its theoretical foundations, methodological position and phenomenal framework. The concluding fourth section draws on the presented positive heuristics to outline the analytical stages and strategies of the post-foundational discourse analysis and discusses suitable methods for sampling and interpreting empirical data. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs150319

  6. [Correlation analysis between biochemical and biophysical markers of endothelium damage in children with diabetes type 1].

    Science.gov (United States)

    Głowińska-Olszewska, Barbara; Urban, Mirosława; Tołwińska, Joanna; Peczyńska, Jadwiga; Florys, Bozena

    2005-01-01

    Endothelial damage is one of the earliest stages in the atherosclerosis process. Adhesion molecules, secreted from dysfunctional endothelial cells are considered as early markers of atherosclerotic disease. Ultrasonographic evaluation of brachial arteries serves to detect biophysical changes in endothelial function, and evaluation of carotid arteries intima-media thickness allows to evaluate the earliest structural changes in the vessels. The aim of the study was to the evaluate levels of selected adhesion molecules (sICAM-1, sVCAM-1, sE-selectin, sP-selectin) and endothelial function with use of brachial artery dilatation study (flow mediated dilation--FMD, nitroglycerine mediated dilation--NTGMD) and IMT in carotid arteries in children and adolescents with diabetes type 1, as well as the correlation analysis between biochemical and biophysical markers of endothelial dysfunction. We studied 76 children and adolescents, with mean age--15.6+/-2.5 years, suffering from diabetes mean 7.8+/-2.8 years, mean HbA1c--8.4+/-1.5%. Control group consisted of 33 healthy children age and gender matched. Adhesion molecules levels were estimated with the use of immunoenzymatic methods (R&D Systems). Endothelial function was evaluated by study of brachial arteries dilation--FMD, NTGMD, with ultrasonographic evaluation (Hewlett Packard Sonos 4500) after Celermajer method, and IMT after Pignoli method. In the study group we found elevated levels of sICAM-1: 309.54+/-64 vs. 277.85+/-52 ng/ml in the control group (p<00.05) and elevated level of sE-selectin: 87.81+/-35 vs. 66.21+/-22 ng/ml (p<00.05). We found significantly impaired FMD in brachial arteries in the study group--7.51+/-4.52 vs. 12.61+/-4.65% (p<00.05) and significantly higher IMT value: 0.51+/-0.07 vs. 0.42+/-0.05 mm (p<00.001). Correlation analysis revealed a significant negative correlation between sE-selectin and FMD - r=-0.33 (p=0.004), and a positive correlation between E-selectin and IMT: r=0.32 (p=0.005). 1. In

  7. The NREL Biochemical and Thermochemical Ethanol Conversion Processes: Financial and Environmental Analysis Comparison

    Directory of Open Access Journals (Sweden)

    Jesse Sky Daystar

    2015-07-01

    Full Text Available The financial and environmental performance of the National Renewable Energy Lab’s (NREL thermochemical and biochemical biofuel conversion processes are examined herein with pine, eucalyptus, unmanaged hardwood, switchgrass, and sweet sorghum. The environmental impacts of the process scenarios were determined by quantifying greenhouse gas (GHG emissions and TRACI impacts. Integrated financial and environmental performance metrics were introduced and used to examine the biofuel production scenarios. The thermochemical and biochemical conversion processes produced the highest financial performance and lowest environmental impacts when paired with pine and sweet sorghum, respectively. The high ash content of switchgrass and high lignin content of loblolly pine lowered conversion yields, resulting in the highest environmental impacts and lowest financial performance for the thermochemical and biochemical conversion processes, respectively. Biofuel produced using the thermochemical conversion process resulted in lower TRACI single score impacts and somewhat lower GHG emissions per megajoule (MJ of fuel than using the biochemical conversion pathway. The cost of carbon mitigation resulting from biofuel production and corresponding government subsidies was determined to be higher than the expected market carbon price. In some scenarios, the cost of carbon mitigation was several times higher than the market carbon price, indicating that there may be other more cost-effective methods of reducing carbon emissions.

  8. Time from first detectable PSA following radical prostatectomy to biochemical recurrence: A competing risk analysis

    NARCIS (Netherlands)

    L. De Boo (Leonora); M. Pintilie (Melania); P. Yip (Paul); J. Baniel (Jack); N.E. Fleshner (Neil); D. Margel (David)

    2015-01-01

    textabstractIntroduction: In this study, we estimated the time from first detectable prostate-specific antigen (PSA) following radical prostatectomy (RP) to commonly used definitions of biochemical recurrence (BCR). We also identified the predictors of time to BCR. Methods: We identified subjects

  9. MINERAL AND BIOCHEMICAL ANALYSIS OF VARIOUS PARTS OF CISSUS QUADRANGULARIS LINN

    OpenAIRE

    Udayakumar, R.; Sundaran, M.; Krishna, Raghuram

    2004-01-01

    Ash, minerals and biochemical contents were determined in various parts of root, stem and leaf of Cissus quadrangularis. The maximum ash content was observed in the root. The maximum concentration of carbohydrate and protein in the root and phosphorus, iron, calcium and lipids in the stem were observed.

  10. Phylogenetic analysis of of Sarcocystis nesbitti (Coccidia: Sarcocystidae) suggests a snake as its probable definitive host

    Science.gov (United States)

    Sarcocystis nesbitti was first described by Mandour in 1969 from rhesus monkey muscle. Its definitive host remains unknown. 18SrRNA gene of Sarcocystis nesbitti was amplified, sequenced, and subjected to phylogenetic analysis. Among those congeners available for comparison, it shares closest affinit...

  11. Rasch analysis suggested three unidimensional domains for Affiliate Stigma Scale: additional psychometric evaluation.

    Science.gov (United States)

    Chang, Chih-Cheng; Su, Jian-An; Tsai, Ching-Shu; Yen, Cheng-Fang; Liu, Jiun-Horng; Lin, Chung-Ying

    2015-06-01

    To examine the psychometrics of the Affiliate Stigma Scale using rigorous psychometric analysis: classical test theory (CTT) (traditional) and Rasch analysis (modern). Differential item functioning (DIF) items were also tested using Rasch analysis. Caregivers of relatives with mental illness (n = 453; mean age: 53.29 ± 13.50 years) were recruited from southern Taiwan. Each participant filled out four questionnaires: Affiliate Stigma Scale, Rosenberg Self-Esteem Scale, Beck Anxiety Inventory, and one background information sheet. CTT analyses showed that the Affiliate Stigma Scale had satisfactory internal consistency (α = 0.85-0.94) and concurrent validity (Rosenberg Self-Esteem Scale: r = -0.52 to -0.46; Beck Anxiety Inventory: r = 0.27-0.34). Rasch analyses supported the unidimensionality of three domains in the Affiliate Stigma Scale and indicated four DIF items (affect domain: 1; cognitive domain: 3) across gender. Our findings, based on rigorous statistical analysis, verified the psychometrics of the Affiliate Stigma Scale and reported its DIF items. We conclude that the three domains of the Affiliate Stigma Scale can be separately used and are suitable for measuring the affiliate stigma of caregivers of relatives with mental illness. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Computer aided plant engineering: An analysis and suggestions for computer use

    International Nuclear Information System (INIS)

    Leinemann, K.

    1979-09-01

    To get indications to and boundary conditions for computer use in plant engineering, an analysis of the engineering process was done. The structure of plant engineering is represented by a network of substaks and subsets of data which are to be manipulated. Main tool for integration of CAD-subsystems in plant engineering should be a central database which is described by characteristical requirements and a possible simple conceptual schema. The main features of an interactive system for computer aided plant engineering are shortly illustrated by two examples. The analysis leads to the conclusion, that an interactive graphic system for manipulation of net-like structured data, usable for various subtasks, should be the base for computer aided plant engineering. (orig.) [de

  13. Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis.

    Science.gov (United States)

    Salati, Simona; Zini, Roberta; Nuzzo, Simona; Guglielmelli, Paola; Pennucci, Valentina; Prudente, Zelia; Ruberti, Samantha; Rontauroli, Sebastiano; Norfo, Ruggiero; Bianchi, Elisa; Bogani, Costanza; Rotunno, Giada; Fanelli, Tiziana; Mannarelli, Carmela; Rosti, Vittorio; Salmoiraghi, Silvia; Pietra, Daniela; Ferrari, Sergio; Barosi, Giovanni; Rambaldi, Alessandro; Cazzola, Mario; Bicciato, Silvio; Tagliafico, Enrico; Vannucchi, Alessandro M; Manfredini, Rossella

    2016-04-01

    Primary myelofibrosis (PMF) is a Myeloproliferative Neoplasm (MPN) characterized by megakaryocyte hyperplasia, progressive bone marrow fibrosis, extramedullary hematopoiesis and transformation to Acute Myeloid Leukemia (AML). A number of phenotypic driver (JAK2, CALR, MPL) and additional subclonal mutations have been described in PMF, pointing to a complex genomic landscape. To discover novel genomic lesions that can contribute to disease phenotype and/or development, gene expression and copy number signals were integrated and several genomic abnormalities leading to a concordant alteration in gene expression levels were identified. In particular, copy number gain in the polyamine oxidase (PAOX) gene locus was accompanied by a coordinated transcriptional up-regulation in PMF patients. PAOX inhibition resulted in rapid cell death of PMF progenitor cells, while sparing normal cells, suggesting that PAOX inhibition could represent a therapeutic strategy to selectively target PMF cells without affecting normal hematopoietic cells' survival. Moreover, copy number loss in the chromatin modifier HMGXB4 gene correlates with a concomitant transcriptional down-regulation in PMF patients. Interestingly, silencing of HMGXB4 induces megakaryocyte differentiation, while inhibiting erythroid development, in human hematopoietic stem/progenitor cells. These results highlight a previously un-reported, yet potentially interesting role of HMGXB4 in the hematopoietic system and suggest that genomic and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage that characterizes PMF patients. © 2015 UICC.

  14. Striatal proteomic analysis suggests that first L-dopa dose equates to chronic exposure.

    Directory of Open Access Journals (Sweden)

    Birger Scholz

    Full Text Available L-3,4-dihydroxypheylalanine (L-dopa-induced dyskinesia represent a debilitating complication of therapy for Parkinson's disease (PD that result from a progressive sensitization through repeated L-dopa exposures. The MPTP macaque model was used to study the proteome in dopamine-depleted striatum with and without subsequent acute and chronic L-dopa treatment using two-dimensional difference in-gel electrophoresis (2D-DIGE and mass spectrometry. The present data suggest that the dopamine-depleted striatum is so sensitive to de novo L-dopa treatment that the first ever administration alone would be able (i to induce rapid post-translational modification-based proteomic changes that are specific to this first exposure and (ii, possibly, lead to irreversible protein level changes that would be not further modified by chronic L-dopa treatment. The apparent equivalence between first and chronic L-dopa administration suggests that priming would be the direct consequence of dopamine loss, the first L-dopa administrations only exacerbating the sensitization process but not inducing it.

  15. Mating type gene analysis in apparently asexual Cercospora species is suggestive of cryptic sex.

    Science.gov (United States)

    Groenewald, Marizeth; Groenewald, Johannes Z; Harrington, Thomas C; Abeln, Edwin C A; Crous, Pedro W

    2006-12-01

    The genus Cercospora consists of numerous important, apparently asexual plant pathogens. We designed degenerate primers from homologous sequences in related species to amplify part of the C. apii, C. apiicola, C. beticola, C. zeae-maydis and C. zeina mating type genes. Chromosome walking was used to determine the full length mating type genes of these species. Primers were developed to amplify and sequence homologous portions of the mating type genes of additional species. Phylogenetic analyses of these sequences revealed little variation among members of the C. apii complex, whereas C. zeae-maydis and C. zeina were found to be dissimilar. The presence of both mating types in approximately even proportions in C. beticola, C. zeae-maydis and C. zeina populations, in contrast to single mating types in C. apii (MAT1) and C. apiicola (MAT2), suggests that a sexual cycle may be active in some of these species.

  16. Three suggestions on the definition of terms for the safety and reliability analysis of digital systems

    International Nuclear Information System (INIS)

    Kim, Man Cheol; Smidts, Carol S.

    2015-01-01

    As digital instrumentation and control systems are being progressively introduced into nuclear power plants, a growing number of related technical issues are coming to light needing to be resolved. As a result, an understanding of relevant terms and basic concepts becomes increasingly important. Under the framework of the OECD/NEA WGRISK DIGREL Task Group, the authors were involved in reviewing definitions of terms forming the supporting vocabulary for addressing issues related to the safety and reliability analysis of digital instrumentation and control (SRA of DI and C). These definitions were extracted from various standards regulating the disciplines that form the technical and scientific basis of SRA DI and C. The authors discovered that different definitions are provided by different standards within a common discipline and used differently across various disciplines. This paper raises the concern that a common understanding of terms and basic concepts has not yet been established to address the very specific technical issues facing SRA DI and C. Based on the lessons learned from the review of the definitions of interest and the analysis of dependency relationships existing between these definitions, this paper establishes a set of recommendations for the development of a consistent terminology for SRA DI and C. - Highlights: ●We reviewed definitions of terms used in reliability analysis of digital systems. ●Different definitions are provided by different standards within a common discipline. ●Acyclic and cyclic structures of dependency in defining terms are compared. ●Three recommendations for the development of a consistent terminology provided

  17. Genome wide expression analysis suggests perturbation of vascular homeostasis during high altitude pulmonary edema.

    Directory of Open Access Journals (Sweden)

    Manish Sharma

    Full Text Available BACKGROUND: High altitude pulmonary edema (HAPE is a life-threatening form of non-cardiogenic edema which occurs in unacclimatized but otherwise normal individuals within two to four days after rapid ascent to altitude beyond 3000 m. The precise pathoetiology and inciting mechanisms regulating HAPE remain unclear. METHODOLOGY/PRINCIPLE FINDINGS: We performed global gene expression profiling in individuals with established HAPE compared to acclimatized individuals. Our data suggests concurrent modulation of multiple pathways which regulate vascular homeostasis and consequently lung fluid dynamics. These pathways included those which regulate vasoconstriction through smooth muscle contraction, cellular actin cytoskeleton rearrangements and endothelial permeability/dysfunction. Some notable genes within these pathways included MYLK; rho family members ARGEF11, ARHGAP24; cell adhesion molecules such as CLDN6, CLDN23, PXN and VCAM1 besides other signaling intermediates. Further, several important regulators of systemic/pulmonary hypertension including ADRA1D, ECE1, and EDNRA were upregulated in HAPE. We also observed significant upregulation of genes involved in paracrine signaling through chemokines and lymphocyte activation pathways during HAPE represented by transcripts of TNF, JAK2, MAP2K2, MAP2K7, MAPK10, PLCB1, ARAF, SOS1, PAK3 and RELA amongst others. Perturbation of such pathways can potentially skew vascular homeostatic equilibrium towards altered vascular permeability. Additionally, differential regulation of hypoxia-sensing, hypoxia-response and OXPHOS pathway genes in individuals with HAPE were also observed. CONCLUSIONS/SIGNIFICANCE: Our data reveals specific components of the complex molecular circuitry underlying HAPE. We show concurrent perturbation of multiple pathways regulating vascular homeostasis and suggest multi-genic nature of regulation of HAPE.

  18. QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance.

    Science.gov (United States)

    Klein, Anthony; Houtin, Hervé; Rond, Céline; Marget, Pascal; Jacquin, Françoise; Boucherot, Karen; Huart, Myriam; Rivière, Nathalie; Boutet, Gilles; Lejeune-Hénaut, Isabelle; Burstin, Judith

    2014-06-01

    Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea. The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9-71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.

  19. Bias due to Preanalytical Dilution of Rodent Serum for Biochemical Analysis on the Siemens Dimension Xpand Plus

    Directory of Open Access Journals (Sweden)

    Jennifer L. Johns

    2018-02-01

    Full Text Available Clinical pathology testing of rodents is often challenging due to insufficient sample volume. One solution in clinical veterinary and exploratory research environments is dilution of samples prior to analysis. However, published information on the impact of preanalytical sample dilution on rodent biochemical data is incomplete. The objective of this study was to evaluate the effects of preanalytical sample dilution on biochemical analysis of mouse and rat serum samples utilizing the Siemens Dimension Xpand Plus. Rats were obtained from end of study research projects. Mice were obtained from sentinel testing programs. For both, whole blood was collected via terminal cardiocentesis into empty tubes and serum was harvested. Biochemical parameters were measured on fresh and thawed frozen samples run straight and at dilution factors 2–10. Dilutions were performed manually, utilizing either ultrapure water or enzyme diluent per manufacturer recommendations. All diluted samples were generated directly from the undiluted sample. Preanalytical dilution caused clinically unacceptable bias in most analytes at dilution factors four and above. Dilution-induced bias in total calcium, creatinine, total bilirubin, and uric acid was considered unacceptable with any degree of dilution, based on the more conservative of two definitions of acceptability. Dilution often caused electrolyte values to fall below assay range precluding evaluation of bias. Dilution-induced bias occurred in most biochemical parameters to varying degrees and may render dilution unacceptable in the exploratory research and clinical veterinary environments. Additionally, differences between results obtained at different dilution factors may confound statistical comparisons in research settings. Comparison of data obtained at a single dilution factor is highly recommended.

  20. Epidemiologic analysis of families with isolated anorectal malformations suggests high prevalence of autosomal dominant inheritance.

    Science.gov (United States)

    Dworschak, Gabriel C; Zwink, Nadine; Schmiedeke, Eberhard; Mortazawi, Kiarasch; Märzheuser, Stefanie; Reinshagen, Konrad; Leonhardt, Johannes; Gómez, Barbara; Volk, Patrick; Rißmann, Anke; Jenetzky, Ekkehart; Reutter, Heiko

    2017-12-13

    Anorectal malformations (ARM) are rare abnormalities that occur in approximately 1 in 3000 live births with around 40% of patients presenting with isolated forms. Multiple familial cases reported, suggest underlying genetic factors that remain largely unknown. The recurrence in relatives is considered rare, however transmission rates of ARM by affected parents have never been determined before. The inheritance pattern of ARM was investigated in our database of patients with isolated ARM. Within our cohort of 327 patients with isolated ARM we identified eight adult patients from eight families who had in total 16 children with their healthy spouse. Of these ten had ARM, resulting in a recurrence risk of approximately one in two live births (10 of 16; 62%). From 226 families with 459 siblings we found two affected siblings in five families. Hence, the recurrence risk of ARM among siblings is approximately one in 92 live births (5 of 459; 1.0%). Comparing the observed recurrence risk in our cohort with the prevalence in the general population, we see a 1500-fold increase in recurrence risk for offspring and a 32-fold increase if a sibling is affected. The recurrence risk of approximately 62% indicates an autosomal dominant mode of inheritance. Reliable figures on recurrence of ARM are becoming increasingly important since improved surgical techniques are able to maintain sexual function resulting in more offspring of patients with ARM. These data allow more precise counseling of families with ARM and support the need for genetic studies.

  1. Analysis of orthopedic injuries in an airplane landing disaster and a suggested mechanism of trauma.

    Science.gov (United States)

    Mirzatolooei, Fardin; Bazzazi, Amirmohammad

    2013-04-01

    Survival after an airplane disaster is rare. We describe the injuries of survivors of an airplane accident and present a common mechanism of trauma for victims. Descriptive data were gathered by interviews with patients, physical examination. Review of charts and patients X-ray films. Informations regarding the flight characteristics were obtained from Iran air safety board. All dead patients were clinically examined by legal medicine department. The suggested mechanism of trauma was established according to present knowledge of mechanism of fractures. From 105 passengers, 27 survived. There was no mortality during hospital course. Between dead passengers, lower extremity fractures were the most common followed by chest wall fractures. Among the survivors, neurosurgical help was needed only in one case for shunt application. Brain concussions and effusions and one hematoma managed conservatively. Two laparotomies were performed for one splenectomy and two hepatoraphy. One pelvic fracture and two femur fractures were occurred. Tibia fractures were the most common (17) followed by spine (14) fractures. Ten tibial fractures were open, and 15 were in distal third. All tibia fractures were fixed with IM locking nails or locking plates. Eight posterior instrumentations were applied for seven burst and two fracture-dislocations. In this landing accident, a combination of vertical loading along with deceleration force produced burst fractures of spine and distal leg fractures.

  2. Comparative skull analysis suggests species-specific captivity-related malformation in lions (Panthera leo).

    Science.gov (United States)

    Saragusty, Joseph; Shavit-Meyrav, Anat; Yamaguchi, Nobuyuki; Nadler, Rona; Bdolah-Abram, Tali; Gibeon, Laura; Hildebrandt, Thomas B; Shamir, Merav H

    2014-01-01

    Lion (Panthera leo) populations have dramatically decreased worldwide with a surviving population estimated at 32,000 across the African savannah. Lions have been kept in captivity for centuries and, although they reproduce well, high rates of stillbirths as well as morbidity and mortality of neonate and young lions are reported. Many of these cases are associated with bone malformations, including foramen magnum (FM) stenosis and thickened tentorium cerebelli. The precise causes of these malformations and whether they are unique to captive lions remain unclear. To test whether captivity is associated with FM stenosis, we evaluated 575 lion skulls of wild (N = 512) and captive (N = 63) origin. Tiger skulls (N = 276; 56 captive, 220 wild) were measured for comparison. While no differences were found between males and females or between subadults and adults in FM height (FMH), FMH of captive lions (17.36±3.20 mm) was significantly smaller and with greater variability when compared to that in wild lions (19.77±2.11 mm). There was no difference between wild (18.47±1.26 mm) and captive (18.56±1.64 mm) tigers in FMH. Birth origin (wild vs. captive) as a factor for FMH remained significant in lions even after controlling for age and sex. Whereas only 20/473 wild lions (4.2%) had FMH equal to or smaller than the 5th percentile of the wild population (16.60 mm), this was evident in 40.4% (23/57) of captive lion skulls. Similar comparison for tigers found no differences between the captive and wild populations. Lions with FMH equal to or smaller than the 5th percentile had wider skulls with smaller cranial volume. Cranial volume remained smaller in both male and female captive lions when controlled for skull size. These findings suggest species- and captivity-related predisposition for the pathology in lions.

  3. The Trends and Prospects of Health Information Standards : Standardization Analysis and Suggestions

    International Nuclear Information System (INIS)

    Kim, Chang Soo

    2008-01-01

    Ubiquitous health care system, which is one of the developing solution technologies of IT, BT and NT, could give us new medical environments in future. Implementing health information systems can be complex, expensive and frustrating. Healthcare professionals seeking to acquire or upgrade systems do not have a convenient, reliable way of specifying a level of adherence to communication standards sufficient to achieve truly efficient interoperability. Great progress has been made in establishing such standards-DICOM, IHE and HL7, notably, are now highly advanced. IHE has defined a common framework to deliver the basic interoperability needed for local and regional health information networks. It has developed a foundational set of standards-based integration profiles for information exchange with three interrelated efforts. HL7 is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. Most SDOs produce standards (protocols) for a particular healthcare domain such as pharmacy, medical devices, imaging or insurance transactions. HL7's domain is clinical and administrative data. HL7 is an international community of healthcare subject matter experts and information scientists collaborating to create standards for the exchange, management and integration of electronic healthcare information. The ASTM specification for Continuity of Care Record was developed by subcommittee E31.28 on electronic health records, which includes clinicians, provider institutions, administrators, patient advocates, vendors, and health industry. In this paper, there are suggestions that provide a test bed, demonstration and specification of how standards such a IHE, HL7, ASTM can be used to provide an integrated environment.

  4. Comparative skull analysis suggests species-specific captivity-related malformation in lions (Panthera leo.

    Directory of Open Access Journals (Sweden)

    Joseph Saragusty

    Full Text Available Lion (Panthera leo populations have dramatically decreased worldwide with a surviving population estimated at 32,000 across the African savannah. Lions have been kept in captivity for centuries and, although they reproduce well, high rates of stillbirths as well as morbidity and mortality of neonate and young lions are reported. Many of these cases are associated with bone malformations, including foramen magnum (FM stenosis and thickened tentorium cerebelli. The precise causes of these malformations and whether they are unique to captive lions remain unclear. To test whether captivity is associated with FM stenosis, we evaluated 575 lion skulls of wild (N = 512 and captive (N = 63 origin. Tiger skulls (N = 276; 56 captive, 220 wild were measured for comparison. While no differences were found between males and females or between subadults and adults in FM height (FMH, FMH of captive lions (17.36±3.20 mm was significantly smaller and with greater variability when compared to that in wild lions (19.77±2.11 mm. There was no difference between wild (18.47±1.26 mm and captive (18.56±1.64 mm tigers in FMH. Birth origin (wild vs. captive as a factor for FMH remained significant in lions even after controlling for age and sex. Whereas only 20/473 wild lions (4.2% had FMH equal to or smaller than the 5th percentile of the wild population (16.60 mm, this was evident in 40.4% (23/57 of captive lion skulls. Similar comparison for tigers found no differences between the captive and wild populations. Lions with FMH equal to or smaller than the 5th percentile had wider skulls with smaller cranial volume. Cranial volume remained smaller in both male and female captive lions when controlled for skull size. These findings suggest species- and captivity-related predisposition for the pathology in lions.

  5. Communication failures in patient sign-out and suggestions for improvement: a critical incident analysis.

    Science.gov (United States)

    Arora, V; Johnson, J; Lovinger, D; Humphrey, H J; Meltzer, D O

    2005-12-01

    The transfer of care for hospitalized patients between inpatient physicians is routinely mediated through written and verbal communication or "sign-out". This study aims to describe how communication failures during this process can lead to patient harm. In interviews employing critical incident technique, first year resident physicians (interns) described (1) any adverse events or near misses due to suboptimal preceding patient sign-out; (2) the worst event due to suboptimal sign-out in which they were involved; and (3) suggestions to improve sign-out. All data were analyzed and categorized using the constant comparative method with independent review by three researchers. Twenty six interns caring for 82 patients were interviewed after receiving sign-out from another intern. Twenty five discrete incidents, all the result of communication failures during the preceding patient sign-out, and 21 worst events were described. Inter-rater agreement for categorization was high (kappa 0.78-1.00). Omitted content (such as medications, active problems, pending tests) or failure-prone communication processes (such as lack of face-to-face discussion) emerged as major categories of failed communication. In nearly all cases these failures led to uncertainty during decisions on patient care. Uncertainty may result in inefficient or suboptimal care such as repeat or unnecessary tests. Interns desired thorough but relevant face-to-face verbal sign-outs that reviewed anticipated issues. They preferred legible, accurate, updated, written sign-out sheets that included standard patient content such as code status or active and anticipated medical problems. Communication failures during sign-out often lead to uncertainty in decisions on patient care. These may result in inefficient or suboptimal care leading to patient harm.

  6. The Trends and Prospects of Health Information Standards : Standardization Analysis and Suggestions

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Chang Soo [Dept. of Radiological Science, College of Health Science, Catholic University of Pusan, Pusan (Korea, Republic of)

    2008-03-15

    Ubiquitous health care system, which is one of the developing solution technologies of IT, BT and NT, could give us new medical environments in future. Implementing health information systems can be complex, expensive and frustrating. Healthcare professionals seeking to acquire or upgrade systems do not have a convenient, reliable way of specifying a level of adherence to communication standards sufficient to achieve truly efficient interoperability. Great progress has been made in establishing such standards-DICOM, IHE and HL7, notably, are now highly advanced. IHE has defined a common framework to deliver the basic interoperability needed for local and regional health information networks. It has developed a foundational set of standards-based integration profiles for information exchange with three interrelated efforts. HL7 is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. Most SDOs produce standards (protocols) for a particular healthcare domain such as pharmacy, medical devices, imaging or insurance transactions. HL7's domain is clinical and administrative data. HL7 is an international community of healthcare subject matter experts and information scientists collaborating to create standards for the exchange, management and integration of electronic healthcare information. The ASTM specification for Continuity of Care Record was developed by subcommittee E31.28 on electronic health records, which includes clinicians, provider institutions, administrators, patient advocates, vendors, and health industry. In this paper, there are suggestions that provide a test bed, demonstration and specification of how standards such a IHE, HL7, ASTM can be used to provide an integrated environment.

  7. Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution.

    Science.gov (United States)

    Kumar, Narender; Mariappan, Vanitha; Baddam, Ramani; Lankapalli, Aditya K; Shaik, Sabiha; Goh, Khean-Lee; Loke, Mun Fai; Perkins, Tim; Benghezal, Mohammed; Hasnain, Seyed E; Vadivelu, Jamuna; Marshall, Barry J; Ahmed, Niyaz

    2015-01-01

    The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host-pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Main Consequences of IFRS Adoption: Analysis of Existing Literature and Suggestions for Further Research

    Directory of Open Access Journals (Sweden)

    Isabel Maria Estima Costa Lourenço

    2015-08-01

    Full Text Available This study characterizes the results of scientific research on the effect of adopting the International Financial Reporting Standards (IFRS that have been published in the most prestigious scientific journals in the field of accounting at the international level and it identifies avenues for further research. Based on the analysis of a set of 67 articles published by the accounting journals that make up the Social Sciences Citation Index (SSCI, published between 2000 and 2013, it is concluded that, as a general rule, IFRS adoption has a positive effect on information quality, the capital market, analysts' ability to predict, comparability, and information use. Nevertheless, this effect depends on some factors, such as country's characteristics (namely, the enforcement level and companies' characteristics. Sharing rules is not, by itself, enough to create a common business language, and management incentives and institutional factors play a major role in framing the characteristics of financial reporting. Finally, some gaps are identified in the literature and avenues for further research are introduced.

  9. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts

    Directory of Open Access Journals (Sweden)

    Normand Philippe

    2008-01-01

    genomes, suggesting that plant cell wall polysaccharide degradation may not be crucial to root infection, or that this degradation varies among strains. We hypothesize that the relative lack of secreted polysaccharide-degrading enzymes in Frankia reflects a strategy used by these bacteria to avoid eliciting host defense responses. The esterases, lipases, and proteases found in the core Frankia secretome might facilitate hyphal penetration through the cell wall, release carbon sources, or modify chemical signals. The core secretome also includes extracellular solute-binding proteins and Frankia-specific hypothetical proteins that may enable the actinorhizal symbiosis.

  10. Integrative analysis of transgenic alfalfa (Medicago sativa L. suggests new metabolic control mechanisms for monolignol biosynthesis.

    Directory of Open Access Journals (Sweden)

    Yun Lee

    2011-05-01

    Full Text Available The entanglement of lignin polymers with cellulose and hemicellulose in plant cell walls is a major biological barrier to the economically viable production of biofuels from woody biomass. Recent efforts of reducing this recalcitrance with transgenic techniques have been showing promise for ameliorating or even obviating the need for costly pretreatments that are otherwise required to remove lignin from cellulose and hemicelluloses. At the same time, genetic manipulations of lignin biosynthetic enzymes have sometimes yielded unforeseen consequences on lignin composition, thus raising the question of whether the current understanding of the pathway is indeed correct. To address this question systemically, we developed and applied a novel modeling approach that, instead of analyzing the pathway within a single target context, permits a comprehensive, simultaneous investigation of different datasets in wild type and transgenic plants. Specifically, the proposed approach combines static flux-based analysis with a Monte Carlo simulation in which very many randomly chosen sets of parameter values are evaluated against kinetic models of lignin biosynthesis in different stem internodes of wild type and lignin-modified alfalfa plants. In addition to four new postulates that address the reversibility of some key reactions, the modeling effort led to two novel postulates regarding the control of the lignin biosynthetic pathway. The first posits functionally independent pathways toward the synthesis of different lignin monomers, while the second postulate proposes a novel feedforward regulatory mechanism. Subsequent laboratory experiments have identified the signaling molecule salicylic acid as a potential mediator of the postulated control mechanism. Overall, the results demonstrate that mathematical modeling can be a valuable complement to conventional transgenic approaches and that it can provide biological insights that are otherwise difficult to obtain.

  11. Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators.

    Science.gov (United States)

    Mende, Susanne; Royer, Loic; Herr, Alexander; Schmiedel, Janet; Deschauer, Marcus; Klopstock, Thomas; Kostic, Vladimir S; Schroeder, Michael; Reichmann, Heinz; Storch, Alexander

    2011-07-01

    The heteroplasmic mitochondrial DNA (mtDNA) mutation A3243G causes the mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome as one of the most frequent mitochondrial diseases. The process of reconfiguration of nuclear gene expression profile to accommodate cellular processes to the functional status of mitochondria might be a key to MELAS disease manifestation and could contribute to its diverse phenotypic presentation. To determine master regulatory protein networks and disease-modifying genes in MELAS syndrome. Analyses of whole blood transcriptomes from 10 MELAS patients using a novel strategy by combining classic Affymetrix oligonucleotide microarray profiling with regulatory and protein interaction network analyses. Hierarchical cluster analysis elucidated that the relative abundance of mutant mtDNA molecules is decisive for the nuclear gene expression response. Further analyses confirmed not only transcription factors already known to be involved in mitochondrial diseases (such as TFAM), but also detected the hypoxia-inducible factor 1 complex, nuclear factor Y and cAMP responsive element-binding protein-related transcription factors as novel master regulators for reconfiguration of nuclear gene expression in response to the MELAS mutation. Correlation analyses of gene alterations and clinico-genetic data detected significant correlations between A3243G-induced nuclear gene expression changes and mutant mtDNA load as well as disease characteristics. These potential disease-modifying genes influencing the expression of the MELAS phenotype are mainly related to clusters primarily unrelated to cellular energy metabolism, but important for nucleic acid and protein metabolism, and signal transduction. Our data thus provide a framework to search for new pathogenetic concepts and potential therapeutic approaches to treat the MELAS syndrome.

  12. Analysis of Neogene deformation between Beaver, Utah and Barstow, California: Suggestions for altering the extensional paradigm

    Science.gov (United States)

    Anderson, R. Ernest; Beard, Sue; Mankinen, Edward A.; Hillhouse, John W.

    2013-01-01

    -scale coupling is critical to understanding major NS shortening and westerly tectonic escape in the Lake Mead area.One north-elongate uplift in the Hingeline shear zone is a positive flower structure along a strike-slip fault, and we postulate that most other large uplifts are diapiric, resulting from extension-normal inflow of ductile substrate, rather than second-order isostatic responses to tectonic unloading. We also postulate that large steep-axis rotations, and some small ones as well, result from basal tractions imparted by gradients in southerly directed subjacent ductile flow rather than by shear coupling imparted by laterally variable elongation strains. The shortening strain recorded in the rotations and related structures probably matches or exceeds the magnitude of lengthening, even for the Lake Mead area where we do not question local large (~65 km) west-directed lengthening. We assess the results of extensive recent earth-science research in the Lake Mead area and conclude that previously published models of N-S convergence, westerly tectonic rafting, and N-S occlusion are valid and record unique tectonic escape accommodation for south-directed displacement of the Great Basin sector of the Basin and Range. Genetic ties between the south-directed displacement and plate-interaction forces are elusive, and we suggest the displacement results from body forces inherent in the Basin and Range.

  13. A detailed radiobiological and dosimetric analysis of biochemical outcomes in a case-control study of permanent prostate brachytherapy patients

    International Nuclear Information System (INIS)

    Butler, Wayne M.; Stewart, Renee R.; Merrick, Gregory S.

    2009-01-01

    The purpose of this study is to determine dosimetric and radiobiological predictors of biochemical control after recalculation of prostate implant dosimetry using updated AAPM Task Group 43 (TG-43) parameters and the radiobiological parameters recommended by TG-137. All biochemical failures among patients implanted with 125 I or 103 Pd sources between 1994 and March 2006 were matched 2:1 with nonfailure controls. The individual matching was by risk group, radionuclide, prescribed dose, and time of implant (one match before and one after the failed patient) resulting in a median follow-up of 10.9 years. Complete dose volume histogram (DVH) data were recalculated for all 55 cases and 110 controls after updating the original source strength by the retrospectively determined ratios of TG-43. Differential DVH data were acquired in 179 increments of prostate volume versus percentage prescribed dose. At each incremental dose level i, the biologically equivalent dose BED i , equivalent uniform dose EUD i , and tumor control probability TCP i were calculated from the implant dose plus any external beam delivered to the patient. Total BED, EUD, and TCP were then derived from the incremental values for comparison with single point dosimetric quality parameters and DVH-based averages. There was no significant difference between failures and controls in terms of total BED (143 vs 142 Gy), EUD (95 vs 94 Gy), or TCP (0.87 vs 0.89). Conditional logistic regression analysis factored out the matching variables and stratified the cohort into each case and its controls, but no radiobiological parameter was predictive of biochemical failure. However, there was a significant difference between radiobiological parameters of 125 I and 103 Pd due to less complete coverage of the target volume by the former isotope. The implant BED and TCP were highly correlated with the D 90 and natural prescription doses and a series of mean DVH-based doses such as the harmonic mean and expressions of the

  14. Biochemical and genetic analysis of the Drk SH2/SH3 adaptor protein of Drosophila.

    OpenAIRE

    Raabe, T; Olivier, J P; Dickson, B J; Liu, X; Gish, G D; Pawson, T; Hafen, E

    1995-01-01

    The Drk SH3-SH2-SH3 adaptor protein has been genetically identified in a screen for rate-limiting components acting downstream of the Sevenless (Sev) receptor tyrosine kinase in the developing eye of Drosophila. It provides a link between the activated Sev receptor and Sos, a guanine nucleotide release factor that activates Ras1. We have used a combined biochemical and genetic approach to study the interactions between Sev, Drk and Sos. We show that Tyr2546 in the cytoplasmic tail of Sev is r...

  15. Analysis of Technetium Species and Fractions in Natural Seaweed Using Biochemical Separation and ICP-MS Measurement

    DEFF Research Database (Denmark)

    Shi, Keliang; Hou, Xiaolin; Qiao, Jixin

    2016-01-01

    An extremely high accumulation and retention of technetium in marine plants, especially brown seaweed, makes it a unique bioindicator of technetium. In the present work, a novel approach was developed for the speciation analysis of technetium in seaweed, wherein a series of biochemical separations....... Besides the inorganic species of TcO4-, most of technetium (>75%) combined with organic components of seaweed such as algin, cellulose, and pigment. This investigation could provide important fundamental knowledge for studying the processes and mechanisms of 99Tc accumulation in the natural seaweed....

  16. Methods in the use of GC/C/IRMS for the analysis of biochemical and pollutant isotope signatures of compounds

    International Nuclear Information System (INIS)

    Macko, S.A.; Engel, M.H.

    2001-01-01

    The potential for application of GC/C/IRMS analysis to any multitude of environmental, ecological or biochemical research areas is only beginning to be realized. Extension of compound-specific isotope analytical data derived from modern organisms and settings to yield interpretations of ancient depositional environments certainly appears possible. Further application of GC/C/IRMS approaches to understand the cycling of carbon and nitrogen, the identification and alteration of pollutants, or resolve metabolic relationships between compounds in living or extinct organisms are all within the scope of future research. (author)

  17. Aldehyde Dehydrogenases in Arabidopsis thaliana: Biochemical Requirements, Metabolic Pathways, and Functional Analysis.

    Science.gov (United States)

    Stiti, Naim; Missihoun, Tagnon D; Kotchoni, Simeon O; Kirch, Hans-Hubert; Bartels, Dorothea

    2011-01-01

    Aldehyde dehydrogenases (ALDHs) are a family of enzymes which catalyze the oxidation of reactive aldehydes to their corresponding carboxylic acids. Here we summarize molecular genetic and biochemical analyses of selected ArabidopsisALDH genes. Aldehyde molecules are very reactive and are involved in many metabolic processes but when they accumulate in excess they become toxic. Thus activity of aldehyde dehydrogenases is important in regulating the homeostasis of aldehydes. Overexpression of some ALDH genes demonstrated an improved abiotic stress tolerance. Despite the fact that several reports are available describing a role for specific ALDHs, their precise physiological roles are often still unclear. Therefore a number of genetic and biochemical tools have been generated to address the function with an emphasis on stress-related ALDHs. ALDHs exert their functions in different cellular compartments and often in a developmental and tissue specific manner. To investigate substrate specificity, catalytic efficiencies have been determined using a range of substrates varying in carbon chain length and degree of carbon oxidation. Mutational approaches identified amino acid residues critical for coenzyme usage and enzyme activities.

  18. Biochemical impact of soccer: an analysis of hormonal, muscle damage, and redox markers during the season.

    Science.gov (United States)

    Silva, João Renato; Rebelo, António; Marques, Franklim; Pereira, Laura; Seabra, André; Ascensão, António; Magalhães, José

    2014-04-01

    This study aimed to analyze changes in performance, muscle function, and stress-related biochemical markers in professional soccer players (n = 14) at 4 timepoints (3 for performance and 4 for stress-related biochemical markers) during the soccer season [Formula: see text] preseason (E1), midseason (E2), end of the season (E3) [Formula: see text] and after the end of the recovery period (E4). Performance in 5- and 30-m sprints, countermovement jump, and agility, and maximal isokinetic knee extension and knee flexion strength were measured (E1 to E3). We observed increased in-season levels of myoglobin (E2 > E1 and E4; p E1 and E4; p player during the competition period), performance, and hormonal and redox parameters (r = 0.456-0.615; p soccer players face significant changes in biomarkers of physiologic strain (muscle damage and oxidative stress-related markers) during the season, but values return to normal during the off-season. Additionally, MAT influences physical, hormonal, and oxidative stress-related parameters in professional soccer players.

  19. Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28.

    Directory of Open Access Journals (Sweden)

    Bonsu Ku

    Full Text Available Dual-specificity phosphatases (DUSPs constitute a subfamily of protein tyrosine phosphatases, and are intimately involved in the regulation of diverse parameters of cellular signaling and essential biological processes. DUSP28 is one of the DUSP subfamily members that is known to be implicated in the progression of hepatocellular and pancreatic cancers, and its biological functions and enzymatic characteristics are mostly unknown. Herein, we present the crystal structure of human DUSP28 determined to 2.1 Å resolution. DUSP28 adopts a typical DUSP fold, which is composed of a central β-sheet covered by α-helices on both sides and contains a well-ordered activation loop, as do other enzymatically active DUSP proteins. The catalytic pocket of DUSP28, however, appears hardly accessible to a substrate because of the presence of nonconserved bulky residues in the protein tyrosine phosphatase signature motif. Accordingly, DUSP28 showed an atypically low phosphatase activity in the biochemical assay, which was remarkably improved by mutations of two nonconserved residues in the activation loop. Overall, this work reports the structural and biochemical basis for understanding a putative oncological therapeutic target, DUSP28, and also provides a unique mechanism for the regulation of enzymatic activity in the DUSP subfamily proteins.

  20. What can we learn from global sensitivity analysis of biochemical systems?

    Science.gov (United States)

    Kent, Edward; Neumann, Stefan; Kummer, Ursula; Mendes, Pedro

    2013-01-01

    Most biological models of intermediate size, and probably all large models, need to cope with the fact that many of their parameter values are unknown. In addition, it may not be possible to identify these values unambiguously on the basis of experimental data. This poses the question how reliable predictions made using such models are. Sensitivity analysis is commonly used to measure the impact of each model parameter on its variables. However, the results of such analyses can be dependent on an exact set of parameter values due to nonlinearity. To mitigate this problem, global sensitivity analysis techniques are used to calculate parameter sensitivities in a wider parameter space. We applied global sensitivity analysis to a selection of five signalling and metabolic models, several of which incorporate experimentally well-determined parameters. Assuming these models represent physiological reality, we explored how the results could change under increasing amounts of parameter uncertainty. Our results show that parameter sensitivities calculated with the physiological parameter values are not necessarily the most frequently observed under random sampling, even in a small interval around the physiological values. Often multimodal distributions were observed. Unsurprisingly, the range of possible sensitivity coefficient values increased with the level of parameter uncertainty, though the amount of parameter uncertainty at which the pattern of control was able to change differed among the models analysed. We suggest that this level of uncertainty can be used as a global measure of model robustness. Finally a comparison of different global sensitivity analysis techniques shows that, if high-throughput computing resources are available, then random sampling may actually be the most suitable technique.

  1. Suggestions on performance of finite element limit analysis for eliminating the necessity of stress classifications in design and defect assessment

    Energy Technology Data Exchange (ETDEWEB)

    Fujioka, T. [Central Research Institute of Electric Power Industry, Tokyo (Japan)

    2001-07-01

    In structural design of a nuclear power component, stress classification from elastic stress analysis resultants is often used. Alternatively, to improve accuracy, finite element limit analysis may be performed. This paper examines some issues relating to the use of limit analysis; specifically, the treatment of multiple applied loads and the definition of the limit load from analysis using hardening plasticity laws. These are addressed both by detailed analysis for a simple geometry and by using the reference stress approach to estimate the inelastic displacement. The proposals are also applicable to a defect assessment of a cracked component, and treatment of distributed loads. It is shown that multiple or distributed loads should be treated as if they were applied proportionally irrespective of the actual nature of loads, and that the limit load from analysis with general plasticity laws may be estimated using a newly suggested reduced elastic slope method. (author)

  2. Suggestions on performance of finite element limit analysis for eliminating the necessity of stress classifications in design and defect assessment

    International Nuclear Information System (INIS)

    Fujioka, T.

    2001-01-01

    In structural design of a nuclear power component, stress classification from elastic stress analysis resultants is often used. Alternatively, to improve accuracy, finite element limit analysis may be performed. This paper examines some issues relating to the use of limit analysis; specifically, the treatment of multiple applied loads and the definition of the limit load from analysis using hardening plasticity laws. These are addressed both by detailed analysis for a simple geometry and by using the reference stress approach to estimate the inelastic displacement. The proposals are also applicable to a defect assessment of a cracked component, and treatment of distributed loads. It is shown that multiple or distributed loads should be treated as if they were applied proportionally irrespective of the actual nature of loads, and that the limit load from analysis with general plasticity laws may be estimated using a newly suggested reduced elastic slope method. (author)

  3. Biochemical System Analysis of Lutein Production by Heterotrophic Chlorella pyrenoidosa in a Fermentor

    Directory of Open Access Journals (Sweden)

    Zheng-Yun Wu

    2009-01-01

    Full Text Available Chlorella is a promising alternative source of lutein, as it can be cultivated heterotrophically with high efficiency. In this study, the carotenoids in Chlorella pyrenoidosa heterotrophically cultivated in a 19-litre fermentor have been analyzed and determined by using HPLC and HPLC-MS. A biochemical system theory (BST model was developed for understanding the regulatory features of carotenoid metabolism during the batch cultivation. Factors that influence lutein production by C. pyrenoidosa were discussed based on the model. It shows that low flux for lycopene formation is the major bottleneck for lutein production, while by-product syntheses and inhibitions affect the cellular lutein content much less. However, with further increase of the cellular lutein content, the inhibition on lycopene formation by lutein may become a limiting factor. Although speculative, these results may provide useful information for further elucidation of the regulatory mechanisms of carotenoid biosynthesis in Chlorella and modifying its metabolic network to enhance lutein production.

  4. Biochemical and topological analysis of bovine sperm cells induced by low power laser irradiation

    Science.gov (United States)

    Dreyer, T. R.; Siqueira, A. F. P.; Magrini, T. D.; Fiorito, P. A.; Assumpção, M. E. O. A.; Nichi, M.; Martinho, H. S.; Milazzotto, M. P.

    2011-07-01

    Low-level laser irradiation (LLLI) increases ATP production and energy supply to the cell which could increase sperm motility, acrossomal reaction and consequently the fertilizing potential. The aim of this study was to characterize the biochemical and topological changes induced by low power laser irradiation on bull sperm cells. Post-thawing sperm were irradiated with a 633nm laser with fluence rates of 30, 150 and 300mJ.cm-2 (power of 5mW for 1, 5 and 10minutes, respectively); 45, 230, and 450mJ.cm-2 (7.5mW for 1, 5 and 10 minutes); and 60, 300 and 600mJ.cm-2 (10mW for 1, 5 and 10 minutes). Biochemical and metabolical changes were analyzed by FTIR and flow cytometry; oxygen reactive species production was assessed by TBARS and the morphological changes were evaluated by AFM. Motility had no difference among times or powers of irradiation. Increasing in ROS generation was observed with power of 5mW compared to 7.5 and 10mW, and with 10min of irradiation in comparison with 5 and 1min of irradiation. This higher ROS generation was related to an increase in acrossomal and plasma membrane damage. FTIR results showed that the amount of lipids was inversely proportional to the quantity of ROS generated. AFM images showed morphological differences in plasma/acrossomal membrane, mainly on the equatorial region. We conclude that LLLI is an effective method to induce changes on sperm cell metabolism but more studies are necessary to establish an optimal dose to increase the fertility potential of these cells.

  5. Eight novel F13A1 gene missense mutations in patients with mild FXIII deficiency: in silico analysis suggests changes in FXIII-A subunit structure/function.

    Science.gov (United States)

    Biswas, Arijit; Ivaskevicius, Vytautas; Thomas, Anne; Varvenne, Michael; Brand, Brigitte; Rott, Hannelore; Haussels, Iris; Ruehl, Heiko; Scholz, Ute; Klamroth, Robert; Oldenburg, Johannes

    2014-10-01

    Mild FXIII deficiency is an under-diagnosed disorder because the carriers of this deficiency are often asymptomatic and reveal a phenotype only under special circumstances like surgery or induced trauma. Mutational reports from this type of deficiency have been rare. In this study, we present the phenotypic and genotypic data of nine patients showing mild FXIII-A deficiency caused by eight novel heterozygous missense mutations (Pro166Leu, Arg171Gln, His342Tyr, Gln415Arg, Leu529Pro, Gln601Lys, Arg703Gln and Arg715Gly) in the F13A1 gene. None of these variants were seen in 200 healthy controls. In silico structural analysis of the local wild-type protein structures (activated and non-activated) from X-ray crystallographic models downloaded from the protein databank identified potential structural/functional effects for the identified mutations. The missense mutations in the core domain are suggested to be directly influencing the catalytic triad. Mutations on other domains might influence other critical factors such as activation peptide cleavage or the barrel domain integrity. In vitro expression and subsequent biochemical studies in the future will be able to confirm the pathophysiological mechanisms proposed for the mutations in this article.

  6. Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis

    Directory of Open Access Journals (Sweden)

    Jolly Emmitt R

    2005-11-01

    Full Text Available Abstract Background A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. Results Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. Conclusion We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation.

  7. Biochemical analysis of plant protection afforded by a nonpathogenic endophytic mutant of Colletotrichum magna

    Energy Technology Data Exchange (ETDEWEB)

    Redman, R.S.; Rodriguez, R.J. (Geological Survey, Seattle, WA (United States) Univ. of Washington, Seattle, WA (United States). Dept. of Botany); Clifton, D.R.; Morrel, J.; Brown, G. (Geological Survey, Seattle, WA (United States)); Freeman, S. (Volcani Center, Bet Dagan (Israel). Dept. of Plant Pathology)

    1999-02-01

    A nonpathogenic mutant of Colletotrichum magna (path-1) was previously shown to protect watermelon (Citrullus lanatus) and cucumber (Cucumis sativus) seedlings from anthracnose disease elicited by wild-type C. magna. Disease protection was observed in stems of path-1-colonized cucurbits but not in cotyledons, indicating that path-1 conferred tissue-specific and/or localized protection. Plant biochemical indicators of a localized and systemic (peroxidase, phenylalanine ammonia-lyase, lignin, and salicylic acid) plant-defense response were investigated in anthracnose-resistant and-susceptible cultivars of cucurbit seedlings exposed to four treatments: (1) water (control), (2) path-1 conidia, (3) wild-type conidia, and (4) challenge conditions (inoculation into path-1 conidia for 48 h and then exposure to wild-type conidia). Collectively, these analyses indicated that disease protection in path-1-colonized plants was correlated with the ability of these plants to mount a defense response more rapidly and to equal or greater levels than plants exposed to wild-type C. magna alone. Watermelon plants colonized with path-1 were also protected against disease caused by Colletotrichum orbiculare and Fusarium oxysporum. A model based on the kinetics of plant-defense activation is presented to explain the mechanism of path-1-conferred disease protection.

  8. Mixotrophic growth and biochemical analysis of Chlorella vulgaris cultivated with diluted monosodium glutamate wastewater.

    Science.gov (United States)

    Ji, Yan; Hu, Wenrong; Li, Xiuqing; Ma, Guixia; Song, Mingming; Pei, Haiyan

    2014-01-01

    Monosodium glutamate wastewater (MSGW) is a potential medium for microbial cultivation because of containing abundant organic nutrient. This paper seeks to evaluate the feasibility of growing Chlorella vulgaris with MSGW and assess the influence of MSGW concentration on the biomass productivity and biochemical compositions. The MSGW diluted in different concentrations was prepared for microalga cultivation. C. vulgaris growth was greatly promoted with MSGW compared with the inorganic BG11 medium. C. vulgaris obtained the maximum biomass concentration (1.02 g/L) and biomass productivity (61.47 mg/Ld) with 100-time diluted MSGW. The harvested biomass was rich in protein (36.01-50.64%) and low in lipid (13.47-25.4%) and carbohydrate (8.94-20.1%). The protein nutritional quality and unsaturated fatty acids content of algal increased significantly with diluted MSGW. These results indicated that the MSGW is a feasible alternative for mass cultivation of C. vulgaris. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

    Science.gov (United States)

    Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

    2010-12-01

    Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

  10. Expression analysis and biochemical characterization of beans plants biofortificated with zinc

    Directory of Open Access Journals (Sweden)

    Sandra Pérez Álvarez

    2017-09-01

    Full Text Available The present work was carried out in greenhouse conditions at the Centro de Investigación en Alimentación y Desarrollo AC in Delicias, Chihuahua, México. Four different concentrations (0, 25, 50 and 100 μM L−1 of Zn chelate and sulfate were used to study the antioxidant system of Phaseolus vulgaris L. Three genes related with antioxidant activity [superoxide dismutase (SOD, glutathione peroxidase (GSH-Px and catalase (CAT] were selected for expression study. Results showed that when Zn chelate at 50 and 100 μM L−1 were applied SOD was repressed and GSH-Px expression was low at 0, 25 and 100 μM L−1 while with sulfate form SOD expression was low and GSH-Px expression was strong in all treatment. CAT was highly expressed in all form and treatments. For a biochemical study the same enzymes were spectrophotometrically measured. SOD activity shows differences in both forms of Zn, chelate form was different at 25, 50 and 100 μM L−1 with less activity at 100 μM L−1 and sulfate treatment shows differences in all concentrations used. GSH-Px activity shows significant differences with sulfate form at 25, 50 μM L−1 where at 50 μM the activity was higher and low at 100 μM L−1, CAT does not exhibit significant differences but with chelate treatment at 50–100 μM L−1 the activity was higher compared to sulfate. Finally, to raise the Zn concentration in bean under biofortification program is a promising strategy in cropping systems in order to increase the ingestion of zinc and antioxidant capacity in the general population and provided the benefits that this element offered in human health.

  11. Neuroprotective effect of edaravone in experimental glaucoma model in rats: a immunofluorescence and biochemical analysis

    Directory of Open Access Journals (Sweden)

    Arzu Toruk Aksar

    2015-04-01

    Full Text Available AIM: To evaluate the neuroprotective activity of systemically administered edaravone in early and late stage of experimental glaucoma in rats. METHODS: In this study, 60 Wistar albino rats were used. Experimental glaucoma model was created by injecting hyaluronic acid to the anterior chamber once a week for 6wk in 46 of 60 subjects. Fourteen subjects without any medication were included as control group. Edaravone administered intraperitoneally 3 mg/kg/d to the 15 of 30 subjects starting at the onset of glaucoma induction and also administered intraperitoneally 3 mg/kg/d to the other 15 subjects starting at three weeks after the onset of glaucoma induction. The other 16 subjects who underwent glaucoma induction was administered any therapy. Retinal ganglion cells (RGCs have been marked with dextran tetramethylrhodamine (DTMR retrograde at the end of the sixth week and after 48h, subjects were sacrificed by the method of cardiac perfusion. Alive RGC density was assessed in the whole-mount retina. Whole-mount retinal tissues homogenized and nitric oxide (NO, malondialdehyde (MDA and total antioxidant capacity (TAC values were measured biochemically. RESULTS: RGCs counted with Image-Pro Plus program, in the treatment group were found to be statistically significantly protected, compared to the glaucoma group (Bonferroni, P<0.05. The neuroprotective activity of edaravone was found to be more influential by administration at the start of the glaucoma process. Statistically significant lower NO levels were determined in the glaucoma group comparing treatment groups (Bonferroni, P<0.05. MDA levels were found to be highest in untreated glaucoma group, TAC levels were found to be lower in the glaucoma induction groups than the control group (Bonferroni, P<0.05. CONCLUSION: Systemic administration of Edaravone in experimental glaucoma showed potent neuroprotective activity. The role of oxidative stress causing RGC damage in glaucoma was supported by this

  12. Biochemical analysis of a papain-like protease isolated from the latex of Asclepias curassavica L.

    Science.gov (United States)

    Liggieri, Constanza; Obregon, Walter; Trejo, Sebastian; Priolo, Nora

    2009-02-01

    Most of the species belonging to Asclepiadaceae family usually secrete an endogenous milk-like fluid in a network of laticifer cells in which sub-cellular organelles intensively synthesize proteins and secondary metabolites. A new papain-like endopeptidase (asclepain c-II) has been isolated and characterized from the latex extracted from petioles of Asclepias curassavica L. (Asclepiadaceae). Asclepain c-II was the minor proteolytic component in the latex, but showed higher specific activity than asclepain c-I, the main active fraction previously studied. Both enzymes displayed quite distinct biochemical characteristics, confirming that they are different enzymes. Crude extract was purified by cation exchange chromatography (FPLC). Two active fractions, homogeneous by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and mass spectrometry, were isolated. Asclepain c-II displayed a molecular mass of 23,590 Da, a pI higher than 9.3, maximum proteolytic activity at pH 9.4-10.2, and showed poor thermostability. The activity of asclepain c-II is inhibited by cysteine proteases inhibitors like E-64, but not by any other protease inhibitors such as 1,10-phenantroline, phenylmethanesulfonyl fluoride, and pepstatine. The Nterminal sequence (LPSFVDWRQKGVVFPIRNQGQCGSCWTFSA) showed a high similarity with those of other plant cysteine proteinases. When assayed on N-alpha-CBZ-amino acid-p-nitrophenyl esters, the enzyme exhibited higher preference for the glutamine derivative. Determinations of kinetic parameters were performed with N-alpha-CBZ-L-Gln-p-nitrophenyl ester as substrate: K(m)=0.1634 mM, k(cat)=121.48 s(-1), and k(cat)/K(m)=7.4 x 10(5) s(-1)/mM.

  13. Analysis of the hematological and biochemical parameters related to lead intoxication.

    Science.gov (United States)

    Yılmaz, Hınç; Keten, Alper; Karacaoğlu, Emre; Tutkun, Engin; Akçan, Ramazan

    2012-11-01

    In parallel with industrial advancements, number of the occupational diseases secondary to chemical exposure is increasing. The chemical agents in the work places affect various organ and tissue systems, leading to chronic diseases. In this study, the cases diagnosed with occupational disease due to exposure to lead were studied and importance of the environmental forensic sciences on this issue was emphasized. A hundred and ninety patients diagnosed with occupational disease related to lead intoxication in Ankara Occupational Diseases Hospital between 01/01/2009 and 31/12/2009 were included in the study. Twenty cases were used as the controls. Sociodemographic characteristics, serum chemical parameters and hematological parameters of the patients were retrospectively assessed. Mean age of the cases included in the study was 35.3±8.69. Hemoglobin (Hb) (p=0.018) and Mean corpuscular volume (MCV) (plead exposure than in the controls. Gamma glutamyl transferase (GGT) was significantly lower in the patients with lead exposure than in the controls (p=0.002), whereas alkaline phosphatase (ALP) was found higher (plead exposure than in the control group (p=0.01), while Thyrotrophin-stimulating hormone (TSH) levels were lower (plead (Pb) was correlated positively with ALP values and negatively with Hb, MCV and TSH. Considering its effects on the biochemical and hematological parameters, a detailed investigation should be carried out in the cases with lead exposure, which occupies an important place among the occupational diseases. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  14. Robot-assisted radical prostatectomy has lower biochemical recurrence than laparoscopic radical prostatectomy: Systematic review and meta-analysis

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    Seon Heui Lee

    2017-05-01

    Full Text Available Purpose: To assess the effectiveness and safety of robot-assisted radical prostatectomy (RARP versus laparoscopic radical prostatectomy (LRP in the treatment of prostate cancer. Materials and Methods: Existing systematic reviews were updated to investigate the effectiveness and safety of RARP. Electronic databases, including Ovid MEDLINE, Ovid Embase, the Cochrane Library, KoreaMed, Kmbase, and others, were searched through July 2014. The quality of the selected systematic reviews was assessed by using the revised assessment of multiple systematic reviews (R-Amstar and the Cochrane Risk of Bias tool. Meta-analysis was performed by using Revman 5.2 (Cochrane Community and Comprehensive Meta-Analysis 2.0 (CMA; Biostat. Cochrane Q and I2 statistics were used to assess heterogeneity. Results: Two systematic reviews and 16 additional studies were selected from a search performed of existing systematic reviews. These included 2 randomized controlled clinical trials and 28 nonrandomized comparative studies. The risk of complications, such as injury to organs by the Clavien-Dindo classification, was lower with RARP than with LRP (relative risk [RR], 0.44; 95% confidence interval [CI], 1.23–0.85; p=0.01. The risk of urinary incontinence was lower (RR, 0.43; 95% CI, 0.31–0.60; p<0.000001 and the potency rate was significantly higher with RARP than with LRP (RR, 1.38; 95% CI, 1.11–1.70; I2 =78%; p=0.003. Regarding positive surgical margins, no significant difference in risk between the 2 groups was observed; however, the biochemical recurrence rate was lower after RARP than after LRP (RR, 0.59; 95% CI, 0.48–0.73; I2 =21%; p<0.00001. Conclusions: RARP appears to be a safe and effective technique compared with LRP with a lower complication rate, better potency, a higher continence rate, and a decreased rate of biochemical recurrence.

  15. Path analysis suggests phytoene accumulation is the key step limiting the carotenoid pathway in white carrot roots

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2005-01-01

    Full Text Available Two F2 carrot (Daucus carota L. populations (orange rooted Brasilia x very dark orange rooted High Carotene Mass - HCM cross and the dark orange rooted cultivated variety B493 x white rooted wild carrot Queen Anne's Lace - QAL cross with very unrelated genetic backgrounds were used to investigate intrinsic factors limiting carotenoid accumulation in carrots by applying phenotypic correlation and path analysis to study the relationships between major root carotenes, root color and several other morphological traits. Most of the correlations between traits were close and agreed in sign between the two populations. Root weight had a moderate to highly significant positive correlation with leaf length, root length and top and middle root diameter. Although phenotypic correlations failed to identify the order of the substrates and products in the carotenoid pathway the correct order of substrates and products (phytoene -> zeta-carotene -> lycopene was identified in the causal diagram of beta-carotene for the Brasilia x HCM population. Path analysis of beta-carotene synthesis in the B493 x QAL population suggested that selection for root carotenes had little effect on plant morphological traits. Causal model of beta-carotene and lycopene in the B493 x QAL population suggested that phytoene synthesis is the key step limiting the carotenoid pathway in white carrots. Path analysis, first presented by Sewall Wright to study quantitative traits, appears to be a powerful statistical approach for the identification of key compounds in complex pathways.

  16. Extensive in silico analysis of Mimivirus coded Rab GTPase homolog suggests a possible role in virion membrane biogenesis

    Directory of Open Access Journals (Sweden)

    Amrutraj eZade

    2015-09-01

    Full Text Available Rab GTPases are the key regulators of intracellular membrane trafficking in eukaryotes. Many viruses and intracellular bacterial pathogens have evolved to hijack the host Rab GTPase functions, mainly through activators and effector proteins, for their benefit. Acanthamoeba polyphaga mimivirus (APMV is one of the largest viruses and belongs to the monophyletic clade of nucleo-cytoplasmic large DNA viruses (NCLDV. The inner membrane lining is integral to the APMV virion structure. APMV assembly involves extensive host membrane modifications, like vesicle budding and fusion, leading to the formation of a membrane sheet that is incorporated into the virion. Intriguingly, APMV and all group I members of the Mimiviridae family code for a putative Rab GTPase protein. APMV is the first reported virus to code for a Rab GTPase (encoded by R214 gene. Our thorough in silico analysis of the subfamily specific (SF region of Mimiviridae Rab GTPase sequences suggests that they are related to Rab5, a member of the group II Rab GTPases, of lower eukaryotes. Because of their high divergence from the existing three isoforms, A, B and C of the Rab5-family, we suggest that Mimiviridae Rabs constitute a new isoform, Rab5D. Phylogenetic analysis indicated probable horizontal acquisition from a lower eukaryotic ancestor followed by selection and divergence. Furthermore, interaction network analysis suggests that vps34 (a Class III P13K homolog, coded by APMV L615, Atg-8 and dynamin (host proteins are recruited by APMV Rab GTPase during capsid assembly. Based on these observations, we hypothesize that APMV Rab plays a role in the acquisition of inner membrane during virion assembly.

  17. Comparative biochemical analysis after steam pretreatment of lignocellulosic agricultural waste biomass from Williams Cavendish banana plant (Triploid Musa AAA group).

    Science.gov (United States)

    Kamdem, Irénée; Jacquet, Nicolas; Tiappi, Florian Mathias; Hiligsmann, Serge; Vanderghem, Caroline; Richel, Aurore; Jacques, Philippe; Thonart, Philippe

    2015-11-01

    The accessibility of fermentable substrates to enzymes is a limiting factor for the efficient bioconversion of agricultural wastes in the context of sustainable development. This paper presents the results of a biochemical analysis performed on six combined morphological parts of Williams Cavendish Lignocellulosic Biomass (WCLB) after steam cracking (SC) and steam explosion (SE) pretreatments. Solid (S) and liquid (L) fractions (Fs) obtained from SC pretreatment performed at 180°C (SLFSC180) and 210°C (SLFSC210) generated, after diluted acid hydrolysis, the highest proportions of neutral sugar (NS) contents, specifically 52.82 ± 3.51 and 49.78 ± 1.39%w/w WCLB dry matter (DM), respectively. The highest proportions of glucose were found in SFSC210 (53.56 ± 1.33%w/w DM) and SFSC180 (44.47 ± 0.00%w/w DM), while the lowest was found in unpretreated WCLB (22.70 ± 0.71%w/w DM). Total NS content assessed in each LF immediately after SC and SE pretreatments was less than 2%w/w of the LF DM, thus revealing minor acid autohydrolysis consequently leading to minor NS production during the steam pretreatment. WCLB subjected to SC at 210 °C (SC210) generated up to 2.7-fold bioaccessible glucan and xylan. SC and SE pretreatments showed potential for the deconstruction of WCLB (delignification, depolymerization, decrystallization and deacetylation), enhancing its enzymatic hydrolysis. The concentrations of enzymatic inhibitors, such as 2-furfuraldehyde and 5-(hydroxymethyl)furfural from LFSC210, were the highest (41 and 21 µg ml(-1), respectively). This study shows that steam pretreatments in general and SC210 in particular are required for efficient bioconversion of WCLB. Yet, biotransformation through biochemical processes (e.g., anaerobic digestion) must be performed to assess the efficiency of these pretreatments. © The Author(s) 2015.

  18. Metabolic flux ratio analysis and cell staining suggest the existence of C4 photosynthesis in Phaeodactylum tricornutum.

    Science.gov (United States)

    Huang, A; Liu, L; Zhao, P; Yang, C; Wang, G C

    2016-03-01

    Mechanisms for carbon fixation via photosynthesis in the diatom Phaeodactylum tricornutum Bohlin were studied recently but there remains a long-standing debate concerning the occurrence of C4 photosynthesis in this species. A thorough investigation of carbon metabolism and the evidence for C4 photosynthesis based on organelle partitioning was needed. In this study, we identified the flux ratios between C3 and C4 compounds in P. tricornutum using (13)C-labelling metabolic flux ratio analysis, and stained cells with various cell-permeant fluorescent probes to investigate the likely organelle partitioning required for single-cell C4 photosynthesis. Metabolic flux ratio analysis indicated the C3/C4 exchange ratios were high. Cell staining indicated organelle partitioning required for single-cell C4 photosynthesis might exist in P. tricornutum. The results of (13)C-labelling metabolic flux ratio analysis and cell staining suggest single-cell C4 photosynthesis exists in P. tricornutum. This study provides insights into photosynthesis patterns of P. tricornutum and the evidence for C4 photosynthesis based on (13)C-labelling metabolic flux ratio analysis and organelle partitioning. © 2015 The Society for Applied Microbiology.

  19. Experimental burn plot trial in the Kruger National Park: history, experimental design and suggestions for data analysis

    Directory of Open Access Journals (Sweden)

    R. Biggs

    2003-12-01

    Full Text Available The experimental burn plot (EBP trial initiated in 1954 is one of few ongoing long-termfire ecology research projects in Africa. The trial aims to assess the impacts of differentfire regimes in the Kruger National Park. Recent studies on the EBPs have raised questions as to the experimental design of the trial, and the appropriate model specificationwhen analysing data. Archival documentation reveals that the original design was modified on several occasions, related to changes in the park's fire policy. These modifications include the addition of extra plots, subdivision of plots and changes in treatmentsover time, and have resulted in a design which is only partially randomised. The representativity of the trial plots has been questioned on account of their relatively small size,the concentration of herbivores on especially the frequently burnt plots, and soil variation between plots. It is suggested that these factors be included as covariates inexplanatory models or that certain plots be excluded from data analysis based on resultsof independent studies of these factors. Suggestions are provided for the specificationof the experimental design when analysing data using Analysis of Variance. It is concluded that there is no practical alternative to treating the trial as a fully randomisedcomplete block design.

  20. Techno-Economic Analysis of Biochemical Scenarios for Production of Cellulosic Ethanol

    Energy Technology Data Exchange (ETDEWEB)

    Kazi, F. K.; Fortman, J.; Anex, R.; Kothandaraman, G.; Hsu, D.; Aden, A.; Dutta, A.

    2010-06-01

    A techno-economic analysis on the production of cellulosic ethanol by fermentation was conducted to understand the viability of liquid biofuel production processes within the next 5-8 years. Initially, 35 technologies were reviewed, then a two-step down selection was performed to choose scenarios to be evaluated in a more detailed economic analysis. The lignocellulosic ethanol process was selected because it is well studied and portions of the process have been tested at pilot scales. Seven process variations were selected and examined in detail. Process designs were constrained to public data published in 2007 or earlier, without projecting for future process improvements. Economic analysis was performed for an 'nth plant' (mature technology) to obtain total investment and product value (PV). Sensitivity analysis was performed on PV to assess the impact of variations in process and economic parameters. Results show that the modeled dilute acid pretreatment process without any downstream process variation had the lowest PV of $3.40/gal of ethanol ($5.15/gallon of gasoline equivalent) in 2007 dollars. Sensitivity analysis shows that PV is most sensitive to feedstock and enzyme costs.

  1. Gene expression analysis and microdialysis suggest hypothalamic triiodothyronine (T3) gates daily torpor in Djungarian hamsters (Phodopus sungorus).

    Science.gov (United States)

    Bank, Jonathan H H; Cubuk, Ceyda; Wilson, Dana; Rijntjes, Eddy; Kemmling, Julia; Markovsky, Hanna; Barrett, Perry; Herwig, Annika

    2017-07-01

    Thyroid hormones play an important role in regulating seasonal adaptations of mammals. Several studies suggested that reduced availability of 3,3',5-triiodothyronine (T3) in the hypothalamus is required for the physiological adaptation to winter in Djungarian hamsters. We have previously shown that T3 is involved in the regulation of daily torpor, but it remains unclear, whether T3 affects torpor by central or peripheral mechanisms. To determine the effect of T3 concentrations within the hypothalamus in regulating daily torpor, we tested the hypothesis that low hypothalamic T3 metabolism would favour torpor and high T3 concentrations would not. In experiment 1 gene expression in torpid hamsters was assessed for transporters carrying thyroid hormones between cerebrospinal fluid and hypothalamic cells and for deiodinases enzymes, activating or inactivating T3 within hypothalamic cells. Gene expression analysis suggests reduced T3 in hypothalamic cells during torpor. In experiment 2, hypothalamic T3 concentrations were altered via microdialysis and torpor behaviour was continuously monitored by implanted body temperature transmitters. Increased T3 concentrations in the hypothalamus reduced expression of torpor as well as torpor bout duration and depth. Subsequent analysis of gene expression in the ependymal layer of the third ventricle showed clear up-regulation of T3 inactivating deiodinase 3 but no changes in several other genes related to photoperiodic adaptations in hamsters. Finally, serum analysis revealed that increased total T3 serum concentrations were not necessary to inhibit torpor expression. Taken together, our results are consistent with the hypothesis that T3 availability within the hypothalamus significantly contributes to the regulation of daily torpor via a central pathway.

  2. A Website to Improve Asthma Care by Suggesting Patient Questions for Physicians: Qualitative Analysis of User Experiences

    Science.gov (United States)

    Sciamanna, Christopher N; Blanch, Danielle C; Mui, Sarah; Lawless, Heather; Manocchia, Michael; Rosen, Rochelle K; Pietropaoli, Anthony

    2007-01-01

    Background Asthma is one of the most prevalent chronic conditions in the United Sates, yet despite the existence of national guidelines, nearly three fourths of patients with asthma do not have adequate control and clinical adherence to guidelines is low. While there are many reasons for this, physician inertia with respect to treatment change is partly to blame. Research suggests that patients who ask for specific tests and treatments are more likely to receive them. Objectives This study investigated the impact and experience of using an interactive patient website designed to give patients individual feedback about their condition and to suggest tailored questions for patients to ask their physician. The website was designed to be used prior to a physician visit, to increase the likelihood that patients would receive recommended tests and treatments. Methods A total of 37 adult patients with asthma participated in semi-structured telephone interviews aimed at eliciting information about their experiences with the website. Transcripts were coded using qualitative data analysis techniques and software. Themes were developed from subsets of codes generated through the analysis. In addition, 26 physicians were surveyed regarding their impressions of the website. Results Opportunities exist for improving website feedback, although the majority of both patient and physician respondents held favorable opinions about the site. Two major themes emerged regarding patients’ experiences with the website. First, many patients who used the website had a positive shift in their attitudes regarding interactions with their physicians. Second, use of the website prompted patients to become more actively involved in their asthma care. No patient reported any negative experiences as a result of using the website. Physicians rated the website positively. Conclusions Patients perceived that the interactive website intervention improved communication and interaction with their

  3. Biochemical and Computational Analysis of the Substrate Specificities of Cfr and RlmN Methyltransferases

    DEFF Research Database (Denmark)

    Ntokou, Eleni; Hansen, Lykke Haastrup; Kongsted, Jacob

    2015-01-01

    -ray structure of RlmN. We used a trinucleotide as target sequence and assessed its positioning at the active site for methylation. The calculations are in accordance with different poses of the trinucleotide in the two enzymes indicating major evolutionary changes to shift the C2/C8 specificities. To explore......Cfr and RlmN methyltransferases both modify adenine 2503 in 23S rRNA (Escherichia coli numbering). RlmN methylates position C2 of adenine while Cfr methylates position C8, and to a lesser extent C2, conferring antibiotic resistance to peptidyl transferase inhibitors. Cfr and RlmN show high sequence...... interchangeability between Cfr and RlmN we constructed various combinations of their genes. The function of the mixed genes was investigated by RNA primer extension analysis to reveal methylation at 23S rRNA position A2503 and by MIC analysis to reveal antibiotic resistance. The catalytic site is expected...

  4. Recent advances in biochemical and molecular analysis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency

    Directory of Open Access Journals (Sweden)

    Jin-Ho Choi

    2016-03-01

    Full Text Available The term congenital adrenal hyperplasia (CAH covers a group of autosomal recessive disorders caused by defects in one of the steroidogenic enzymes involved in the synthesis of cortisol or aldosterone from cholesterol in the adrenal glands. Approximately 95% of all CAH cases are caused by 21-hydroxylase deficiency encoded by the CYP21A2 gene. The disorder is categorized into classical forms, including the salt-wasting and the simple virilizing types, and nonclassical forms based on the severity of the disease. The severity of the clinical features varies according to the level of residual 21-hydroxylase activity. Newborn screening for CAH is performed in many countries to prevent salt-wasting crises in the neonatal period, to prevent male sex assignment in affected females, and to reduce long-term morbidities, such as short stature, gender confusion, and psychosexual disturbances. 17α-hydroxyprogesterone is a marker for 21-hydroxylase deficiency and is measured using a radioimmunoassay, an enzyme-linked immunosorbent assay, or a fluoroimmunoassay. Recently, liquid chromatography linked with tandem mass spectrometry was developed for rapid, highly specific, and sensitive analysis of multiple analytes. Urinary steroid analysis by gas chromatography mass spectrometry also provides qualitative and quantitative data on the excretion of steroid hormone metabolites. Molecular analysis of CYP21A2 is useful for genetic counseling, confirming diagnosis, and predicting prognoses. In conclusion, early detection using neonatal screening tests and treatment can prevent the worst outcomes of 21-hydroxylase deficiency.

  5. Spermine oxidase (SMO) activity in breast tumor tissues and biochemical analysis of the anticancer spermine analogues BENSpm and CPENSpm

    International Nuclear Information System (INIS)

    Cervelli, Manuela; Grillo, Rosalba; Woster, Patrick M; Casero, Robert A Jr; Mariottini, Paolo; Bellavia, Gabriella; Fratini, Emiliano; Amendola, Roberto; Polticelli, Fabio; Barba, Marco; Federico, Rodolfo; Signore, Fabrizio; Gucciardo, Giacomo

    2010-01-01

    Polyamine metabolism has a critical role in cell death and proliferation representing a potential target for intervention in breast cancer (BC). This study investigates the expression of spermine oxidase (SMO) and its prognostic significance in BC. Biochemical analysis of Spm analogues BENSpm and CPENSpm, utilized in anticancer therapy, was also carried out to test their property in silico and in vitro on the recombinant SMO enzyme. BC tissue samples were analyzed for SMO transcript level and SMO activity. Student's t test was applied to evaluate the significance of the differences in value observed in T and NT samples. The structure modeling analysis of BENSpm and CPENSpm complexes formed with the SMO enzyme and their inhibitory activity, assayed by in vitro experiments, were examined. Both the expression level of SMO mRNA and SMO enzyme activity were significantly lower in BC samples compared to NT samples. The modeling of BENSpm and CPENSpm complexes formed with SMO and their inhibition properties showed that both were good inhibitors. This study shows that underexpression of SMO is a negative marker in BC. The SMO induction is a remarkable chemotherapeutical target. The BENSpm and CPENSpm are efficient SMO inhibitors. The inhibition properties shown by these analogues could explain their poor positive outcomes in Phases I and II of clinical trials

  6. Spermine oxidase (SMO activity in breast tumor tissues and biochemical analysis of the anticancer spermine analogues BENSpm and CPENSpm

    Directory of Open Access Journals (Sweden)

    Gucciardo Giacomo

    2010-10-01

    Full Text Available Abstract Background Polyamine metabolism has a critical role in cell death and proliferation representing a potential target for intervention in breast cancer (BC. This study investigates the expression of spermine oxidase (SMO and its prognostic significance in BC. Biochemical analysis of Spm analogues BENSpm and CPENSpm, utilized in anticancer therapy, was also carried out to test their property in silico and in vitro on the recombinant SMO enzyme. Methods BC tissue samples were analyzed for SMO transcript level and SMO activity. Student's t test was applied to evaluate the significance of the differences in value observed in T and NT samples. The structure modeling analysis of BENSpm and CPENSpm complexes formed with the SMO enzyme and their inhibitory activity, assayed by in vitro experiments, were examined. Results Both the expression level of SMO mRNA and SMO enzyme activity were significantly lower in BC samples compared to NT samples. The modeling of BENSpm and CPENSpm complexes formed with SMO and their inhibition properties showed that both were good inhibitors. Conclusions This study shows that underexpression of SMO is a negative marker in BC. The SMO induction is a remarkable chemotherapeutical target. The BENSpm and CPENSpm are efficient SMO inhibitors. The inhibition properties shown by these analogues could explain their poor positive outcomes in Phases I and II of clinical trials.

  7. Raman Spectroscopic Analysis of Biochemical Changes in Individual Triglyceride-Rich Lipoproteins in the Pre- and Postprandial State

    Energy Technology Data Exchange (ETDEWEB)

    Chan, J; Motton, D; Rutledge, J; Keim, N; Huser, T

    2004-09-13

    Individual triglyceride-rich lipoprotein (TGRL) particles derived from human volunteers are non-destructively analyzed by laser tweezers Raman microspectroscopy and information on their composition and distribution is obtained. The Raman signature of single optically trapped very low-density lipoproteins (VLDL), a subclass of TGRL, which play an important role in cardiovascular disease, exhibits distinct peaks associated with molecular vibrations of fatty acids, proteins, lipids, and structural rearrangements of lipids. Our analysis of pre- and postprandial VLDL exhibits the signature of biochemical changes in individual lipoprotein particles following the consumption of meals. Interaction of VLDL with endothelium leads to the breakdown of complex triacylglycerols and the formation of a highly ordered core of free saturated fatty acids in the particle. A particle distribution analysis reveals trends in the degree to which this process has occurred in particles at different times during the postprandial period. Differences in particle distributions based on the different ratios of polyunsaturated to saturated fats in the consumed meals are also easily discerned. Individual lipoprotein particles hydrolyzed in-vitro through addition of lipoprotein lipase (LpL) exhibit strikingly similar changes in their Raman spectra. These results demonstrate the feasibility of monitoring the dynamics of lipid metabolism of individual TGRL particles as they interact with LpL in the endothelial cell wall using Raman spectroscopy.

  8. Different energy metabolism in two human small cell lung cancer subpopulations examined by 31P magnetic resonance spectroscopy and biochemical analysis in vivo and in vitro

    DEFF Research Database (Denmark)

    Kristjansen, P E; Spang-Thomsen, M; Quistorff, B

    1991-01-01

    Two human small cell lung cancer tumor lines, maintained as solid tumor xenografts on nude mice and as in vitro cell cultures, were studied by in vivo 31P magnetic resonance spectroscopy and by biochemical analysis of extracts of solid tumors and cell cultures. The tumor lines CPH SCCL 54A and CPH...

  9. When Does Maluma/Takete Fail? Two Key Failures and a Meta-Analysis Suggest That Phonology and Phonotactics Matter.

    Science.gov (United States)

    Styles, Suzy J; Gawne, Lauren

    2017-01-01

    Eighty-seven years ago, Köhler reported that the majority of students picked the same answer in a quiz: Which novel word form ('maluma' or 'takete') went best with which abstract line drawing (one curved, one angular). Others have consistently shown the effect in a variety of contexts, with only one reported failure by Rogers and Ross. In the spirit of transparency, we report our own failure in the same journal. In our study, speakers of Syuba, from the Himalaya in Nepal, do not show a preference when matching word forms 'kiki' and 'bubu' to spiky versus curvy shapes. We conducted a meta-analysis of previous studies to investigate the relationship between pseudoword legality and task effects. Our combined analyses suggest a common source for both of the failures: 'wordiness' - We believe these tests fail when the test words do not behave according to the sound structure of the target language.

  10. Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    William W. Lau

    2016-12-01

    Full Text Available Background: The proliferation of publicly accessible large-scale biological data together with increasing availability of bioinformatics tools have the potential to transform biomedical research. Here we report a crowdsourcing Jamboree that explored whether a team of volunteer biologists without formal bioinformatics training could use OMiCC, a crowdsourcing web platform that facilitates the reuse and (meta- analysis of public gene expression data, to compile and annotate gene expression data, and design comparisons between disease and control sample groups. Methods: The Jamboree focused on several common human autoimmune diseases, including systemic lupus erythematosus (SLE, multiple sclerosis (MS, type I diabetes (DM1, and rheumatoid arthritis (RA, and the corresponding mouse models. Meta-analyses were performed in OMiCC using comparisons constructed by the participants to identify 1 gene expression signatures for each disease (disease versus healthy controls at the gene expression and biological pathway levels, 2 conserved signatures across all diseases within each species (pan-disease signatures, and 3 conserved signatures between species for each disease and across all diseases (cross-species signatures. Results: A large number of differentially expressed genes were identified for each disease based on meta-analysis, with observed overlap among diseases both within and across species. Gene set/pathway enrichment of upregulated genes suggested conserved signatures (e.g., interferon across all human and mouse conditions. Conclusions: Our Jamboree exercise provides evidence that when enabled by appropriate tools, a "crowd" of biologists can work together to accelerate the pace by which the increasingly large amounts of public data can be reused and meta-analyzed for generating and testing hypotheses. Our encouraging experience suggests that a similar crowdsourcing approach can be used to explore other biological questions.

  11. Biochemical and mutational analysis of a novel nicotinamidase from Oceanobacillus iheyensis HTE831.

    Science.gov (United States)

    Sánchez-Carrón, Guiomar; García-García, María Inmaculada; Zapata-Pérez, Rubén; Takami, Hideto; García-Carmona, Francisco; Sánchez-Ferrer, Alvaro

    2013-01-01

    Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD(+) salvage pathway. This paper reports a new nicotinamidase from the deep-sea extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831 (OiNIC). The enzyme was active towards nicotinamide and several analogues, including the prodrug pyrazinamide. The enzyme was more nicotinamidase (kcat/Km  = 43.5 mM(-1)s(-1)) than pyrazinamidase (kcat/Km  = 3.2 mM(-1)s(-1)). Mutational analysis was carried out on seven critical amino acids, confirming for the first time the importance of Cys133 and Phe68 residues for increasing pyrazinamidase activity 2.9- and 2.5-fold, respectively. In addition, the change in the fourth residue involved in the ion metal binding (Glu65) was detrimental to pyrazinamidase activity, decreasing it 6-fold. This residue was also involved in a new distinct structural motif DAHXXXDXXHPE described in this paper for Firmicutes nicotinamidases. Phylogenetic analysis revealed that OiNIC is the first nicotinamidase described for the order Bacillales.

  12. Biochemical and mutational analysis of a novel nicotinamidase from Oceanobacillus iheyensis HTE831.

    Directory of Open Access Journals (Sweden)

    Guiomar Sánchez-Carrón

    Full Text Available Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD(+ salvage pathway. This paper reports a new nicotinamidase from the deep-sea extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831 (OiNIC. The enzyme was active towards nicotinamide and several analogues, including the prodrug pyrazinamide. The enzyme was more nicotinamidase (kcat/Km  = 43.5 mM(-1s(-1 than pyrazinamidase (kcat/Km  = 3.2 mM(-1s(-1. Mutational analysis was carried out on seven critical amino acids, confirming for the first time the importance of Cys133 and Phe68 residues for increasing pyrazinamidase activity 2.9- and 2.5-fold, respectively. In addition, the change in the fourth residue involved in the ion metal binding (Glu65 was detrimental to pyrazinamidase activity, decreasing it 6-fold. This residue was also involved in a new distinct structural motif DAHXXXDXXHPE described in this paper for Firmicutes nicotinamidases. Phylogenetic analysis revealed that OiNIC is the first nicotinamidase described for the order Bacillales.

  13. Neutron-activation analysis for investigation of biochemical manganese in soils cotton soweol zone of Uzbekistan

    International Nuclear Information System (INIS)

    Zhumamuratov, A.; Tillaev, T.; Khatamov, Sh.; Suvanov, M.; Osinskaya, N.S.; Rakhmanova, T.P.

    2004-01-01

    Full text: For many years we neutron activation analysis of soils sampled from different areas of landscape-geochemical regions of Uzbekistan including zone of extreme ecological catastrophe of Aral. Content of manganese and some other elements in the 'soil-cotton' system was investigated. Neutron-activation method of manganese determining with productivity up to 400 samples on shift with detection limit of 1,1 10 -5 % and discrepancies not more than 10%. Was developed extremely uniform distribution of manganese in cotton sowed soils of the Republic (340-1800mg/kg) is determined. Practically all soils of cotton-sowed zone of Republic are with lack of manganese. Distribution of manganese on soil profile of separate organs of cotton (leaves seeds etc.) was studied. Correlation between gross concentration of manganese and its active part extracted by distilled water on the basis of quantity analysis was found. Successive comparison of gross content of manganese in the soil with crop capacity of cotton in different zones of Republic made it possible to find interconnection between these quantities, which proves necessity of using micro-additions of manganese in the soils where its low concentration is detected

  14. Comparative binding characteristics of Tc-CPI, Tc-TBI, and Tc-MIBI in cultured heart cells: Correlation with biochemical analysis and animal images

    International Nuclear Information System (INIS)

    Piwnica-Worms, D.; Kronauge, J.F.; Holman, B.L.; Davison, A.; Jones, A.G.

    1987-01-01

    Hexakis (isonitrile)technetium (I) complexes are a new class of cationic, lipophilic myocaridal perfusion imaging agents. To better understand their cellular mechanisms of uptake and washout, chick heart cells grown in culture were used as a model myocardial system. Tc-MIBI showed uptake to a plateau at a rate similar to Tc-CPI (t1/2 = 4.1 +- 0.7 minutes); however, the plateau was 63% greater. Tc-TBI uptake approached a plateau 900% greater than Tc-CPI binding. Heart cell studies showed washout of Tc-CPI>Tc-TBI>Tc-MIBI, which correlated with kinetic analysis of rabbit myocardial images. Biochemical in vitro analysis in human plasma demonstrated 75% enzymatic ester hydrolysis of Tc-CPI by 3 minutes, but no hydrolysis of Tc-TBI and Tc-MIBI. The results suggest that metabolism of the ester function of Tc-CPI following myocardial uptake may in part account for the more rapid cellular washout rates of Tc-CPI compared with Tc-TBI and Tc-MIBI

  15. Biochemical Analysis of Two Single Mutants that Give Rise to a Polymorphic G6PD A-Double Mutant

    Directory of Open Access Journals (Sweden)

    Edson Jiovany Ramírez-Nava

    2017-10-01

    Full Text Available Glucose-6-phosphate dehydrogenase (G6PD is a key regulatory enzyme that plays a crucial role in the regulation of cellular energy and redox balance. Mutations in the gene encoding G6PD cause the most common enzymopathy that drives hereditary nonspherocytic hemolytic anemia. To gain insights into the effects of mutations in G6PD enzyme efficiency, we have investigated the biochemical, kinetic, and structural changes of three clinical G6PD variants, the single mutations G6PD A+ (Asn126AspD and G6PD Nefza (Leu323Pro, and the double mutant G6PD A− (Asn126Asp + Leu323Pro. The mutants showed lower residual activity (≤50% of WT G6PD and displayed important kinetic changes. Although all Class III mutants were located in different regions of the three-dimensional structure of the enzyme and were not close to the active site, these mutants had a deleterious effect over catalytic activity and structural stability. The results indicated that the G6PD Nefza mutation was mainly responsible for the functional and structural alterations observed in the double mutant G6PD A−. Moreover, our study suggests that the G6PD Nefza and G6PD A− mutations affect enzyme functions in a similar fashion to those reported for Class I mutations.

  16. Biochemical analysis of induced resistance in chickpea against broomrape (Orobanche foetida by rhizobia inoculation

    Directory of Open Access Journals (Sweden)

    Yassine MABROUK

    2016-05-01

    Full Text Available This study examined the capacity of Rhizobium sp. strain PchAZM to reduce parasitism of chickpea by Orobanche foetida under greenhouse conditions, and assessed the relative impact of rhizobia on the expression of chickpea defense response against broomrape. Growth chamber experiments using Petri dishes revealed that rhizobia infection on chickpea roots reduced broomrape seed germination, and restricted the broomrape attachment to host roots while retarding tubercle formation and development by the parasite. In pot experiments, chickpea roots inoculated with rhizobia reduced the total number of broomrape by up to 90%. Broomrape necrosis was observed both before and after parasite attachment to inoculated chickpea roots in Petri dishes and pot experiments. Reduction in infection was accompanied by enhanced levels of the defence-related enzymes phenylalanine ammonia lyase (PAL and peroxidase (POX. Increased levels of phenolics were recorded in the roots of rhizobia-inoculated plants grown in the presence of broomrape. The results suggest that rhizobia could be used for protection of chickpea against O. foetida.

  17. Biochemical and Molecular Analysis of Some Commercial Samples of Chilli Peppers from Mexico

    Directory of Open Access Journals (Sweden)

    Ivonne Guadalupe Troconis-Torres

    2012-01-01

    Full Text Available The genus Capsicum provides antioxidant compounds, such as phenolics and carotenoids, into the diet. In Mexico, there is a wide diversity of species and varieties of chilli peppers, a fruit which has local cultural and gastronomic importance. In the present study, the relationship of the carotenoid and phenolic profiles with the RAPD fingerprint of three different commercial cultivars of chilli peppers of seven regions of Mexico was investigated. Through RAPD, the species of chilli were differentiated by means of different primers (OPE-18, MFG-17, MFG-18, C51, and C52. The genetic distance found with OPE 18 was in the order of 2.6. The observed differences were maintained when the chromatographic profile of carotenoids, and the molecular markers were analyzed, which suggest a close relationship between carotenoids and the genetic profile. While the chromatographic profile of phenols and the molecular markers were unable to differentiate between genotypes of chilli peppers. In addition, by using infrared spectroscopy and statistical PCA, differences explained by geographic origin were found. Thus, this method could be an alternative for identification of chilli species with respect to their geographic origin.

  18. Using of a combined approach by biochemical and image analysis to develop a new method to estimate seed maturity stage for Bordeaux area grapevine

    Directory of Open Access Journals (Sweden)

    Amélie RABOT

    2017-03-01

    Full Text Available Aim: The importance of phenolic maturity (depending on tannins and anthocyans of the grape is crucial at harvest and determines the final quality of wine. The work presented here aims to characterize the evolution of phenolic maturity of seeds for 3 varieties combining macroscopic analysis and biochemical analyzes of these tannins at phenological stages of interest. Methods and results: Using R software for macroscopic analyzes have been shown that the color varies dramatically (from green to dark brown in the two months between the bunch closure and maturity. Biochemical analysis (HPLC measurement shows that tannins in seeds are increasing from bunch closure to early veraison and decrease after this step until maturity. Conclusion: All together these results have shown that the color variation is correlated to the tannins content in the seeds. Significance of the study: Nowadays, no easy ways of prediction of phenolic maturity are known. The aim of this work is to use these results (usually considered independently to have an knowledge of seed level of phenolic maturity necessary without biochemical analysis to establish a date of great harvest for the most favorable conditions for the extraction of tannins required for the organoleptic quality of a wine .The originality of this work is to use the combined visual seeds and its biochemical composition in tannins (correlation established by CPA. Forward, these results will help to develop a decision support tool based on simply system to acquiring seed image easily usable by winemakers.

  19. Comparative Biochemical and Functional Analysis of Viral and Human Secreted Tumor Necrosis Factor (TNF) Decoy Receptors*

    Science.gov (United States)

    Pontejo, Sergio M.; Alejo, Ali; Alcami, Antonio

    2015-01-01

    The blockade of tumor necrosis factor (TNF) by etanercept, a soluble version of the human TNF receptor 2 (hTNFR2), is a well established strategy to inhibit adverse TNF-mediated inflammatory responses in the clinic. A similar strategy is employed by poxviruses, encoding four viral TNF decoy receptor homologues (vTNFRs) named cytokine response modifier B (CrmB), CrmC, CrmD, and CrmE. These vTNFRs are differentially expressed by poxviral species, suggesting distinct immunomodulatory properties. Whereas the human variola virus and mouse ectromelia virus encode one vTNFR, the broad host range cowpox virus encodes all vTNFRs. We report the first comprehensive study of the functional and binding properties of these four vTNFRs, providing an explanation for their expression profile among different poxviruses. In addition, the vTNFRs activities were compared with the hTNFR2 used in the clinic. Interestingly, CrmB from variola virus, the causative agent of smallpox, is the most potent TNFR of those tested here including hTNFR2. Furthermore, we demonstrate a new immunomodulatory activity of vTNFRs, showing that CrmB and CrmD also inhibit the activity of lymphotoxin β. Similarly, we report for the first time that the hTNFR2 blocks the biological activity of lymphotoxin β. The characterization of vTNFRs optimized during virus-host evolution to modulate the host immune response provides relevant information about their potential role in pathogenesis and may be used to improve anti-inflammatory therapies based on soluble decoy TNFRs. PMID:25940088

  20. Comparative Biochemical and Functional Analysis of Viral and Human Secreted Tumor Necrosis Factor (TNF) Decoy Receptors.

    Science.gov (United States)

    Pontejo, Sergio M; Alejo, Ali; Alcami, Antonio

    2015-06-26

    The blockade of tumor necrosis factor (TNF) by etanercept, a soluble version of the human TNF receptor 2 (hTNFR2), is a well established strategy to inhibit adverse TNF-mediated inflammatory responses in the clinic. A similar strategy is employed by poxviruses, encoding four viral TNF decoy receptor homologues (vTNFRs) named cytokine response modifier B (CrmB), CrmC, CrmD, and CrmE. These vTNFRs are differentially expressed by poxviral species, suggesting distinct immunomodulatory properties. Whereas the human variola virus and mouse ectromelia virus encode one vTNFR, the broad host range cowpox virus encodes all vTNFRs. We report the first comprehensive study of the functional and binding properties of these four vTNFRs, providing an explanation for their expression profile among different poxviruses. In addition, the vTNFRs activities were compared with the hTNFR2 used in the clinic. Interestingly, CrmB from variola virus, the causative agent of smallpox, is the most potent TNFR of those tested here including hTNFR2. Furthermore, we demonstrate a new immunomodulatory activity of vTNFRs, showing that CrmB and CrmD also inhibit the activity of lymphotoxin β. Similarly, we report for the first time that the hTNFR2 blocks the biological activity of lymphotoxin β. The characterization of vTNFRs optimized during virus-host evolution to modulate the host immune response provides relevant information about their potential role in pathogenesis and may be used to improve anti-inflammatory therapies based on soluble decoy TNFRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Infantile Refsum's disease: biochemical findings suggesting multiple peroxisomal dysfunction

    NARCIS (Netherlands)

    Poll-The, B. T.; Saudubray, J. M.; Ogier, H.; Schutgens, R. B.; Wanders, R. J.; Schrakamp, G.; van den Bosch, H.; Trijbels, J. M.; Poulos, A.; Moser, H. W.

    1986-01-01

    Infantile Refsum's disease was diagnosed in three male patients, presenting with facial dysmorphia, retinitis pigmentosa, neurosensory hearing loss, hepatomegaly, osteopenia and delayed growth and psychomotor development. An elevated plasma phytanic acid concentration and a deficient phytanic acid

  2. Molecular and biochemical analysis of conjugation and adolescence in Tetrahymena thermophila

    International Nuclear Information System (INIS)

    Rogers, M.B.

    1986-01-01

    A previously unrecognized stage in the development of sexual maturity in Tetrahymena thermophila, adolescence, has been described. When the progeny of successfully mated cells are grown logarithmically, they are unable to form mating pairs for about 65 generations. This period is known as immaturity. During the next stage, adolescence, the progeny pair with mature cells but not with other adolescent cells despite the presence of complementary mating types. Adolescence persists for 20-25 generations before the cells attain maturity (the ability to mate with any cell of different mating type). Once paired with mature cells, adolescents successfully complete conjugation was shown genetically. Mating pairs formed between adolescent and mature cells are indistinguishable from those formed between mature cells by the criteria of cytology and two-dimensional gel electrophoresis of proteins extracted from mating pairs pulse-labelled with [ 35 S]methionine. An analysis of proteins induced during the first ten hours of conjugation was carried out using two-dimensional gel electrophoresis. The protein patterns obtained from all controls were similar. The synthesis of numerous large and basic proteins were induced during conjugation. The majority of the proteins were detected during meiosis and none were mating type specific. A library of micronuclear DNA was constructed in the plasmic PUC18. The library was screened by differential colony hybridization using cDNA complementary to polyA + RNA isolated from conjugating and control cells. Eight recombinant clones were isolated which contain sequences transcriptionally induced in conjugating cells

  3. Biochemical characterisation and dietary fibre analysis of sugar beet supplemented cookies

    International Nuclear Information System (INIS)

    Pasha, I.; Jahangir, M.F.; Akhter, S.; Manzoor, M.S.

    2016-01-01

    This study was planned to utilize sugar beet powder as a rich source of dietary fibre in cookies. Purposely, five treatments namely T1, T2, T3, T4 and T5 with 4%, 8%, 12%, 16% and 20% sugar beet powder addition in wheat flour were chosen to estimate fibre, antioxidant profiling and engineering properties of cookies. Results showed an increased content of all above mentioned parameters. With the increment in sugar beet powder addition in treatments, dietary fibre analysis have shown that total dietary fibre (TDF), insoluble dietary fibre (IDF) and soluble dietary fibre (SDF) have depicted increasing trend with maximum for T5 for all dietary fibre types. Significant results were obtained for in vitro antioxidant studies including total phenolic content (TPC) and DPPH that showed increasing trend with T1 0.6 mg GAE/g and maximum values for T5 with 2.0 mg GAE/g for TPC and for DPPH with T5 being maximum value of 1.7% and minimum for T1 with 1.3%. T5 treatment with 20% sugar beet gave best physicochemical results but disturbed sensory properties while T3 with 12% sugar beet powder showed good physicochemical and sensory characteristics. Therefore, T3 with 12% level is considered as the best source of dietary fibre in bakery products and can be considered as the prospective choice to address metabolic syndromes. (author)

  4. Biochemical Stability Analysis of Nano Scaled Contrast Agents Used in Biomolecular Imaging Detection of Tumor Cells

    Science.gov (United States)

    Kim, Jennifer; Kyung, Richard

    Imaging contrast agents are materials used to improve the visibility of internal body structures in the imaging process. Many agents that are used for contrast enhancement are now studied empirically and computationally by researchers. Among various imaging techniques, magnetic resonance imaging (MRI) has become a major diagnostic tool in many clinical specialties due to its non-invasive characteristic and its safeness in regards to ionizing radiation exposure. Recently, researchers have prepared aqueous fullerene nanoparticles using electrochemical methods. In this paper, computational simulations of thermodynamic stabilities of nano scaled contrast agents that can be used in biomolecular imaging detection of tumor cells are presented using nanomaterials such as fluorescent functionalized fullerenes. In addition, the stability and safety of different types of contrast agents composed of metal oxide a, b, and c are tested in the imaging process. Through analysis of the computational simulations, the stabilities of the contrast agents, determined by optimized energies of the conformations, are presented. The resulting numerical data are compared. In addition, Density Functional Theory (DFT) is used in order to model the electron properties of the compound.

  5. Biochemical and structural analysis of the hyperpolarization-activated K(+) channel MVP.

    Science.gov (United States)

    Randich, Amelia M; Cuello, Luis G; Wanderling, Sherry S; Perozo, Eduardo

    2014-03-18

    In contrast to the majority of voltage-gated ion channels, hyperpolarization-activated channels remain closed at depolarizing potentials and are activated at hyperpolarizing potentials. The basis for this reverse polarity is thought to be a result of differences in the way the voltage-sensing domain (VSD) couples to the pore domain. In the absence of structural data, the molecular mechanism of this reverse polarity coupling remains poorly characterized. Here we report the characterization of the structure and local dynamics of the closed activation gate (lower S6 region) of MVP, a hyperpolarization-activated potassium channel from Methanococcus jannaschii, by electron paramagnetic resonance (EPR) spectroscopy. We show that a codon-optimized version of MVP has high expression levels in Escherichia coli, is purified as a stable tetramer, and exhibits expected voltage-dependent activity when reconstituted in liposomes. EPR analysis of the mid to lower S6 region revealed positions exhibiting strong spin-spin coupling, indicating that the activation gate of MVP is closed at 0 mV. A comparison of local environmental parameters along the activation gate for MVP and KcsA indicates that MVP adopts a different closed conformation. These structural details set the stage for future evaluations of reverse electromechanical coupling in MVP.

  6. Biochemical and Structural Analysis of the Hyperpolarization-Activated K+ Channel MVP

    Science.gov (United States)

    2015-01-01

    In contrast to the majority of voltage-gated ion channels, hyperpolarization-activated channels remain closed at depolarizing potentials and are activated at hyperpolarizing potentials. The basis for this reverse polarity is thought to be a result of differences in the way the voltage-sensing domain (VSD) couples to the pore domain. In the absence of structural data, the molecular mechanism of this reverse polarity coupling remains poorly characterized. Here we report the characterization of the structure and local dynamics of the closed activation gate (lower S6 region) of MVP, a hyperpolarization-activated potassium channel from Methanococcus jannaschii, by electron paramagnetic resonance (EPR) spectroscopy. We show that a codon-optimized version of MVP has high expression levels in Escherichia coli, is purified as a stable tetramer, and exhibits expected voltage-dependent activity when reconstituted in liposomes. EPR analysis of the mid to lower S6 region revealed positions exhibiting strong spin–spin coupling, indicating that the activation gate of MVP is closed at 0 mV. A comparison of local environmental parameters along the activation gate for MVP and KcsA indicates that MVP adopts a different closed conformation. These structural details set the stage for future evaluations of reverse electromechanical coupling in MVP. PMID:24490868

  7. Biochemical analysis of respiratory metabolism in the heterofermentative Lactobacillus spicheri and Lactobacillus reuteri.

    Science.gov (United States)

    Ianniello, R G; Zheng, J; Zotta, T; Ricciardi, A; Gänzle, M G

    2015-09-01

    This study evaluated the aerobic and respiratory metabolism in Lactobacillus reuteri and Lactobacillus spicheri, two heterofermentative species used in sourdough fermentation. In silico genome analysis, production of metabolites and gene expression of pyruvate oxidase, pyruvate dehydrogenase and cytochrome oxidase were assessed in anaerobic and aerobic cultures of Lact. reuteri and Lact. spicheri. Respiring homofermentative Lactobacillus casei N87 and Lact. rhamnosus N132 were used for comparison. Aerobiosis and respiration increased the biomass production of heterofermentative strains compared to anaerobic cultivation. Respiration led to acetoin production by Lact. rhamnosus and Lact. casei, but not in heterofermentative strains, in which lactate and acetate were the major end-products. Lactobacillus spicheri LP38 showed the highest oxygen uptake. Pyruvate oxidase, respiratory cytochromes, NADH oxidase and NADH peroxidase were present in the genome of Lact. spicheri LP38. Both Lact. spicheri LP38 and Lact. rhamnosus N132 overexpressed pox in aerobic cultures, while cydA was up-regulated only when haeme was supplied; pdh was repressed during aerobic growth. Aerobic and respiratory growth provided physiological and metabolic advantages also in heterofermentative lactobacilli. The exploitation of oxygen-tolerant phenotypes of Lact. spicheri may be useful for the development of improved starter cultures. © 2015 The Society for Applied Microbiology.

  8. Enzyme and biochemical producing fungi

    DEFF Research Database (Denmark)

    Lübeck, Peter Stephensen; Lübeck, Mette; Nilsson, Lena

    2010-01-01

    factories for sustainable production of important molecules. For developing fungi into efficient cell factories, the project includes identification of important factors that control the flux through the pathways using metabolic flux analysis and metabolic engineering of biochemical pathways....

  9. Structural and chemical analysis of process residue from biochemical conversion of wheat straw (Triticum aestivum L.) to ethanol

    DEFF Research Database (Denmark)

    Hansen, Mads Anders Tengstedt; Jørgensen, Henning; Laursen, Kristian Holst

    2013-01-01

    Biochemical conversion of lignocellulose to fermentable carbohydrates for ethanol production is now being implemented in large-scale industrial production. Applying hydrothermal pretreatment and enzymatic hydrolysis for the conversion process, a residue containing substantial amounts of lignin...

  10. Comparative analysis of whole mount processing and systematic sampling of radical prostatectomy specimens: pathological outcomes and risk of biochemical recurrence.

    Science.gov (United States)

    Salem, Shady; Chang, Sam S; Clark, Peter E; Davis, Rodney; Herrell, S Duke; Kordan, Yakup; Wills, Marcia L; Shappell, Scott B; Baumgartner, Roxelyn; Phillips, Sharon; Smith, Joseph A; Cookson, Michael S; Barocas, Daniel A

    2010-10-01

    Whole mount processing is more resource intensive than routine systematic sampling of radical retropubic prostatectomy specimens. We compared whole mount and systematic sampling for detecting pathological outcomes, and compared the prognostic value of pathological findings across pathological methods. We included men (608 whole mount and 525 systematic sampling samples) with no prior treatment who underwent radical retropubic prostatectomy at Vanderbilt University Medical Center between January 2000 and June 2008. We used univariate and multivariate analysis to compare the pathological outcome detection rate between pathological methods. Kaplan-Meier curves and the log rank test were used to compare the prognostic value of pathological findings across pathological methods. There were no significant differences between the whole mount and the systematic sampling groups in detecting extraprostatic extension (25% vs 30%), positive surgical margins (31% vs 31%), pathological Gleason score less than 7 (49% vs 43%), 7 (39% vs 43%) or greater than 7 (12% vs 13%), seminal vesicle invasion (8% vs 10%) or lymph node involvement (3% vs 5%). Tumor volume was higher in the systematic sampling group and whole mount detected more multiple surgical margins (each p systematic sampling yield similar pathological information. Each method stratifies patients into comparable risk groups for biochemical recurrence. Thus, while whole mount is more resource intensive, it does not appear to result in improved detection of clinically important pathological outcomes or prognostication. Copyright © 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  11. Prediction of phospholipidosis-inducing potential of drugs by in vitro biochemical and physicochemical assays followed by multivariate analysis.

    Science.gov (United States)

    Kuroda, Yukihiro; Saito, Madoka

    2010-03-01

    An in vitro method to predict phospholipidosis-inducing potential of cationic amphiphilic drugs (CADs) was developed using biochemical and physicochemical assays. The following parameters were applied to principal component analysis, as well as physicochemical parameters: pK(a) and clogP; dissociation constant of CADs from phospholipid, inhibition of enzymatic phospholipid degradation, and metabolic stability of CADs. In the score plot, phospholipidosis-inducing drugs (amiodarone, propranolol, imipramine, chloroquine) were plotted locally forming the subspace for positive CADs; while non-inducing drugs (chlorpromazine, chloramphenicol, disopyramide, lidocaine) were placed scattering out of the subspace, allowing a clear discrimination between both classes of CADs. CADs that often produce false results by conventional physicochemical or cell-based assay methods were accurately determined by our method. Basic and lipophilic disopyramide could be accurately predicted as a nonphospholipidogenic drug. Moreover, chlorpromazine, which is often falsely predicted as a phospholipidosis-inducing drug by in vitro methods, could be accurately determined. Because this method uses the pharmacokinetic parameters pK(a), clogP, and metabolic stability, which are usually obtained in the early stages of drug development, the method newly requires only the two parameters, binding to phospholipid, and inhibition of lipid degradation enzyme. Therefore, this method provides a cost-effective approach to predict phospholipidosis-inducing potential of a drug. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  12. Biochemical and kinetic analysis of the GH3 family beta-xylosidase from Aspergillus awamori X-100.

    Science.gov (United States)

    Eneyskaya, Elena V; Ivanen, Dina R; Bobrov, Kirill S; Isaeva-Ivanova, Lyudmila S; Shabalin, Konstantin A; Savel'ev, Andrew N; Golubev, Alexander M; Kulminskaya, Anna A

    2007-01-15

    The beta-xylosidase from Aspergillus awamori X-100 belonging to the family 3 glycoside hydrolase revealed a distinctive transglycosylating ability to produce xylooligosaccharides with degree of polymerization more than 7. In order to explain this fact, the enzyme has been subjected to the detailed biochemical study. The enzymatic hydrolysis of p-nitrophenyl beta-D-xylopyranoside was found to occur with overall retention of substrate anomeric configuration suggesting cleavage of xylosidic bonds through a double-displacement mechanism. Kinetic study with aryl beta-xylopyranosides substrates, in which leaving group pK(a)s were in the range of 3.96-10.32, revealed monotonic function of log(k(cat)) and no correlation of log(k(cat)/Km) versus pKa values indicating deglycosylation as a rate-limiting step for the enzymatic hydrolysis. The classical bell-shaped pH dependence of k(cat)/Km indicated two ionizable groups in the beta-xylosidase active site with apparent pKa values of 2.2 and 6.4. The kinetic parameters of hydrolysis, Km and k(cat), of p-nitrophenyl beta-D-1,4-xylooligosaccharides were very close to those for hydrolysis of p-nitrophenyl-beta-D-xylopyranoside. Increase of p-nitrophenyl-beta-D-xylopyranoside concentration up to 80 mM led to increasing of the reaction velocity resulting in k(cat)(app)=81 s(-1). Addition of alpha-methyl D-xylopyranoside to the reaction mixture at high concentration of p-nitrophenyl-beta-D-xylopyranoside (50 mM) caused an acceleration of the beta-xylosidase-catalyzed reactions and appearance of a new transglycosylation product, alpha-methyl D-xylopyranosyl-1,4-beta-D-xylopyranoside, that was identified by 1H NMR spectroscopy. The kinetic model suggested for the enzymatic reaction was consistent with the results obtained.

  13. THE STRATEGIC PLANNING (SWOT ANALYSIS OUTCOMES AND SUGGESTIONS ACCORDING TO THE STUDENTS AND THE LECTURERS WITHIN THE DISTANCE EDUCATION SYSTEM

    Directory of Open Access Journals (Sweden)

    Tugba Yanpar YELKEN

    2012-04-01

    Full Text Available In recent years, strategic planning has become one of the subjects that many institutions work on to ensure the intuitions’ appropriate management based on realistic results. Therefore, this planning has to be taken into account and should provide planning direction on the bases of its results. Basically, the manager of strategic planning, leadership and strategic thinking and to act to help planners designed the tools, processes and concepts is a group. At the same time, the organization of the development and effective strategies will help to place. The purpose of this research is to provide SWOT (Strengths, Weaknesses, Opportunities and Threats analysis and to present new suggestions based on the opinions of students in the distance education system. In this work, we have applied Survey Method. The study group has consisted of 70 students and 11 instructors of Mersin Vocational School of Higher Education (MVSHE. All the data was surveyed during the spring semester of 2009. In the development of the questionnaire, a relevant literature has been investigated. Also, expert opinion has also been provided for the survey materials and survey articles. The questionnaire is finalized according to the expert’s opinion. The questionnaire was applied in the internet environment to both the students and the instructors. The outcomes of the survey have been evaluated quantatively along the direction of the survey’s fundamental question: “What are your views on strategic planning (SWOT of distance education?” The suggestions have been made about the distance learning education based on the findings of the survey.

  14. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase

    Directory of Open Access Journals (Sweden)

    Dugas Sandra L

    2003-07-01

    Full Text Available Abstract Background The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects. Results Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the γ-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (γ-Proteobacteria possess similar plasmid-encoded arsC sequences. Conclusion The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

  15. The prostate health index PHI predicts oncological outcome and biochemical recurrence after radical prostatectomy - analysis in 437 patients.

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    Maxeiner, Andreas; Kilic, Ergin; Matalon, Julia; Friedersdorff, Frank; Miller, Kurt; Jung, Klaus; Stephan, Carsten; Busch, Jonas

    2017-10-03

    The purpose of this study was to investigate the Prostate-Health-Index (PHI) for pathological outcome prediction following radical prostatectomy and also for biochemical recurrence prediction in comparison to established parameters such as Gleason-score, pathological tumor stage, resection status (R0/1) and prostate-specific antigen (PSA). Out of a cohort of 460 cases with preoperative PHI-measurements (World Health Organization calibration: Beckman Coulter Access-2-Immunoassay) between 2001 and 2014, 437 patients with complete follow up data were included. From these 437 patients, 87 (19.9%) developed a biochemical recurrence. Patient characteristics were compared by using chi-square test. Predictors were analyzed by multivariate adjusted logistic and Cox regression. The median follow up for a biochemical recurrence was 65 (range 3-161) months. PHI, PSA, [-2]proPSA, PHI- and PSA-density performed as significant variables (p PHI, PSA, %fPSA, [-2]proPSA, PHI- and PSA-density significantly discriminated between stages PHI. In biochemical recurrence prediction PHI, PSA, [-2]proPSA, PHI- and PSA-density were the strongest predictors. In conclusion, due to heterogeneity of time spans to biochemical recurrence, longer follow up periods are crucial. This study with a median follow up of more than 5 years, confirmed a clinical value for PHI as an independent biomarker essential for biochemical recurrence prediction.

  16. Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces

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    Brown Scott

    2010-07-01

    Full Text Available Abstract Background Interleukin-4 (IL4 is a secreted immunoregulatory cytokine critically involved in host protection from parasitic helminths 1. Reasoning that helminths may have evolved mechanisms to antagonize IL4 to maximize their dispersal, we explored mammalian IL4 evolution. Results This analysis revealed evidence of diversifying selection at 15 residues, clustered in epitopes responsible for IL4 binding to its Type I and Type II receptors. Such a striking signature of selective pressure suggested either recurrent episodes of pathogen antagonism or ligand/receptor co-evolution. To test the latter possibility, we performed detailed functional analysis of IL4 allotypes expressed by Mus musculus musculus and Mus musculus castaneus, which happen to differ at 5 residues (including three at positively selected sites in and adjacent to the site 1 epitope that binds the IL4Rα subunit shared by the Type I and Type II IL4 receptors. We show that this intra-species variation affects the ability of IL4 neither to bind IL4 receptor alpha (IL4Rα nor to signal biological responses through its Type I receptor. Conclusions Our results -- reminiscent of clustered positively selected sites revealing functionally important residues at host-virus interaction interfaces -- are consistent with IL4 having evolved to avoid recurrent pathogen antagonism, while maintaining the capacity to bind and signal through its cognate receptor. This work exposes what may be a general feature of evolutionary conflicts fought by pathogen antagonists at host protein-protein interaction interfaces involved in immune signaling: the emergence of receptor-binding ligand epitopes capable of buffering amino acid variation.

  17. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

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    Jeliazko R. Jeliazkov

    2018-03-01

    Full Text Available Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.

  18. Haplotype analysis suggest that the MLH1 c.2059C > T mutation is a Swedish founder mutation.

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    von Salomé, Jenny; Liu, Tao; Keihäs, Markku; Morak, Moni; Holinski-Feder, Elke; Berry, Ian R; Moilanen, Jukka S; Baert-Desurmont, Stéphanie; Lindblom, Annika; Lagerstedt-Robinson, Kristina

    2017-12-29

    Lynch syndrome (LS) predisposes to a spectrum of cancers and increases the lifetime risk of developing colorectal- or endometrial cancer to over 50%. Lynch syndrome is dominantly inherited and is caused by defects in DNA mismatch-repair genes MLH1, MSH2, MSH6 or PMS2, with the vast majority detected in MLH1 and MSH2. Recurrent LS-associated variants observed in apparently unrelated individuals, have either arisen de novo in different families due to mutation hotspots, or are inherited from a founder (a common ancestor) that lived several generations back. There are variants that recur in some populations while also acting as founders in other ethnic groups. Testing for founder mutations can facilitate molecular diagnosis of Lynch Syndrome more efficiently and more cost effective than screening for all possible mutations. Here we report a study of the missense mutation MLH1 c.2059C > T (p.Arg687Trp), a potential founder mutation identified in eight Swedish families and one Finnish family with Swedish ancestors. Haplotype analysis confirmed that the Finnish and Swedish families shared a haplotype of between 0.9 and 2.8 Mb. While MLH1 c.2059C > T exists worldwide, the Swedish haplotype was not found among mutation carriers from Germany or France, which indicates a common founder in the Swedish population. The geographic distribution of MLH1 c.2059C > T in Sweden suggests a single, ancient mutational event in the northern part of Sweden.

  19. Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea).

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    Yang, Ji; Gu, Hongya; Yang, Ziheng

    2004-01-01

    Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A-E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (omega = d(N)/ d(S)) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.

  20. Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation

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    Lundberg Cathryn

    2008-01-01

    Full Text Available Abstract Background Gene expression measurements from breast cancer (BrCa tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic clinical arrays show little overlap in the sets of genes identified. One approach to identify a set of consistently dysregulated candidate genes in these tumors is to employ meta-analysis of multiple independent microarray datasets. This allows one to compare expression data from a diverse collection of breast tumor array datasets generated on either cDNA or oligonucleotide arrays. Results We gathered expression data from 9 published microarray studies examining estrogen receptor positive (ER+ and estrogen receptor negative (ER- BrCa tumor cases from the Oncomine database. We performed a meta-analysis and identified genes that were universally up or down regulated with respect to ER+ versus ER- tumor status. We surveyed both the proximal promoter and 3' untranslated regions (3'UTR of our top-ranking genes in each expression group to test whether common sequence elements may contribute to the observed expression patterns. Utilizing a combination of known transcription factor binding sites (TFBS, evolutionarily conserved mammalian promoter and 3'UTR motifs, and microRNA (miRNA seed sequences, we identified numerous motifs that were disproportionately represented between the two gene classes suggesting a common regulatory network for the observed gene expression patterns. Conclusion Some of the genes we identified distinguish key transcripts previously seen in array studies, while others are newly defined. Many of the genes identified as overexpressed in ER- tumors were previously identified as expression markers for neoplastic transformation in multiple human cancers. Moreover, our motif analysis identified a collection of

  1. Histo-chemical and biochemical analysis reveals association of er1 mediated powdery mildew resistance and redox balance in pea.

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    Mohapatra, Chinmayee; Chand, Ramesh; Navathe, Sudhir; Sharma, Sandeep

    2016-09-01

    Powdery mildew caused by Erysiphe pisi is one of the important diseases responsible for heavy yield losses in pea crop worldwide. The most effective method of controlling the disease is the use of resistant varieties. The resistance to powdery mildew in pea is recessive and governed by a single gene er1. The objective of present study is to investigate if er1 mediated powdery mildew resistance is associated with changes in the redox status of the pea plant. 16 pea genotypes were screened for powdery mildew resistance in field condition for two years and, also, analyzed for the presence/absence of er1 gene. Histochemical analysis with DAB and NBT staining indicates accumulation of reactive oxygen species (ROS) in surrounding area of powdery mildew infection which was higher in susceptible genotypes as compared to resistant genotypes. A biochemical study revealed that the activity of superoxide dismutase (SOD) and catalase, enzymes involved in scavenging ROS, was increased in, both, resistant and susceptible genotypes after powdery mildew infection. However, both enzymes level was always higher in resistant than susceptible genotypes throughout time course of infection. Moreover, irrespective of any treatment, the total phenol (TP) and malondialdehyde (MDA) content was significantly high and low in resistant genotypes, respectively. The powdery mildew infection elevated the MDA content but decreased the total phenol in pea genotypes. Statistical analysis showed a strong positive correlation between AUDPC and MDA; however, a negative correlation was observed between AUDPC and SOD, CAT and TP. Heritability of antioxidant was also high. The study identified few novel genotypes resistant to powdery mildew infection that carried the er1 gene and provided further clue that er1 mediated defense response utilizes antioxidant machinery to confer powdery mildew resistance in pea. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  2. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management.

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    Hindrikson, Maris; Remm, Jaanus; Pilot, Malgorzata; Godinho, Raquel; Stronen, Astrid Vik; Baltrūnaité, Laima; Czarnomska, Sylwia D; Leonard, Jennifer A; Randi, Ettore; Nowak, Carsten; Åkesson, Mikael; López-Bao, José Vicente; Álvares, Francisco; Llaneza, Luis; Echegaray, Jorge; Vilà, Carles; Ozolins, Janis; Rungis, Dainis; Aspi, Jouni; Paule, Ladislav; Skrbinšek, Tomaž; Saarma, Urmas

    2017-08-01

    The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we

  3. Integrated biochemical, molecular genetic, and bioacoustical analysis of mesoscale variability of the euphausiid Nematoscelis difficilis in the California Current

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    Bucklin, Ann; Wiebe, Peter H.; Smolenack, Sara B.; Copley, Nancy J.; Clarke, M. Elizabeth

    2002-03-01

    Integrated assessment of the euphausiid Nematoscelis difficilis (Crustacea; Euphausiacea) and the zooplankton assemblage of the California Current was designed to investigate individual, population, and community responses to mesoscale variability in biological and physical characters of the ocean. Zooplankton samples and observational data were collected along a cross-shelf transect of the California Current in association with the California Cooperative Fisheries Investigations (CalCOFI) Survey during October 1996. The transect crossed three domains defined by temperature and salinity: nearshore, mid-Current, and offshore. Individual N. difficilis differed in physiological condition along the transect, with higher size-corrected concentrations of four central metabolic enzymes (citrate synthetase, hexokinase, lactate dehydrogenase (LDH), and phosphoglucose isomerase (PGI)) for euphausiids collected in nearshore waters than in mid-Current and offshore waters. There was little variation in the DNA sequences of the genes encoding PGI and LDH (all DNA changes were either silent or heterozygous base substitutions), suggesting that differences in enzyme concentration did not result from underlying molecular genetic variation. The population genetic makeup of N. difficilis varied from sample to sample based on haplotype frequencies of mitochondrial cytochrome oxidase I (mtCOI; P=0.029). There were significant differences between pooled nearshore and offshore samples, based on allele frequencies at two sites of common substitutions in the mtCOI sequence ( P=0.020 and 0.026). Silhouette and bioacoustical backscattering measurements of the zooplankton assemblage of the top 100 m showed marked diel vertical migration of the scattering layer, of which euphausiids were a small but significant fraction. The biochemical and molecular assays are used as indices of complex physiological (i.e., growth and condition) and genetic (i.e., mortality) processes; the bioacoustical

  4. Biogeochemical analysis of ancient Pacific Cod bone suggests Hg bioaccumulation was linked to paleo sea level rise and climate change

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    Maribeth S. Murray

    2015-02-01

    Full Text Available Deglaciation at the end of the Pleistocene initiated major changes in ocean circulation and distribution. Within a brief geological time, large areas of land were inundated by sea-level rise and today global sea level is 120 m above its minimum stand during the last glacial maximum. This was the era of modern sea shelf formation; climate change caused coastal plain flooding and created broad continental shelves with innumerable consequences to marine and terrestrial ecosystems and human populations. In Alaska, the Bering Sea nearly doubled in size and stretches of coastline to the south were flooded, with regional variability in the timing and extent of submergence. Here we suggest how past climate change and coastal flooding are linked to mercury bioaccumulation that could have had profound impacts on past human populations and that, under conditions of continued climate warming, may have future impacts. Biogeochemical analysis of total mercury (tHg and 13C/15N ratios in the bone collagen of archaeologically recovered Pacific Cod (Gadus macrocephalus bone shows high levels of tHg during early/mid-Holocene. This pattern cannot be linked to anthropogenic activity or to food web trophic changes, but may result from natural phenomena such as increases in productivity, carbon supply and coastal flooding driven by glacial melting and sea-level rise. The coastal flooding could have led to increased methylation of Hg in newly submerged terrestrial land and vegetation. Methylmercury is bioaccumulated through aquatic food webs with attendant consequences for the health of fish and their consumers, including people. This is the first study of tHg levels in a marine species from the Gulf of Alaska to provide a time series spanning nearly the entire Holocene and we propose that past coastal flooding resulting from climate change had the potential to input significant quantities of Hg into marine food webs and subsequently to human consumers.

  5. Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum.

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    Vilela, Mariane de Mendonça; Del Bem, Luiz Eduardo; Van Sluys, Marie-Anne; de Setta, Nathalia; Kitajima, João Paulo; Cruz, Guilherme Marcelo Queiroga; Sforça, Danilo Augusto; de Souza, Anete Pereira; Ferreira, Paulo Cavalcanti Gomes; Grativol, Clícia; Cardoso-Silva, Claudio Benicio; Vicentini, Renato; Vincentz, Michel

    2017-02-01

    Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Planktonic foraminiferal oxygen isotope analysis by ion microprobe technique suggests warm tropical sea surface temperatures during the Early Paleogene

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    Kozdon, Reinhard; Kelly, D. Clay; Kita, Noriko T.; Fournelle, John H.; Valley, John W.

    2011-09-01

    Cool tropical sea surface temperatures (SSTs) are reported for warm Paleogene greenhouse climates based on the δ18O of planktonic foraminiferal tests. These results are difficult to reconcile with models of greenhouse gas-forced climate. It has been suggested that this "cool tropics paradox" arises from postdepositional alteration of foraminiferal calcite, yielding erroneously high δ18O values. Recrystallization of foraminiferal tests is cryptic and difficult to quantify, and the compilation of robust δ18O records from moderately altered material remains challenging. Scanning electron microscopy of planktonic foraminiferal chamber-wall cross sections reveals that the basal area of muricae, pustular outgrowths on the chamber walls of species belonging to the genus Morozovella, contain no mural pores and may be less susceptible to postdepositional alteration. We analyzed the δ18O in muricae bases of morozovellids from the central Pacific (Ocean Drilling Program Site 865) by ion microprobe using 10 μm pits with an analytical reproducibility of ±0.34‰ (2 standard deviations). In situ measurements of δ18O in these domains yield consistently lower values than those published for conventional multispecimen analyses. Assuming that the original δ18O is largely preserved in the basal areas of muricae, this new δ18O record indicates Early Paleogene (˜49-56 Ma) tropical SSTs in the central Pacific were 4°-8°C higher than inferred from the previously published δ18O record and that SSTs reached at least ˜33°C during the Paleocene-Eocene thermal maximum. This study demonstrates the utility of ion microprobe analysis for generating more reliable paleoclimate records from moderately altered foraminiferal tests preserved in deep-sea sediments.

  7. An Analysis of the Regulatory Environment Governing Hearsay Electronic Evidence in South Africa: Suggestions for Reform – Part One

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    Lee Swales

    2018-03-01

    Full Text Available The purpose of this two-part article is to examine the regulatory environment governing hearsay electronic evidence in South Africa – with a view to providing clear, practical suggestions for regulatory reform in the context of the South African Law Reform Commission's most recent Discussion Paper on electronic evidence. Technology has become an indispensable part of modern life. In particular, the Internet has facilitated new forms of business enterprise, and shifted basic communication norms. From a legal perspective, technology has presented several novel challenges for courts and legal practitioners to deal with – one of these key challenges relates to electronic evidence and in particular the application of the hearsay rules to the digital environment. The South African Law Reform Commission has identified the application of the hearsay rule as one of the core concerns with regard to electronic evidence, and certain academic analysis has revealed inefficiency in the current legal position which may involve multiple sources of law. Moreover, the Law Society of South Africa has stated that there is some confusion amongst members of the profession in relation to hearsay as it applies to electronic evidence. With the pervasive and burgeoning nature of technology, and with the Internet in mind, it is natural to assume that electronic evidence will be relevant in most forms of legal proceedings in future, and hearsay electronic evidence in particular will play an increasingly important role in years to come. Consequently, part one of this article will consider the key definitional concept in relation to electronic evidence – data messages - and examine whether the definition should be revised. In addition, part one of this article will answer two further critical questions posed by the South African Law Reform Commission in relation to data messages and hearsay evidence, namely: should a data message constitute hearsay? And, how should one

  8. Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum).

    Science.gov (United States)

    Popovsky-Sarid, Sigal; Borovsky, Yelena; Faigenboim, Adi; Parsons, Eugene P; Lohrey, Gregory T; Alkalai-Tuvia, Sharon; Fallik, Elazar; Jenks, Matthew A; Paran, Ilan

    2017-02-01

    Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.

  9. Retrospective analysis of the quality of reports by author-suggested and non-author-suggested reviewers in journals operating on open or single-blind peer review models.

    Science.gov (United States)

    Kowalczuk, Maria K; Dudbridge, Frank; Nanda, Shreeya; Harriman, Stephanie L; Patel, Jigisha; Moylan, Elizabeth C

    2015-09-29

    To assess whether reports from reviewers recommended by authors show a bias in quality and recommendation for editorial decision, compared with reviewers suggested by other parties, and whether reviewer reports for journals operating on open or single-blind peer review models differ with regard to report quality and reviewer recommendations. Retrospective analysis of the quality of reviewer reports using an established Review Quality Instrument, and analysis of reviewer recommendations and author satisfaction surveys. BioMed Central biology and medical journals. BMC Infectious Diseases and BMC Microbiology are similar in size, rejection rates, impact factors and editorial processes, but the former uses open peer review while the latter uses single-blind peer review. The Journal of Inflammation has operated under both peer review models. Two hundred reviewer reports submitted to BMC Infectious Diseases, 200 reviewer reports submitted to BMC Microbiology and 400 reviewer reports submitted to the Journal of Inflammation. For each journal, author-suggested reviewers provided reports of comparable quality to non-author-suggested reviewers, but were significantly more likely to recommend acceptance, irrespective of the peer review model (previewer reports measured by the Review Quality Instrument was 5% higher than for BMC Microbiology (p=0.042). For the Journal of Inflammation, the quality of reports was the same irrespective of the peer review model used. Reviewers suggested by authors provide reports of comparable quality to non-author-suggested reviewers, but are significantly more likely to recommend acceptance. Open peer review reports for BMC Infectious Diseases were of higher quality than single-blind reports for BMC Microbiology. There was no difference in quality of peer review in the Journal of Inflammation under open peer review compared with single blind. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a

  10. Comparative analysis of molecular signatures suggests the use of gabapentin for the management of endometriosis-associated pain

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    Bellessort B

    2018-04-01

    the progress of endometriosis. CACNA2D3, a component of the α2δ family of voltage-dependent calcium channel complex, was strongly overexpressed both in mutant mouse uteri and in endometriosis implants, were also CACNA2D1 and CACNA2D2, other members of the α2δ family involved in nociception, are upregulated. Conclusion: Comparative analysis of gene expression signatures from endometriosis and mouse models showed that calcium channel subunits α2δ involved in nociception can be targets for the treatment of endometriosis-associated pain. CACNA2D3 has been associated with pain sensitization and heat nociception in animal models. In patients, CACNA2D3 variants were associated with reduced sensitivity to acute noxious stimuli. As α2δs were targets of gabapentinoid analgesics, the results suggested the use of these drugs for the treatment of endometriosis-associated pain. Indeed, recent small-scale clinical studies have shown that gabapentin could be effective in women with CPP. The findings of this study reinforce the need for a large definitive trial. Keywords: endometriosis, gabapentin, CACNA2D3, Dlx5, pain

  11. Analysis of knockout mice suggests a role for VGF in the control of fat storage and energy expenditure

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    Chakraborty Tandra

    2009-10-01

    Full Text Available Abstract Background Previous studies of mixed background mice have demonstrated that targeted deletion of Vgf produces a lean, hypermetabolic mouse that is resistant to diet-, lesion-, and genetically-induced obesity. To investigate potential mechanism(s and site(s of action of VGF, a neuronal and endocrine secreted protein and neuropeptide precursor, we further analyzed the metabolic phenotypes of two independent VGF knockout lines on C57Bl6 backgrounds. Results Unlike hyperactive VGF knockout mice on a mixed C57Bl6-129/SvJ background, homozygous mutant mice on a C57Bl6 background were hypermetabolic with similar locomotor activity levels to Vgf+/Vgf+ mice, during day and night cycles, indicating that mechanism(s other than hyperactivity were responsible for their increased energy expenditure. In Vgf-/Vgf- knockout mice, morphological analysis of brown and white adipose tissues (BAT and WAT indicated decreased fat storage in both tissues, and decreased adipocyte perimeter and area in WAT. Changes in gene expression measured by real-time RT-PCR were consistent with increased fatty acid oxidation and uptake in BAT, and increased lipolysis, decreased lipogenesis, and brown adipocyte differentiation in WAT, suggesting that increased sympathetic nervous system activity in Vgf-/Vgf- mice may be associated with or responsible for alterations in energy expenditure and fat storage. In addition, uncoupling protein 1 (UCP1 and UCP2 protein levels, mitochondrial number, and mitochondrial cristae density were upregulated in Vgf-/Vgf- BAT. Using immunohistochemical and histochemical techniques, we detected VGF in nerve fibers innervating BAT and Vgf promoter-driven reporter expression in cervical and thoracic spinal ganglia that project to and innervate the chest wall and tissues including BAT. Moreover, VGF peptide levels were quantified by radioimmunoassay in BAT, and were found to be down-regulated by a high fat diet. Lastly, despite being hypermetabolic

  12. Serial analysis of resected prostate cancer suggests up-regulation of type 1 IGF receptor with disease progression.

    Science.gov (United States)

    Turney, Benjamin W; Turner, Gareth D H; Brewster, Simon F; Macaulay, Valentine M

    2011-05-01

    • To compare immunostaining protocols using different antibodies for the type 1 insulin-like growth factor receptor (IGF-1R) in channel transurethal resection of the prostate (chTURP) chips, and to investigate how IGF-1R expression varies with time in serial prostate cancer specimens from individual patients. • We studied IGF-1R expression in 44 prostate cancer specimens from 18 patients who had undergone serial chTURP at least 3 months apart. • Retrospective analysis of the hospital notes was undertaken to obtain clinical information, including age, Gleason score, prostate-specific antigen (PSA) level, hormone treatment and metastatic disease status at the time of each operation. • After an optimization process using three commercially-available IGF-1R antibodies, we used two antibodies for semiquantititve immunostaining of serial chTURP chips. • Santa Cruz antibody sc713 gave positive staining in IGF-1R null R- cells, and was not used further. Antibodies from Cell Signaling Technology (Beverly, MA, USA) (CS) and NeoMarkers Inc. (Fremont, CA, USA) (NM) did not stain R- cells and, in prostate tissue, showed staining of the glandular epithelium, with negligible stromal staining. All 44 chTURP samples contained identifiable malignant tissue and, of these, 73% and 64% scored moderately or strongly (score 3 or 4) with the CS and NM antibodies respectively. • There was significant correlation of IGF-1R scores of malignant tissue between the two antibodies (P < 0.001). By contrast, staining of benign glands showed poor correlation between antibodies: CS gave significantly weaker staining than malignant epithelium in the same sections (P < 0.001), whereas NM showed poor discrimination between malignant and benign glands. IGF-1R staining scores generated by the CS antibody were used to analyze the clinical data. • Most patients (six of seven) with falling IGF-1R staining scores were responding to androgen deprivation therapy (confirmed by PSA response

  13. The role of overall treatment time in the outcome of radiotherapy of prostate cancer: An analysis of biochemical failure in 4839 men treated between 1987 and 1995

    International Nuclear Information System (INIS)

    Thames, Howard D.; Kuban, Deborah; Levy, Larry B.; Horwitz, Eric M.; Kupelian, Patrick; Martinez, Alvaro; Michalski, Jeffrey; Pisansky, Thomas; Sandler, Howard; Shipley, William; Zelefsky, Michael; Zietman, Anthony

    2010-01-01

    Purpose: Assess the importance of overall time (OT) and dose for biochemical failure (BF) after external-beam radiotherapy of prostate cancer in a retrospective analysis of a nine-institution database with 4839 patients. Patients and methods: Relevant baseline factors (T stage, Gleason score, initial PSA) were available for 4338 men. Cox models were used to estimate the effects of dose and OT corrected for baseline factors, treatment year, institution and interactions, and differences in post-treatment PSA-measurement intervals. After exclusion of very short and long intervals, patient numbers were 1445 events/3426 at risk (endpoint all BFs), and 1177 events/3354 at risk (endpoint exclusion of BFs that were likely distant failures). Separate analyses were carried out by risk group for men who received <70 Gy and ≥70 Gy. Results: Neither dose nor OT was significant when the analysis was restricted to doses <70 Gy, while for patients treated to 70 Gy or higher there were significant influences of both dose and OT on outcome in low- and intermediate-risk patients. These effects were quantified as a relative increase after 5 years followup of 6% in BFs for a 1-week increase in OT, a relative decrease of 15% in BFs for a 6-Gy increase in dose, and a dose equivalent of proliferation of 0.24 Gy/day. As the dose per fraction was nearly constant, the data contain no information on the α/β ratio. Conclusion: The results show that OT and dose are significant determinants of outcome of radiotherapy in low- and intermediate-risk patients treated to 70 Gy or higher, and suggest that meaningful improvements in outcome may be targeted by modest increases in total dose and decreases in OT.

  14. Molecular cloning, biochemical characterization, and expression analysis of two glutathione S-transferase paralogs from the big-belly seahorse (Hippocampus abdominalis).

    Science.gov (United States)

    Tharuka, M D Neranjan; Bathige, S D N K; Lee, Jehee

    2017-12-01

    Glutathione S-transferases (GSTs, EC 2.5.1.18) are important Phase II detoxifying enzymes that catalyze hydrophobic, electrophilic xenobiotic substance with the conjugation of reduced glutathione (GSH). In this study, GSTμ and GSTρ paralogs of GST in the big belly seahorse (Hippocampus abdominalis; HaGSTρ, HaGSTμ) were biochemically, molecularly, functionally characterized to determine their detoxification range and protective capacities upon different pathogenic stresses. HaGSTρ and HaGSTμ are composed of coding sequences of 681bp and 654bp, which encode proteins 225 and 217 amino acids, with predicted molecular masses of 26.06kDa and 25.74kDa respectively. Sequence analysis revealed that both HaGSTs comprise the characteristic GSH-binding site in the thioredoxin-like N-terminal domain and substrate binding site in the C-terminal domain. The recombinant HaGSTρ and HaGSTμ proteins catalyzed the model GST substrate 1-chloro-2, 4-dinitrobenzene (CDNB). Enzyme kinetic analysis revealed different K m and V max values for each rHaGST, suggesting that they have different conjugation rates. The optimum conditions (pH, temperature) and inhibitory assays of each protein demonstrated different optimal ranges. However, HaGSTμ was highly expressed in the ovary and gill, whereas HaGSTρ was highly expressed in the gill and pouch. mRNA expression of HaGSTρ and HaGSTμ was significantly elevated upon lipopolysaccharide, Poly (I:C), and Edwardsiella tarda challenges in liver and in blood cells as well as with Streptococcus iniae challenge in blood cells. From these collective experimental results, we propose that HaGSTρ and HaGSTμ are effective in detoxifying xenobiotic toxic agents, and importantly, their mRNA expression could be stimulated by immunological stress signals in the aquatic environment. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

    Directory of Open Access Journals (Sweden)

    Nancy Martínez-Montiel

    Full Text Available The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization

  16. In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

    Science.gov (United States)

    Martínez-Montiel, Nancy; Morales-Lara, Laura; Hernández-Pérez, Julio M; Martínez-Contreras, Rebeca D

    2016-01-01

    The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability

  17. Biochemical analysis of the Hormoconis resinae fungal mycelium in the corrosion of aeronautical aluminium alloys

    Directory of Open Access Journals (Sweden)

    Araya, R.

    2007-06-01

    Full Text Available Biochemical analyses of the Hormoconis resinae fungal mycelium would explain behaviour differences of corrosive and non-corrosive strains on Al and its aeronautical alloys. In previous works its aggressiveness had been studied through SEM-EDX surface analysis, electrochemical techniques and immersion testing. In this paper separation of the proteins of the mycelium produced by a non-corrosive strain and its culture along three generations was performed. Cultures were prepared in batch in the presence and absence of pure Al and AA 2024, AA 7005 and AA 7075 alloys. The mycelia grown throughout the three generations increasingly
    recovered usual characteristics at the third replication, included their corrosiveness on Al and its alloys previously shown by all our strains. Amongst the bio-molecule fractions isolated and analysed during this preliminary study only the proteins revealed changes with the generation grown. When this fungal strain was cultured in the presence of alloy metal sheets electrophoresis of the protean fraction was correlative with the distinct mycelia behaviour observed, including corrosiveness on Al and its alloys.

    Las diferencias entre el comportamiento corrosivo y no corrosivo de una cepa del hongo Hormoconis resinae sobre aluminio y sus aleaciones aeronáuticas se explicarían a través de análisis bioquímicos del micelio. En trabajos previos, el comportamiento corrosivo se estudió mediante análisis de superficie SEM-EDX, técnicas electroquímicas y ensayos de inmersión. En este trabajo, se llevó a cabo la separación de proteínas del micelio producido por una cepa que perdió su corrosividad y su cultivo a través de tres generaciones. Cultivos en batch, en presencia y ausencia de aluminio y sus aleaciones AA 2024, AA 7005 y AA 7075, a través de tres generaciones del micelio crecido, fueron recuperando sus características, incluida su habitual corrosividad, en la tercera replicaci

  18. Interpretive analysis of 85 systematic reviews suggests that narrative syntheses and meta‐analyses are incommensurate in argumentation

    Science.gov (United States)

    O'Mara‐Eves, A.; Thomas, J.; Brunton, G.; Caird, J.; Petticrew, M.

    2016-01-01

    Using Toulmin's argumentation theory, we analysed the texts of systematic reviews in the area of workplace health promotion to explore differences in the modes of reasoning embedded in reports of narrative synthesis as compared with reports of meta‐analysis. We used framework synthesis, grounded theory and cross‐case analysis methods to analyse 85 systematic reviews addressing intervention effectiveness in workplace health promotion. Two core categories, or ‘modes of reasoning’, emerged to frame the contrast between narrative synthesis and meta‐analysis: practical–configurational reasoning in narrative synthesis (‘what is going on here? What picture emerges?’) and inferential–predictive reasoning in meta‐analysis (‘does it work, and how well? Will it work again?’). Modes of reasoning examined quality and consistency of the included evidence differently. Meta‐analyses clearly distinguished between warrant and claim, whereas narrative syntheses often presented joint warrant–claims. Narrative syntheses and meta‐analyses represent different modes of reasoning. Systematic reviewers are likely to be addressing research questions in different ways with each method. It is important to consider narrative synthesis in its own right as a method and to develop specific quality criteria and understandings of how it is carried out, not merely as a complement to, or second‐best option for, meta‐analysis. © 2016 The Authors. Research Synthesis Methods published by John Wiley & Sons Ltd. PMID:27860329

  19. Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons.

    Science.gov (United States)

    Garmyn, Dominique; Augagneur, Yoann; Gal, Laurent; Vivant, Anne-Laure; Piveteau, Pascal

    2012-01-01

    Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.

  20. Efficacy of transsphenoidal surgery in achieving biochemical cure of growth hormone-secreting pituitary adenomas among patients with cavernous sinus invasion: a systematic review and meta-analysis.

    Science.gov (United States)

    Briceno, Vanessa; Zaidi, Hasan A; Doucette, Joanne A; Onomichi, Kaho B; Alreshidi, Amer; Mekary, Rania A; Smith, Timothy R

    2017-05-01

    Growth hormone-secreting pituitary adenomas in adults can result in severe craniofacial disfigurement and potentially fatal medical complications. Surgical resection leading to remission of the disease is dependent on complete surgical resection of the tumor. Lesions that invade the cavernous sinus may not be safely accessible via an endonasal transsphenoidal surgery (TSS), and the rates of biochemical remission of patients with residual disease vary widely in the literature. We conducted a meta-analysis to examine the prevalence of biochemical remission after TSS among patients with growth hormone-secreting pituitary adenomas with and without cavernous sinus invasion. Embase, PubMed, and Cochrane Library databases were searched for relevant publications. Fourteen studies with 972 patients with biochemically confirmed growth hormone-secreting pituitary adenomas were included in the meta-analysis. The overall remission prevalence under a fixed-effect model was 47.6% (95% CI = 40.8-54.4%) for patients with invasive macroadenomas (I 2  = 74.6%, p < 0.01); 76.4% (95% CI = 72.2-80.1%) for patients with non-invasive macroadenomas (I 2  = 59.6%, p = 0.03); and 74.2% (95% CI = 66.3-80.7%) for patients with non-invasive microadenomas (I 2  = 36.4, p = 0.10). The significant difference among the three groups resulted from the difference between patients with or without cavernous sinus invasion (p = 0.01) and not from the size of adenomas among those without cavernous sinus invasion (p = 0.66). The prevalence of biochemical remission in patients with cavernous sinus invasion was lower than in patients without cavernous sinus invasion after TSS for acromegaly.

  1. Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers: a diagnostic approach based on cluster analysis.

    Science.gov (United States)

    Egsgaard, Line Lindhardt; Eskehave, Thomas Navndrup; Bay-Jensen, Anne C; Hoeck, Hans Christian; Arendt-Nielsen, Lars

    2015-01-01

    Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary.

  2. Fast and Cost-Effective Biochemical Spectrophotometric Analysis of Solution of Insect “Blood” and Body Surface Elution

    Directory of Open Access Journals (Sweden)

    Aleksandra Łoś

    2018-05-01

    Full Text Available Using insect hemolymph (“blood” and insect body surface elutions, researchers can perform rapid and cheap biochemical analyses to determine the insect’s immunology status. The authors of this publication describe a detailed methodology for a quick marking of the concentration of total proteins and evaluation of the proteolytic system activity (acid, neutral, and alkaline proteases and protease inhibitors, as well as a methodology for quick “liver” tests in insects: alanine aminotransferase (ALT, aspartate aminotransferase (AST, alkaline phosphatase (ALP, and urea and glucose concentration analyses. The meaning and examples of an interpretation of the results of the presented methodology for biochemical parameter determination are described for the example of honey bees.

  3. Phytochemical analysis and In-vitro Biochemical Characterization of aqueous and methanolic extract of Triphala, a conventional herbal remedy

    Directory of Open Access Journals (Sweden)

    Romana Parveen

    2018-03-01

    Results revealed the presence of valuable bioactive compounds such as flavonoids, alkaloids, phenols, etc which might be responsible for biochemical activities. Extracts exhibited satisfactory radical-scavenging activity comparable with ascorbic acid. Methanolic extracts demonstrated higher antioxidant activity compared to aqueous extract. Extracts showed promising antibacterial potential against tested strain comparable to ampicillin. Hence, it can be concluded that triphala may be a promising candidate in pharmaceuticals and future medicine.

  4. Fast and Cost-Effective Biochemical Spectrophotometric Analysis of Solution of Insect “Blood” and Body Surface Elution

    OpenAIRE

    Aleksandra Łoś; Aneta Strachecka

    2018-01-01

    Using insect hemolymph (“blood”) and insect body surface elutions, researchers can perform rapid and cheap biochemical analyses to determine the insect’s immunology status. The authors of this publication describe a detailed methodology for a quick marking of the concentration of total proteins and evaluation of the proteolytic system activity (acid, neutral, and alkaline proteases and protease inhibitors), as well as a methodology for quick “liver” tests in insects: alanine aminotransferase ...

  5. Bifurcation Analysis of an Existing Mathematical Model Reveals Novel Treatment Strategies and Suggests Potential Cure for Type 1 Diabetes

    DEFF Research Database (Denmark)

    Nielsen, Kenneth Hagde Mandrup; Ottesen, Johnny T.; Pociot, Flemming

    2014-01-01

    Type 1 diabetes is a disease with serious personal and socioeconomic consequences that has attracted the attention of modellers recently. But as models of this disease tend to be complicated, there has been only limited mathematical analysis to date. Here we address this problem by providing...... a bifurcation analysis of a previously published mathematical model for the early stages of type 1 diabetes in diabetes-prone NOD mice, which is based on the data available in the literature. We also show positivity and the existence of a family of attracting trapping regions in the positive 5D cone, converging...... or activated macrophages, increasing the phagocytic ability of resting and activated macrophages simultaneously and lastly, adding additional macrophages to the site of inflammation. The latter seems counter-intuitive at first glance, but nevertheless it appears to be the most promising, as evidenced by recent...

  6. Ancient DNA analysis suggests negligible impact of the Wari Empire expansion in Peru's central coast during the Middle Horizon

    OpenAIRE

    Valverde, G.; Romero, M.; Espinoza, I.; Cooper, A.; Fehren-Schmitz, L.; Llamas, B.; Haak, W.

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650?1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, wh...

  7. Natural history definition and a suggested clinical approach to Buerger's disease: a case-control study with survival analysis.

    Science.gov (United States)

    Fazeli, Bahare; Ravari, Hassan; Assadi, Reza

    2012-08-01

    The aim of this study was first to describe the natural history of Buerger's disease (BD) and then to discuss a clinical approach to this disease based on multivariate analysis. One hundred eight patients who corresponded with Shionoya's criteria were selected from 2000 to 2007 for this study. Major amputation was considered the ultimate adverse event. Survival analyses were performed by Kaplan-Meier curves. Independent variables including gender, duration of smoking, number of cigarettes smoked per day, minor amputation events and type of treatments, were determined by multivariate Cox regression analysis. The recorded data demonstrated that BD may present in four forms, including relapsing-remitting (75%), secondary progressive (4.6%), primary progressive (14.2%) and benign BD (6.2%). Most of the amputations occurred due to relapses within the six years after diagnosis of BD. In multivariate analysis, duration of smoking of more than 20 years had a significant relationship with further major amputation among patients with BD. Smoking cessation programs with experienced psychotherapists are strongly recommended for those areas in which Buerger's disease is common. Patients who have smoked for more than 20 years should be encouraged to quit smoking, but should also be recommended for more advanced treatment for limb salvage.

  8. High-dose rate brachytherapy in the treatment of prostate cancer: acute toxicity and biochemical behavior analysis

    International Nuclear Information System (INIS)

    Esteves, Sergio Carlos Barros; Oliveira, Antonio Carlos Zuliani de; Cardoso, Herbeni; Tagawa, Eduardo Komai; Castelo, Roberto; D'Imperio, Marcio

    2006-01-01

    Objective: this study focuses on the biochemical response of the following variables: prostate volume, prostate-specific antigen (PSA) value, Gleason scores, staging, the risk of the disease, and hormone therapy. Objective: in the period between February of 1998 and July of 2001, 46 patients with prostate cancer were treated with radiotherapy, in a combination of teletherapy and high-dose rate (HDR) brachytherapy. The age ranged from 51 to 79 years (averaging 66.4 years). T1c stage was the most frequent one: 30 (65%). The Gleason score was below 7 in 78% of the patients. PSA ranged from 3.4 to 33.3, being below 10 in 39% of the cases. The average prostatic volume was 32.3 cc. Twenty-eight percent of the patients received hormone therapy. Teletherapy dose ranged from 45 to 50.4 Gy, associated to four fractions of 4 Gy of HDR brachytherapy. Results: the follow-up period varied from 6 to 43 months. Four patients missed the follow-up and four died (one due to the disease). Out of the 39 patients that were analyzed, 76% presented a less than 1.5 PSA. None of the analyzed variables were found to be of statistical significance (p > 0.05) regarding biochemical control. Conclusion: the use of HDR brachytherapy was found to be effective in the treatment of prostate cancer and, in this study, the variables considered as prognostic factors did not interfere in the biochemical control. (author)

  9. Gene expression profiling, pathway analysis and subtype classification reveal molecular heterogeneity in hepatocellular carcinoma and suggest subtype specific therapeutic targets.

    Science.gov (United States)

    Agarwal, Rahul; Narayan, Jitendra; Bhattacharyya, Amitava; Saraswat, Mayank; Tomar, Anil Kumar

    2017-10-01

    A very low 5-year survival rate among hepatocellular carcinoma (HCC) patients is mainly due to lack of early stage diagnosis, distant metastasis and high risk of postoperative recurrence. Hence ascertaining novel biomarkers for early diagnosis and patient specific therapeutics is crucial and urgent. Here, we have performed a comprehensive analysis of the expression data of 423 HCC patients (373 tumors and 50 controls) downloaded from The Cancer Genome Atlas (TCGA) followed by pathway enrichment by gene ontology annotations, subtype classification and overall survival analysis. The differential gene expression analysis using non-parametric Wilcoxon test revealed a total of 479 up-regulated and 91 down-regulated genes in HCC compared to controls. The list of top differentially expressed genes mainly consists of tumor/cancer associated genes, such as AFP, THBS4, LCN2, GPC3, NUF2, etc. The genes over-expressed in HCC were mainly associated with cell cycle pathways. In total, 59 kinases associated genes were found over-expressed in HCC, including TTK, MELK, BUB1, NEK2, BUB1B, AURKB, PLK1, CDK1, PKMYT1, PBK, etc. Overall four distinct HCC subtypes were predicted using consensus clustering method. Each subtype was unique in terms of gene expression, pathway enrichment and median survival. Conclusively, this study has exposed a number of interesting genes which can be exploited in future as potential markers of HCC, diagnostic as well as prognostic and subtype classification may guide for improved and specific therapy. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. A case-control analysis of common variants in GIP with type 2 diabetes and related biochemical parameters in a South Indian population

    Directory of Open Access Journals (Sweden)

    Kumar Harish

    2010-07-01

    Full Text Available Abstract Background Glucose-dependent insulinotropic polypeptide (GIP is one of the incretins, which plays a crucial role in the secretion of insulin upon food stimulus and in the regulation of postprandial glucose level. It also exerts an effect on the synthesis and secretion of lipoprotein lipase, from adipocytes, important for lipid metabolism. The aim of our study was to do a case-control association analysis of common variants in GIP in association with type 2 diabetes and related biochemical parameters. Method A total of 2000 subjects which includes 1000 (584M/416F cases with type 2 diabetes and 1000 (470M/530F normoglycemic control subjects belonging to Dravidian ethnicity from South India were recruited to assess the effect of single nucleotide polymorphisms (SNPs in GIP (rs2291725, rs2291726, rs937301 on type 2 diabetes in a case-control manner. The SNPs were genotyped by using tetra primer amplification refractory mutation system-PCR (ARMS PCR. For statistical analysis, our study population was divided into sub-groups based on gender (male and female. Association analysis was carried out using chi-squared test and the comparison of biochemical parameters among the three genotypes were performed using analysis of covariance (ANCOVA. Result Initial analysis revealed that, out of the total three SNPs selected for the present study, two SNPs namely rs2291726 and rs937301 were in complete linkage disequilibrium (LD with each other. Therefore, only two SNPs, rs2291725 and rs2291726, were genotyped for the association studies. No significant difference in the allele frequency and genotype distribution of any of the SNPs in GIP were observed between cases and controls (P > 0.05. Analysis of biochemical parameters among the three genotypes showed a significant association of total cholesterol (P = 0.042 and low density lipoprotein (LDL with the G allele of the SNP rs2291726 in GIP (P = 0.004, but this was observed only in the case of female

  11. Integrated physiological, biochemical and molecular analysis identifies important traits and mechanisms associated with differential response of rice genotypes to elevated temperature

    Directory of Open Access Journals (Sweden)

    Boghireddy eSailaja

    2015-11-01

    Full Text Available In changing climate, heat stress caused by high temperature poses a serious threat to rice cultivation. A multiple organizational analysis at physiological, biochemical and molecular level is required to fully understand the impact of elevated temperature in rice. This study was aimed at deciphering the elevated temperature response in eleven popular and mega rice cultivars widely grown in India. Physiological and biochemical traits specifically membrane thermostability (MTS, antioxidants, and photosynthesis were studied at vegetative and reproductive phases which were used to establish a correlation with grain yield under stress. Several useful traits in different genotypes were identified which will be important resource to develop high temperature tolerant rice cultivars. Interestingly, Nagina22 emerged as best performer in terms of yield as well as expression of physiological and biochemical traits at elevated temperature. It showed lesser relative injury, lesser reduction in chlorophyll content, increased super oxide dismutase, catalase and peroxidase activity, lesser reduction in net photosynthetic rate (PN, high transpiration rate (E and other photosynthetic/ fluorescence parameters contributing to least reduction in spikelet fertility and grain yield at elevated temperature. Further, expression of 14 genes including heat shock transcription factors and heat shock proteins was analyzed in Nagina22 (tolerant and Vandana (susceptible at flowering phase, strengthening the fact that N22 performs better at molecular level also during elevated temperature. This study shows that elevated temperature response is complex and involves multiple biological processes which are needed to be characterized to address the challenges of future climate extreme conditions.

  12. Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

    CERN Document Server

    Laurinavichius, K S

    1998-01-01

    Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

  13. Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Henriksen, Peter; Wagner, Sebastian Alexander; Weinert, Brian Tate

    2012-01-01

    Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine...... acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S....... cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved...

  14. Analysis of educational research at a medical faculty in Germany and suggestions for strategic development – a case study

    Science.gov (United States)

    Prediger, Sarah; Harendza, Sigrid

    2016-01-01

    Background: Evidence-based medical education is playing an increasingly important role in the choice of didactic methods and the development of medical curricula and assessments. In Germany, a growing number of educational research projects has accompanied an ongoing change in the medical education process. The aim of this project was to assess medical education research activities at one medical faculty to develop procedural recommendations for the support and development of best evidence medical education. Methods: Using a newly developed online questionnaire, the 65 institutes and departments of the medical faculty of Hamburg University at Hamburg University Medical-Center (UKE) were asked to report their medical education research and service projects, medical education publications, medical education theses, financial support for educational projects, and supportive structures that they would consider helpful in the future. The data were grouped, and a SWOT analysis was performed. Results: In total, 60 scientists who were involved in 112 medical education research publications between 1998 and 2014 were identified at the UKE. Twenty-five of them had published at least one manuscript as first or last author. Thirty-three UKE institutions were involved in educational service or research projects at the time of the study, and 75.8% of them received internal or external funding. Regular educational research meetings and the acquisition of co-operation partners were mentioned most frequently as beneficial supportive structures for the future. Conclusion: An analysis to define the status quo of medical education research at a medical faculty seems to be a helpful first step for the development of a strategy and structure to further support researchers in medical education. PMID:27990467

  15. Analysis of educational research at a medical faculty in Germany and suggestions for strategic development - a case study.

    Science.gov (United States)

    Prediger, Sarah; Harendza, Sigrid

    2016-01-01

    Background: Evidence-based medical education is playing an increasingly important role in the choice of didactic methods and the development of medical curricula and assessments. In Germany, a growing number of educational research projects has accompanied an ongoing change in the medical education process. The aim of this project was to assess medical education research activities at one medical faculty to develop procedural recommendations for the support and development of best evidence medical education. Methods: Using a newly developed online questionnaire, the 65 institutes and departments of the medical faculty of Hamburg University at Hamburg University Medical-Center (UKE) were asked to report their medical education research and service projects, medical education publications, medical education theses, financial support for educational projects, and supportive structures that they would consider helpful in the future. The data were grouped, and a SWOT analysis was performed. Results: In total, 60 scientists who were involved in 112 medical education research publications between 1998 and 2014 were identified at the UKE. Twenty-five of them had published at least one manuscript as first or last author. Thirty-three UKE institutions were involved in educational service or research projects at the time of the study, and 75.8% of them received internal or external funding. Regular educational research meetings and the acquisition of co-operation partners were mentioned most frequently as beneficial supportive structures for the future. Conclusion: An analysis to define the status quo of medical education research at a medical faculty seems to be a helpful first step for the development of a strategy and structure to further support researchers in medical education.

  16. Analysis of recent failures of disease modifying therapies in Alzheimer's disease suggesting a new methodology for future studies.

    Science.gov (United States)

    Amanatkar, Hamid Reza; Papagiannopoulos, Bill; Grossberg, George Thomas

    2017-01-01

    Pharmaceutical companies and the NIH have invested heavily in a variety of potential disease-modifying therapies for Alzheimer's disease (AD) but unfortunately all double-blind placebo-controlled Phase III studies of these drugs have failed to show statistically significant results supporting their clinical efficacy on cognitive measures. These negative results are surprising as most of these medications have the capability to impact the biomarkers which are associated with progression of Alzheimer's disease. Areas covered: This contradiction prompted us to review all study phases of Intravenous Immunoglobulin (IVIG), Bapineuzumab, Solanezumab, Avagacestat and Dimebolin to shed more light on these recent failures. We critically analyzed these studies, recommending seven lessons from these failures which should not be overlooked. Expert commentary: We suggest a new methodology for future treatment research in Alzheimer's disease considering early intervention with more focus on cognitive decline as a screening tool, more sophisticated exclusion criteria with more reliance on biomarkers, stratification of subjects based on the rate of cognitive decline aiming less heterogeneity, and a longer study duration with periodic assessment of cognition and activities of daily living during the study and also after a washout period.

  17. Implications of geoengineering under the 1.5 °C target: Analysis and policy suggestions

    Directory of Open Access Journals (Sweden)

    Ying Chen

    2017-06-01

    Full Text Available The Paris Agreement introduced a 1.5 °C target to control the rise in global temperature, but clear arrangements for feasible implementation pathways were not made. Achieving the 1.5 °C target imposes high requirements on global emission reduction. Nationally Determined Contributions of all Parties are far from the 1.5 °C target, and conventional emission reduction technologies and policies will also have difficulty in fulfilling this task. In this context, geoengineering is gaining interest in the international arena. The Paris Agreement includes afforestation, carbon capture, utilization and storage, and negative emission technologies such as bio-energy with carbon capture and store. All of these techniques are CO2 removal technologies that belong to geoengineering. Solar radiation management, which is highly controversial, has also attracted increased attention in recent years. Although the outline of the IPCC Special Report on 1.5 °C does not include a specific section on geoengineering issues yet, geoengineering is an unconventional technical option that cannot be avoided in research and discussions on impact assessment, technical options, ethics, and international governance under the 1.5 °C target. On the basis of analyzing and discussing abovementioned issues, this paper proposes several policy suggestions for China to strengthen research on and response to geoengineering.

  18. Phylogenetic analysis and survey of Apis cerana strain of Sacbrood virus (AcSBV) in Taiwan suggests a recent introduction.

    Science.gov (United States)

    Huang, Wei-Fone; Mehmood, Shahid; Huang, Shaokang; Chen, Yue-Wen; Ko, Chong-Yu; Su, Songkun

    2017-06-01

    The Sacbrood virus (SBV) is widely distributed in European honey bees, Apis mellifera. AcSBV, a distinct SBV strain in Asian honey bees (A. cerana) causes larva death before pupation and often depopulates colonies, leading to collapse. It is the most severe disease in A. cerana beekeeping. AcSBV infects A. cerana in most natural habitats, yet occurrences were not reported in Taiwan before 2015 and were not a concern for local beekeepers. However, in 2016, A. cerana beekeepers in central Taiwan reported SBV-like symptoms. We screened samples of larvae using RT-PCR and surveyed asymptomatic apiaries in north Taiwan. Phylogenetic analyses suggested that AcSBV isolates from central Taiwan were introduced; all isolates had high similarity in sequences to AcSBV genomes identified in mainland China, Vietnam, and Korea and distinct differences to SBV sequence identified in Taiwan. The overall prevalence in symptomatic colonies was low. No latent infections were detected in asymptomatic colonies. The AcSBV epizootic may not yet have reached its highest potential. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Proteomic analysis of mature soybean seeds from the Chernobyl area suggests plant adaptation to the contaminated environment.

    Science.gov (United States)

    Danchenko, Maksym; Skultety, Ludovit; Rashydov, Namik M; Berezhna, Valentyna V; Mátel, L'ubomír; Salaj, Terézia; Pret'ová, Anna; Hajduch, Martin

    2009-06-01

    The explosion in one of the four reactors of the Chernobyl Nuclear Power Plant (CNPP, Chernobyl) caused the worst nuclear environmental disaster ever seen. Currently, 23 years after the accident, the soil in the close vicinity of CNPP is still significantly contaminated with long-living radioisotopes, such as (137)Cs. Despite this contamination, the plants growing in Chernobyl area were able to adapt to the radioactivity, and survive. The aim of this study was to investigate plant adaptation mechanisms toward permanently increased level of radiation using a quantitative high-throughput proteomics approach. Soybeans of a local variety (Soniachna) were sown in contaminated and control fields in the Chernobyl region. Mature seeds were harvested and the extracted proteins were subjected to two-dimensional gel electrophoresis (2-DE). In total, 9.2% of 698 quantified protein spots on 2-D gel were found to be differentially expressed with a p-value Chernobyl soil conditions was proposed. Our results suggest that adaptation toward heavy metal stress, protection against radiation damage, and mobilization of seed storage proteins are involved in plant adaptation mechanism to radioactivity in the Chernobyl region.

  20. Analysis of the Beta-Tubulin Gene and morphological changes of the Microsporidium Anncaliia algerae both Suggest Albendazole Sensitivity*

    Science.gov (United States)

    Santiana, Marianita; Pau, Cyrilla; Takvorian, Peter M.; Cali, Ann

    2014-01-01

    The Microsporidium, Anncaliia algerae, an obligate intracellular parasite, has been identified as an opportunistic human pathogen but treatment has not been evaluated for infections with this organism. Albendazole, an anti-tubulin polymerization drug used against parasitic worm infections, has been the medication of choice used to treat some microsporidial infections affecting humans, with varying results ranging from clearing infection (Encephalitozoon) to resistance (Enterocytozoon). This study illustrates the effect of albendazole treatment on A. algerae infection in Rabbit Kidney (RK13) cells and Human Fetal Lung (HFL-1) fibroblasts. Albendazole appears to have an attenuating effect on A. algerae infection and albendazole’s IC50 in RK13 cells is 0.1μg/ml. Long-term treatment inhibits up to 98% of spore production, but interrupting treatment re-establishes the infection without new exposure to the parasite as supported by microscopic observations. The parasite’s Beta-Tubulin gene was purified, cloned, and sequenced. Five of the six specific amino acids, associated with benzimidazole sensitivity, are conserved in A. algerae. These findings suggest that A. algerae is sensitive to albendazole; however, the organism is not completely cleared from cultures. PMID:25105446

  1. BISEN: Biochemical simulation environment

    NARCIS (Netherlands)

    Vanlier, J.; Wu, F.; Qi, F.; Vinnakota, K.C.; Han, Y.; Dash, R.K.; Yang, F.; Beard, D.A.

    2009-01-01

    The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for

  2. Late gadolinium uptake demonstrated with magnetic resonance in patients where automated PERFIT analysis of myocardial SPECT suggests irreversible perfusion defect

    International Nuclear Information System (INIS)

    Rosendahl, Lene; Blomstrand, Peter; Ohlsson, Jan L; Björklund, Per-Gunnar; Ahlander, Britt-Marie; Starck, Sven-Åke; Engvall, Jan E

    2008-01-01

    Myocardial perfusion single photon emission computed tomography (MPS) is frequently used as the reference method for the determination of myocardial infarct size. PERFIT ® is a software utilizing a three-dimensional gender specific, averaged heart model for the automatic evaluation of myocardial perfusion. The purpose of this study was to compare the perfusion defect size on MPS, assessed with PERFIT, with the hyperenhanced volume assessed by late gadolinium enhancement magnetic resonance imaging (LGE) and to relate their effect on the wall motion score index (WMSI) assessed with cine magnetic resonance imaging (cine-MRI) and echocardiography (echo). LGE was performed in 40 patients where clinical MPS showed an irreversible uptake reduction suggesting a myocardial scar. Infarct volume, extent and major coronary supply were compared between MPS and LGE as well as the relationship between infarct size from both methods and WMSI. MPS showed a slightly larger infarct volume than LGE (MPS 29.6 ± 23.2 ml, LGE 22.1 ± 16.9 ml, p = 0.01), while no significant difference was found in infarct extent (MPS 11.7 ± 9.4%, LGE 13.0 ± 9.6%). The correlation coefficients between methods in respect to infarct size and infarct extent were 0.71 and 0.63 respectively. WMSI determined with cine-MRI correlated moderately with infarct volume and infarct extent (cine-MRI vs MPS volume r = 0.71, extent r = 0.71, cine-MRI vs LGE volume r = 0.62, extent r = 0.60). Similar results were achieved when wall motion was determined with echo. Both MPS and LGE showed the same major coronary supply to the infarct area in a majority of patients, Kappa = 0.84. MPS and LGE agree moderately in the determination of infarct size in both absolute and relative terms, although infarct volume is slightly larger with MPS. The correlation between WMSI and infarct size is moderate

  3. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Science.gov (United States)

    Valverde, Guido; Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars; Llamas, Bastien; Haak, Wolfgang

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD), Wari (Middle Horizon, 800-1000 AD) and Ychsma (Late Intermediate Period, 1000-1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.

  4. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Directory of Open Access Journals (Sweden)

    Guido Valverde

    Full Text Available The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD, Wari (Middle Horizon, 800-1000 AD and Ychsma (Late Intermediate Period, 1000-1450 AD. We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.

  5. Analysis of the state of vegetation in the municipality of Jagodina (Serbia through remote sensing and suggestions for protection

    Directory of Open Access Journals (Sweden)

    Milanović Miško M.

    2016-01-01

    Full Text Available Both environmental control and appropriate measurement results present basis for the quality protection of geospatial elements. Providing environmental monitoring activities and creating control network is the obligation of each state, whereas local communities provide observation and control of air quality, water quality, waste quality, soil quality, vegetation and land cover control, etc. This has been the reason for the analysis of vegetation of the municipality of Jagodina in Serbia. By processing satellite images, data on the sources of pollution and polluting materials of the vegetation have been discovered. These include spot (stationary, linear (mobile and stationary and surface (stationary and mobile sources. While processing satellite images by the Idrisi software, we have acquired results that indicate certain vegetation modifications (images obtained through infrared spectral imaging. Results obtained through remote sensing indicate the necessity to define adequate vegetation monitoring, to complete a register of pollutants, to set up information system and define ways of data presentation in order to manage a single, complete register of environmental pollutants in the municipality of Jagodina.

  6. Transcriptome analysis and RNA interference of cockroach phototransduction indicate three opsins and suggest a major role for TRPL channels

    Directory of Open Access Journals (Sweden)

    Andrew S French

    2015-07-01

    Full Text Available Our current understanding of insect phototransduction is based on a small number of species, but insects occupy many different visual environments. We created the retinal transcriptome of a nocturnal insect, the cockroach, Periplaneta americana to identify proteins involved in the earliest stages of compound eye phototransduction, and test the hypothesis that different visual environments are reflected in different molecular contributions to function. We assembled five novel mRNAs: two green opsins, one UV opsin, and one each TRP and TRPL ion channel homologs. One green opsin mRNA (pGO1 was 100-1000 times more abundant than the other opsins (pGO2 and pUVO, while pTRPL mRNA was 10 times more abundant than pTRP, estimated by transcriptome analysis or quantitative PCR (qPCR. Electroretinograms were used to record photoreceptor responses. Gene-specific in vivo RNA interference (RNAi was achieved by injecting long (596-708 bp double-stranded RNA into head hemolymph, and verified by qPCR. RNAi of the most abundant green opsin reduced both green opsins by more than 97% without affecting UV opsin, and gave a maximal reduction of 75% in ERG amplitude seven days after injection that persisted for at least 19 days. RNAi of pTRP and pTRPL genes each specifically reduced the corresponding mRNA by 90%. Electroretinogram reduction by pTRPL RNAi was slower than for opsin, reaching 75% attenuation by 21 days, without recovery at 29 days. pTRP RNAi attenuated ERG much less; only 30% after 21 days. Combined pTRP plus pTRPL RNAi gave only weak evidence of any cooperative interactions. We conclude that silencing retinal genes by in vivo RNAi using long dsRNA is effective, that visible light transduction in Periplaneta is dominated by pGO1, and that pTRPL plays a major role in cockroach phototransduction.

  7. PRE VACCINATION MEASLES OUTBREAKS IN ENGLAND AND WALES: NONLINEAR ASSOCIATION ANALYSIS SUGGESTS A LEADING ROLE FOR PRESTON

    Directory of Open Access Journals (Sweden)

    Lourdes Hernández Martinez

    2006-08-01

    Full Text Available ABSTRACTMeasles data from pre-vaccination era in England and Wales were submitted to nonlinear association analysis. The method's rationale lies on the supposal that strong association between two time series when one of them is shifted in time respect to the other might be taken as an evidence for spatial-temporal causality. A threshold value for the nonlinear determination coefficient ( was set as criterion of strong association ( > 0.55.The common pattern for most of the cities was that outbreaks in a given place might be anticipated by some cities whereas followed by others. Only Preston preceded other cities and never followed any other. This result might be plausible since this port is an important node of human exchange with other cities. The associations respect to Preston were markedly nonlinear and the spread from there was slower, perhaps due to climatic causes. We conclude that nonlinear association approach is a promising way of exploring spatial-temporal epidemics data. RESUMEN:Se estudiaron, mediante un método de análisis de asociación no lineal, datos de incidencia de sarampión en Inglaterra y Gales correspondientes a la era pre-vacunación. La idea del método se centra en suponer que una asociación fuerte entre dos series temporales cuando una esta desplazada en el eje del tiempo respecto a la otra puede ser tomada como evidencia de causalidad. Se predeterminó un valor umbral para el coeficiente de determinación no lineal ( como criterio de asociación fuerte ( > 0.55.Para la mayor parte de las ciudades los brotes epidémicos se anticipaban a los de otras ciudades, pero eran posteriores a unas terceras. Solamente Preston precedía a otras ciudades y nunca siguió a otra. Este resultado pudiera ser relevante por cuanto este puerto es un nodo importante de intercambio humano con otras ciudades. Las asociaciones respecto a Preston eran marcadamente no lineales y la propagación desde Preston era más lenta, quizás debido

  8. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list.

    Science.gov (United States)

    Kotera, Masaaki; Nishimura, Yosuke; Nakagawa, Zen-ichi; Muto, Ai; Moriya, Yuki; Okamoto, Shinobu; Kawashima, Shuichi; Katayama, Toshiaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2014-12-01

    Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

  9. Biochemical Analysis Reveals the Multifactorial Mechanism of Histone H3 Clipping by Chicken Liver Histone H3 Protease

    KAUST Repository

    Chauhan, Sakshi

    2016-09-02

    Proteolytic clipping of histone H3 has been identified in many organisms. Despite several studies, the mechanism of clipping, the substrate specificity, and the significance of this poorly understood epigenetic mechanism are not clear. We have previously reported histone H3 specific proteolytic clipping and a protein inhibitor in chicken liver. However, the sites of clipping are still not known very well. In this study, we attempt to identify clipping sites in histone H3 and to determine the mechanism of inhibition by stefin B protein, a cysteine protease inhibitor. By employing site-directed mutagenesis and in vitro biochemical assays, we have identified three distinct clipping sites in recombinant human histone H3 and its variants (H3.1, H3.3, and H3t). However, post-translationally modified histones isolated from chicken liver and Saccharomyces cerevisiae wild-type cells showed different clipping patterns. Clipping of histone H3 N-terminal tail at three sites occurs in a sequential manner. We have further observed that clipping sites are regulated by the structure of the N-terminal tail as well as the globular domain of histone H3. We also have identified the QVVAG region of stefin B protein to be very crucial for inhibition of the protease activity. Altogether, our comprehensive biochemical studies have revealed three distinct clipping sites in histone H3 and their regulation by the structure of histone H3, histone modifications marks, and stefin B.

  10. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.

    Directory of Open Access Journals (Sweden)

    Melody K Morris

    2011-03-01

    Full Text Available Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL, converts a prior knowledge network (obtained from literature or interactome databases into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a generating experimentally testable biological hypotheses concerning pathway crosstalk, (b establishing capability for quantitative prediction of protein activity, and (c prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone.

  11. A Dose–Response Analysis of Biochemical Control Outcomes After {sup 125}I Monotherapy for Patients With Favorable-Risk Prostate Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Shiraishi, Yutaka, E-mail: shiraishi@rad.med.keio.ac.jp [Department of Radiology, Keio University School of Medicine, Tokyo (Japan); Department of Radiology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Yorozu, Atsunori [Department of Radiology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Ohashi, Toshio [Department of Radiology, Keio University School of Medicine, Tokyo (Japan); Toya, Kazuhito [Department of Radiology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Saito, Shiro; Nishiyama, Toru; Yagi, Yasuto [Department of Urology, National Hospital Organization Tokyo Medical Center, Tokyo (Japan); Shigematsu, Naoyuki [Department of Radiology, Keio University School of Medicine, Tokyo (Japan)

    2014-12-01

    Purpose: To define the optimal dose for {sup 125}I prostate implants by correlating postimplantation dosimetry findings with biochemical failure and toxicity. Methods and Materials: Between 2003 and 2009, 683 patients with prostate cancer were treated with {sup 125}I prostate brachytherapy without supplemental external beam radiation therapy and were followed up for a median time of 80 months. Implant dose was defined as the D90 (the minimal dose received by 90% of the prostate) on postoperative day 1 and 1 month after implantation. Therefore, 2 dosimetric variables (day 1 D90 and day 30 D90) were analyzed for each patient. We investigated the dose effects on biochemical control and toxicity. Results: The 7-year biochemical failure-free survival (BFFS) rate for the group overall was 96.4% according to the Phoenix definition. A multivariate analysis found day 1 D90 and day 30 D90 to be the most significant factors affecting BFFS. The cutoff points for day 1 D90 and day 30 D90, calculated from ROC curves, were 163 Gy and 175 Gy, respectively. By use of univariate analysis, various dosimetric cutoff points for day 30 D90 were tested. We found that day 30 D90 cutoff points from 130 to 180 Gy appeared to be good for the entire cohort. Greater D90s were associated with an increase in late genitourinary or gastrointestinal toxicity ≥ grade 2, but the increase was not statistically significant. Conclusions: Improvements in BFFS rates were seen with increasing D90 levels. Day 30 D90 doses of 130 to 180 Gy were found to serve as cutoff levels. For low-risk and low-tier intermediate-risk prostate cancer patients, high prostate D90s, even with doses exceeding 180 Gy, achieve better treatment results and are feasible.

  12. PREDICTORS OF BIOCHEMICAL REMISSION AND RECURRENCE AFTER SURGICAL AND RADIATION TREATMENTS OF CUSHING DISEASE: A SYSTEMATIC REVIEW AND META-ANALYSIS.

    Science.gov (United States)

    Abu Dabrh, Abd Moain Abu; Singh Ospina, Naykky M; Al Nofal, Alaa; Farah, Wigdan H; Barrionuevo, Patricia; Sarigianni, Maria; Mohabbat, Arya B; Benkhadra, Khalid; Carranza Leon, Barbara G; Gionfriddo, Michael R; Wang, Zhen; Mohammed, Khaled; Ahmed, Ahmed T; Elraiyah, Tarig A; Haydour, Qusay; Alahdab, Fares; Prokop, Larry J; Murad, Mohammad Hassan

    2016-04-01

    We conducted a systematic review and meta-analysis to synthesize the evidence about predictors that may affect biochemical remission and recurrence after transsphenoidal surgery (TSS), radiosurgery (RS), and radiotherapy (RT) in Cushing disease. We searched multiple databases through December 2014 including original controlled and uncontrolled studies that enrolled patients with Cushing disease who received TSS (first-line), RS, or RT. We extracted data independently, in duplicates. Outcomes of interest were biochemical remission and recurrence. A meta-analysis was conducted using the random-effects model to estimate event rates with 95% confidence intervals (CIs). First-line TSS was associated with high remission (76% [95% CI, 72 to 79%]) and low recurrence rates (10% [95% CI, 6 to 16%]). Remission after TSS was higher in patients with microadenomas or positive-adrenocorticotropic hormone tumor histology. RT was associated with a high remission rate (RS, 68% [95% CI, 61 to 77%]; RT, 66% [95% CI, 58 to 75%]) but also with a high recurrence rate (RS, 32% [95% CI, 16 to 60%]; RT, 26% [95% CI, 14 to 48%]). Remission after RS was higher at short-term follow-up (≤2 years) and with high-dose radiation, while recurrence was higher in women and with lower-dose radiation. Remission was after RT in adults who received TSS prior to RT, and with lower radiation doses. There was heterogeneity (nonstandardization) in the criteria and cutoff points used to define biochemical remission and recurrence. First-line TSS is associated with high remission and low recurrence, while RS and RT are associated with reasonable remission rates but important recurrence rates. The current evidence warrants low confidence due to the noncomparative nature of the studies, high heterogeneity, and imprecision.

  13. Biochemical and Biophysical Methods for Analysis of Poly(ADP-Ribose) Polymerase 1 and Its Interactions with Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Chassé, Maggie H.; Muthurajan, Uma M.; Clark, Nicholas J.; Kramer, Michael A.; Chakravarthy, Srinivas; Irving, Thomas; Luger, Karolin [Children; (IIT); (Colorado); (Amgen)

    2018-01-18

    Poly (ADP-Ribose) Polymerase I (PARP-1) is a first responder to DNA damage and participates in the regulation of gene expression. The interaction of PARP-1 with chromatin and DNA is complex and involves at least two different modes of interaction. In its enzymatically inactive state, PARP-1 binds native chromatin with similar affinity as it binds free DNA ends. Automodification of PARP-1 affects interaction with chromatin and DNA to different extents. Here we describe a series of biochemical and biophysical techniques to quantify and dissect the different binding modes of PARP-1 with its various substrates. The techniques listed here allow for high throughput and quantitative measurements of the interaction of different PARP-1 constructs (inactive and automodified) with chromatin and DNA damage models.

  14. Hypnosis, suggestion, and suggestibility: an integrative model.

    Science.gov (United States)

    Lynn, Steven Jay; Laurence, Jean-Roch; Kirsch, Irving

    2015-01-01

    This article elucidates an integrative model of hypnosis that integrates social, cultural, cognitive, and neurophysiological variables at play both in and out of hypnosis and considers their dynamic interaction as determinants of the multifaceted experience of hypnosis. The roles of these variables are examined in the induction and suggestion stages of hypnosis, including how they are related to the experience of involuntariness, one of the hallmarks of hypnosis. It is suggested that studies of the modification of hypnotic suggestibility; cognitive flexibility; response sets and expectancies; the default-mode network; and the search for the neurophysiological correlates of hypnosis, more broadly, in conjunction with research on social psychological variables, hold much promise to further understanding of hypnosis.

  15. Gel-free/label-free proteomic, photosynthetic, and biochemical analysis of cowpea (Vigna unguiculata [L.] Walp.) resistance against Cowpea severe mosaic virus (CPSMV).

    Science.gov (United States)

    Varela, Anna Lidia N; Komatsu, Setsuko; Wang, Xin; Silva, Rodolpho G G; Souza, Pedro Filho N; Lobo, Ana Karla M; Vasconcelos, Ilka M; Silveira, Joaquim A G; Oliveira, Jose T A

    2017-06-23

    Cowpea severe mosaic virus (CPSMV) causes significant losses in cowpea (Vigna unguiculata) production. In this present study biochemical, physiological, and proteomic analysis were done to identify pathways and defense proteins that are altered during the incompatible interaction between the cowpea genotype BRS-Marataoã and CPSMV. The leaf protein extracts from mock- (MI) and CPSMV-inoculated plantlets (V) were evaluated at 2 and 6days post-inoculation (DPI). Data support the assumptions that increases in biochemical (high hydrogen peroxide, antioxidant enzymes, and secondary compounds) and physiological responses (high photosynthesis index and chlorophyll content), confirmed by label-free comparative proteomic approach, in which quantitative changes in proteasome proteins, proteins related to photosynthesis, redox homeostasis, regulation factors/RNA processing proteins were observed may be implicated in the resistance of BRS-Marataoã to CPSMV. This pioneering study provides information for the selection of specific pathways and proteins, altered in this incompatible relationship, which could be chosen as targets for detailed studies to advance our understanding of the molecular, physiological, and biochemistry basis of the resistance mechanism of cowpea and design approachs to engineer plants that are more productive. This is a pioneering study in which an incompatible relationship between a resistant cowpea and Cowpea severe mosaic virus (CPSMV) was conducted to comparatively evaluate proteomic profiles by Gel-free/label-free methodology and some physiological and biochemical parameters to shed light on how a resistant cowpea cultivar deals with the virus attack. Specific proteins and associated pathways were altered in the cowpea plants challenged with CPSMV and will contribute to our knowledge on the biological process tailored by cowpea in response to CPSMV. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Biochemical analysis of murine leukemia viruses isolated from radiation-induced leukemias of strain BALB/c

    International Nuclear Information System (INIS)

    Ellis, R.W.; Hopkins, N.; Fleissner, E.

    1980-01-01

    Murine leukemia viruses isolated from radiation-induced BALB/c leukemias were characterized with respect to viral proteins and RNA. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the viral structural proteins revealed that for p12, p15, p30, and gp70, three to four electrophoretic variants of each could be detected. There was no correlation found between any of these mobilities and N- or B-tropism of the viruses. Proteins of all xenotropic viral isolates were identical in their gel electrophoretic profiles. The similar phenotypes of multiple viral clones from individual leukemias and of isolates grown in different cells suggest that the polymorphism of ecotropic viruses was generated in vivo rather than during in vitro virus growth. By two-dimensional fingerprinting of RNase T1-resistant oligonucleotides from 70S viral RNA, the previously reported association of N- and B-tropism with two distinct oligonucleotides was confirmed. The presence of two other oligonucleotides was correlated with positive and negative phenotypes of the virus-coded G/sub IX/ cell surface antigen. The RNAs of two B-tropic isolates with distinctive p15 and p12 phenotypes differed from the RNA of a prototype N-tropic virus by the absence of three oligonucleotides mapping in the 5' portion (gag region) of the prototype RNA. In addition, one small-plaque B-tropic virus displayed extensive changes in the RNA sequences associated with the env region of the prototype

  17. Biochemical and Structural Analysis of an Eis Family Aminoglycoside Acetyltransferase from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Green, Keith D.; Biswas, Tapan; Chang, Changsoo; Wu, Ruiying; Chen, Wenjing; Janes, Brian K.; Chalupska, Dominika; Gornicki, Piotr; Hanna, Philip C.; Tsodikov, Oleg V.; Joachimiak, Andrzej; Garneau-Tsodikova, Sylvie

    2015-05-26

    Proteins from the enhanced intracellular survival (Eis) family are versatile acetyltransferases that acetylate amines at multiple positions of several aminoglycosides (AGs). Their upregulation confers drug resistance. Homologues of Eis are present in diverse bacteria, including many pathogens. Eis from Mycobacterium tuberculosis (Eis_Mtb) has been well characterized. In this study, we explored the AG specificity and catalytic efficiency of the Eis family protein from Bacillus anthracis (Eis_Ban). Kinetic analysis of specificity and catalytic efficiency of acetylation of six AGs indicates that Eis_Ban displays significant differences from Eis_Mtb in both substrate binding and catalytic efficiency. The number of acetylated amines was also different for several AGs, indicating a distinct regiospecificity of Eis_Ban. Furthermore, most recently identified inhibitors of Eis_Mtb did not inhibit Eis_Ban, underscoring the differences between these two enzymes. To explain these differences, we determined an Eis_Ban crystal structure. The comparison of the crystal structures of Eis_Ban and Eis_Mtb demonstrates that critical residues lining their respective substrate binding pockets differ substantially, explaining their distinct specificities. Our results suggest that acetyltransferases of the Eis family evolved divergently to garner distinct specificities while conserving catalytic efficiency, possibly to counter distinct chemical challenges. The unique specificity features of these enzymes can be utilized as tools for developing AGs with novel modifications and help guide specific AG treatments to avoid Eis-mediated resistance.

  18. Quantitative Raman spectral changes of the differentiation of mesenchymal stem cells into islet-like cells by biochemical component analysis and multiple peak fitting

    Science.gov (United States)

    Su, Xin; Fang, Shaoyin; Zhang, Daosen; Zhang, Qinnan; He, Yingtian; Lu, Xiaoxu; Liu, Shengde; Zhong, Liyun

    2015-12-01

    Mesenchymal stem cells (MSCs) differentiate into islet-like cells, providing a possible solution for type I diabetes treatment. To search for the precise molecular mechanism of the directional differentiation of MSC-derived islet-like cells, biomolecular composition, and structural conformation information during MSC differentiation, is required. Because islet-like cells lack specific surface markers, the commonly employed immunostaining technique is not suitable for their identification, physical separation, and enrichment. Combining Raman spectroscopic data, a fitting accuracy-improved biochemical component analysis, and multiple peaks fitting approach, we identified the quantitative biochemical and intensity change of Raman peaks that show the differentiation of MSCs into islet-like cells. Along with increases in protein and glycogen content, and decreases in deoxyribonucleic acid and ribonucleic acid content, in islet-like cells relative to MSCs, it was found that a characteristic peak of insulin (665 cm-1) has twice the intensity in islet-like cells relative to MSCs, indicating differentiation of MSCs into islet-like cells was successful. Importantly, these Raman signatures provide useful information on the structural and pathological states during MSC differentiation and help to develop noninvasive and label-free Raman sorting methods for stem cells and their lineages.

  19. Speaking with and without words : An analysis of foster children’s expressions and behaviors that are suggestive of prior sexual abuse

    NARCIS (Netherlands)

    Wubs, Susanna; Batstra, Laura; Grietens, Hans

    2018-01-01

    This exploratory study reports on foster children’s informal self-disclosures of previously unknown histories of sexual abuse. Data were collected from 40 children’s files, and an inductive thematic analysis of verbal and behavioral expressions was conducted. Findings suggest that foster children’s

  20. Biochemical and functional analysis of two Plasmodium falciparum blood-stage 6-cys proteins: P12 and P41.

    Directory of Open Access Journals (Sweden)

    Tana Taechalertpaisarn

    Full Text Available The genomes of Plasmodium parasites that cause malaria in humans, other primates, birds, and rodents all encode multiple 6-cys proteins. Distinct 6-cys protein family members reside on the surface at each extracellular life cycle stage and those on the surface of liver infective and sexual stages have been shown to play important roles in hepatocyte growth and fertilization respectively. However, 6-cys proteins associated with the blood-stage forms of the parasite have no known function. Here we investigate the biochemical nature and function of two blood-stage 6-cys proteins in Plasmodium falciparum, the most pathogenic species to afflict humans. We show that native P12 and P41 form a stable heterodimer on the infective merozoite surface and are secreted following invasion, but could find no evidence that this complex mediates erythrocyte-receptor binding. That P12 and P41 do not appear to have a major role as adhesins to erythrocyte receptors was supported by the observation that antisera to these proteins did not substantially inhibit erythrocyte invasion. To investigate other functional roles for these proteins their genes were successfully disrupted in P. falciparum, however P12 and P41 knockout parasites grew at normal rates in vitro and displayed no other obvious phenotypic changes. It now appears likely that these blood-stage 6-cys proteins operate as a pair and play redundant roles either in erythrocyte invasion or in host-immune interactions.

  1. Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases.

    Science.gov (United States)

    Vardakou, Maria; Salmon, Melissa; Faraldos, Juan A; O'Maille, Paul E

    2014-01-01

    Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.

  2. Open to Suggestion.

    Science.gov (United States)

    Journal of Reading, 1987

    1987-01-01

    Offers (1) suggestions for improving college students' study skills; (2) a system for keeping track of parent, teacher, and community contacts; (3) suggestions for motivating students using tic tac toe; (4) suggestions for using etymology to improve word retention; (5) a word search grid; and (6) suggestions for using postcards in remedial reading…

  3. The Analysis of Curriculum Development Studies Which are Applied For Effective Science Teaching at Primary Level in Turkey and Suggestions to Problems Encountered

    OpenAIRE

    Rahmi YAĞBASAN; Murat DEMİRBAŞ

    2005-01-01

    In this study, curriculum development studies for effective science teaching were analyzed in Turkey, solution suggestions were made by determining the confronted problems. The studies for curriculum analysis toward science teaching were done by covering applications of modern science teaching started in 1970s, curriculum of science teaching made in 1990s and applications of science teaching curriculum put into practice in 2000. It was determined that new science teaching studies that will be...

  4. Metabolomic Analysis of Biochemical Changes in the Plasma of High-Fat Diet and Streptozotocin-Induced Diabetic Rats after Treatment with Isoflavones Extract of Radix Puerariae

    Directory of Open Access Journals (Sweden)

    Yan Zhang

    2016-01-01

    Full Text Available The main purpose of this study was to investigate the protective effects of total isoflavones from Radix Puerariae (PTIF in diabetic rats. Diabetes was induced by a high-fat diet and intraperitoneal injection of low-dose streptozotocin (STZ; 40 mg/kg. At 26 weeks onwards, PTIF 421 mg/kg was administrated to the rats once daily consecutively for 10 weeks. Metabolic profiling changes were analyzed by Ultraperformance Liquid Chromatography-Quadrupole-Exactive Orbitrap-Mass Spectrometry (UPLC-Q-Exactive Orbitrap-MS. The principal component discriminant analysis (PCA-DA, partial least-squares discriminant analysis (PLS-DA, and orthogonal partial least-squares discriminant analysis (OPLS-DA were used for multivariate analysis. Moreover, free amino acids in serum were determined by high-performance liquid chromatography with fluorescence detector (HPLC-FLD. Additionally, oxidative stress and inflammatory cytokines were evaluated. Eleven potential metabolite biomarkers, which are mainly related to the coagulation, lipid metabolism, and amino acid metabolism, have been identified. PCA-DA scores plots indicated that biochemical changes in diabetic rats were gradually restored to normal after administration of PTIF. Furthermore, the levels of BCAAs, glutamate, arginine, and tyrosine were significantly increased in diabetic rats. Treatment with PTIF could regulate the disturbed amino acid metabolism. Consequently, PTIF has great therapeutic potential in the treatment of DM by improving metabolism disorders and inhibiting oxidative damage.

  5. Suicidality and interrogative suggestibility.

    Science.gov (United States)

    Pritchard-Boone, Lea; Range, Lillian M

    2005-01-01

    All people are subject to memory suggestibility, but suicidal individuals may be especially so. The link between suicidality and suggestibility is unclear given mixed findings and methodological weaknesses of past research. To test the link between suicidality and interrogative suggestibility, 149 undergraduates answered questions about suicidal thoughts and reasons for living, and participated in a direct suggestibility procedure. As expected, suggestibility correlated with suicidality but accounted for little overall variance (4%). Mental health professionals might be able to take advantage of client suggestibility by directly telling suicidal persons to refrain from suicidal thoughts or actions.

  6. Biochemical analysis of cerebrospinal fluid in the laboratories of deployed medical treatment facilities: are Multistix 10 SG strip and iSTAT useful?

    Science.gov (United States)

    Lefrere, Bertrand; Plantamura, J; Renard, C; Ceppa, F; Delacour, H

    2017-12-01

    During military deployment, the diagnosis and the management of acute bacterial meningitis can be problematic, as deployed Medical Treatment Facilities (MTFs) often have a limited laboratory diagnostic capability. However, French Role 2 and 3 MTFs have point-of-care (POC) testing to perform urinary (Multistix 10 SG strip) and blood (iSTAT handheld analyser) biochemical testing mentioned in AMedP8.5. The purpose of this study was to compare the accuracy of this urine test strip and of the iSTAT CHEM8 and CG4 cartridges with a standard hospital bench top analyser in order to determine if these POC devices have a potential role in the biochemical analysis of cerebrospinal fluid (CSF protein, CSF glucose and CSF lactate, respectively). Agreement between the index methods and the reference methods (suitable kits on the Cobas 6 000 System) was evaluated by parallel testing of 30 CSF samples by both techniques. For CSF protein, agreement between the strip and the reference method was evaluated determining the κ coefficient. For CSF glucose and CSF lactate subgroups, least squares linear regressions were calculated and Bland-Altman analyses were performed. The Multistix 10 SG strip can be used to make a semiquantitative determination of CSF protein. A good agreement between the strip and the reference method was observed (κ coefficient: 0.93 (IC 95 0.82 to 1)). This strip is thus well adapted to demonstrate an elevation of CSF protein level as observed in acute bacterial meningitis. The iSTAT CHEM8 and CG4+ cartridges correlated well with the reference methods for the determination of CSF glucose and CSF lactate, respectively (r 2 >0.98) but exhibited a negative bias (∼ -7% and ∼ -15%, respectively). The combined use of the Multistix 10 SG strip and of the iSTAT system appears to be an attractive solution for the biochemical investigation of CSF in medical treatment facilities with limited laboratory diagnostic capability. Published by the BMJ Publishing Group

  7. Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays.

    Science.gov (United States)

    Hou, Sen; Sun, Lili; Wieczorek, Stefan A; Kalwarczyk, Tomasz; Kaminski, Tomasz S; Holyst, Robert

    2014-01-15

    Fluorescent double-stranded DNA (dsDNA) molecules labeled at both ends are commonly produced by annealing of complementary single-stranded DNA (ssDNA) molecules, labeled with fluorescent dyes at the same (3' or 5') end. Because the labeling efficiency of ssDNA is smaller than 100%, the resulting dsDNA have two, one or are without a dye. Existing methods are insufficient to measure the percentage of the doubly-labeled dsDNA component in the fluorescent DNA sample and it is even difficult to distinguish the doubly-labeled DNA component from the singly-labeled component. Accurate measurement of the percentage of such doubly labeled dsDNA component is a critical prerequisite for quantitative biochemical measurements, which has puzzled scientists for decades. We established a fluorescence correlation spectroscopy (FCS) system to measure the percentage of doubly labeled dsDNA (PDL) in the total fluorescent dsDNA pool. The method is based on comparative analysis of the given sample and a reference dsDNA sample prepared by adding certain amount of unlabeled ssDNA into the original ssDNA solution. From FCS autocorrelation functions, we obtain the number of fluorescent dsDNA molecules in the focal volume of the confocal microscope and PDL. We also calculate the labeling efficiency of ssDNA. The method requires minimal amount of material. The samples have the concentration of DNA in the nano-molar/L range and the volume of tens of microliters. We verify our method by using restriction enzyme Hind III to cleave the fluorescent dsDNA. The kinetics of the reaction depends strongly on PDL, a critical parameter for quantitative biochemical measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Comparative biochemical analysis during the anaerobic digestion of lignocellulosic biomass from six morphological parts of Williams Cavendish banana (Triploid Musa AAA group) plants.

    Science.gov (United States)

    Kamdem, Irénée; Hiligsmann, Serge; Vanderghem, Caroline; Bilik, Igor; Paquot, Michel; Thonart, Philippe

    2013-12-01

    We studied banana lignocellulosic biomass (BALICEBIOM) that is abandoned after fruit harvesting, and assessed its biochemical methane potential, because of its potential as an energy source. We monitored biogas production from six morphological parts (MPs) of the "Williams Cavendish" banana cultivar using a modified operating procedure (KOP) using KOH. Volatile fatty acid (VFA) production was measured using high performance liquid chromatography. The bulbs, leaf sheaths, petioles-midribs, leaf blades, rachis stems, and floral stalks gave total biogas production of 256, 205, 198, 126, 253, and 221 ml g⁻¹ dry matter, respectively, and total biomethane production of 150, 141, 127, 98, 162, and 144 ml g⁻¹, respectively. The biogas production rates and yields depended on the biochemical composition of the BALICEBIOM and the ability of anaerobic microbes to access fermentable substrates. There were no significant differences between the biogas analysis results produced using KOP and gas chromatography. Acetate was the major VFA in all the MP sample culture media. The bioconversion yields for each MP were below 50 %, showing that these substrates were not fully biodegraded after 188 days. The estimated electricity that could be produced from biogas combustion after fermenting all of the BALICEBIOM produced annually by the Cameroon Development Corporation-Del Monte plantations for 188 days is approximately 10.5 × 10⁶ kW h (which would be worth 0.80-1.58 million euros in the current market). This bioenergy could serve the requirements of about 42,000 people in the region, although CH₄ productivity could be improved.

  9. Physiological and biochemical and resistance changes and issr polymorphic analysis exposed to 12C6+ heavy ion radiation on calla lily

    International Nuclear Information System (INIS)

    Chen Zhen; Xu Bingliang; Tian Gu; Pu Chongjian; Xu Qiong

    2013-01-01

    Physiological and biochemical changes and ISSR Polymorphic of calla lily caused by exposure to 12 C 6+ heavy-ion radiation were studied. The results showed that bulb germination rate and plant height had significant negative correlation with radiation dose, while MDA content had high significant positive correlation with radiation dose. With increasing radiation dose, the activities of CAT, POD and resistance showed a trend of decrease after an initial increasing. Optimum doses of irradiation were 10 ∼ 20 Gy. ISSR molecular marker of the control and variant plants induced by the 12 C 6+ heavy-ion radiation suggested that 121 bands were amplified with 22 ISSR primers among two calla lily varieties, 55 bands were polymorphic and the polymorphism rate reached to 45%, the 12 C 6+ heavy-ion radiation could cause mutation of genome DNA in calla lily. It is suggested that effect of irradiation on calla lily plant was damage and suppression. Optimum doses of irradiation of 12 C 6+ Heavy ion might be applied for breeding method on Calla lily. (authors)

  10. A universal electronical adaptation of automats for biochemical analysis to a central processing computer by applying CAMAC-signals

    International Nuclear Information System (INIS)

    Schaefer, R.

    1975-01-01

    A universal expansion of a CAMAC-subsystem - BORER 3000 - for adapting analysis instruments in biochemistry to a processing computer is described. The possibility of standardizing input interfaces for lab instruments with such circuits is discussed and the advantages achieved by applying the CAMAC-specifications are described

  11. Analysis of Biochemical Control and Prognostic Factors in Patients Treated With Either Low-Dose Three-Dimensional Conformal Radiation Therapy or High-Dose Intensity-Modulated Radiotherapy for Localized Prostate Cancer

    International Nuclear Information System (INIS)

    Vora, Sujay A.; Wong, William W.; Schild, Steven E.; Ezzell, Gary A.; Halyard, Michele Y.

    2007-01-01

    Purpose: To identify prognostic factors and evaluate biochemical control rates for patients with localized prostate cancer treated with either high-dose intensity-modulated radiotherapy (IMRT) or conventional-dose three-dimensional conformal radiotherapy 3D-CRT. Methods: Four hundred sixteen patients with a minimum follow-up of 3 years (median, 5 years) were included. Two hundred seventy-one patients received 3D-CRT with a median dose of 68.4 Gy (range, 66-71 Gy). The next 145 patients received IMRT with a median dose of 75.6 Gy (range, 70.2-77.4 Gy). Biochemical control rates were calculated according to both American Society for Therapeutic Radiology and Oncology (ASTRO) consensus definitions. Prognostic factors were identified using both univariate and multivariate analyses. Results: The 5-year biochemical control rate was 60.4% for 3D-CRT and 74.1% for IMRT (p < 0.0001, first ASTRO Consensus definition). Using the ASTRO Phoenix definition, the 5-year biochemical control rate was 74.4% and 84.6% with 3D-RT and IMRT, respectively (p = 0.0326). Univariate analyses determined that PSA level, T stage, Gleason score, perineural invasion, and radiation dose were predictive of biochemical control. On multivariate analysis, dose, Gleason score, and perineural invasion remained significant. Conclusion: On the basis of both ASTRO definitions, dose, Gleason score, and perineural invasion were predictive of biochemical control. Intensity-modulated radiotherapy allowed delivery of higher doses of radiation with very low toxicity, resulting in improved biochemical control

  12. Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice.

    Science.gov (United States)

    Lakatos, Anita; Goldberg, Natalie R S; Blurton-Jones, Mathew

    2017-03-10

    We previously demonstrated that transplantation of murine neural stem cells (NSCs) can improve motor and cognitive function in a transgenic model of Dementia with Lewy Bodies (DLB). These benefits occurred without changes in human α-synuclein pathology and were mediated in part by stem cell-induced elevation of brain-derived neurotrophic factor (BDNF). However, instrastriatal NSC transplantation likely alters the brain microenvironment via multiple mechanisms that may synergize to promote cognitive and motor recovery. The underlying neurobiology that mediates such restoration no doubt involves numerous genes acting in concert to modulate signaling within and between host brain cells and transplanted NSCs. In order to identify functionally connected gene networks and additional mechanisms that may contribute to stem cell-induced benefits, we performed weighted gene co-expression network analysis (WGCNA) on striatal tissue isolated from NSC- and vehicle-injected wild-type and DLB mice. Combining continuous behavioral and biochemical data with genome wide expression via network analysis proved to be a powerful approach; revealing significant alterations in immune response, neurotransmission, and mitochondria function. Taken together, these data shed further light on the gene network and biological processes that underlie the therapeutic effects of NSC transplantation on α-synuclein induced cognitive and motor impairments, thereby highlighting additional therapeutic targets for synucleinopathies.

  13. Biochemical markers of bone turnover

    International Nuclear Information System (INIS)

    Kim, Deog Yoon

    1999-01-01

    Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays

  14. An audit of the contribution to post-mortem examination diagnosis of individual analyte results obtained from biochemical analysis of the vitreous.

    Science.gov (United States)

    Mitchell, Rebecca; Charlwood, Cheryl; Thomas, Sunethra Devika; Bellis, Maria; Langlois, Neil E I

    2013-12-01

    Biochemical analysis of the vitreous humor from the eye is an accepted accessory test for post-mortem investigation of cause of death. Modern biochemical analyzers allow testing of a range of analytes from a sample. However, it is not clear which analytes should be requested in order to prevent unnecessary testing (and expense). The means and standard deviation of the values obtained from analysis of the vitreous humor for sodium, potassium, chloride, osmolality, glucose, ketones (β-hydroxybutyrate), creatinine, urea, calcium, lactate, and ammonia were calculated from which the contribution of each analyte was reviewed in the context of post-mortem findings and final cause of death. For sodium 32 cases were regarded as high (more than one standard deviation above the mean), from which 9 contributed to post-mortem diagnosis [drowning (4), heat related death (2), diabetic hyperglycemia (2), and dehydration (1)], but 25 low values (greater than one standard deviation below the mean) made no contribution. For chloride 29 high values contributed to 4 cases--3 drowning and 1 heat-related, but these were all previously identified by a high sodium level. There were 29 high and 35 low potassium values, none of which contributed to determining the final cause of death. Of 22 high values of creatinine, 12 contributed to a diagnosis of renal failure. From 32 high values of urea, 18 contributed to 16 cases of renal failure (2 associated with diabetic hyperglycemia), 1 heat-related death, and one case with dehydration. Osmolarity contributed to 12 cases (5 heat-related, 4 diabetes, 2 renal failure, and 1 dehydration) from 36 high values. There was no contribution from 32 high values and 19 low values of calcium and there was no contribution from 4 high and 2 low values of ammonia. There were 11 high values of glucose, which contributed to the diagnosis of 6 cases of diabetic hyperglycemia and 21 high ketone levels contributed to 8 cases: 4 diabetic ketosis, 3 hypothermia, 3

  15. Quantitative analysis of Plasmodium ookinete motion in three dimensions suggests a critical role for cell shape in the biomechanics of malaria parasite gliding motility.

    Science.gov (United States)

    Kan, Andrey; Tan, Yan-Hong; Angrisano, Fiona; Hanssen, Eric; Rogers, Kelly L; Whitehead, Lachlan; Mollard, Vanessa P; Cozijnsen, Anton; Delves, Michael J; Crawford, Simon; Sinden, Robert E; McFadden, Geoffrey I; Leckie, Christopher; Bailey, James; Baum, Jake

    2014-05-01

    Motility is a fundamental part of cellular life and survival, including for Plasmodium parasites--single-celled protozoan pathogens responsible for human malaria. The motile life cycle forms achieve motility, called gliding, via the activity of an internal actomyosin motor. Although gliding is based on the well-studied system of actin and myosin, its core biomechanics are not completely understood. Currently accepted models suggest it results from a specifically organized cellular motor that produces a rearward directional force. When linked to surface-bound adhesins, this force is passaged to the cell posterior, propelling the parasite forwards. Gliding motility is observed in all three life cycle stages of Plasmodium: sporozoites, merozoites and ookinetes. However, it is only the ookinetes--formed inside the midgut of infected mosquitoes--that display continuous gliding without the necessity of host cell entry. This makes them ideal candidates for invasion-free biomechanical analysis. Here we apply a plate-based imaging approach to study ookinete motion in three-dimensional (3D) space to understand Plasmodium cell motility and how movement facilitates midgut colonization. Using single-cell tracking and numerical analysis of parasite motion in 3D, our analysis demonstrates that ookinetes move with a conserved left-handed helical trajectory. Investigation of cell morphology suggests this trajectory may be based on the ookinete subpellicular cytoskeleton, with complementary whole and subcellular electron microscopy showing that, like their motion paths, ookinetes share a conserved left-handed corkscrew shape and underlying twisted microtubular architecture. Through comparisons of 3D movement between wild-type ookinetes and a cytoskeleton-knockout mutant we demonstrate that perturbation of cell shape changes motion from helical to broadly linear. Therefore, while the precise linkages between cellular architecture and actomyosin motor organization remain unknown, our

  16. High production, purification, biochemical characterization and gene analysis of a novel catalase from the thermophilic bacterium Ureibacillus thermosphaericus FZSF03.

    Science.gov (United States)

    Jia, Xianbo; Lin, Xinjian; Tian, Yandan; Chen, Jichen; You, Minsheng

    2017-10-01

    A catalase-producing thermophilic bacterium, Ureibacillus thermosphaericus FZSF03, was isolated from high-temperature compost. Catalase production in this strain increased 31 times and reached 57,630U/mL after optimization in a shake flask, which might represent the highest catalase activity level among reported wild strains. This catalase was further purified and identified. The purified enzyme showed a specific activity of 219,360U/mg, higher than many other catalases. The molecular weight of this enzyme is 52kDa according to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the enzyme was identified as a monofunctional haeme catalase of Ureibacillus thermosphaericus by liquid chromatography-mass spectrometry (LC-MS)/MS. The optimal reaction temperature for this catalase was found to be 60°C. Stability was observed at 60°C and at a pH of 10.0, indicating the superiority of this enzyme at a high temperature and under alkaline conditions. Therefore, this catalase is a prospective candidate for industrial production and applications. The gene encoding this catalase is 1503bp. As the amino acid sequence shows low similarity with other catalases, we suggest that this is a novel monofunctional haeme catalase. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari

    2007-05-01

    Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

  18. [Physiological and biochemical analysis of the transformants of aerobic methylobacteria expressing the dcm A gene of dichloromethane dehydrogenase].

    Science.gov (United States)

    Firsova, Iu E; Doronina, N V; Trotsenko, Iu A

    2004-01-01

    The transformants of Methylobacterium dichloromethanicum DM4 (DM4-2cr-/pME8220 and DM4-2cr-/pME8221) and of Methylobacterium extorquens AM1 (AM1/pME8220 and AM1/pME8221) that express the dcm A gene of dichloromethane dehalogenase undergo lysis when incubated in the presence of dichloromethane and are sensitive to acidic shock. The lysis of the transformants was found to be related neither to the accumulation of Cl- ions, CH2O, and HCOOH, nor to the impairment of glutathione synthesis or to the maintenance of intracellular pH. The (exo-) Klenow fragment-mediated incorporation of [alpha-32P]dATP into the DNA of the transformants DM4-2cr-/pME8220 and AM1/pME8220 was considerably greater when the transformed cells were incubated with CH2Cl2 than when they were incubated with CH3OH, indicating the occurrence of a significant increase in the total length of gaps. At the same time, the strain AM1 (which lacks dichloromethane dehalogenase) and the dichloromethane-degrading strain DM4 incubated with CH2Cl2 showed an insignificant increase in the total length of the gaps. The transformed cells are likely to lyse due to the relatively inefficient repair of DNA lesions that are induced in response to the alkylating action of S-chloromethylglutathione, an intermediate product of CH2Cl2 degradation. The data obtained suggest that the bacterial mineralization of dichloromethane requires an efficient DNA repair system.

  19. High-throughput quantitative biochemical characterization of algal biomass by NIR spectroscopy; multiple linear regression and multivariate linear regression analysis.

    Science.gov (United States)

    Laurens, L M L; Wolfrum, E J

    2013-12-18

    One of the challenges associated with microalgal biomass characterization and the comparison of microalgal strains and conversion processes is the rapid determination of the composition of algae. We have developed and applied a high-throughput screening technology based on near-infrared (NIR) spectroscopy for the rapid and accurate determination of algal biomass composition. We show that NIR spectroscopy can accurately predict the full composition using multivariate linear regression analysis of varying lipid, protein, and carbohydrate content of algal biomass samples from three strains. We also demonstrate a high quality of predictions of an independent validation set. A high-throughput 96-well configuration for spectroscopy gives equally good prediction relative to a ring-cup configuration, and thus, spectra can be obtained from as little as 10-20 mg of material. We found that lipids exhibit a dominant, distinct, and unique fingerprint in the NIR spectrum that allows for the use of single and multiple linear regression of respective wavelengths for the prediction of the biomass lipid content. This is not the case for carbohydrate and protein content, and thus, the use of multivariate statistical modeling approaches remains necessary.

  20. Biochemical and structural analysis of a site directed mutant of manganese dependent aminopeptidase P from Streptomyces lavendulae

    Directory of Open Access Journals (Sweden)

    ARYA NANDAN

    2015-08-01

    Full Text Available Aminopeptidase P (APP removes N-terminal amino acids from peptides and proteins when the penultimate residue is proline. To understand the structure-function relationships of aminopeptidase P of Streptomyces lavendulae, a conserved arginine residue was replaced with lysine (R453K by site-directed mutagenesis. The overexpressed wild and mutant enzymes were of nearly 60 kDa and purified by nickel affinity chromatography. Kinetic analysis of R453K variant using Gly-Pro-pNA as the substrate revealed an increase in Km with a decrease in Vmax, leading to overall decrease in the catalytic efficiency, indicating that the guanidinium group of arginine plays an important role in substrate binding in APP. We constructed three dimensional models for the catalytic domains of wild and mutant enzyme and it revealed an interaction in R453 of native enzyme through hydrogen bonding with the adjacent residues making a substrate binding cavity whereas K453 did not participate in any hydrogen bonding. Hence, R453 in APP of S. lavenduale must be playing a critical role in the hydrolysis of the substrate.

  1. The interpretation of forensic biochemical expert test made in human body fluids: scientific - legal analysis in the research on sexual offenses

    International Nuclear Information System (INIS)

    Chaves Carballo, Diana

    2014-01-01

    The contributions of science and technology have covered the whole of human life, and relationships of coexistence are even found in the various disciplines of knowledge through legal forensics. Therefore, it is increasingly imperative that the law enforcement agents are interdisciplinary professionals, with knowledge beyond the legal knowledge to enable them make the most of the scientific knowledge in judicial proceedings. Among the natural sciences applied to right, forensic biochemistry has contributed an extremely relevant test for the investigation of various sexual offenses, much has been so, that the Organismo de Investigacion Judicial of Costa Rica has in its Departamento de Laboratorios de Ciencias Forenses with specialized sections in this discipline. A diversity of skills are performed of presumptive and confirmatory character for the presence of biological fluids, sexually transmitted diseases and identification of DNA by genetic markers. Updated information is given with respect to the correct interpretation of forensic biochemical expertises achievable for identification of semen, blood and human saliva in the investigation of sexual offenses. A scientific and legal language is used allowing the most of this information in the criminal process. The main objective has been to interpret, legal and scientifically, forensic biochemical expert evidence performed in human body fluids during the investigation of sexual offenses. A legal, doctrinal and scientific review is presented with compilation of related jurisprudence and criminology reports analysis of Seccion de Bioquimica of the Departamento de Laboratorios Forenses of the Organismo de Investigacion Juridica issued during the investigation of sexual offenses. Two types of attainable skills have existed for the identification of biological fluids, each with a different binding. In addition, it has been clear, due to the lexicon employed when making a forensic biochemist opinion, that to make a proper

  2. Genome-wide Gene Expression Analysis of Mucosal Colonic Biopsies and Isolated Colonocytes Suggests a Continuous Inflammatory State in the Lamina Propria of Patients with Quiescent Ulcerative Colitis

    DEFF Research Database (Denmark)

    Bjerrum, Jacob Tveiten; Hansen, Morten; Olsen, Jørgen

    2010-01-01

    colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n = 8), quiescent UC (n = 9), and with irritable bowel......Background: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated......-discriminant analysis using the SIMCA-P 11 software (Umetrics, Umea, Sweden). Results: A clear separation between active UC, quiescent UC, and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC...

  3. Molecular analysis of endo-β-mannanase genes upon seed imbibition suggest a cross-talk between radicle and micropylar endosperm during germination of Arabidopsis thaliana

    Science.gov (United States)

    Iglesias-Fernández, Raquel; del Carmen Rodríguez-Gacio, María; Barrero-Sicilia, Cristina; Carbonero, Pilar

    2011-01-01

    The endo-β-mannanase (MAN) family is represented in the Arabidopsis genome by eight members, all with canonical signal peptides and only half of them being expressed in germinating seeds. The transcripts of these genes were localized in the radicle and micropylar endosperm (ME) before radicle protrusion and this expression disappears as soon as the endosperm is broken by the emerging radicle tip. However, only three of these MAN genes, AtMAN5, AtMAN7 and especially AtMAN6 influence the germination time (t50) as assessed by the analysis of the corresponding knock-out lines. The data suggest a possible interaction between embryo and ME regarding the role of MAN during the Arabidopsis germination process. PMID:21301215

  4. Mechanical factors and vitamin D deficiency in schoolchildren with low back pain: biochemical and cross-sectional survey analysis

    Directory of Open Access Journals (Sweden)

    Alghadir AH

    2017-04-01

    serum bone-specific alkaline phosphatase compared with moderate and healthy schoolchildren. Stepwise regression analysis revealed that age, gender, demographic parameters, PA, vitamin D levels, Ca, CK, and LDH associated with ~56.8%–86.7% of the incidence of LBP among schoolchildren.Conclusion: In children and adolescents, LBP was shown to be linked with limited sun exposure, inadequate vitamin D diets, adiposity, lower PA, sedentary lifestyles, vitamin 25 (OH D deficiency, and lower levels of Ca, CK, and LDH. Keywords: low back pain, LBP, mechanical factors, 25(OHD concentrations, muscle pain, physical activity

  5. PET/CT with {sup 11}C-choline for evaluation of prostate cancer patients with biochemical recurrence: meta-analysis and critical review of available data

    Energy Technology Data Exchange (ETDEWEB)

    Fanti, Stefano; Castellucci, Paolo [S. Orsola-Malpighi University Hospital, Department of Nuclear Medicine, Bologna (Italy); Minozzi, Silvia [Lazio Regional Health Service, Cochrane Review Group on Drugs and Alcohol, Department of Epidemiology, Rome (Italy); Balduzzi, Sara [University of Modena and Reggio Emilia, Department of Diagnostic Medicine, Clinical and Public Health, Modena (Italy); Herrmann, Ken [David Geffen School of Medicine at UCLA, Department of Molecular and Medical Pharmacology, Los Angeles, CA (United States); University Hospital Wuerzburg, Department of Nuclear Medicine, Wuerzburg (Germany); Krause, Bernd Joachim [Universitaetsmedizin Rostock, Department of Nuclear Medicine, Rostock (Germany); Oyen, Wim [Radboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen (Netherlands); Chiti, Arturo [Humanitas Research Hospital, Nuclear Medicine, Rozzano, Milano (Italy); Humanitas University, Rozzano, Milano (Italy)

    2016-01-15

    For the last decade PET and PET/CT with {sup 11}C-choline have been proposed for the evaluation of prostate cancer (PC), but the diagnostic performance of {sup 11}C-choline PET/CT is still a matter of debate. We performed a comprehensive review of the most important clinical application of {sup 11}C-choline PET, restaging of patients with biochemical relapse, following a rigorous methodological approach and including assessment of the risk of bias. We conducted a systematic review and meta-analysis of the literature assessing {sup 11}C-choline PET/CT for its accuracy in the diagnosis and ability to detect the site of recurrence of PC in the restaging of patients with biochemical recurrence after initial treatment with curative intent. We performed a comprehensive literature search of PubMed and the Cochrane Library to determine the accuracy for the detection of the site of recurrence (prostate bed recurrences, metastatic spread to locoregional pelvic lymph nodes or distant metastases). Only studies with a reference standard (for prostatic bed histopathology, for histopathology or biopsy of distant metastases or a composite reference standard with clinical follow-up of at least 12 months, correlative imaging and clinical data) were included. Overall 425 studies were retrieved, of which 43 were judged as potentially relevant and 29 with 2,686 participants were finally included. Of these 29 studies, 18 reported results for any relapse, All 18 studies, with a total of 2,126 participants, reported detection rates. The pooled rate was 62 % (95 % CI 53 - 71 %). Of the 18 studies, 12 with 1,270 participants reported useful data to derive sensitivity and specificity. The pooled sensitivity was 89 % (95 % CI 83 - 93 %) and the pooled specificity was 89 % (95 % CI 73 - 96 %). Of 11 studies reporting results for local relapse, 9 with 993 participants reported detection rates. The pooled rate was 27 % (95 % CI 16 - 38 %). Six studies with 491 participants reported sensitivity

  6. Analysis of biosurfactants from industrially viable Pseudomonas strain isolated from crude oil suggests how rhamnolipids congeners affect emulsification property and antimicrobial activity.

    Science.gov (United States)

    Das, Palashpriya; Yang, Xin-Ping; Ma, Luyan Z

    2014-01-01

    Rhamnolipid biosurfactants produced mainly by Pseudomonas sp. had been reported to possess a wide range of potential industrial application. These biosurfactants are produced as monorhamnolipid (MRL) and di-rhamnolipid (DRL) congeners. The present study deals with rhamnolipid biosurfactants produced by three bacterial isolates from crude oil. Biosurfactants produced by one of the strains (named as IMP67) was found to be very efficacious based on its critical micelle concentration value and hydrocarbon emulsification property. Strikingly, antimicrobial, and anti-biofilm potential of this biosurfactant were higher than biosurfactants produced by other two strains. Thin layer chromatography analysis and rhamnose quantification showed that the rhamnolipids of IMP67 had more MRL congeners than biosurfactants of the other two strains. Emulsification and antimicrobial actions were affected by manual change of MRL and DRL congener proportions. Increase of MRL proportion enhanced emulsification index and antimicrobial property to Gram negative bacteria. This result indicated that the ratio of MRL and DRL affected the emulsification potentials of rhamnolipids, and suggested that high emulsification potentials might enhance rhamnolipids to penetrate the cell wall of Gram negative bacteria. In line with this finding, rhamnolipids of IMP67 also reduced the MIC of some antibiotics against bacteria, suggesting their synergistic role with the antibiotics.

  7. Analysis of biosurfactants from industrially-viable Pseudomonas strain isolated from crude oil suggests how rhamnolipids congeners affect on emulsification property and antimicrobial activity

    Directory of Open Access Journals (Sweden)

    Palashpriya eDas

    2014-12-01

    Full Text Available Rhamnolipid biosurfactants produced mainly by Pseudomonas sp. had been reported to possess a wide range of potential industrial application. These biosurfactants are produced as monorhamnolipid (MRL and di-rhamnolipid (DRL congeners. The present study deals with rhamnolipid biosurfactants produced by three bacterial isolates from crude oil. Biosurfactants produced by one of the strains (named as IMP67 was found to be very efficacious based on its critical micelle concentration (CMC value and hydrocarbon emulsification property. Strikingly, antimicrobial and anti-biofilm potential of this biosurfactant were higher than biosurfactants produced by other two strains. Thin layer chromatography (TLC analysis and rhamnose quantification showed that the rhamnolipids of IMP67 had more MRL congeners than biosurfactants of the other two strains. Emulsification and antimicrobial actions were affected by manual change of MRL and DRL congener proportions. Increase of MRL proportion enhanced emulsification index and antimicrobial property to Gram negative bacteria. This result indicated that the ratio of MRL and DRL affect the emulsification potentials of rhamnolipids, and suggested that high emulsification potentials might enhance rhamnolipids to penetrate the cell wall of Gram negative bacteria. In consistent, rhamnolipids of IMP67 reduced the MIC of some antibiotics against bacteria, suggesting the potential of biosurfactant as antibiotics synergist.

  8. Raman spectroscopic biochemical mapping of tissues

    Science.gov (United States)

    Stone, Nicholas; Hart Prieto, Maria C.; Kendall, Catherine A.; Shetty, Geeta; Barr, Hugh

    2006-02-01

    Advances in technologies have brought us closer to routine spectroscopic diagnosis of early malignant disease. However, there is still a poor understanding of the carcinogenesis process. For example it is not known whether many cancers follow a logical sequence from dysplasia, to carcinoma in situ, to invasion. Biochemical tissue changes, triggered by genetic mutations, precede morphological and structural changes. These can be probed using Raman or FTIR microspectroscopy and the spectra analysed for biochemical constituents. Local microscopic distribution of various constituents can then be visualised. Raman mapping has been performed on a number of tissues including oesophagus, breast, bladder and prostate. The biochemical constituents have been calculated at each point using basis spectra and least squares analysis. The residual of the least squares fit indicates any unfit spectral components. The biochemical distribution will be compared with the defined histopathological boundaries. The distribution of nucleic acids, glycogen, actin, collagen I, III, IV, lipids and others appear to follow expected patterns.

  9. Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8.

    Directory of Open Access Journals (Sweden)

    Archana Shenoy

    2009-09-01

    Full Text Available The Microprocessor, containing the RNA binding protein Dgcr8 and RNase III enzyme Drosha, is responsible for processing primary microRNAs to precursor microRNAs. The Microprocessor regulates its own levels by cleaving hairpins in the 5'UTR and coding region of the Dgcr8 mRNA, thereby destabilizing the mature transcript.To determine whether the Microprocessor has a broader role in directly regulating other coding mRNA levels, we integrated results from expression profiling and ultra high-throughput deep sequencing of small RNAs. Expression analysis of mRNAs in wild-type, Dgcr8 knockout, and Dicer knockout mouse embryonic stem (ES cells uncovered mRNAs that were specifically upregulated in the Dgcr8 null background. A number of these transcripts had evolutionarily conserved predicted hairpin targets for the Microprocessor. However, analysis of deep sequencing data of 18 to 200nt small RNAs in mouse ES, HeLa, and HepG2 indicates that exonic sequence reads that map in a pattern consistent with Microprocessor activity are unique to Dgcr8.We conclude that the Microprocessor's role in directly destabilizing coding mRNAs is likely specifically targeted to Dgcr8 itself, suggesting a specialized cellular mechanism for gene auto-regulation.

  10. Suggestive Objects at Work

    DEFF Research Database (Denmark)

    Ratner, Helene Gad

    2009-01-01

    In Western secular societies, spiritual life is no longer limited to classical religious institutions but can also be found at workplace organizations. While spirituality is conventionally understood as a subjective and internal process, this paper proposes the concept of ‘suggestive objects......’, constructed by combining insights from Gabriel Tarde's sociology with Bruno Latour's actor-network theory, to theorize the material dimension of organizational spirituality. The sacred in organizations arises not from the internalization of collective values but through the establishment of material...... scaffolding. This has deep implications for our understanding of the sacred, including a better appreciation of the way that suggestive objects make the sacred durable, the way they organize it....

  11. Genome-wide investigation and expression analysis suggest diverse roles and genetic redundancy of Pht1 family genes in response to Pi deficiency in tomato.

    Science.gov (United States)

    Chen, Aiqun; Chen, Xiao; Wang, Huimin; Liao, Dehua; Gu, Mian; Qu, Hongye; Sun, Shubin; Xu, Guohua

    2014-03-11

    Phosphorus (P) deficiency is one of the major nutrient stresses limiting plant growth. The uptake of P by plants is well considered to be mediated by a number of high-affinity phosphate (Pi) transporters belonging to the Pht1 family. Although the Pht1 genes have been extensively identified in several plant species, there is a lack of systematic analysis of the Pht1 gene family in any solanaceous species thus far. Here, we report the genome-wide analysis, phylogenetic evolution and expression patterns of the Pht1 genes in tomato (Solanum lycopersicum). A total of eight putative Pht1 genes (LePT1 to 8), distributed on three chromosomes (3, 6 and 9), were identified through extensive searches of the released tomato genome sequence database. Chromosomal organization and phylogenetic tree analysis suggested that the six Pht1 paralogues, LePT1/3, LePT2/6 and LePT4/5, which were assigned into three pairs with very close physical distance, were produced from recent tandem duplication events that occurred after Solanaceae splitting with other dicot families. Expression analysis of these Pht1 members revealed that except LePT8, of which the transcript was undetectable in all tissues, the other seven paralogues showed differential but partial-overlapping expression patterns. LePT1 and LePT7 were ubiquitously expressed in all tissues examined, and their transcripts were induced abundantly in response to Pi starvation; LePT2 and LePT6, the two paralogues harboring identical coding sequence, were predominantly expressed in Pi-deficient roots; LePT3, LePT4 and LePT5 were strongly activated in the roots colonized by arbuscular mycorrhizal fungi under low-P, but not high-P condition. Histochemical analysis revealed that a 1250-bp LePT3 promoter fragment and a 471-bp LePT5 promoter fragment containing the two elements, MYCS and P1BS, were sufficient to direct the GUS reporter expression in mycorrhizal roots and were limited to distinct cells harboring AM fungal structures

  12. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae.

    Science.gov (United States)

    Cao, Yunpeng; Han, Yahui; Meng, Dandan; Li, Dahui; Jin, Qing; Lin, Yi; Cai, Yongping

    2017-01-01

    The ethylene-insensitive3/ethylene-insensitive3-like ( EIN3/EIL ) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear ( Pyrus bretschneideri ), mei ( Prunus mume ), peach ( Prunus persica ) and strawberry ( Fragaria vesca ), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

  13. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae

    Directory of Open Access Journals (Sweden)

    Yunpeng Cao

    2017-05-01

    Full Text Available The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri, mei (Prunus mume, peach (Prunus persica and strawberry (Fragaria vesca, respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

  14. Measures of Biochemical Sociology

    Science.gov (United States)

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  15. Baryogenesis model suggesting antigalaxies

    International Nuclear Information System (INIS)

    Kirilova, D.P.

    1998-12-01

    A non-GUT baryogenesis model, according to which our Universe may contain clusters of antigalaxies is discussed. A mechanism of separation of vast quantities of matter from such of antimatter is described. The provided analysis showed that for a natural range of model parameters a sufficient separation between matter and antimatter regions, required from observational data, can be obtained. (author)

  16. A broad-spectrum analysis of the effects of teflubenzuron exposure on the biochemical activities and microbial community structure of soil.

    Science.gov (United States)

    Cycoń, Mariusz; Wójcik, Marcin; Borymski, Sławomir; Piotrowska-Seget, Zofia

    2012-10-15

    We evaluated the response of soil bacteria to applications of the insecticide teflubenzuron at the field rate dosage (FR; 0.15 mg/kg of soil) and at a higher dosage (10*FR; 1.5 mg/kg of soil). When applied at the FR dosage, teflubenzuron had no effect on several biochemical parameters of the soil, including substrate-induced respiration (SIR), dehydrogenase (DHA) and phosphatase activities (PHOS), and N-NO(3)(-) and N-NH(4)(+) concentrations. Additionally, no differences were observed in the culturable fraction of the soil bacteria (the number of heterotrophic, nitrifying, denitrifying and N(2)-fixing bacteria; the growth strategy; the ecophysiological and colony development indices; and the physiological state). In contrast, treatment with the 10*FR dosage of the insecticide significantly increased SIR, DHA, PHOS and N-NH(4)(+) levels and the number of heterotrophic and denitrifying bacteria. Decreases in urease activity (URE) and the number of nitrifying and N(2)-fixing bacteria were also observed. A phospholipid fatty acid (PLFA) method-based analysis of the entire soil microorganism population revealed that teflubenzuron treatment affected the total fatty acid level as well as those considered to be of Gram-positive bacteria, Gram-negative bacteria and fungi. This effect was observed on days 1 and 14 post-treatment. A principal component analysis (PCA) of the PLFAs showed that teflubenzuron treatment significantly shifted the microbial community structure; however, all of the observed effects were transient. Studies on the degradation of teflubenzuron revealed that this process is characterised by a short lag phase and a rate constant (k) of 0.020/day. This degradation rate follows first-order kinetics, and the DT50 was 33.5 days. This is the first study that thoroughly examines the functional and structural status of both the culturable and non-culturable fractions of the soil microbial community after teflubenzuron application. Copyright © 2012 Elsevier Ltd

  17. Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions.

    Science.gov (United States)

    Pezer, Željka; Chung, Amanda G; Karn, Robert C; Laukaitis, Christina M

    2017-06-01

    The Androgen-binding protein ( Abp ) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus ( Mmd ) and Mus musculus musculus ( Mmm ), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd , primarily representing the presence/absence of the final duplications described for the mouse genome. Clustering of Mmd individuals based on this variation did not reflect their geographical origin, suggesting no population divergence in the Abp gene cluster. However, copy number variation patterns differ substantially between Mmd and other mouse taxa. Large blocks of Abp genes are absent in Mmm , Mus musculus castaneus and an outgroup, Mus spretus , although with differences in variation and breakpoint locations. Our analysis calls into question the reliance on a reference genome for interpreting the detailed organization of genes in taxa more distant from the Mmd reference genome. The polymorphic nature of the gene family expansion in all four taxa suggests that the number of Abp genes, especially in the central gene region, is not critical to the survival and reproduction of the mouse. However, Abp haplotypes of variable length may serve as a source of raw genetic material for new signals influencing reproductive communication and thus speciation of mice. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Stochastic analysis of biochemical systems

    CERN Document Server

    Anderson, David F

    2015-01-01

    This book focuses on counting processes and continuous-time Markov chains motivated by examples and applications drawn from chemical networks in systems biology.  The book should serve well as a supplement for courses in probability and stochastic processes.  While the material is presented in a manner most suitable for students who have studied stochastic processes up to and including martingales in continuous time, much of the necessary background material is summarized in the Appendix. Students and Researchers with a solid understanding of calculus, differential equations, and elementary probability and who are well-motivated by the applications will find this book of interest.    David F. Anderson is Associate Professor in the Department of Mathematics at the University of Wisconsin and Thomas G. Kurtz is Emeritus Professor in the Departments of Mathematics and Statistics at that university. Their research is focused on probability and stochastic processes with applications in biology and other ar...

  19. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues

    2014-08-01

    Full Text Available Ouroboros: Playing A Biochemical RODRIGUES,D.T.1,2;GAYER, M.C.1,2; ESCOTO, D.F.1; DENARDIN, E.L.G.2, ROEHRS, R.1,2 1Interdisciplinary Research Group on Teaching Practice, Graduate Program in Biochemistry, Unipampa, RS, Brazil 2Laboratory of Physicochemical Studies and Natural Products, Post Graduate Program in Biochemistry, Unipampa, RS, Brazil Introduction: Currently, teachers seek different alternatives to enhance the teaching-learning process. Innovative teaching methodologies are increasingly common tools in educational routine. The use of games, electronic or conventional, is an effective tool to assist in learning and also to raise the social interaction between students. Objective: In this sense our work aims to evaluate the card game and "Ouroboros" board as a teaching and learning tool in biochemistry for a graduating class in Natural Sciences. Materials and methods: The class gathered 22 students of BSc in Natural Sciences. Each letter contained a question across the board that was drawn to a group to answer within the allotted time. The questions related concepts of metabolism, organic and inorganic chemical reactions, bioenergetics, etc.. Before the game application, students underwent a pre-test with four issues involving the content that was being developed. Soon after, the game was applied. Then again questions were asked. Data analysis was performed from the ratio of the number of correct pre-test and post-test answers. Results and discussion: In the pre-test 18.1% of the students knew all issues, 18.1% got 3 correct answers, 40.9% answered only 2 questions correctly and 22.7% did not hit any. In post-test 45.4% answered all the questions right, 31.8% got 3 questions and 22.7% got 2 correct answers. The results show a significant improvement of the students about the field of content taught through the game. Conclusion: Generally, traditional approaches of chemistry and biochemistry are abstract and complex. Thus, through games

  20. Improving Marine Ecosystem Models with Biochemical Tracers

    Science.gov (United States)

    Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

    2018-01-01

    Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

  1. Rolling circle amplification-based analysis of Sri Lankan cassava mosaic virus isolates from Tamil Nadu, India, suggests a low level of genetic variability.

    Science.gov (United States)

    Kushawaha, Akhilesh Kumar; Rabindran, Ramalingam; Dasgupta, Indranil

    2018-03-01

    Cassava mosaic disease is a widespread disease of cassava in south Asia and the African continent. In India, CMD is known to be caused by two single-stranded DNA viruses (geminiviruses), Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosdaic virus (SLCMV). Previously, the diversity of ICMV and SLCMV in India has been studied using PCR, a sequence-dependent method. To have a more in-depth study of the variability of the above viruses and to detect any novel geminiviruses associated with CMD, sequence-independent amplification using rolling circle amplification (RCA)-based methods were used. CMD affected cassava plants were sampled across eighty locations in nine districts of the southern Indian state of Tamil Nadu. Twelve complete sequence of coat protein genes of the resident geminiviruses, comprising 256 amino acid residues were generated from the above samples, which indicated changes at only six positions. RCA followed by RFLP of the 80 samples indicated that most samples (47) contained only SLCMV, followed by 8, which were infected jointly with ICMV and SLCMV. In 11 samples, the pattern did not match the expected patterns from either of the two viruses and hence, were variants. Sequence analysis of an average of 700 nucleotides from 31 RCA-generated fragments of the variants indicated identities of 97-99% with the sequence of a previously reported infectious clone of SLCMV. The evidence suggests low levels of genetic variability in the begomoviruses infecting cassava, mainly in the form of scattered single nucleotide changes.

  2. Brachytherapy Improves Biochemical Failure–Free Survival in Low- and Intermediate-Risk Prostate Cancer Compared With Conventionally Fractionated External Beam Radiation Therapy: A Propensity Score Matched Analysis

    International Nuclear Information System (INIS)

    Smith, Graham D.; Pickles, Tom; Crook, Juanita; Martin, Andre-Guy; Vigneault, Eric; Cury, Fabio L.; Morris, Jim; Catton, Charles; Lukka, Himu; Warner, Andrew; Yang, Ying; Rodrigues, George

    2015-01-01

    Purpose: To compare, in a retrospective study, biochemical failure-free survival (bFFS) and overall survival (OS) in low-risk and intermediate-risk prostate cancer patients who received brachytherapy (BT) (either low-dose-rate brachytherapy [LDR-BT] or high-dose-rate brachytherapy with external beam radiation therapy [HDR-BT+EBRT]) versus external beam radiation therapy (EBRT) alone. Methods and Materials: Patient data were obtained from the ProCaRS database, which contains 7974 prostate cancer patients treated with primary radiation therapy at four Canadian cancer institutions from 1994 to 2010. Propensity score matching was used to obtain the following 3 matched cohorts with balanced baseline prognostic factors: (1) low-risk LDR-BT versus EBRT; (2) intermediate-risk LDR-BT versus EBRT; and (3) intermediate-risk HDR-BT+EBRT versus EBRT. Kaplan-Meier survival analysis was performed to compare differences in bFFS (primary endpoint) and OS in the 3 matched groups. Results: Propensity score matching created acceptable balance in the baseline prognostic factors in all matches. Final matches included 2 1:1 matches in the intermediate-risk cohorts, LDR-BT versus EBRT (total n=254) and HDR-BT+EBRT versus EBRT (total n=388), and one 4:1 match in the low-risk cohort (LDR-BT:EBRT, total n=400). Median follow-up ranged from 2.7 to 7.3 years for the 3 matched cohorts. Kaplan-Meier survival analysis showed that all BT treatment options were associated with statistically significant improvements in bFFS when compared with EBRT in all cohorts (intermediate-risk EBRT vs LDR-BT hazard ratio [HR] 4.58, P=.001; intermediate-risk EBRT vs HDR-BT+EBRT HR 2.08, P=.007; low-risk EBRT vs LDR-BT HR 2.90, P=.004). No significant difference in OS was found in all comparisons (intermediate-risk EBRT vs LDR-BT HR 1.27, P=.687; intermediate-risk EBRT vs HDR-BT+EBRT HR 1.55, P=.470; low-risk LDR-BT vs EBRT HR 1.41, P=.500). Conclusions: Propensity score matched analysis showed that BT options led

  3. Proteomics analysis suggests broad functional changes in potato leaves triggered by phosphites and a complex indirect mode of action against Phytophthora infestans.

    Science.gov (United States)

    Lim, Sanghyun; Borza, Tudor; Peters, Rick D; Coffin, Robert H; Al-Mughrabi, Khalil I; Pinto, Devanand M; Wang-Pruski, Gefu

    2013-11-20

    Phosphite (salts of phosphorous acid; Phi)-based fungicides are increasingly used in controlling oomycete pathogens, such as the late blight agent Phytophthora infestans. In plants, low amounts of Phi induce pathogen resistance through an indirect mode of action. We used iTRAQ-based quantitative proteomics to investigate the effects of phosphite on potato plants before and after infection with P. infestans. Ninety-three (62 up-regulated and 31 down-regulated) differentially regulated proteins, from a total of 1172 reproducibly identified proteins, were identified in the leaf proteome of Phi-treated potato plants. Four days post-inoculation with P. infestans, 16 of the 31 down-regulated proteins remained down-regulated and 42 of the 62 up-regulated proteins remained up-regulated, including 90% of the defense proteins. This group includes pathogenesis-related, stress-responsive, and detoxification-related proteins. Callose deposition and ultrastructural analyses of leaf tissues after infection were used to complement the proteomics approach. This study represents the first comprehensive proteomics analysis of the indirect mode of action of Phi, demonstrating broad effects on plant defense and plant metabolism. The proteomics data and the microscopy study suggest that Phi triggers a hypersensitive response that is responsible for induced resistance of potato leaves against P. infestans. Phosphie triggers complex functional changes in potato leaves that are responsible for the induced resistance against Phytophthora infestans. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Literature-Informed Analysis of a Genome-Wide Association Study of Gestational Age in Norwegian Women and Children Suggests Involvement of Inflammatory Pathways

    Science.gov (United States)

    Bacelis, Jonas; Juodakis, Julius; Sengpiel, Verena; Zhang, Ge; Myhre, Ronny; Muglia, Louis J.; Nilsson, Staffan; Jacobsson, Bo

    2016-01-01

    Background Five-to-eighteen percent of pregnancies worldwide end in preterm birth, which is the major cause of neonatal death and morbidity. Approximately 30% of the variation in gestational age at birth can be attributed to genetic factors. Genome-wide association studies (GWAS) have not shown robust evidence of association with genomic loci yet. Methods We separately investigated 1921 Norwegian mothers and 1199 children from pregnancies with spontaneous onset of delivery. Individuals were further divided based on the onset of delivery: initiated by labor or prelabor rupture of membranes. Genetic association with ultrasound-dated gestational age was evaluated using three genetic models and adaptive permutations. The top-ranked loci were tested for enrichment in 12 candidate gene-sets generated by text-mining PubMed abstracts containing pregnancy-related keywords. Results The six GWAS did not reveal significant associations, with the most extreme empirical p = 5.1 × 10−7. The top loci from maternal GWAS with deliveries initiated by labor showed significant enrichment in 10 PubMed gene-sets, e.g., p = 0.001 and 0.005 for keywords "uterus" and "preterm" respectively. Enrichment signals were mainly caused by infection/inflammation-related genes TLR4, NFKB1, ABCA1, MMP9. Literature-informed analysis of top loci revealed further immunity genes: IL1A, IL1B, CAMP, TREM1, TFRC, NFKBIA, MEFV, IRF8, WNT5A. Conclusion Our analyses support the role of inflammatory pathways in determining pregnancy duration and provide a list of 32 candidate genes for a follow-up work. We observed that the top regions from GWAS in mothers with labor-initiated deliveries significantly more often overlap with pregnancy-related genes than would be expected by chance, suggesting that increased sample size would benefit similar studies. PMID:27490719

  5. Yield of diagnostic tests for celiac disease in individuals with symptoms suggestive of irritable bowel syndrome: systematic review and meta-analysis.

    Science.gov (United States)

    Ford, Alexander C; Chey, William D; Talley, Nicholas J; Malhotra, Ashish; Spiegel, Brennan M R; Moayyedi, Paul

    2009-04-13

    Individuals with irritable bowel syndrome (IBS) report abdominal pain, bloating, and diarrhea, symptoms similar to those in celiac disease. Studies suggest that the prevalence of celiac disease is increased in individuals with IBS; however, evidence is conflicting, and current guidelines do not always recommend screening for celiac disease in these individuals. We conducted a systematic review and meta-analysis to estimate prevalence of celiac disease in unselected adults who met diagnostic criteria for IBS. MEDLINE (1950 to May 31, 2008) and EMBASE (1980 to May 31, 2008) were searched. Case series and case-control studies that used serologic tests for celiac disease were eligible for inclusion. Prevalence of positive serologic indications of celiac disease and biopsy-proved celiac disease were extracted and pooled for all studies and were compared between cases and controls using an odds ratio and 95% confidence interval. Fourteen studies were identified comprising 4204 individuals, of whom 2278 (54%) met diagnostic criteria for IBS. Pooled prevalence of positive IgA-class antigliadin antibodies, either positive endomysial antibodies or tissue transglutaminase, and biopsy-proved celiac disease were 4.0% (95% confidence interval, 1.7-7.2), 1.63% (0.7-3.0), and 4.1% (1.9-7.0), respectively. Pooled odds ratios (95% confidence intervals) for positive IgA-class antigliadin antibodies, either positive endomysial antibodies or tissue transglutaminase, and biopsy-proved celiac disease in cases meeting diagnostic criteria for IBS compared with controls without IBS were 3.40 (1.62-7.13), 2.94 (1.36-6.35), and 4.34 (1.78-10.6). Prevalence of biopsy-proved celiac disease in cases meeting diagnostic criteria for IBS was more than 4-fold that in controls without IBS.

  6. [Cost-effectiveness analysis of interferon beta-1b as treatment for patients with clinically isolated syndrome suggestive of multiple sclerosis in Spain].

    Science.gov (United States)

    Piñol, C

    2016-05-01

    The BENEFIT study has demonstrated the benefits of early treatment with interferon beta 1b (IFNβ-1b). The objective of this study was to estimate the efficiency of early vs delayed IFNβ-1b treatment in patients with clinically isolated syndrome (CIS) suggestive of multiple sclerosis (MS) in Spain. A Markov model reflecting the social perspective was developed with time horizons ranging from 2 years to lifetime. A cohort of 1000 patients with CIS, whose health status had been measured on the Expanded Disability Symptom Scale (EDSS), included patients who received early IFNβ-1b treatment and those who did not. Data from the BENEFIT study were used to model EDSS progression and transitions to MS. Costs were estimated from published literature. Patient utilities were derived from EQ-5D data and published data. Mortality was estimated using life tables and EDSS data. Costs (€ at 2013 rates) and outcomes were discounted at 3% per annum. A probabilistic sensitivity analysis was performed. In the base case, both the incremental cost utility ratio (ICUR) and the incremental cost effectiveness ratio (ICER) of IFNβ-1b versus no treatment were dominant (more effective and less costly) from a social perspective. From the perspective of the Spanish Health System, the ICUR was € 40,702/QALY and the ICER was € 13/relapse avoided. Early treatment with IFNβ-1b after a CIS versus delayed treatment is efficient from a social perspective, but it may not be efficient from the perspective of the NHS which does not take non health-related costs into account. Copyright © 2014 Sociedad Española de Neurología. Published by Elsevier España, S.L.U. All rights reserved.

  7. Y-chromosome status identification suggests a recipient origin of posttransplant non-small cell lung carcinomas: chromogenic in situ hybridization analysis.

    Science.gov (United States)

    Chen, Wei; Brodsky, Sergey V; Zhao, Weiqiang; Otterson, Gregory A; Villalona-Calero, Miguel; Satoskar, Anjali A; Hasan, Ayesha; Pelletier, Ronald; Ivanov, Iouri; Ross, Patrick; Nadasdy, Tibor; Shilo, Konstantin

    2014-05-01

    Owing to the need of lifelong immunosuppression, solid-organ transplant recipients are known to have an increased risk of posttransplant malignancies including lung cancer. Posttransplant neoplastic transformation of donor-derived cells giving rise to hematopoietic malignancies, Kaposi sarcoma, and basal cell carcinoma in nongraft tissues has been reported. The goal of this study was to assess the cell origin (donor versus recipient derived) of posttransplant non-small cell lung carcinomas (NSCLCs) in kidney and heart transplant recipients. An institutional database search identified 2557 kidney and heart transplant recipients in 8 consecutive years. Among this cohort, 20 (0.8%) renal and 18 (0.7%) heart transplant recipients developed NSCLC. The study cohort comprised 6 of 38 NSCLCs arising in donor-recipient sex-mismatched transplant patients. The tumor cell origin was evaluated by chromogenic in situ hybridization with Y-chromosome probe on formalin-fixed, paraffin-embedded tissues. Y-chromosome was identified in 97% ± 1% (range from 92% to 99%) of all types of nucleated cells in male control tissues. In all 5 NSCLCs from male recipients of female donor organ, Y-chromosome was identified in 97% ± 2% (range from 92% to 100%) of tumor cells, statistically equivalent to normal control (P recipient of male kidney. These findings suggest a recipient derivation of NSCLC arising in kidney and heart transplant recipients. A combination of histologic evaluation and chromogenic in situ hybridization with Y-chromosome analysis allows reliable determination of tissue origin in sex-mismatched solid-organ transplant recipients and may aid in management of posttransplant malignancy in such cases. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Functional microarray analysis suggests repressed cell-cell signaling and cell survival-related modules inhibit progression of head and neck squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Soares Fernando A

    2011-04-01

    Full Text Available Abstract Background Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph node metastasis (N+ and recurrent head and neck squamous cell carcinoma (HNSCC may increase our understanding of the complex biology of this disease. Methods Tumor samples were obtained from untreated HNSCC patients undergoing surgery. Patients were classified according to pathologic lymph node status (positive or negative or tumor recurrence (recurrent or non-recurrent tumor after treatment (surgery with neck dissection followed by radiotherapy. Using microarray gene expression, we screened tumor samples according to modules comprised by genes in the same pathway or functional category. Results The most frequent alterations were the repression of modules in negative lymph node (N0 and in non-recurrent tumors rather than induction of modules in N+ or in recurrent tumors. N0 tumors showed repression of modules that contain cell survival genes and in non-recurrent tumors cell-cell signaling and extracellular region modules were repressed. Conclusions The repression of modules that contain cell survival genes in N0 tumors reinforces the important role that apoptosis plays in the regulation of metastasis. In addition, because tumor samples used here were not microdissected, tumor gene expression data are represented together with the stroma, which may reveal signaling between the microenvironment and tumor cells. For instance, in non-recurrent tumors, extracellular region module was repressed, indicating that the stroma and tumor cells may have fewer interactions, which disable metastasis development. Finally, the genes highlighted in our analysis can be implicated in more than one pathway or characteristic, suggesting that therapeutic approaches to prevent tumor progression should target more than one gene or pathway

  9. Systematic review with meta-analysis: risk factors for non-alcoholic fatty liver disease suggest a shared altered metabolic and cardiovascular profile between lean and obese patients.

    Science.gov (United States)

    Sookoian, S; Pirola, C J

    2017-07-01

    The pathogenesis of non-alcoholic fatty liver disease (NAFLD) is closely associated with the co-occurrence of multiple pathological conditions characterising the metabolic syndrome (MetS), obesity in particular. However, NAFLD also develops in lean subjects, whose risk factors remain poorly defined. We performed a meta-analysis of 15 studies, along with the data pertaining to our own population (n=336 patients). Data from lean (n=1966) and obese (n=5938) patients with NAFLD were analysed; lean (n=9946) and obese (n=6027) subjects without NAFLD served as controls. Relative to the lean non-NAFLD controls, lean patients with NAFLD were older (3.79±0.72 years, P=1.36×10 -6 ) and exhibited the entire spectrum of the MetS risk factors. Specifically, they had a significant (P=10 -10 ) increase in plasma glucose levels (6.44±1.12 mg/dL) and HOMA-IR (0.52±0.094-unit increment), blood lipids (triglycerides: 48.37±3.6, P=10 -10 and total cholesterol: 7.04±3.8, mg/dL, P=4.2×10 -7 ), systolic (5.64±0.7) and diastolic (3.37±0.9) blood pressure (mm Hg), P=10 -10 , and waist circumference (5.88±0.4 cm, P=10 -10 ); values denote difference in means±SE. Nevertheless, the overall alterations in the obese group were much more severe when compared to lean subjects, regardless of the presence of NAFLD. Meta-regression suggested that NAFLD is a modifier of the level of blood lipids. Lean and obese patients with NAFLD share a common altered metabolic and cardiovascular profile. The former, while having normal body weight, showed excess of abdominal adipose tissue as well as other MetS features. © 2017 John Wiley & Sons Ltd.

  10. Factors Influencing Nonabsolute Indications for Surgery in Patients With Lower Urinary Tract Symptoms Suggestive of Benign Prostatic Hyperplasia: Analysis Using Causal Bayesian Networks

    Directory of Open Access Journals (Sweden)

    Myong Kim

    2014-12-01

    Full Text Available Purpose To identify the factors affecting the surgical decisions of experienced physicians when treating patients with lower urinary tract symptoms that are suggestive of benign prostatic hyperplasia (LUTS/BPH. Methods Patients with LUTS/BPH treated by two physicians between October 2004 and August 2013 were included in this study. The causal Bayesian network (CBN model was used to analyze factors influencing the surgical decisions of physicians and the actual performance of surgery. The accuracies of the established CBN models were verified using linear regression (LR analysis. Results A total of 1,108 patients with LUTS/BPH were analyzed. The mean age and total prostate volume (TPV were 66.2 (±7.3, standard deviation years and 47.3 (±25.4 mL, respectively. Of the total 1,108 patients, 603 (54.4% were treated by physician A and 505 (45.6% were treated by physician B. Although surgery was recommended to 699 patients (63.1%, 589 (53.2% actually underwent surgery. Our CBN model showed that the TPV (R=0.432, treating physician (R=0.370, bladder outlet obstruction (BOO on urodynamic study (UDS (R=0.324, and International Prostate Symptom Score (IPSS question 3 (intermittency; R=0.141 were the factors directly influencing the surgical decision. The transition zone volume (R=0.396, treating physician (R=0.340, and BOO (R=0.300 directly affected the performance of surgery. Compared to the LR model, the area under the receiver operating characteristic curve of the CBN surgical decision model was slightly compromised (0.803 vs. 0.847, P<0.001, whereas that of the actual performance of surgery model was similar (0.801 vs. 0.820, P=0.063 to the LR model. Conclusions The TPV, treating physician, BOO on UDS, and the IPSS item of intermittency were factors that directly influenced decision-making in physicians treating patients with LUTS/BPH.

  11. Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes.

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    Casey R Richardson

    2010-05-01

    Full Text Available MicroRNAs (miRNAs and trans-acting small-interfering RNAs (tasi-RNAs are small (20-22 nt long RNAs (smRNAs generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery.We explored rice (Oryza sativa sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis 'orphan' hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the "ancient" (deeply conserved class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for "new" rapidly-evolving MIRNA genes.Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non-coding RNAs in plants and potentially other

  12. An analysis of clinical and treatment related prognostic factors on outcome using biochemical control as an end-point in patients with prostate cancer treated with external beam irradiation

    International Nuclear Information System (INIS)

    Horwitz, Eric M.; Vicini, Frank A.; Ziaja, Ellen L.; Dmuchowski, Carl F.; Stromberg, Jannifer S.; Gustafson, Gary S.; Martinez, Alvaro A.

    1997-01-01

    Purpose: We reviewed our institution's experience in treating patients with clinically localized prostate cancer with external beam irradiation (RT) to determine if previously analyzed clinical and treatment related prognostic factors affected outcome when biochemical control was used as an end-point to evaluate results. Materials and methods: Between 1 January 1987 and 31 December 1991, 470 patients with clinically localized prostate cancer were treated with external beam RT using localized prostate fields at William Beaumont Hospital. Biochemical control was defined as PSA nadir ≤1.5 ng/ml within 1 year of treatment. After achieving nadir, if two consecutive increases of PSA were noted, the patient was scored a failure at the time of the first increase. Prognostic factors, including the total number of days in treatment, the method of diagnosis, a history of any pretreatment transurethral resection of the prostate (TURP) and the type of boost were analyzed. Results: Median follow-up was 48 months. No statistically significant difference in rates of biochemical control were noted for treatment time, overall time (date of biopsy to completion of RT), history of any pretreatment TURP, history of diagnosis by TURP, or boost techniques. Patients diagnosed by TURP had a significant improvement in the overall rate of biochemical control (P < 0.03) compared to transrectal/transperineal biopsy. The 5-year actuarial rates were 58 versus 39%, respectively. This improvement was not evident when pretreatment PSA, T stage, or Gleason score were controlled for. On multivariate analysis, no variable was associated with outcome. When analysis was limited to a more favorable group of patients (T1/T2 tumors, pretreatment PSA ≤20 ng/ml and Gleason score <7), none of these variables were significantly predictive of biochemical control when controlling for pretreatment PSA, T stage and Gleason score. Conclusions: No significant effect of treatment time, overall time, pretreatment

  13. Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer's disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids.

    Science.gov (United States)

    Bautista-Aguilera, Oscar M; Esteban, Gerard; Chioua, Mourad; Nikolic, Katarina; Agbaba, Danica; Moraleda, Ignacio; Iriepa, Isabel; Soriano, Elena; Samadi, Abdelouahid; Unzeta, Mercedes; Marco-Contelles, José

    2014-01-01

    The design, synthesis, and biochemical evaluation of donepezil-pyridyl hybrids (DPHs) as multipotent cholinesterase (ChE) and monoamine oxidase (MAO) inhibitors for the potential treatment of Alzheimer's disease (AD) is reported. The 3D-quantitative structure-activity relationship study was used to define 3D-pharmacophores for inhibition of MAO A/B, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) enzymes and to design DPHs as novel multi-target drug candidates with potential impact in the therapy of AD. DPH14 (Electrophorus electricus AChE [EeAChE]: half maximal inhibitory concentration [IC50] =1.1±0.3 nM; equine butyrylcholinesterase [eqBuChE]: IC50 =600±80 nM) was 318-fold more potent for the inhibition of AChE, and 1.3-fold less potent for the inhibition of BuChE than the reference compound ASS234. DPH14 is a potent human recombinant BuChE (hBuChE) inhibitor, in the same range as DPH12 or DPH16, but 13.1-fold less potent than DPH15 for the inhibition of human recombinant AChE (hAChE). Compared with donepezil, DPH14 is almost equipotent for the inhibition of hAChE, and 8.8-fold more potent for hBuChE. Concerning human monoamine oxidase (hMAO) A inhibition, only DPH9 and 5 proved active, compound DPH9 being the most potent (IC50 [MAO A] =5,700±2,100 nM). For hMAO B, only DPHs 13 and 14 were moderate inhibitors, and compound DPH14 was the most potent (IC50 [MAO B] =3,950±940 nM). Molecular modeling of inhibitor DPH14 within EeAChE showed a binding mode with an extended conformation, interacting simultaneously with both catalytic and peripheral sites of EeAChE thanks to a linker of appropriate length. Absortion, distribution, metabolism, excretion and toxicity analysis showed that structures lacking phenyl-substituent show better druglikeness profiles; in particular, DPHs13-15 showed the most suitable absortion, distribution, metabolism, excretion and toxicity properties. Novel donepezil-pyridyl hybrid DPH14 is a potent, moderately selective h

  14. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai

    2013-05-01

    Full Text Available Introduction: Animations of biochemical processes and virtual laboratory environments lead to true molecular simulations. The use of interactive software’s in education can improve cognitive capacity, better learning and, mainly, it makes information acquisition easier. Material and Methods: This work presents the development of a biochemical hypermedia to understanding of the galactose metabolism. It was developed with the help of concept maps, ISIS Draw, ADOBE Photoshop and FLASH MX Program. Results and Discussion: A step by step animation process shows the enzymatic reactions of galactose conversion to glucose-1-phosphate (to glycogen synthesis, glucose-6-phosphate (glycolysis intermediary, UDP-galactose (substrate to mucopolysaccharides synthesis and collagen’s glycosylation. There are navigation guide that allow scrolling the mouse over the names of the components of enzymatic reactions of via the metabolism of galactose. Thus, explanatory text box, chemical structures and animation of the actions of enzymes appear to navigator. Upon completion of the module, the user’s response to the proposed exercise can be checked immediately through text box with interactive content of the answer. Conclusion: This hypermedia was presented for undergraduate students (UFSC who revealed that it was extremely effective in promoting the understanding of the theme.

  15. Analysis of school authorities´ concepts and suggestions on bullying - doi: 10.4025/actascieduc.v36i1.21940

    Directory of Open Access Journals (Sweden)

    José Leon Crochík

    2014-02-01

    Full Text Available Interviews by school authorities from five public primary schools inSão Paulo,São Paulo State,Brazilwere analyzed. The contents of the interviews by school principals and pedagogical coordinators investigated (1 the manner they understood bullying, especially with regard to their determinations; (2 their proposals for combating the problem; (3 the relationship between their understanding of the phenomenon and the suggestions against it. Results showed that the authorities that perceived the social determination on school violence had the best structured suggestions against the phenomenon, with regard to its understanding by students and teachers. On the other hand, others, foregrounded on a more reductionist stance which made difficult the perception of bulling within the school milieu, suggested activities which were not relevant to the factors that produced it and thus not efficacious in their attacking the phenomenon.

  16. Analysis of the Variability of Epstein-Barr Virus Genes in Infectious Mononucleosis: Investigation of the Potential Correlation with Biochemical Parameters of Hepatic Involvement

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    Banko Ana

    2016-09-01

    Full Text Available Background: Primary Epstein-Barr virus (EBV infection is usually asymptomatic, although at times it results in the benign lymphoproliferative disease, infectious mononucleosis (IM, during which almost half of patients develop hepatitis. The aims of the present study are to evaluate polymorphisms of EBV genes circulating in IM isolates from this geographic region and to investigate the correlation of viral sequence patterns with the available IM biochemical parameters.

  17. Fusion protein gene nucleotide sequence similarities, shared antigenic sites and phylogenetic analysis suggest that phocid distemper virus 2 and canine distemper virus belong to the same virus entity.

    NARCIS (Netherlands)

    I.K.G. Visser (Ilona); R.W.J. van der Heijden (Roger); M.W.G. van de Bildt (Marco); M.J.H. Kenter (Marcel); C. Örvell; A.D.M.E. Osterhaus (Albert)

    1993-01-01

    textabstractNucleotide sequencing of the fusion protein (F) gene of phocid distemper virus-2 (PDV-2), recently isolated from Baikal seals (Phoca sibirica), revealed an open reading frame (nucleotides 84 to 2075) with two potential in-frame ATG translation initiation codons. We suggest that the

  18. Effect of the combination of metformin hydrochloride and melatonin on oxidative stress before and during pregnancy, and biochemical and histopathological analysis of the livers of rats after treatment for polycystic ovary syndrome

    International Nuclear Information System (INIS)

    Lemos, Ana Janaina Jeanine M.; Peixoto, Christina A.; Teixeira, Álvaro Aguiar C.; Luna, Rayana Leal A.; Rocha, Sura Wanessa S.; Santos, Hilda Michelly P.; Silva, Amanda Karolina S.; Nunes, Ana Karolina S.; Wanderley-Teixeira, Valéria

    2014-01-01

    The aim of the present study was to analyze the effect of a combination of metformin hydrochloride and melatonin on oxidative stress together with a biochemical and histopathological analysis of the livers of Wistar rats induced with PCOS. The results indicated that a combination of the drugs was more effective in the reduction of plasmatic levels of liver enzyme alanine aminotransferase, nitric oxide and total glutathione, and decreased the inflammatory response and histopathological damage, producing results that were significantly similar to animals from the control group. A mixture of the drugs produced more effective results against liver toxicity caused by PCOS, encouraging the normalization of biochemical parameters. During pregnancy, there was reduced oxidative stress compared to monotherapeutic use of these drugs. Interestingly, the combination of the drugs caused a physiological reaction similar to responses identified in healthy rats without induction of the PCOS control group. However, the clinical and physiological effectiveness of the combination should be further explored, especially with respect to the possible side effects on offspring. - Highlights: • Studies have documented increased oxidative stress in patients with PCOS. • It has been noted that women with PCOS have a high prevalence of liver alterations. • Liver disease in pregnancy may be pre-existing increasing the newborn mortality. • Metformin/melatonin associated reduced oxidative stress in liver in pregnant rats. • Association of metformin/melatonin normalizes hepatic biochemical parameters

  19. Effect of the combination of metformin hydrochloride and melatonin on oxidative stress before and during pregnancy, and biochemical and histopathological analysis of the livers of rats after treatment for polycystic ovary syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Lemos, Ana Janaina Jeanine M. [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil); Unit of Medical and Health Sciences, Universidade Federal de Campina Grande (Brazil); Peixoto, Christina A. [Centro de Pesquisa Aggeu Magalhães-Fiocruz Recife (Brazil); Teixeira, Álvaro Aguiar C. [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil); Luna, Rayana Leal A.; Rocha, Sura Wanessa S. [Centro de Pesquisa Aggeu Magalhães-Fiocruz Recife (Brazil); Santos, Hilda Michelly P. [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil); Silva, Amanda Karolina S.; Nunes, Ana Karolina S. [Centro de Pesquisa Aggeu Magalhães-Fiocruz Recife (Brazil); Wanderley-Teixeira, Valéria, E-mail: valeria@dmfa.ufrpe.br [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil)

    2014-10-01

    The aim of the present study was to analyze the effect of a combination of metformin hydrochloride and melatonin on oxidative stress together with a biochemical and histopathological analysis of the livers of Wistar rats induced with PCOS. The results indicated that a combination of the drugs was more effective in the reduction of plasmatic levels of liver enzyme alanine aminotransferase, nitric oxide and total glutathione, and decreased the inflammatory response and histopathological damage, producing results that were significantly similar to animals from the control group. A mixture of the drugs produced more effective results against liver toxicity caused by PCOS, encouraging the normalization of biochemical parameters. During pregnancy, there was reduced oxidative stress compared to monotherapeutic use of these drugs. Interestingly, the combination of the drugs caused a physiological reaction similar to responses identified in healthy rats without induction of the PCOS control group. However, the clinical and physiological effectiveness of the combination should be further explored, especially with respect to the possible side effects on offspring. - Highlights: • Studies have documented increased oxidative stress in patients with PCOS. • It has been noted that women with PCOS have a high prevalence of liver alterations. • Liver disease in pregnancy may be pre-existing increasing the newborn mortality. • Metformin/melatonin associated reduced oxidative stress in liver in pregnant rats. • Association of metformin/melatonin normalizes hepatic biochemical parameters.

  20. Experiment K-6-09. Morphological and biochemical investigation of microgravity-induced nerve and muscle breakdown. Part 1: Investigation of nerve and muscle breakdown during spaceflight; Part 2: Biochemical analysis of EDL and PLT muscles

    Science.gov (United States)

    Riley, D. A.; Ellis, S.; Bain, J.; Sedlak, F.; Slocum, G.; Oganov, V.

    1990-01-01

    The present findings on rat hindlimb muscles suggest that skeletal muscle weakness induced by prolonged spaceflight can result from a combination of muscle fiber atrophy, muscle fiber segmental necrosis, degeneration of motor nerve terminals and destruction of microcirculatory vessels. Damage was confined to the red adductor longus (AL) and soleus muscles. The midbelly region of the AL muscle had more segmental necrosis and edema than the ends. Macrophages and neutrophils were the major mononucleated cells infiltrating and phagocytosing the cellular debris. Toluidine blue-positive mast cells were significantly decreased in Flight AL muscles compared to controls; this indicated that degranulation of mast cells contributed to tissue edema. Increased ubiquitination of disrupted myofibrils may have promoted myofilament degradation. Overall, mitochondria content and SDH activity were normal, except for a decrease in the subsarcolemmal region. The myofibrillar ATPase activity shifted toward the fast type in the Flight AL muscles. Some of the pathological changes may have occurred or been exacerbated during the 2 day postflight period of readaptation to terrestrial gravity. While simple atrophy should be reversible by exercise, restoration of pathological changes depends upon complex processes of regeneration by stem cells. Initial signs of muscle and nerve fiber regeneration were detected. Even though regeneration proceeds on Earth, the space environment may inhibit repair and cause progressive irreversible deterioration during long term missions. Muscles obtained from Flight rats sacrificed immediately (within a few hours) after landing are needed to distinguish inflight changes from postflight readaptation.

  1. Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding

    Science.gov (United States)

    Me´ndez, Eduardo; Cerda´, María F.

    2016-01-01

    Students of physical chemistry in biochemical disciplines need biochemical examples to capture the need, not always understood, of a difficult area in their studies. The use of thermodynamic data in the chemical reference state may lead to incorrect interpretations in the analysis of biochemical examples when the analysis does not include relevant…

  2. Proteome analysis of a Lactococcus lactis strain overexpressing gapA suggests that the gene product is an auxiliary glyceraldehyde 3-phosphate dehydrogenase

    DEFF Research Database (Denmark)

    Willemoes, Martin; Kilstrup, Mogens; Roepstorff, P.

    2002-01-01

    revealed two neighbouring protein spots, GapBI and GapBII, with amino terminal sequences identical to the product of gapA from the L. lactis subspecies cremoris strain LM0230 and that of the two IL1403 sequences. In order to assign the two protein spots to their respective genes we constructed an L. lactis...... was specific for NAD. No NADP dependent activity was detected. Proteome analysis of the gapA overexpressing strain revealed two new protein spots, GapAI and GapAII, not previously detected in proteome analysis of MG1363. Results from mass spectrometry analysis of GapA and GapB and comparison with the deduced......The sequence of the genome from the Lactococcus lactis subspecies lactis strain IL1403 shows the presence of two reading frames, gapA and gapB, putatively encoding glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Previous proteomic analysis of the L. lactis subspecies cremoris strain MG1363 has...

  3. Implantable biochemical fuel cell

    Energy Technology Data Exchange (ETDEWEB)

    Richter, G; Rao, J R

    1978-01-05

    Implantable biochemical fuel cells for the operation of heart pacemakers or artificial hearts convert oxidisable body substances such as glucose on the anode side and reduce the oxygen contained in body fluids at the cathode. The anode and cathode are separated by membranes which are impermeable to albumen and blood corpuscles in body fluids. A chemical shortcircuit cannot occur in practice if, according to the invention, one or more selective oxygen electrodes with carbon as catalyst are arranged so that the mixture which diffuses into the cell from body fluids during operation reaches the fuel cell electrode through the porous oxygen electrode. The membranes used must be permeable to water. Cellulose, polymerised polyvinyl alcohol or an ion exchanger with a buffering capacity between pH5 and 8 act as permeable materials.

  4. Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM.

    Science.gov (United States)

    Amin, N; Byrne, E; Johnson, J; Chenevix-Trench, G; Walter, S; Nolte, I M; Vink, J M; Rawal, R; Mangino, M; Teumer, A; Keers, J C; Verwoert, G; Baumeister, S; Biffar, R; Petersmann, A; Dahmen, N; Doering, A; Isaacs, A; Broer, L; Wray, N R; Montgomery, G W; Levy, D; Psaty, B M; Gudnason, V; Chakravarti, A; Sulem, P; Gudbjartsson, D F; Kiemeney, L A; Thorsteinsdottir, U; Stefansson, K; van Rooij, F J A; Aulchenko, Y S; Hottenga, J J; Rivadeneira, F R; Hofman, A; Uitterlinden, A G; Hammond, C J; Shin, S-Y; Ikram, A; Witteman, J C M; Janssens, A C J W; Snieder, H; Tiemeier, H; Wolfenbuttel, B H R; Oostra, B A; Heath, A C; Wichmann, E; Spector, T D; Grabe, H J; Boomsma, D I; Martin, N G; van Duijn, C M

    2012-11-01

    Coffee consumption is a model for addictive behavior. We performed a meta-analysis of genome-wide association studies (GWASs) on coffee intake from 8 Caucasian cohorts (N=18 176) and sought replication of our top findings in a further 7929 individuals. We also performed a gene expression analysis treating different cell lines with caffeine. Genome-wide significant association was observed for two single-nucleotide polymorphisms (SNPs) in the 15q24 region. The two SNPs rs2470893 and rs2472297 (P-values=1.6 × 10(-11) and 2.7 × 10(-11)), which were also in strong linkage disequilibrium (r(2)=0.7) with each other, lie in the 23-kb long commonly shared 5' flanking region between CYP1A1 and CYP1A2 genes. CYP1A1 was found to be downregulated in lymphoblastoid cell lines treated with caffeine. CYP1A1 is known to metabolize polycyclic aromatic hydrocarbons, which are important constituents of coffee, whereas CYP1A2 is involved in the primary metabolism of caffeine. Significant evidence of association was also detected at rs382140 (P-value=3.9 × 10(-09)) near NRCAM-a gene implicated in vulnerability to addiction, and at another independent hit rs6495122 (P-value=7.1 × 10(-09))-an SNP associated with blood pressure-in the 15q24 region near the gene ULK3, in the meta-analysis of discovery and replication cohorts. Our results from GWASs and expression analysis also strongly implicate CAB39L in coffee drinking. Pathway analysis of differentially expressed genes revealed significantly enriched ubiquitin proteasome (P-value=2.2 × 10(-05)) and Parkinson's disease pathways (P-value=3.6 × 10(-05)).

  5. Biochemical Markers in Neurocritical Care

    Directory of Open Access Journals (Sweden)

    Omidvar Rezae

    2016-07-01

    Full Text Available During the past two decades, a variety of serum or cerebrospinal fluid (CSF biochemical markers in daily clinical practice have been recommended to diagnose and monitor diverse diseases or pathologic situations. It will be essential to develop a panel of biomarkers, to be suitable for evaluation of treatment efficacy, representing distinct phases of injury and recovery and consider the temporal profile of those. Among the possible and different biochemical markers, S100b appeared to fulfill many of optimized criteria of an ideal marker. S100b, a cytosolic low molecular weight dimeric calciumbinding protein from chromosome 21, synthesized in glial cells throughout the CNS, an homodimeric diffusible, belongs to a family of closely related protein, predominantly expressed by astrocytes and Schwann cells and a classic immunohistochemical marker for these cells, is implicated in brain development and neurophysiology. Of the 3 isoforms of S-100, the BB subunit (S100B is present in high concentrations in central and peripheral glial and Schwann cells, Langerhans and anterior pituitary cells, fat, muscle, and bone marrow tissues. The biomarker has shown to be a sensitive marker of clinical and subclinical cerebral damage, such as stroke, traumatic brain injury, and spinal cord injury. Increasing evidence suggests that the biomarker plays a double function as an intracellular regulator and an extracellular signal of the CNS. S100b is found in the cytoplasm in a soluble form and also is associated with intracellular membranes, centrosomes, microtubules, and type III intermediate filaments. Their genomic organization now is known, and many of their target proteins have been identified, although the mechanisms of regulating S100b secretion are not completely understood and appear to be related to many factors, such as the proinflammatory cytokines, tumor necrosis factor alpha (TNF-a, interleukin (IL-1b, and metabolic stress. 

  6. Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis

    Directory of Open Access Journals (Sweden)

    Eroukova Veronika

    2008-12-01

    Full Text Available Abstract Background Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, ~4700 strains for increased sensitivity to paromomycin, which targets the process of protein synthesis. Results As expected, our analysis indicated that the majority of deletion strains (134 with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45, cellular component biogenesis and organization (28, DNA maintenance (21, transport (20, others (38 and unknown (39. These may represent minor cellular target sites (side-effects for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. Conclusion We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s.

  7. Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis.

    Science.gov (United States)

    Alamgir, Md; Eroukova, Veronika; Jessulat, Matthew; Xu, Jianhua; Golshani, Ashkan

    2008-12-03

    Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, approximately 4700 strains) for increased sensitivity to paromomycin, which targets the process of protein synthesis. As expected, our analysis indicated that the majority of deletion strains (134) with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45), cellular component biogenesis and organization (28), DNA maintenance (21), transport (20), others (38) and unknown (39). These may represent minor cellular target sites (side-effects) for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s).

  8. Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca

    Directory of Open Access Journals (Sweden)

    Yunpeng Cao

    2017-06-01

    Full Text Available WUSCHEL-related homeobox (WOX family is one of the largest group of transcription factors (TFs specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively. According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.

  9. Suggested improvements to the definitions of Standardized Plant Analysis of Risk-Human Reliability Analysis (SPAR-H) performance shaping factors, their levels and multipliers and the nominal tasks

    International Nuclear Information System (INIS)

    Laumann, Karin; Rasmussen, Martin

    2016-01-01

    This paper discusses the definitions and content of eight performance shaping factors (PSFs) used in Standardized Plant Analysis of Risk-Human Reliability Analysis (SPAR-H) and their levels and multipliers. Definitions of nominal tasks are also discussed. The discussion is based on a review of literature on PSFs, interviews with consultants who have carried out SPAR-H analysis in the petroleum industry and an evaluation of human reliability analysis reports based on SPAR-H analysis. We concluded that SPAR-H definitions and descriptions of the PSFs are unclear and overlap too much, making it difficult for the analyst to choose between them and select the appropriate level. This reduces inter-rater reliability and thus the consistency of SPAR-H analyses. New definitions of the PSFs, levels and multipliers are suggested with the aim to develop more specific definitions of the PSFs in order to increase the inter-rater reliability of SPAR-H. Another aim was to construct more varied and more nuanced levels and multipliers to improve the capacity of SPAR-H analysis to capture the degree of difficulty faced by operators in different scenarios. We also suggest that only one of two nominal SPAR-H tasks should be retained owing to the difficulty in distinguishing between them. - Highlights: • The SPAR-H guidelines should be revised. • Descriptions of the PSFs should be improved. • New definitions should reduce overlap between the PSFs. • The multipliers are based on an “old” method and should be revised. • Some PSF levels and multipliers in SPAR-H are not logical.

  10. Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination.

    Science.gov (United States)

    Jia, Lei; Li, Lin; Gui, Tao; Liu, Siyang; Li, Hanping; Han, Jingwan; Guo, Wei; Liu, Yongjian; Li, Jingyun

    2016-09-21

    With increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms. Near full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated. Pearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination. These results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our

  11. Analysis of the ACTN3 heterozygous genotype suggests that α-actinin-3 controls sarcomeric composition and muscle function in a dose-dependent fashion.

    Science.gov (United States)

    Hogarth, Marshall W; Garton, Fleur C; Houweling, Peter J; Tukiainen, Taru; Lek, Monkol; Macarthur, Daniel G; Seto, Jane T; Quinlan, Kate G R; Yang, Nan; Head, Stewart I; North, Kathryn N

    2016-03-01

    A common null polymorphism (R577X) in ACTN3 causes α-actinin-3 deficiency in ∼ 18% of the global population. There is no associated disease phenotype, but α-actinin-3 deficiency is detrimental to sprint and power performance in both elite athletes and the general population. However, despite considerable investigation to date, the functional consequences of heterozygosity for ACTN3 are unclear. A subset of studies have shown an intermediate phenotype in 577RX individuals, suggesting dose-dependency of α-actinin-3, while others have shown no difference between 577RR and RX genotypes. Here, we investigate the effects of α-actinin-3 expression level by comparing the muscle phenotypes of Actn3(+/-) (HET) mice to Actn3(+/+) [wild-type (WT)] and Actn3(-/-) [knockout (KO)] littermates. We show reduction in α-actinin-3 mRNA and protein in HET muscle compared with WT, which is associated with dose-dependent up-regulation of α-actinin-2, z-band alternatively spliced PDZ-motif and myotilin at the Z-line, and an incremental shift towards oxidative metabolism. While there is no difference in force generation, HET mice have an intermediate endurance capacity compared with WT and KO. The R577X polymorphism is associated with changes in ACTN3 expression consistent with an additive model in the human genotype-tissue expression cohort, but does not influence any other muscle transcripts, including ACTN2. Overall, ACTN3 influences sarcomeric composition in a dose-dependent fashion in mouse skeletal muscle, which translates directly to function. Variance in fibre type between biopsies likely masks this phenomenon in human skeletal muscle, but we suggest that an additive model is the most appropriate for use in testing ACTN3 genotype associations. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Gene expression analysis of overwintering mountain pine beetle larvae suggests multiple systems involved in overwintering stress, cold hardiness, and preparation for spring development

    Directory of Open Access Journals (Sweden)

    Jeanne A. Robert

    2016-07-01

    Full Text Available Cold-induced mortality has historically been a key aspect of mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae, population control, but little is known about the molecular basis for cold tolerance in this insect. We used RNA-seq analysis to monitor gene expression patterns of mountain pine beetle larvae at four time points during their overwintering period—early-autumn, late-autumn, early-spring, and late-spring. Changing transcript profiles over the winter indicates a multipronged physiological response from larvae that is broadly characterized by gene transcripts involved in insect immune responses and detoxification during the autumn. In the spring, although transcripts associated with developmental process are present, there was no particular biological process dominating the transcriptome.

  13. A model of residential energy end-use in Canada: Using conditional demand analysis to suggest policy options for community energy planners

    International Nuclear Information System (INIS)

    Newsham, Guy R.; Donnelly, Cara L.

    2013-01-01

    We applied conditional demand analysis (CDA) to estimate the average annual energy use of various electrical and natural gas appliances, and derived energy reductions associated with certain appliance upgrades and behaviours. The raw data came from 9773 Canadian households, and comprised annual electricity and natural gas use, and responses to >600 questions on dwelling and occupant characteristics, appliances, heating and cooling equipment, and associated behaviours. Replacing an old (>10 years) refrigerator with a new one was estimated to save 100 kW h/year; replacing an incandescent lamp with a CFL/LED lamp was estimated to save 20 kW h/year; and upgrading an old central heating system with a new one was estimated to save 2000 kW h/year. This latter effect was similar to that of reducing the number of walls exposed to the outside. Reducing the winter thermostat setpoint during occupied, waking hours was estimated to lower annual energy use by 200 kW h/°C-reduction, and lowering the thermostat setting overnight in winter relative to the setting during waking hours (night-time setback) was estimated to have a similar effect. This information may be used by policy-makers to optimize incentive programs, information campaigns, or other energy use change instruments. - Highlights: ► Conditional demand analysis (CDA) applied to data from 9773 Canadian households. ► Energy savings associated with certain appliance upgrades estimated. ► Energy savings associated with thermostat behaviours estimated. ► Policy-makers can use findings to optimize incentives and information campaigns

  14. A model-based telecoupling analysis for the Patagonian shelf: a new suggested template on how to study global seabirds-fisheries interactions for sustainability

    Science.gov (United States)

    Huettmann, F.; Raya Rey, A.

    2016-12-01

    The Southwest Atlantic Ocean, and the extended Patagonian shelf in particular, presents us with a very complex ecosystem of global relevance for food security and global peace. It is a highly productive area and it maintains a great diversity and abundance of seabird species. Fisheries have been identified as a main stressor for the marine ecosystems and as one of the main causes of seabird population declines. Using the framework of telecoupling - a sophisticated description of natural and socioeconomic interactions over large distances - here we present a fresh holistic look at the dynamic fisheries and (endangered) seabird interactions for the Patagonian shelf. While data are sparse, we employ machine learning-based predictions for a more holistic overview. We found that these waters of the Patagonian Shelf are significantly affected by many nations and outside players. We found that the input, output and spill-over of the Patagonian shelf ecosystem are distributed virtually all over the globe. In addition, we also found `losers' (=nations and their citizens that are left out entirely from this global resource and its governance). Our findings are based on best-available public trade and fish harvest analysis for this region, linked with predictive modeling (machine learning and geographic information systems GIS) to generalize for nine seabird species. We conveniently extend this analysis with a perspective from the financial sector and policy that enables the Patagonian fisheries as international investment and development projects. As increasingly recognized elsewhere, we believe that telecoupling can serve as a new but rather sophisticated study template highlighting wider complexities, bottlenecks and sensitivities for a vastly improved conservation research on oceans and global sustainability questions.

  15. Subcellular localization analysis of the closely related Fps/Fes and Fer protein-tyrosine kinases suggests a distinct role for Fps/Fes in vesicular trafficking.

    Science.gov (United States)

    Zirngibl, R; Schulze, D; Mirski, S E; Cole, S P; Greer, P A

    2001-05-15

    The subcellular localizations of the Fps/Fes and closely related Fer cytoplasmic tyrosine kinases were studied using green fluorescent protein (GFP) fusions and confocal fluorescence microscopy. In contrast to previous reports, neither kinase localized to the nucleus. Fer was diffusely cytoplasmic throughout the cell cycle. Fps/Fes also displayed a diffuse cytoplasmic localization, but in addition it showed distinct accumulations in cytoplasmic vesicles as well as in a perinuclear region consistent with the Golgi. This localization was very similar to that of TGN38, a known marker of the trans Golgi. The localization of Fps/Fes and TGN38 were both perturbed by brefeldin A, a fungal metabolite that disrupts the Golgi apparatus. Fps/Fes was also found to colocalize to various extents with several Rab proteins, which are members of the monomeric G-protein superfamily involved in vesicular transport between specific subcellular compartments. Using Rabs that are involved in endocytosis (Rab5B and Rab7) or exocytosis (Rab1A and Rab3A), we showed that Fps/Fes is localized in both pathways. These results suggest that Fps/Fes may play a general role in the regulation of vesicular trafficking. Copyright 2001 Academic Press.

  16. Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases.

    Science.gov (United States)

    Grigorenko, Bella L; Knyazeva, Marina A; Nemukhin, Alexander V

    2016-11-01

    We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c-di-GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme-substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c-di-GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c-di-GMP. The most difficult task was to find a pathway for a proton transfer to the O3' atom of c-di-GMP to promote the O3'P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provides the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis, and kinetic experimental studies on the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Biochemical and Cellular Assessment of Acetabular Chondral Flaps Identified During Hip Arthroscopy.

    Science.gov (United States)

    Hariri, Sanaz; Truntzer, Jeremy; Smith, Robert Lane; Safran, Marc R

    2015-06-01

    To analyze chondral flaps debrided during hip arthroscopy to determine their biochemical and cellular composition. Thirty-one full-thickness acetabular chondral flaps were collected during hip arthroscopy. Biochemical analysis was undertaken in 21 flaps from 20 patients, and cellular viability was determined in 10 flaps from 10 patients. Biochemical analysis included concentrations of (1) DNA (an indicator of chondrocyte content), (2) hydroxyproline (an indicator of collagen content), and (3) glycosaminoglycan (an indicator of chondrocyte biosynthesis). Higher values for these parameters indicated more healthy tissue. The flaps were examined to determine the percentage of viable chondrocytes. The percentage of acetabular chondral flap specimens that had concentrations within 1 SD of the mean values reported in previous normal cartilage studies was 38% for DNA, 0% for glycosaminoglycan, and 43% for hydroxyproline. The average cellular viability of our acetabular chondral flap specimens was 39% (SD, 14%). Only 2 of the 10 specimens had more than half the cells still viable. There was no correlation between (1) the gross examination of the joint or knowledge of the patient's demographic characteristics and symptoms and (2) biochemical properties and cell viability of the flap, with one exception: a degenerative appearance of the surrounding cartilage correlated with a higher hydroxyproline concentration. Although full-thickness acetabular chondral flaps can appear normal grossly, the biochemical properties and percentage of live chondrocytes in full-thickness chondral flaps encountered in hip arthroscopy show that this tissue is not normal. There has been recent interest in repairing chondral flaps encountered during hip arthroscopy. These data suggest that acetabular chondral flaps are not biochemically and cellularly normal. Although these flaps may still be valuable mechanically and/or as a scaffold in some conductive or inductive capacity, further study is

  18. Biochemical and Structural Analysis of Hormone-sensitive Lipase Homolog EstE7: Insight into the Stabilized Dimerization of HSL-Homolog Proteins

    International Nuclear Information System (INIS)

    Nam, Ki Hyun; Park, Sung Ha; Lee, Won Ho; Hwang, Kwang Yeon

    2010-01-01

    Hormone sensitive lipase (HSL) plays a major role in energy homeostasis and lipid metabolism. Several crystal structures of HSL-homolog proteins have been identified, which has led to a better understanding of its molecular function. HSLhomolog proteins exit as both monomer and dimer, but the biochemical and structural basis for such oligomeric states has not been successfully elucidated. Therefore, we determined the crystal structure of HSL-homolog protein EstE7 from a metagenome library at 2.2 A resolution and characterized the oligomeric states of EstE7 both structurally and biochemically. EstE7 protein prefers the dimeric state in solution, which is supported by its higher enzymatic activity in the dimeric state. In the crystal form, EstE7 protein shows two-types of dimeric interface. Specifically, dimerization via the external β8-strand occurred through tight association between two pseudosymmetric folds via salt bridges, hydrogen bonds and van der Waals interactions. This dimer formation was similar to that of other HSL-homolog protein structures such as AFEST, BEFA, and EstE1. We anticipate that our results will provide insight into the oligomeric state of HSLhomolog proteins

  19. Genetic diversity of notary-national uniform rape seed yield trial and brassica napus varieties using raped markers and biochemical analysis

    International Nuclear Information System (INIS)

    Bakhat, J.; Fareed, A.; Swati, Z.A.; Shafi, M.

    2011-01-01

    In Pakistan, Brassica is the second most important source of oil after cotton. Seventeen NURYT (National Uniform Rape Seed Yield Trial) lines and 5 Brassica napus varieties were assessed through RAPD primers and biochemical assays. Seven different Randomly Amplified Polymorphic DNA markers (RAPD) were employed during the present study. A total of 30 RAPD bands were scored by these primers. Size of the scorable fragments ranged from approximately 250 to 2000 bp. Diversity index was estimated to be 42%. Mean genetic distance estimates ranged between 0.10 and 1.00. For the assessment of various biochemical parameters, Near Infrared Reflectance Spectroscopy (NIRS) was used. Oil content ranged from 38.30 to 49% and protein content from 19.80 to 29.10% among the 22 genotypes. Maximum protein content was assayed in genotype RBN 3046 while minimum in Hyola 405. Glucosinolates ranged between 2 and 84% for genotype CRH 60/08 and CRH05/08 showing the maximum and minimum values respectively. Oleic acid (52 to 72.5%), linolenic acid (7.07 and 9.90%) and erucic acid content (9.57 to 38.3%) was also recorded during the present study. (author)

  20. Physiological and Proteomic Analysis of the Rice Mutant cpm2 Suggests a Negative Regulatory Role of Jasmonic Acid in Drought Tolerance

    Directory of Open Access Journals (Sweden)

    Rohit Dhakarey

    2017-11-01

    Full Text Available It is widely known that numerous adaptive responses of drought-stressed plants are stimulated by chemical messengers known as phytohormones. Jasmonic acid (JA is one such phytohormone. But there are very few reports revealing its direct implication in drought related responses or its cross-talk with other phytohormones. In this study, we compared the morpho-physiological traits and the root proteome of a wild type (WT rice plant with its JA biosynthesis mutant coleoptile photomorphogenesis 2 (cpm2, disrupted in the allene oxide cyclase (AOC gene, for insights into the role of JA under drought. The mutant had higher stomatal conductance, higher water use efficiency and higher shoot ABA levels under severe drought as compared to the WT. Notably, roots of cpm2 were better developed compared to the WT under both, control and drought stress conditions. Root proteome was analyzed using the Tandem Mass Tag strategy to better understand this difference at the molecular level. Expectedly, AOC was unique but notably highly abundant under drought in the WT. Identification of other differentially abundant proteins (DAPs suggested increased energy metabolism (i.e., increased mobilization of resources and reactive oxygen species scavenging in cpm2 under drought. Additionally, various proteins involved in secondary metabolism, cell growth and cell wall synthesis were also more abundant in cpm2 roots. Proteome-guided transcript, metabolite, and histological analyses provided further insights into the favorable adaptations and responses, most likely orchestrated by the lack of JA, in the cpm2 roots. Our results in cpm2 are discussed in the light of JA crosstalk to other phytohormones. These results together pave the path for understanding the precise role of JA during drought stress in rice.

  1. A suggested procedure for resolving an anomaly in least-squares data analysis known as ''Peelle's Pertinent Puzzle'' and the general implications for nuclear data evaluation

    International Nuclear Information System (INIS)

    Chiba, Satoshi; Smith, D.L.

    1991-09-01

    Modern nuclear-data evaluation methodology is based largely on statistical inference, with the least-squares technique being chosen most often to generate best estimates for physical quantities and their uncertainties. It has been observed that those least-squares evaluations which employ covariance matrices based on absolute errors that are derived directly from the reported experimental data often tend to produce results which appear to be too low. This anomaly is discussed briefly in this report, and a procedure for resolving it is suggested. The method involves employing data uncertainties which are derived from errors expressed in percent. These percent errors are used, in conjunction with reasonable a priori estimates for the quantities to be evaluated, to derive the covariance matrices which are required for applications of the least-squares procedure. This approach appears to lead to more rational weighting of the experimental data and, thus, to more realistic evaluated results than are obtained when the errors are based on the actual data. The procedure is very straightforward when only one parameter must be estimated. However, for those evaluation exercises involving more than one parameter, this technique demands that a priori estimates be provided at the outset for all of the parameters in question. Then, the least-squares method is applied iteratively to produce a sequence of sets of estimated values which are anticipated to convergence toward a particular set of parameters which one then designates as the ''best'' evaluated results from the exercise. It is found that convergence usually occurs very rapidly when the a priori estimates approximate the final solution reasonably well

  2. Genome-wide association analysis and replication of coronary artery disease in South Korea suggests a causal variant common to diverse populations

    Science.gov (United States)

    Cho, Eun Young; Jang, Yangsoo; Shin, Eun Soon; Jang, Hye Yoon; Yoo, Yeon-Kyeong; Kim, Sook; Jang, Ji Hyun; Lee, Ji Yeon; Yun, Min Hye; Park, Min Young; Chae, Jey Sook; Lim, Jin Woo; Shin, Dong Jik; Park, Sungha; Lee, Jong Ho; Han, Bok Ghee; Rae, Kim Hyung; Cardon, Lon R; Morris, Andrew P; Lee, Jong Eun; Clarke, Geraldine M

    2010-01-01

    Background Recent genome-wide association (GWA) studies have identified and replicated several genetic loci associated with the risk of development of coronary artery disease (CAD) in samples from populations of Caucasian and Asian descent. However, only chromosome 9p21 has been confirmed as a major susceptibility locus conferring risk for development of CAD across multiple ethnic groups. The authors aimed to find evidence of further similarities and differences in genetic risk of CAD between Korean and other populations. Methods The authors performed a GWA study comprising 230 cases and 290 controls from a Korean population typed on 490 032 single nucleotide polymorphisms (SNPs). A total of 3148 SNPs were taken forward for genotyping in a subsequent replication study using an independent sample of 1172 cases and 1087 controls from the same population. Results The association previously observed on chromosome 9p21 was independently replicated (p=3.08e–07). Within this region, the same risk haplotype was observed in samples from both Korea and of Western European descent, suggesting that the causal mutation carried on this background occurred on a single ancestral allele. Other than 9p21, the authors were unable to replicate any of the previously reported signals for association with CAD. Furthermore, no evidence of association was found at chromosome 1q41 for risk of myocardial infarction, previously identified as conferring risk in a Japanese population. Conclusion A common causal variant is likely to be responsible for risk of CAD in Korean and Western European populations at chromosome 9p21.3. Further investigations are required to confirm non-replication of any other cross-race genetic risk factors. PMID:27325954

  3. Expertly validated models and phylogenetically-controlled analysis suggests responses to climate change are related to species traits in the order lagomorpha.

    Directory of Open Access Journals (Sweden)

    Katie Leach

    Full Text Available Climate change during the past five decades has impacted significantly on natural ecosystems, and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs have been used widely to project changes in species' bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical, and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed 'modellable' within our framework were projected under future climate scenarios (58 species. Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares, and jackrabbits likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov's Pika (Ochotona koslowi. Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of

  4. Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation.

    Science.gov (United States)

    Oliveira, Jorge S; Araújo, Wydemberg J; Figueiredo, Ricardo M; Silva-Portela, Rita C B; de Brito Guerra, Alaine; da Silva Araújo, Sinara Carla; Minnicelli, Carolina; Carlos, Aline Cardoso; de Vasconcelos, Ana Tereza Ribeiro; Freitas, Ana Teresa; Agnez-Lima, Lucymara F

    2017-07-27

    Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects. A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential. In this work we have focused on the

  5. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru’s Central Coast during the Middle Horizon

    Science.gov (United States)

    Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650–1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region’s demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500–700 AD), Wari (Middle Horizon, 800–1000 AD) and Ychsma (Late Intermediate Period, 1000–1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast. PMID:27248693

  6. An exposure-response analysis based on rifampin suggests CYP3A4 induction is driven by AUC: an in vitro investigation.

    Science.gov (United States)

    Chang, Cheng; Yang, Xin; Fahmi, Odette A; Riccardi, Keith A; Di, Li; Obach, R Scott

    2017-08-01

    1. Induction is an important mechanism contributing to drug-drug interactions. It is most commonly evaluated in the human hepatocyte assay over 48-h or 72-h incubation period. However, whether the overall exposure (i.e. Area Under the Curve (AUC) or C ave ) or maximum exposure (i.e. C max ) of the inducer is responsible for the magnitude of subsequent induction has not been thoroughly investigated. Additionally, in vitro induction assays are typically treated as static systems, which could lead to inaccurate induction potency estimation. Hence, European Medicines Agency (EMA) guidance now specifies quantitation of drug levels in the incubation. 2. This work treated the typical in vitro evaluation of rifampin induction as an in vivo system by generating various target engagement profiles, measuring free rifampin concentration over 3 d of incubation and evaluating the impact of these factors on final induction response. 3. This rifampin-based analysis demonstrates that the induction process is driven by time-averaged target engagement (i.e. AUC-driven). Additionally, depletion of rifampin in the incubation medium over 3 d as well as non-specific/specific binding were observed. 4. These findings should help aid the discovery of clinical candidates with minimal induction liability and further expand our knowledge in the quantitative translatability of in vitro induction assays.

  7. Recent Male-Mediated Gene Flow over a Linguistic Barrier in Iberia, Suggested by Analysis of a Y-Chromosomal DNA Polymorphism

    Science.gov (United States)

    Hurles, Matthew E.; Veitia, Reiner; Arroyo, Eduardo; Armenteros, Manuel; Bertranpetit, Jaume; Pérez-Lezaun, Anna; Bosch, Elena; Shlumukova, Maria; Cambon-Thomsen, Anne; McElreavey, Ken; López de Munain, Adolfo; Röhl, Arne; Wilson, Ian J.; Singh, Lalji; Pandya, Arpita; Santos, Fabrício R.; Tyler-Smith, Chris; Jobling, Mark A.

    1999-01-01

    Summary We have examined the worldwide distribution of a Y-chromosomal base-substitution polymorphism, the T/C transition at SRY-2627, where the T allele defines haplogroup 22; sequencing of primate homologues shows that the ancestral state cannot be determined unambiguously but is probably the C allele. Of 1,191 human Y chromosomes analyzed, 33 belong to haplogroup 22. Twenty-nine come from Iberia, and the highest frequencies are in Basques (11%; n=117) and Catalans (22%; n=32). Microsatellite and minisatellite (MSY1) diversity analysis shows that non-Iberian haplogroup-22 chromosomes are not significantly different from Iberian ones. The simplest interpretation of these data is that haplogroup 22 arose in Iberia and that non-Iberian cases reflect Iberian emigrants. Several different methods were used to date the origin of the polymorphism: microsatellite data gave ages of 1,650, 2,700, 3,100, or 3,450 years, and MSY1 gave ages of 1,000, 2,300, or 2,650 years, although 95% confidence intervals on all of these figures are wide. The age of the split between Basque and Catalan haplogroup-22 chromosomes was calculated as only 20% of the age of the lineage as a whole. This study thus provides evidence for direct or indirect gene flow over the substantial linguistic barrier between the Indo-European and non–Indo-European–speaking populations of the Catalans and the Basques, during the past few thousand years. PMID:10521311

  8. In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce.

    Science.gov (United States)

    Yakovlev, Igor A; Fossdal, Carl G

    2017-01-01

    regulation, which in turn could provide a feedback process leading to the formation of epigenetic marks. We suggest that TIR, NBS and LRR domain containing proteins could fulfill more general functions for signal transduction from external environmental stimuli and conversion them into molecular response. Fine-tuning of the miRNA production likely participates in both developmental regulation and epigenetic memory formation in Norway spruce.

  9. In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce

    Directory of Open Access Journals (Sweden)

    Igor A. Yakovlev

    2017-09-01

    involved in epigenetic regulation, which in turn could provide a feedback process leading to the formation of epigenetic marks. We suggest that TIR, NBS and LRR domain containing proteins could fulfill more general functions for signal transduction from external environmental stimuli and conversion them into molecular response. Fine-tuning of the miRNA production likely participates in both developmental regulation and epigenetic memory formation in Norway spruce.

  10. Genetic signature analysis of Perkinsus marinus in Mexico suggests possible translocation from the Atlantic Ocean to the Pacific coast of Mexico.

    Science.gov (United States)

    Ek-Huchim, Juan Pablo; Aguirre-Macedo, Ma Leopoldina; Améndola-Pimenta, Monica; Vidal-Martínez, Victor Manuel; Pérez-Vega, Juan Antonio; Simá-Alvarez, Raúl; Jiménez-García, Isabel; Zamora-Bustillos, Roberto; Rodríguez-Canul, Rossanna

    2017-08-02

    DNA-NTS sequences described herein were restricted to specific locations displaying different geographical connections within the Gulf of Mexico; the Carmen-Pajonal-Machona Pm1 haplotype from the state of Tabasco shared a cluster with P. marinus isolates reported from the Mexican Pacific coast. The rDNA-NTS sequences of P. marinus from the state of Tabasco shared high similarity with the reference rDNA-NTS sequences from the Mexican Pacific coast. The high similarity suggests a transfer of oysters infected with P. marinus from the Mexican part of the Gulf of Mexico into the Mexican Pacific coast.

  11. Targeted α-Therapy of Metastatic Castration-Resistant Prostate Cancer with 225Ac-PSMA-617: Swimmer-Plot Analysis Suggests Efficacy Regarding Duration of Tumor Control.

    Science.gov (United States)

    Kratochwil, Clemens; Bruchertseifer, Frank; Rathke, Hendrik; Hohenfellner, Markus; Giesel, Frederik L; Haberkorn, Uwe; Morgenstern, Alfred

    2018-05-01

    The aim of this evaluation was to identify the first indicators of efficacy for 225 Ac-labeled prostate-specific membrane antigen (PSMA)-617 therapy in a retrospectively analyzed group of patients. Methods: Forty patients with metastatic castration-resistant prostate cancer were selected for treatment with three 100 kBq/kg cycles of 225 Ac-PSMA-617 at 2-mo intervals. Prostate-specific antigen (PSA) and blood cell count were measured every 4 wk. PSMA PET/CT or PSMA SPECT/CT were used for baseline staging and imaging follow-up at month 6. Follow-up included the duration of PSA response and radiologic progression-free survival at month 6. Patient histories were reviewed for the duration of previous treatment lines, and a swimmer plot was used to intraindividually compare the duration of tumor control by PSMA therapy versus prior treatment modalities. Results: Thirty-one of 40 patients were treated per protocol. Five patients discontinued treatment because of nonresponse, and 4 because of xerostomia. Of the 38 patients surviving at least 8 wk, 24 (63%) had a PSA decline of more than 50%, and 33 (87%) had a PSA response of any degree. The median duration of tumor control under 225 Ac-PSMA-617 last-line therapy was 9.0 mo; 5 patients had an enduring response of more than 2 y. Because all patients had advanced disease, this result compares favorably with the tumor control rates associated with earlier-phase disease; the most common preceding first-, second-, third-, and fourth-line therapies were abiraterone (median duration 10.0 mo), docetaxel (6.5 mo), enzalutamide (6.5 mo), and cabazitaxel (6.0 mo), respectively. Conclusion: A positive response for surrogate parameters demonstrates remarkable antitumor activity for 225 Ac-PSMA-617. Swimmer-plot analysis indicates a promising duration of tumor control, especially considering the unfavorable prognostic profile of the selected advanced-stage patients. Xerostomia was the main reason patients discontinued therapy or refused

  12. Evaluation of biochemical changes in unstimulated salivary, calcium ...

    African Journals Online (AJOL)

    TORNADO

    2012-01-26

    Jan 26, 2012 ... salivary, calcium, phosphorous and total protein during ... teins in saliva are important components and any chan- ... Sialochemical analysis .... quantities of protein utilizing the principal of protein-dye binding. Anal biochem.

  13. Biochemical and physicochemical analysis of fish protein isolate recovered from red snapper (Lutjanus sp.) by-product using isoelectric solubilization/precipitation method

    Science.gov (United States)

    Pramono, H.; Pujiastuti, D. Y.; Sahidu, A. M.

    2018-04-01

    The effect of acid- and alkali-process on biochemical and physicochemical characteristics of fish protein isolate from red snapper (Lutjanus sp) by-product was evaluated. Protein recovered by alkali process (16.79%) was higher compared to acid process (13.75%). Reduction of lipid content and total volatile basic nitrogen (TVB-N) exhibited in both treatments indicated both process improved fish protein isolate recovered from red snapper by-product. In addition, the increasing of water holding capacity and oil binding capacity were observed. However, high peroxide value of fish protein isolate was showed in both treatment. This finding indicated that acid and alkali process can be used as a useful method to recover proteins from red snapper by-product. Alkali process gave a protein isolate with better overall quality compared to acid process.

  14. Types of suggestibility: Relationships among compliance, indirect, and direct suggestibility.

    Science.gov (United States)

    Polczyk, Romuald; Pasek, Tomasz

    2006-10-01

    It is commonly believed that direct suggestibility, referring to overt influence, and indirect suggestibility, in which the intention to influence is hidden, correlate poorly. This study demonstrates that they are substantially related, provided that they tap similar areas of influence. Test results from 103 students, 55 women and 48 men, were entered into regression analyses. Indirect suggestibility, as measured by the Sensory Suggestibility Scale for Groups, and compliance, measured by the Gudjonsson Compliance Scale, were predictors of direct suggestibility, assessed with the Barber Suggestibility Scale. Spectral analyses showed that indirect suggestibility is more related to difficult tasks on the BSS, but compliance is more related to easy tasks on this scale.

  15. Analysis of the Variability of Epstein-Barr Virus Genes in Infectious Mononucleosis: Investigation of the Potential Correlation with Biochemical Parameters of Hepatic Involvement.

    Science.gov (United States)

    Banko, Ana; Lazarevic, Ivana; Stevanovic, Goran; Cirkovic, Andja; Karalic, Danijela; Cupic, Maja; Banko, Bojan; Milovanovic, Jovica; Jovanovic, Tanja

    2016-09-01

    Primary Epstein-Barr virus (EBV) infection is usually asymptomatic, although at times it results in the benign lymphoproliferative disease, infectious mononucleosis (IM), during which almost half of patients develop hepatitis. The aims of the present study are to evaluate polymorphisms of EBV genes circulating in IM isolates from this geographic region and to investigate the correlation of viral sequence patterns with the available IM biochemical parameters. The study included plasma samples from 128 IM patients. The genes EBNA2, LMP1 , and EBNA1 were amplified using nested-PCR. EBNA2 genotyping was performed by visualization of PCR products using gel electrophoresis. Investigation of LMP1 and EBNA1 included sequence, phylogenetic, and statistical analyses. The presence of EBV DNA in plasma samples showed correlation with patients' necessity for hospitalization (p=0.034). The majority of EBV isolates was genotype 1. LMP1 variability showed 4 known variants, and two new deletions (27-bp and 147-bp). Of the 3 analyzed attributes of LMP1 isolates, the number of 33-bp repeats less than the reference 4.5 was the only one that absolutely correlated with the elevated levels of transaminases. EBNA1 variability was presented by prototype subtypes. A particular combination of EBNA2, LMP1 , and EBNA1 polymorphisms, deleted LMP1/P-thr and non-deleted LMP1/P-ala , as well as genotype 1/ 4.5 33-bp LMP1 repeats or genotype 2/ 4.5 33-bp LMP1 repeats showed correlation with elevated AST (aspartate aminotransferase) and ALT (alanine transaminase). This is the first study which identified the association between EBV variability and biochemical parameters in IM patients. These results showed a possibility for the identification of hepatic related diagnostic EBV markers.

  16. Gluconeogenesis: An ancient biochemical pathway with a new twist.

    Science.gov (United States)

    Miyamoto, Tetsuya; Amrein, Hubert

    2017-07-03

    Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans, but also in insects. The gluconeogenic-specific enzyme glucose-6-phosphatase (G6Pase) first appears in Cnidaria, but is also present in Echinodermata, Mollusca and Vertebrata. Intriguingly, some species of nematodes and arthropods possess the genes for both pathways. Moreover, expression data from Drosophila suggests that G6Pase and, hence, gluconeogenesis, initially had a neuronal function. We speculate that in insects-and possibly in some vertebrates-gluconeogenesis may be used as a means of neuronal signaling.

  17. Suggestibility and suggestive modulation of the Stroop effect.

    Science.gov (United States)

    Kirsch, Irving

    2011-06-01

    Although the induction of a hypnotic state does not seem necessary for suggestive modulation of the Stroop effect, this important phenomenon has seemed to be dependent on the subject's level of hypnotic suggestibility. Raz and Campbell's (2011) study indicates that suggestion can modulate the Stroop effect substantially in very low suggestible subjects, as well as in those who are highly suggestible. This finding casts doubt on the presumed mechanism by which suggestive modulation is brought about. Research aimed at uncovering the means by which low suggestible individuals are able to modulate the Stroop effect would be welcome, as would assessment of this effect in moderately suggestible people. Copyright © 2010 Elsevier Inc. All rights reserved.

  18. Biochemical Neuroscience Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This biochemistry lab is set up for protein analysis using Western blot, enzyme linked immunosorbent assays, immunohistochemistry, and bead-based immunoassays. The...

  19. Molecular and biochemical toxicology

    National Research Council Canada - National Science Library

    Smart, Robert C; Hodgson, Ernest

    2008-01-01

    ... Expression and Regulation 2.6.1 Northern Analysis 2.6.2 Nuclear Run-On 2.6.3 Promoter Deletion Analysis/Reporter Gene Assays 2.6.4 Microarrays 2.6.5 Reverse Transcriptase-PCR (RT-PCR) and Real-Time P...

  20. Effect of the combination of metformin hydrochloride and melatonin on oxidative stress before and during pregnancy, and biochemical and histopathological analysis of the livers of rats after treatment for polycystic ovary syndrome.

    Science.gov (United States)

    Lemos, Ana Janaina Jeanine M; Peixoto, Christina A; Teixeira, Alvaro Aguiar C; Luna, Rayana Leal A; Rocha, Sura Wanessa S; Santos, Hilda Michelly P; Silva, Amanda Karolina S; Nunes, Ana Karolina S; Wanderley-Teixeira, Valéria

    2014-10-01

    The aim of the present study was to analyze the effect of a combination of metformin hydrochloride and melatonin on oxidative stress together with a biochemical and histopathological analysis of the livers of Wistar rats induced with PCOS. The results indicated that a combination of the drugs was more effective in the reduction of plasmatic levels of liver enzyme alanine aminotransferase, nitric oxide and total glutathione, and decreased the inflammatory response and histopathological damage, producing results that were significantly similar to animals from the control group. A mixture of the drugs produced more effective results against liver toxicity caused by PCOS, encouraging the normalization of biochemical parameters. During pregnancy, there was reduced oxidative stress compared to monotherapeutic use of these drugs. Interestingly, the combination of the drugs caused a physiological reaction similar to responses identified in healthy rats without induction of the PCOS control group. However, the clinical and physiological effectiveness of the combination should be further explored, especially with respect to the possible side effects on offspring. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Somatic embryogenesis, scanning electron microscopy, histology and biochemical analysis at different developing stages of embryogenesis in six date palm (Phoenix dactylifera L.) cultivars.

    Science.gov (United States)

    Aslam, Junaid; Khan, Saeed Ahmad; Cheruth, Abdul Jaleel; Mujib, Abdul; Sharma, Maheshwar Pershad; Srivastava, Prem Shanker

    2011-10-01

    An efficient somatic embryogenesis system has been established in six date palm (Phoenix dactylifera L.) cultivars (Barhee, Zardai, Khalasah, Muzati, Shishi and Zart). Somatic embryogenesis (SE) was growth regulators and cultivars dependent. Friable embryogenic callus was induced from excised shoot tips on MS medium supplemented with various auxins particularly 2,4-dichlorophenoxyacetic acid (2,4-D, 1.5 mg 1(-l)). Suspension culture increased embryogenesis potentiality. Only a-naphthaleneacetic acid (NAA, 0.5 mg 1(-1)) produced somatic embryos in culture. Somatic embryos germinated and converted into plantlets in N(6)-benzyladenine (BAP, 0.75 mg 1(-l)) added medium following a treatment with thidiazuron (TDZ, 1.0 mg 1(-l)) for maturation. Scanning electron microscopy showed early stages of somatic embryo particularly, globular types, and was in masses. Different developing stages of embryogenesis (heart, torpedo and cotyledonary) were observed under histological preparation of embryogenic callus. Biochemical screening at various stages of somatic embryogenesis (embryogenic callus, somatic embryos, matured, germinated embryos and converted plantlets) of date palm cultivars has been conducted and discussed in detail. The result discussed in this paper indicates that somatic embryos were produced in numbers and converted plantlets can be used as a good source of alternative propagation. Genetic modification to the embryo precursor cell may improve the fruit quality and yield further.

  2. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

    Science.gov (United States)

    Mulepati, Sabin; Bailey, Scott

    2011-09-09

    RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

  3. Reconstructing biochemical pathways from time course data.

    Science.gov (United States)

    Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

    2007-03-01

    Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

  4. Biochemical Evaluation of Withania somnifera Root Powder on Adjuvant-Induced Arthritis in Rats

    Directory of Open Access Journals (Sweden)

    Mahaboobkhan Rasool

    2015-04-01

    Full Text Available The present investigation was carried out to evaluate the biochemical effect of Withania somnifera Linn. Solanaceae, commonly known as ashwagandha on adjuvant induced arthritic rats. Results were compared to Indomethacin, a non steroidal anti-inflammatory drug. Arthritis was induced by an intra dermal injection of Complete Freund’s Adjuvant (0.1 ml into the right hind paw of Wistar albino rats. Withania somnifera root powder (1000 mg/kg/day and Indomethacin (3 mg/kg/day were orally administered for 8 days (from 11th to 18th day after adjuvant injection. After the experimental period, all the animals were sacrificed and serum, liver and spleen samples were collected for further biochemical analysis. A significant increase in the activities of gluconeogenic enzymes, tissue marker enzymes, blood glucose level, WBC, platelet count, erythrocyte sedimentation rate, and acute phase proteins (hyaluronic acid, fibrinogen and ceruloplasmin was observed in adjuvant-induced arthritic rats, whereas the activities of glycolytic enzymes, body weight, levels of hemoglobin, RBC count, and packed cell volume were found to be decreased. These biochemical alterations observed in arthritic animals were ameliorated significantly after the administration of Withania somnifera root powder (1000 mg/kg/b.wt and Indomethacin (3 mg/kg/b.wt. Our results suggest that Withania somnifera root powder is capable of rectifying the above biochemical changes in adjuvant arthritis and it may prove to be useful in treating rheumatoid arthritis.

  5. Clinical and Biochemical Pitfalls in the Diagnosis of Peroxisomal Disorders.

    Science.gov (United States)

    Klouwer, Femke C C; Huffnagel, Irene C; Ferdinandusse, Sacha; Waterham, Hans R; Wanders, Ronald J A; Engelen, Marc; Poll-The, Bwee Tien

    2016-08-01

    Peroxisomal disorders are a heterogeneous group of genetic metabolic disorders, caused by a defect in peroxisome biogenesis or a deficiency of a single peroxisomal enzyme. The peroxisomal disorders include the Zellweger spectrum disorders, the rhizomelic chondrodysplasia punctata spectrum disorders, X-linked adrenoleukodystrophy, and multiple single enzyme deficiencies. There are several core phenotypes caused by peroxisomal dysfunction that clinicians can recognize. The diagnosis is suggested by biochemical testing in blood and urine and confirmed by functional assays in cultured skin fibroblasts, followed by mutation analysis. This review describes the phenotype of the main peroxisomal disorders and possible pitfalls in (laboratory) diagnosis to aid clinicians in the recognition of this group of diseases. Georg Thieme Verlag KG Stuttgart · New York.

  6. Deepening Sleep by Hypnotic Suggestion

    Science.gov (United States)

    Cordi, Maren J.; Schlarb, Angelika A.; Rasch, Björn

    2014-01-01

    Study Objectives: Slow wave sleep (SWS) plays a critical role in body restoration and promotes brain plasticity; however, it markedly declines across the lifespan. Despite its importance, effective tools to increase SWS are rare. Here we tested whether a hypnotic suggestion to “sleep deeper” extends the amount of SWS. Design: Within-subject, placebo-controlled crossover design. Setting: Sleep laboratory at the University of Zurich, Switzerland. Participants: Seventy healthy females 23.27 ± 3.17 y. Intervention: Participants listened to an auditory text with hypnotic suggestions or a control tape before napping for 90 min while high-density electroencephalography was recorded. Measurements and Results: After participants listened to the hypnotic suggestion to “sleep deeper” subsequent SWS was increased by 81% and time spent awake was reduced by 67% (with the amount of SWS or wake in the control condition set to 100%). Other sleep stages remained unaffected. Additionally, slow wave activity was significantly enhanced after hypnotic suggestions. During the hypnotic tape, parietal theta power increases predicted the hypnosis-induced extension of SWS. Additional experiments confirmed that the beneficial effect of hypnotic suggestions on SWS was specific to the hypnotic suggestion and did not occur in low suggestible participants. Conclusions: Our results demonstrate the effectiveness of hypnotic suggestions to specifically increase the amount and duration of slow wave sleep (SWS) in a midday nap using objective measures of sleep in young, healthy, suggestible females. Hypnotic suggestions might be a successful tool with a lower risk of adverse side effects than pharmacological treatments to extend SWS also in clinical and elderly populations. Citation: Cordi MJ, Schlarb AA, Rasch B. Deepening sleep by hypnotic suggestion. SLEEP 2014;37(6):1143-1152. PMID:24882909

  7. Biochemical reactions of the organism

    International Nuclear Information System (INIS)

    Fedorova, A.V.

    1984-01-01

    Effects of mercury, strontium chloride, GMDA, trichlorfon as well as some radionuclides ( 89 Sr, 137 Cs, 203 Hg) were studied on rats. Changes in biochemical parameters (histamine content, activity of cholinesterase and histaminase) are noted. Most noticeable changes were observed in enzymatic activity. Distortion of enzymatic systems and accumulation of intermediate exchange and decay products of tissues in excess quantities affecting other systems can be the reason for changes in the organism. The observed changes in biochemical parameters should be necessarily taken into account at hygienic regulations of harmful effects of enviroment

  8. Representational constraints on children's suggestibility.

    Science.gov (United States)

    Ceci, Stephen J; Papierno, Paul B; Kulkofsky, Sarah

    2007-06-01

    In a multistage experiment, twelve 4- and 9-year-old children participated in a triad rating task. Their ratings were mapped with multidimensional scaling, from which euclidean distances were computed to operationalize semantic distance between items in target pairs. These children and age-mates then participated in an experiment that employed these target pairs in a story, which was followed by a misinformation manipulation. Analyses linked individual and developmental differences in suggestibility to children's representations of the target items. Semantic proximity was a strong predictor of differences in suggestibility: The closer a suggested distractor was to the original item's representation, the greater was the distractor's suggestive influence. The triad participants' semantic proximity subsequently served as the basis for correctly predicting memory performance in the larger group. Semantic proximity enabled a priori counterintuitive predictions of reverse age-related trends to be confirmed whenever the distance between representations of items in a target pair was greater for younger than for older children.

  9. Circadian Clocks: Unexpected Biochemical Cogs.

    Science.gov (United States)

    Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

    2015-10-05

    A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ∼ 24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Circadian Clocks: Unexpected Biochemical Cogs

    OpenAIRE

    Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

    2015-01-01

    A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ~24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes.

  11. Validation of artificial neural network models for predicting biochemical markers associated with male infertility.

    Science.gov (United States)

    Vickram, A S; Kamini, A Rao; Das, Raja; Pathy, M Ramesh; Parameswari, R; Archana, K; Sridharan, T B

    2016-08-01

    Seminal fluid is the secretion from many glands comprised of several organic and inorganic compounds including free amino acids, proteins, fructose, glucosidase, zinc, and other scavenging elements like Mg(2+), Ca(2+), K(+), and Na(+). Therefore, in the view of development of novel approaches and proper diagnosis to male infertility, overall understanding of the biochemical and molecular composition and its role in regulation of sperm quality is highly desirable. Perhaps this can be achieved through artificial intelligence. This study was aimed to elucidate and predict various biochemical markers present in human seminal plasma with three different neural network models. A total of 177 semen samples were collected for this research (both fertile and infertile samples) and immediately processed to prepare a semen analysis report, based on the protocol of the World Health Organization (WHO [2010]). The semen samples were then categorized into oligoasthenospermia (n=35), asthenospermia (n=35), azoospermia (n=22), normospermia (n=34), oligospermia (n=34), and control (n=17). The major biochemical parameters like total protein content, fructose, glucosidase, and zinc content were elucidated by standard protocols. All the biochemical markers were predicted by using three different artificial neural network (ANN) models with semen parameters as inputs. Of the three models, the back propagation neural network model (BPNN) yielded the best results with mean absolute error 0.025, -0.080, 0.166, and -0.057 for protein, fructose, glucosidase, and zinc, respectively. This suggests that BPNN can be used to predict biochemical parameters for the proper diagnosis of male infertility in assisted reproductive technology (ART) centres. AAS: absorption spectroscopy; AI: artificial intelligence; ANN: artificial neural networks; ART: assisted reproductive technology; BPNN: back propagation neural network model; DT: decision tress; MLP: multilayer perceptron; PESA: percutaneous

  12. Clinical and biochemical heterogeneity between patients with glycogen storage disease type IA: the added value of CUSUM for metabolic control.

    Science.gov (United States)

    Peeks, Fabian; Steunenberg, Thomas A H; de Boer, Foekje; Rubio-Gozalbo, M Estela; Williams, Monique; Burghard, Rob; Rajas, Fabienne; Oosterveer, Maaike H; Weinstein, David A; Derks, Terry G J

    2017-09-01

    To study heterogeneity between patients with glycogen storage disease type Ia (GSD Ia), a rare inherited disorder of carbohydrate metabolism caused by the deficiency of glucose-6-phosphatase (G6Pase). Descriptive retrospective study of longitudinal clinical and biochemical data and long-term complications in 20 GSD Ia patients. We included 11 patients with homozygous G6PC mutations and siblings from four families carrying identical G6PC genotypes. To display subtle variations for repeated triglyceride measurements with respect to time for individual patients, CUSUM-analysis graphs were constructed. Patients with different homozygous G6PC mutations showed important differences in height, BMI, and biochemical parameters (i.e., lactate, uric acid, triglyceride, and cholesterol concentrations). Furthermore, CUSUM-analysis predicts and displays subtle changes in longitudinal blood triglyceride concentrations. Siblings in families also displayed important differences in biochemical parameters (i.e., lactate, uric acid, triglycerides, and cholesterol concentrations) and long-term complications (i.e., liver adenomas, nephropathy, and osteopenia/osteoporosis). Differences between GSD Ia patients reflect large clinical and biochemical heterogeneity. Heterogeneity between GSD Ia patients with homozygous G6PC mutations indicate an important role of the G6PC genotype/mutations. Differences between affected siblings suggest an additional role (genetic and/or environmental) of modifying factors defining the GSD Ia phenotype. CUSUM-analysis can facilitate single-patient monitoring of metabolic control and future application of this method may improve precision medicine for patients both with GSD and remaining inherited metabolic diseases.

  13. Classification of hadith into positive suggestion, negative suggestion, and information

    Science.gov (United States)

    Faraby, Said Al; Riviera Rachmawati Jasin, Eliza; Kusumaningrum, Andina; Adiwijaya

    2018-03-01

    As one of the Muslim life guidelines, based on the meaning of its sentence(s), a hadith can be viewed as a suggestion for doing something, or a suggestion for not doing something, or just information without any suggestion. In this paper, we tried to classify the Bahasa translation of hadith into the three categories using machine learning approach. We tried stemming and stopword removal in preprocessing, and TF-IDF of unigram, bigram, and trigram as the extracted features. As the classifier, we compared between SVM and Neural Network. Since the categories are new, so in order to compare the results of the previous pipelines, we created a baseline classifier using simple rule-based string matching technique. The rule-based algorithm conditions on the occurrence of words such as “janganlah, sholatlah, and so on” to determine the category. The baseline method achieved F1-Score of 0.69, while the best F1-Score from the machine learning approach was 0.88, and it was produced by SVM model with the linear kernel.

  14. Interrogative suggestibility in opiate users.

    Science.gov (United States)

    Murakami, A; Edelmann, R J; Davis, P E

    1996-09-01

    The present study investigated interrogative suggestibility in opiate users. A group of patients undergoing a methadone detoxification programme in an in-patient drug treatment unit (Detox group, n = 21), and a group of residents who had come off drugs and were no longer suffering from withdrawal syndrome (Rehab group, n = 19) were compared on interrogative suggestibility and various other psychological factors. Significant differences were found between the two groups, with the Detox group having more physical and psychological problems, and a higher total suggestibility score in comparison with the Rehab group. These findings are discussed in relation to the context of police interrogations and the reliability of confessions made by suspects and witnesses dependent on opiates.

  15. Diet History Questionnaire: Suggested Citations

    Science.gov (United States)

    Use of the Diet History Questionnaire and Diet*Calc Analysis Software for publication purposes should contain a citation which includes version information for the software, questionnaire, and nutrient database.

  16. Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit colour

    NARCIS (Netherlands)

    Ballester, A.R.; Molthoff, J.W.; Vos, de C.H.; Lintel Hekkert, B.; Orzaez, D.; Fernandez-Moreno, J.P.; Tripodi, S.; Grandillo, S.; Martin, C.; Heldens, J.; Ykema, M.; Granell, A.; Bovy, A.G.

    2010-01-01

    The color of tomato fruit is mainly determined by carotenoids and flavonoids. Phenotypic analysis of an introgression line (IL) population derived from a cross between Solanum lycopersicum 'Moneyberg' and the wild species Solanum chmielewskii revealed three ILs with a pink fruit color. These lines

  17. Treatment of landfill leachate biochemical effluent using the nano-Fe3O4/Na2S2O8 system: Oxidation performance, wastewater spectral analysis, and activator characterization.

    Science.gov (United States)

    Liu, Zhanmeng; Li, Xian; Rao, Zhiwei; Hu, Fengping

    2018-02-15

    Nano-Fe 3 O 4 was used as heterogeneous catalyst to activate Na 2 S 2 O 8 for the generation of the sulfate radicals (SO 4 - ) to oxidize the residual pollutants in landfill leachate biochemical effluent. The oxidation performance, wastewater spectral analysis and activator characterization were discussed. Oxidation experimental result shows that nano-Fe 3 O 4 has obvious catalytic effect on Na 2 S 2 O 8 and can significantly enhance the oxidation efficiencies of Na 2 S 2 O 8 on landfill leachate biochemical effluent, with COD and color removals above 63% and 95%, respectively. Based on the analyses of three-dimensional excitation emission matrix fluorescence spectrum (3DEEM), ultraviolet-visible spectra (UV-vis), and Fourier Transform infrared spectroscopy (FTIR) of wastewater samples before and after treatment, it can be concluded that the pollution level of dissolved organic matter (DOM) declined and that the humic acid (HA) fractions were efficiently degraded into small molecules of fulvic acid (FA) fractions with less weight and stable structure. Compared to the raw wastewater sample, the aromaticity and substituent groups of the DOM were lessened in the treated wastewater sample. Moreover, the main structure of the organics and functional groups were changed by the Fe 3 O 4 /Na 2 S 2 O 8 system, with substantial decrease of conjugated double bonds. The micro morphology of nano-Fe 3 O 4 was characterized before and after reaction by the methods of scanning electron microscope spectra (SEM), X-ray diffraction pattern (XRD), and X-ray photoelectron spectroscopy (XPS). The XRD pattern analysis showed that nano-Fe 3 O 4 was oxidized into r-Fe 2 O 3 and that the particle size of it also became smaller after reaction. XPS was employed to analyze the content and iron valence on the nano-Fe 3 O 4 surface, and it can be found that the ratio of Fe 3+ /Fe 2+ decreased from 1.8 before reaction to 0.8 after reaction. From the SEM analysis after the treatment, it was

  18. The study of the changes in the biochemical and mineral contents of bones of Catla catla due to lead intoxication.

    Science.gov (United States)

    Palaniappan, P L R M; Krishnakumar, N; Vadivelu, M; Vijayasundaram, V

    2010-02-01

    In the present study, an attempt has been made to analyze the changes in the biochemical and mineral contents of lead-intoxicated bones of Catla catla at subchronic (15.5 ppm) exposure, and also to determine whether the effects of Pb intoxication can be reversed with the chelating agent meso 2, 3-dimercaptosuccinic acid (DMSA) on the bones of freshwater fingerlings Catla catla by using Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), and atomic absorption spectrophotometer techniques. The FT-IR spectra of the lead-exposed bones show significant alteration in the biochemical constituents. The XRD analysis showed a decrease in crystallinity due to lead exposure. Further, the Ca, Mg, and P contents of the lead-exposed bones were less than those of the control group, and there was an increase in the mineral contents of the bones after DMSA treatment. In conclusion, the present study suggests that the subchronic lead exposure results in severe loss of bone minerals. The overall decrease in the FT-IR band intensity of Pb-exposed bones relative to the control indicates a decrease in the biochemical constituents like proteins and lipids. The increase in the band intensity after treatment with chelating agent DMSA indicates increased biochemical constituents, showing that the subchronic effects of lead can be reversed by DMSA. The amide I bands observed at 1654 cm(-1) in the present study suggest that the protein is dominated by alpha-helical structure.

  19. Biochemical Process Development and Integration | Bioenergy | NREL

    Science.gov (United States)

    Biochemical Process Development and Integration Biochemical Process Development and Integration Our conversion and separation processes to pilot-scale integrated process development and scale up. We also Publications Accounting for all sugar produced during integrated production of ethanol from lignocellulosic

  20. Genotoxic and biochemical effects of Yohimbe after short-term treatment in somatic and germ cells of Swiss Albino Mice

    International Nuclear Information System (INIS)

    Al-Yahya, Abdulaziz A.

    2006-01-01

    Yohimbe was evaluated for its effects on cytological and biochemical toxicity in male Swiss albino mice. Adult male mice were mice were treated with different doses (750, 1500 and 3000 mg yohombe/kg., body weight/day) in form of an aqueous suspension for 7 consecutive days by gavage. The following parameters were evaluated: (i) cytological studies on micronucleus test, (ii) cytological analysis of spermatozoa abnormalities, (iii) Cytogentic analysis of meiotic chromosomes in the tests, (iv) quantification of proteins, ribose nucleic acid (RNA) and deoxyribose nucleic acid (DNA) in hepatic and testicular cells and (v) estimation of malondialdehyde (MDA) and nonprotein sulfhydryl (NP-SH) in hepatic and testicular cells. The treatment caused significant changes in the frequency of micronuclei in the femoral cells and induced spermatozoal abnormalities and testicular chromosomal aberrations. The study on biochemical parameters showed an increase of MDA and depletion of NP-SH, proteins, RNA and DNA in both hepatic and testicular cells. The data elucidated the role of free radical species in cytological and biochemical changes in both somatic and germ cells of Swiss albino mice. The exact mechanism of the genesis of lipid peroxides is not known, however, this might be related to the influence of yohimbine (the principal constituent of yohimbe) to enhance some catecholamines, including norepineprine which possess destructive stimuli on biological systems. It is suggested that, in view of the observed cytological and biochemical effects of yohimbe, it may be subjected to a thorough evaluation of toxicity before making it available for human use. (author)

  1. Simulating the influence of plasma protein on measured receptor affinity in biochemical assays reveals the utility of Schild analysis for estimating compound affinity for plasma proteins.

    Science.gov (United States)

    Blakeley, D; Sykes, D A; Ensor, P; Bertran, E; Aston, P J; Charlton, S J

    2015-11-01

    Plasma protein binding (PPB) influences the free fraction of drug available to bind to its target and is therefore an important consideration in drug discovery. While traditional methods for assessing PPB (e.g. rapid equilibrium dialysis) are suitable for comparing compounds with relatively weak PPB, they are not able to accurately discriminate between highly bound compounds (typically >99.5%). The aim of the present work was to use mathematical modelling to explore the potential utility of receptor binding and cellular functional assays to estimate the affinity of compounds for plasma proteins. Plasma proteins are routinely added to in vitro assays, so a secondary goal was to investigate the effect of plasma proteins on observed ligand-receptor interactions. Using the principle of conservation of mass and the law of mass action, a cubic equation was derived describing the ligand-receptor complex [LR] in the presence of plasma protein at equilibrium. The model demonstrates the profound influence of PPB on in vitro assays and identifies the utility of Schild analysis, which is usually applied to determine receptor-antagonist affinities, for calculating affinity at plasma proteins (termed KP ). We have also extended this analysis to functional effects using operational modelling and demonstrate that these approaches can also be applied to cell-based assay systems. These mathematical models can potentially be used in conjunction with experimental data to estimate drug-plasma protein affinities in the earliest phases of drug discovery programmes. © 2015 The British Pharmacological Society.

  2. Biochemical toxicology of environmental agents

    International Nuclear Information System (INIS)

    Bruin, A. de

    1976-01-01

    A thorough and up-to-date account of the molecular-biological aspects of harmful agents - both chemical and physical - is given. This current treatise is principally intended to serve as an informative reference work for researchers in various areas of the field. In the pursuit of this aim, a devision of the entire field into 42 chapters has been made. Each chapter starts with a short introductory account dealing with the biochemical essentials of the particular subject. Radiation effects are discussed briefly at the end of each treatise. In order to make the treatise useful as a source book, a substantial collection of pertinent literature references is provided which are numbered in order of citation in the text. Initial chapters are devoted to the metabolic fate of the major classes of xenobiotic compounds. Peripheral topics, closely related to metabolism and dealing with modification of xenobiotic-metabolizing ability, as well as interaction phenomena follow (chs. 5-8). Subjects that draw heavily on the practical field of occupational hygiene are dealt with in chapters 9 and 10. The systematic treatment of how chemical and physical agents interact with the various biochemical and enzymatic systems they encounter during their passage through the organism occupies quantitatively the main part of the book (chs. 11-36). Finally, radiation biochemistry is discussed from the viewpoint of its high degree of scientific advancement, and secondly because the type of biochemical changes produced in vivo by X-rays closely parallel those evoked by chemical agents

  3. A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

    DEFF Research Database (Denmark)

    McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A.

    2014-01-01

    in metabolomes between anaerobic and aerobic growth of Escherichia coli. Constraint‐based modeling was utilized to deduce a target list of compounds for downstream method development. An analytical and experimental methodology was developed and tailored to the compound chemistry and growth conditions of interest....... This included the construction of a rapid sampling apparatus for use with anaerobic cultures. The resulting genome‐scale data sets for anaerobic and aerobic growth were validated by comparison to previous small‐scale studies comparing growth of E. coli under the same conditions. The metabolomics data were......‐oxidation pathway for synthesis of fatty acids. This analysis also identified enzyme promiscuity for the pykA gene, that is critical for anaerobic growth, and which has not been previously incorporated into metabolic models of E coli. Biotechnol....

  4. Analysis of Flavonoids in Lotus (Nelumbo nucifera Leaves and Their Antioxidant Activity Using Macroporous Resin Chromatography Coupled with LC-MS/MS and Antioxidant Biochemical Assays

    Directory of Open Access Journals (Sweden)

    Ming-Zhi Zhu

    2015-06-01

    Full Text Available Lotus (Nelumbo nucifera leaves, a traditional Chinese medicinal herb, are rich in flavonoids. In an effort to thoroughly analyze their flavonoid components, macroporous resin chromatography coupled with HPLC-MS/MS was employed to simultaneously enrich and identify flavonoids from lotus leaves. Flavonoids extracted from lotus leaves were selectively enriched in the macroporous resin column, eluted subsequently as fraction II, and successively subjected to analysis with the HPLC-MS/MS and bioactivity assays. Altogether, fourteen flavonoids were identified, four of which were identified from lotus leaves for the first time, including quercetin 3-O-rhamnopyranosyl-(1→2-glucopyranoside, quercetin 3-O-arabinoside, diosmetin 7-O-hexose, and isorhamnetin 3-O-arabino- pyranosyl-(1→2-glucopyranoside. Further bioactivity assays revealed that these flavonoids from lotus leaves possess strong antioxidant activity, and demonstrate very good potential to be explored as food supplements or even pharmaceutical products to improve human health.

  5. Biochemical Markers for Assessing Aquatic Contamination

    Directory of Open Access Journals (Sweden)

    Zdeňka Svobodová

    2007-11-01

    Full Text Available Biochemical markers, specifically enzymes of the first phase of xenobiotic transformation - cytochrome P450 and ethoxyresorufin-O-deethylase (EROD - were used to determine the quantities of persistent organic pollutants (POPs in fish muscle (PCB, HCB, HCH, OCS, DDT. Eight rivers were monitored (Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina; and the River Blanice was used as a control. The indicator species selected was the chub (Leuciscus cephalus L.. There were no significant differences in cytochrome P450 content between the locations monitored. The highest concentration of cytochrome P450 in fish liver was in the Vltava (0.241 nmol mg-1 protein, and the lowest was in the Orlice (0.120 nmol mg-1 protein. Analysis of EROD activity showed a significant difference between the Blanice and the Vltava (P< 0.05, and also between the Orlice and the Vltava (P< 0.01, the Orlice and the Bílina (P< 0.01, and the Orlice and the Ohře (P< 0.05. The highest EROD activity in fish liver was in the Vltava (576.4 pmol min-1 mg-1 protein, and the lowest was in the Orlice (63.05 pmol min-1 mg-1 protein. In individual locations, results of chemical monitoring and values of biochemical markers were compared. A significant correlation (P< 0.05 was found between biochemical markers and OCS, and PCB. Among the tributaries studied those that contaminated the Elbe most were the Vltava and the Bílina. These tributaries should not be considered the main sources of industrial contamination of the River Elbe, because the most important contamination sources were along the river Elbe itself.

  6. CcMP-II, a new hemorrhagic metalloproteinase from Cerastes cerastes snake venom: purification, biochemical characterization and amino acid sequence analysis.

    Science.gov (United States)

    Boukhalfa-Abib, Hinda; Laraba-Djebari, Fatima

    2015-01-01

    Snake venom metalloproteinases (SVMPs) are the most abundant components in snake venoms. They are important in the induction of systemic alterations and local tissue damage after envenomation. CcMP-II, which is a metalloproteinase purified from Cerastes cerastes snake venom, was obtained by a combination of gel filtration, ion-exchange and affinity chromatographies. It was homogeneous on SDS-PAGE, with a molecular mass estimated to 35kDa and presents a pI of 5.6. CcMP-II has an N-terminal sequence of EDRHINLVSVADHRMXTKY, with high levels of homology with those of the members of class P-II of SVMPs, which comprises metalloproteinase and disintegrin-like domains together. This proteinase displayed a fibrinogenolytic and hemorrhagic activities. The proteolytic and hemorrhagic activities of CcMP-II were inhibited by EDTA and 1,10-phenanthroline. However, these activities were not affected by aprotinine and PMSF, suggesting that CcMP-II is a zinc-dependent hemorrhagic metalloproteinase with an α-fibrinogenase activity. The hemorrhagic metalloproteinase CcMP-II was also able to hydrolyze extracellular matrix components, such as type IV collagen and laminin. These results indicate that CcMP-II is implicated in the local and systemic bleeding, contributing thus in the toxicity of C. cerastes venom. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Potential bird dispersers of Psychotria in a area of Atlantic forest on Ilha Grande, RJ, Southeastern Brazil: a biochemical analysis of the fruits

    Directory of Open Access Journals (Sweden)

    E. M. Almeida

    Full Text Available The present study assessed the fruiting pattern, bird foraging behavior, and sugar content of ripe fruits of two sympatric species of Rubiaceae (Psychotria brasiliensis and P. nuda. This study was carried out in an Atlantic forest area on Ilha Grande, RJ, between August 1998 and July 1999. Fruit production occurred year round, with a peak of mature P. brasiliensis fruits in December 1998 and another of P. nuda in February of 1999. Lipaugus lanioides (Cotingidae, Baryphtengus ruficapillus (Momotidae and Saltator similis (Emberizidae made the most frequent foraging visits to fruiting P. brasiliensis, so that L. lanioides and B. ruficapillus removed the fruits with sallying maneuvers while S. similis gleaned the fruits. Lipaugus lanioides was by far the most important consumer, and potentially the main disperser of P. brasiliensis. Birds of this genus are heavy frugivores in the tropical forests and are widely assumed to be important seed dispersers. The fruits were analyzed quantitatively and qualitatively in relation to the amounts of sucrose and starch. Psychotria brasiliensis (the visited species showed the smallest quantity of sucrose and the highest amount of starch. These findings suggest that what may influence the birds' choice of fruit is the proportion of starch in the Psychotria species studied here rather than the carbohydrate composition.

  8. Biochemical markers predictive for bone marrow involvement in systemic mastocytosis

    NARCIS (Netherlands)

    Donker, Marjolein L.; van Doormaal, Jasper J.; van Doormaal, Frederiek F.; Kluin, Philip M.; van der Veer, Eveline; de Monchy, Jan G. R.; Kema, Ido P.; Kluin-Nelemans, Hanneke C.

    Systemic mastocytosis is characterized by bone marrow involvement, which requires a bone marrow biopsy for diagnostic work-up. We questioned whether bone marrow involvement could be predicted using biochemical markers. We selected patients with various symptoms suggestive of indolent systemic

  9. Pheochromocytoma-paraganglioma: Biochemical and genetic diagnosis.

    Science.gov (United States)

    Cano Megías, Marta; Rodriguez Puyol, Diego; Fernández Rodríguez, Loreto; Sención Martinez, Gloria Lisette; Martínez Miguel, Patricia

    Pheochromocytomas and paragangliomas are tumours derived from neural crest cells, which can be diagnosed by biochemical measurement of metanephrine and methoxytyramine. Advances in genetic research have identified many genes involved in the pathogenesis of these tumours, suggesting that up to 35-45% may have an underlying germline mutation. These genes have a singular transcriptional signature and can be grouped into 2 clusters (or groups): cluster 1 (VHL and SHDx), involved in angiogenesis and hypoxia pathways; and cluster 2 (MEN2 and NF1), linked to the kinase signalling pathway. In turn, these genes are associated with a characteristic biochemical phenotype (noradrenergic and adrenergic), and clinical features (location, biological behaviour, age of presentation, etc.) in a large number of cases. Early diagnosis of these tumours, accompanied by a correct genetic diagnosis, should eventually become a priority to enable better treatment, early detection of complications, proper screening of family members and related tumours, as well as an improvement in the overall prognosis of these patients. Copyright © 2016 Sociedad Española de Nefrología. Published by Elsevier España, S.L.U. All rights reserved.

  10. Comparative analysis of distinctive transcriptome profiles with biochemical evidence in bisphenol S- and benzo[a]pyrene-exposed liver tissues of the olive flounder Paralichthys olivaceus.

    Directory of Open Access Journals (Sweden)

    Jee-Hyun Jung

    Full Text Available Flounder is a promising model species for environmental monitoring of coastal regions. To assess the usefulness of liver transcriptome profiling, juvenile olive flounder Paralichthys olivaceus were exposed to two pollutants, bisphenol S (BPS and benzo[a]pyrene (BaP, which have different chemical characteristics and have distinct modes of metabolic action in teleost. Six hours after intraperitoneal injection with BPS (50 mg/kg bw or BaP (20 mg/kg bw, liver transcriptomes were analyzed using the Illumina Hiseq 3000 platform. Interestingly, the transcriptome was highly sensitive and was distinctively expressed in response to each chemical. The primary effect of BPS was significantly increased transcription of egg process and vitellogenesis related genes, including vitellogenins (vtg1, vtg2, zona pellucida sperm-binding proteins (zp3, zp4, and estrogen receptors (erα, erβ, with increases in plasma 17β-estradiol (E2 and vitellogenin (VTG concentrations. Following BaP treatment, detoxification- and biotransformation-related genes such as cyp1a1 and UDP-glucuronosyltransferase (ugt1a1 were significantly increased, with an increase in EROD activity. In both transcriptomes, mRNA expression of genes involved in antioxidant defense systems was increased, while genes involved in innate immunity were decreased upon BPS or BaP exposure with a decrease in complement activity. This study provides useful insight into the chemical-specific hepatic transcriptional response of P. olivaceus and suggests a basis for further studies examining biomarker application of liver transcriptomes for environmental pollution.

  11. A soluble RecN homologue provides means for biochemical and genetic analysis of DNA double-strand break repair in Escherichia coli.

    Science.gov (United States)

    Grove, Jane I; Wood, Stuart R; Briggs, Geoffrey S; Oldham, Neil J; Lloyd, Robert G

    2009-12-03

    RecN is a highly conserved, SMC-like protein in bacteria. It plays an important role in the repair of DNA double-strand breaks and is therefore a key factor in maintaining genome integrity. The insolubility of Escherichia coli RecN has limited efforts to unravel its function. We overcame this limitation by replacing the resident coding sequence with that of Haemophilus influenzae RecN. The heterologous construct expresses Haemophilus RecN from the SOS-inducible E. coli promoter. The hybrid gene is fully functional, promoting survival after I-SceI induced DNA breakage, gamma irradiation or exposure to mitomycin C as effectively as the native gene, indicating that the repair activity is conserved between these two species. H. influenzae RecN is quite soluble, even when expressed at high levels, and is readily purified. Its analysis by ionisation-mass spectrometry, gel filtration and glutaraldehyde crosslinking indicates that it is probably a dimer under physiological conditions, although a higher multimer cannot be excluded. The purified protein displays a weak ATPase activity that is essential for its DNA repair function in vivo. However, no DNA-binding activity was detected, which contrasts with RecN from Bacillus subtilis. RecN proteins from Aquifex aeolicus and Bacteriodes fragilis also proved soluble. Neither binds DNA, but the Aquifex RecN has weak ATPase activity. Our findings support studies indicating that RecN, and the SOS response in general, behave differently in E. coli and B. subtilis. The hybrid recN reported provides new opportunities to study the genetics and biochemistry of how RecN operates in E. coli.

  12. High serum folate is associated with reduced biochemical recurrence after radical prostatectomy: Results from the SEARCH Database

    Directory of Open Access Journals (Sweden)

    Daniel M. Moreira

    2013-06-01

    Full Text Available Introduction To analyze the association between serum levels of folate and risk of biochemical recurrence after radical prostatectomy among men from the Shared Equal Access Regional Cancer Hospital (SEARCH database. Materials and Methods Retrospective analysis of 135 subjects from the SEARCH database treated between 1991-2009 with available preoperative serum folate levels. Patients' characteristics at the time of the surgery were analyzed with ranksum and linear regression. Uni- and multivariable analyses of folate levels (log-transformed and time to biochemical recurrence were performed with Cox proportional hazards. Results The median preoperative folate level was 11.6ng/mL (reference = 1.5-20.0ng/mL. Folate levels were significantly lower among African-American men than Caucasians (P = 0.003. In univariable analysis, higher folate levels were associated with more recent year of surgery (P < 0.001 and lower preoperative PSA (P = 0.003. In univariable analysis, there was a trend towards lower risk of biochemical recurrence among men with high folate levels (HR = 0.61, 95%CI = 0.37-1.03, P = 0.064. After adjustments for patients characteristics' and pre- and post-operative clinical and pathological findings, higher serum levels of folate were independently associated with lower risk for biochemical recurrence (HR = 0.42, 95%CI = 0.20-0.89, P = 0.023. Conclusion In a cohort of men undergoing radical prostatectomy at several VAs across the country, higher serum folate levels were associated with lower PSA and lower risk for biochemical failure. While the source of the folate in the serum in this study is unknown (i.e. diet vs. supplement, these findings, if confirmed, suggest a potential role of folic acid supplementation or increased consumption of folate rich foods to reduce the risk of recurrence.

  13. The effects of Islamic fasting on blood hematological-biochemical parameters

    Directory of Open Access Journals (Sweden)

    Mohamad Reza Sedaghat

    2017-06-01

    Conclusion:This study on healthy subjects suggests that fasting could affect some hematological-biochemical parameters but not all of them. Also, these changes in hematological-biochemical parameters were within the normal range and Ramadan fasting seems to be safe for healthy subjects.

  14. [Biochemical principles of early saturnism recognition].

    Science.gov (United States)

    Tsimakuridze, M P; Mansuradze, E A; Zurashvili, D G; Tsimakuridze, M P

    2009-03-01

    The aim of the work is to determine the major sensitive criteria of biochemical indicators that allow timely discovery of negative influence of lead on organism and assist in early diagnosis of primary stages of saturnism. The workers of Georgian typographies, performing technological processes of letterpress printing were observed. Professional groups having contact with lead aerosols (main group of 66 people) and the workers of the same typography not being in touch with the poison (control group of 24 people) were studied. It was distinguished that, protracted professional contact with lead causes moderate increase of lead, coproporphyrin and DALA in daily urine in most cases; it is more clearly evidenced in the professional groups of lead smelters and lino operators and less clearly among typesetter and printers. Upon the checkup of people, having a direct contact with lead, biochemical analysis of urine should be given a preference, especially the determination of quantitative content of lead and coproporphyrin in urine with the aim of revealing the lead carrier, which is one of the first signals for occupational lookout and medical monitoring of the similar contingent.

  15. Near-infrared Raman spectroscopy for assessing biochemical changes of cervical tissue associated with precarcinogenic transformation.

    Science.gov (United States)

    Duraipandian, Shiyamala; Mo, Jianhua; Zheng, Wei; Huang, Zhiwei

    2014-11-07

    Raman spectroscopy measures the inelastically scattered light from tissue that is capable of identifying native tissue biochemical constituents and their changes associated with disease transformation. This study aims to characterize the Raman spectroscopic properties of cervical tissue associated with the multi-stage progression of cervical precarcinogenic sequence. A rapid-acquisition fiber-optic near-infrared (NIR) Raman diagnostic system was employed for tissue Raman spectral measurements at 785 nm excitation. A total of 68 Raman spectra (23 benign, 29 low-grade squamous intraepithelial lesions (LSIL) and 16 high grade squamous intraepithelial lesions (HSIL)) were measured from 25 cervical tissue biopsy specimens, as confirmed by colposcopy-histopathology. The semi-quantitative biochemical modeling based on the major biochemicals (i.e., DNA, proteins (histone, collagen), lipid (triolein) and carbohydrates (glycogen)) in cervical tissue uncovers the stepwise accumulation of biomolecular changes associated with progressive cervical precarcinogenesis. Multi-class partial least squares-discriminant analysis (PLS-DA) together with leave-one tissue site-out, cross-validation yielded the diagnostic sensitivities of 95.7%, 82.8% and 81.3%; specificities of 100.0%, 92.3% and 88.5%,for discrimination among benign, LSIL and HSIL cervical tissues, respectively. This work suggests that the Raman spectral biomarkers have identified the potential to be used for monitoring the multi-stage cervical precarcinogenesis, forming the foundation of applying NIR Raman spectroscopy for the early diagnosis of cervical precancer in vivo at the molecular level.

  16. Biochemical Abnormalities in Batten's Syndrome

    DEFF Research Database (Denmark)

    Clausen, Jytte Lene; Nielsen, Gunnar Gissel; Jensen, Gunde Egeskov

    1978-01-01

    The present data indicate that a group of ten patients with Batten's syndrome showed reduced activity of erythrocyte glutathione (GSH) peroxidase (Px) (glutathione: H2O2 oxidoreductase, EC 1.1.1.9.) using H2O2 as peroxide donor. Assay of erythrocyte GSHPx using H2O2, cumene hydroperoxide and t......-butyl hydroperoxide as donors also makes it possible biochemically to divide Batten's syndrome into two types: (1) one type with decreased values when H2O2 and cumene hydroperoxide are used, and (2) one type with increased values when t-butyl hydroperoxide is used. Furthermore an increased content of palmitic, oleic...

  17. Slot-waveguide biochemical sensor.

    Science.gov (United States)

    Barrios, Carlos A; Gylfason, Kristinn B; Sánchez, Benito; Griol, Amadeu; Sohlström, H; Holgado, M; Casquel, R

    2007-11-01

    We report an experimental demonstration of an integrated biochemical sensor based on a slot-waveguide microring resonator. The microresonator is fabricated on a Si3N4-SiO2 platform and operates at a wavelength of 1.3 microm. The transmission spectrum of the sensor is measured with different ambient refractive indices ranging from n=1.33 to 1.42. A linear shift of the resonant wavelength with increasing ambient refractive index of 212 nm/refractive index units (RIU) is observed. The sensor detects a minimal refractive index variation of 2x10(-4) RIU.

  18. Three-dimensional structural analysis of the group B polysaccharide of Neisseria meningitidis 6275 by two-dimensional NMR: The polysaccharide is suggested to exist in helical conformations in solution

    Energy Technology Data Exchange (ETDEWEB)

    Yamasaki, Ryohei; Bacon, B. (Univ. of California, San Francisco (USA) Veterans Administration Medical Center, San Francisco, CA (USA))

    1991-01-22

    The solution conformations of the group B polysaccharide of Neisseria meningitidis were analyzed by DQF-COSY and pure absorption 2D NOE NMR with three mixing times. The pyranose ring of the sialic acid residue was found to be in the {sup 2}C{sub 5} conformation. The DQF-COSY analysis indicated that the orientations of H6 and H7 and of H7 and H8 are both gauche. In order to overcome the difficulties in analyzing the NOE data due to the two sets of proton overlaps, molecular modeling of {alpha}-2,8-linked sialic acid oligomers was carried out to investigate possible conformers, and theoretical NOE calculations were performed by using CORMA (complete relaxation matrix analysis). The analysis suggests that the polysaccharide adopts helical structures for which the {phi} (defined by O6-C2-O8-C8) and {psi} (C2-O8-C8-C7) angles are in the following ranges: {phi}-60 to 0{degree}, {psi} 115-175{degree} or {phi} 90-120{degree}, {psi}55-175{degree}. The weak affinity of anti-B antibodies for smaller {alpha}-2,8-linked oligosaccharides may be due to the fact that such oligomers are more flexible and may not form an ordered structure as the poly(sialic acid) does.

  19. Biochemical changes induced by five pathogenic fungi on seeds of ...

    African Journals Online (AJOL)

    Different biochemical analysis were carried out to determine the changes induced by some fungi inoculated on Hibiscus sabdariffa linn seed for 14days. The inoculated fungi are Aspergillus niger Van Tieghem, Aspergillus flavus Link Ex fr, Fusarium oxysporum Schlecht, Penicillium chrysogenum Thom and Penicillium ...

  20. Haematological and biochemical values of 10 green iguanas (Iguana iguana).

    Science.gov (United States)

    Divers, S J; Redmayne, G; Aves, E K

    1996-03-02

    Ten clinically healthy green iguanas (Iguana iguana) imported from South America were examined, and haematological and biochemical measurements were made on samples of blood. This paper describes the methods of blood sampling, handling and laboratory analysis, and presents the results as a set of normal blood ranges for the green iguana.

  1. Xanthine, hypoxanthine and muscle pain. Histochemical and biochemical observations

    Energy Technology Data Exchange (ETDEWEB)

    Isaacs, H; Badenhorst, M; Pickering, A [University of the Witwatersrand, Johannesburg (South Africa). Department of Physiology; Heffron, J J.A. [University of the Witwatersrand, Johannesburg (South Africa). Department of Physiological Chemistry; Berman, L

    1975-06-21

    A suspected case of xanthine oxidase deficiency has been further investigated. The patient complained of arthralgia and myalgia. Further studies included histochemical and ultramicroscopic analysis of muscle sarcoplasmic recticulum, and biochemical studies. High levels of xanthine and hypoxanthine were found, while uric acid was absent in the muscle extracts.

  2. Study on the alteration of bubaline blood biochemical composition ...

    African Journals Online (AJOL)

    Bubaline blood biochemistry as affected by slaughter was the agenda for this work. Blood samples were collected from 30 buffaloes from abattoirs before and at slaughter. After biochemical and statistical analysis (mean was compared with t-test), it was observed that the albumin, lactate dehydrogenase and creatine kinase ...

  3. Evaluation of haematological and plasma biochemical effects of ...

    African Journals Online (AJOL)

    TAYO AJIBADE

    2012-11-01

    Nov 1, 2012 ... African Journal of Biotechnology Vol. 11(88), pp. ... biochemical values revealed significant increase in total protein, albumin and aspartate amino transferase. However ... functions and damages to cellular membrane normally leads to the .... way analysis of variance (ANOVA) for statistical significance was.

  4. Molecular and biochemical studies of some yeast strains

    African Journals Online (AJOL)

    user

    2011-02-21

    Feb 21, 2011 ... Kluyveromyces lactis (Y.9) and Pichia jadinii (Y.10) contained almost double the amount of total amino ... Differences between ... biochemical analysis (total protein profile and total amino acids) were used as tools to select the best yeast strains in Saudi Arabia and Egypt as a rich source of animal protein.

  5. Seasonal variation in the biochemical composition of red seaweed

    Indian Academy of Sciences (India)

    Abstract. The biochemical composition of red seaweeds,Catenella repens was investigated in this present study along with subsequent analysis of relevant physico-chemical variables.In this study, the relationship between the nutritive components of this species and the ambient environmental parameters was established.

  6. Biochemical mechanisms determine the functional compatibility of heterologous genes

    DEFF Research Database (Denmark)

    Porse, Andreas; Schou, Thea S.; Munck, Christian

    2018-01-01

    -gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast...... factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance....

  7. Biochemical analysis of NSs from different tospoviruses.

    Science.gov (United States)

    Hedil, Marcio; de Ronde, Dryas; Kormelink, Richard

    2017-10-15

    Tospoviruses suppress antiviral RNA interference by coding for an RNA silencing suppressor (NSs) protein. Previously, using NSs-containing crude plant and insect cell extracts, the affinity of NSs for double-stranded (ds)RNA molecules was demonstrated by electrophoretic mobility shifts assays (EMSAs). While NSs from tomato spotted wilt virus (TSWV) and groundnut ringspot virus (GRSV) were able to bind small and long dsRNA molecules, the one from tomato yellow ring virus (TYRV), a distinct Asian tospovirus, only bound small dsRNA. Here, using bacterially expressed and purified NSs from GRSV and TYRV, it is shown that they are both able to bind to small and long dsRNA. Binding of siRNAs by NSs revealed two consecutive shifts, i.e. a first shift at low NSs concentrations followed by a second larger one at higher concentrations. When NSs of TSWV resistance inducing (RI) and resistance breaking (RB) isolates were analyzed using extracts from infected plants only a major siRNA shift was observed. In contrast, plant extracts containing the respective transiently expressed NSs proteins showed only the lower shift with NSs RI but no shift with NSs RB . The observed affinity for RNA duplexes, as well as the two-stepwise shift pattern, is discussed in light of NSs as a suppressor of silencing and its importance for tospovirus infection. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  8. Biochemical analysis of NSs from different tospoviruses

    OpenAIRE

    Hedil, Marcio; Ronde, de, Dryas; Kormelink, Richard

    2017-01-01

    Tospoviruses suppress antiviral RNA interference by coding for an RNA silencing suppressor (NSs) protein. Previously, using NSs-containing crude plant and insect cell extracts, the affinity of NSs for double-stranded (ds)RNA molecules was demonstrated by electrophoretic mobility shifts assays (EMSAs). While NSs from tomato spotted wilt virus (TSWV) and groundnut ringspot virus (GRSV) were able to bind small and long dsRNA molecules, the one from tomato yellow ring virus (TYRV), a distinct Asi...

  9. Biochemical analysis of NSs from different tospoviruses

    NARCIS (Netherlands)

    Hedil, Marcio; Ronde, de Dryas; Kormelink, Richard

    2017-01-01

    Tospoviruses suppress antiviral RNA interference by coding for an RNA silencing suppressor (NSs) protein. Previously, using NSs-containing crude plant and insect cell extracts, the affinity of NSs for double-stranded (ds)RNA molecules was demonstrated by electrophoretic mobility shifts assays

  10. MICROMORPHOLOGICALCHARACTERISTICS OF THE LIVER AND BIOCHEMICAL ANALYSES IN THE BLOOD OF RATS TREATED BY GENTAMICIN AND VERAPAMIL

    Directory of Open Access Journals (Sweden)

    Milan Stoiljkovic

    2006-04-01

    Full Text Available The use of antimicrobial drugs, especially gentamicin and calcium blocker verapamil, may cause transitional functional damage of the liver.The aim of this study is to explore micro-morphological changes in the liver and biochemical changes in the blood of rats treated with gentamicin and verapamil. The research included 20 rats divided in experimental and control group. The experimental group (10 rats was treated with gentamicin (100 mg/kg/BW/24h and verapamil (3 mg/kgBW/24 h for 8 days. The control group (10 rats received physiological solution (1 ml/kgBW/24 h at the same time. We analyzed micro-morphological changes in the liver and biochemical parameters in blood: transaminase, bilirubin and glucose.In the control group, there was a normal lobular liver structure. All hepatocytes had polygonal shape, pink cytoplasm and the location of nucleus was central or paracentral. Biochemical blood analysis showed normal level of transaminase (SGOT 29.5 +/- 7.4 iu/l; SGPT 31.7 +/- 6.9 iu/l, total bilirubin (3.1 +/- 0.9 mmol/l and glucose (4.9 +/- 0.9 mmol/l. In the experimental group of animals, hepatocytes of all three zones were equally damaged. In the cytoplasm, we found vacuolar degeneration, reduced condensation of chromatine in nucleus and light nucleoplasm. Hepatocytes of the periportal zone had acidofillic degeneration, picnotic and hiperchromatic nuclei. Biochemical blood analysis showed high level of transaminase (SGOT 46.4 +/- 4.7 iu/l; SGPT 50.8+/-6.1 iu/l, total bilirubin (12.8+/-1.7 mmol/l and glucose (9.3+/-1.8 mmol/l. There is a statistically significant difference in biochemical parameters between the two groups (p < 0,001. The results of our experimental study suggest that there is an obvious correlation between application of gentamicin and verapamil and these changes.

  11. The biochemical anatomy of cortical inhibitory synapses.

    Directory of Open Access Journals (Sweden)

    Elizabeth A Heller

    Full Text Available Classical electron microscopic studies of the mammalian brain revealed two major classes of synapses, distinguished by the presence of a large postsynaptic density (PSD exclusively at type 1, excitatory synapses. Biochemical studies of the PSD have established the paradigm of the synapse as a complex signal-processing machine that controls synaptic plasticity. We report here the results of a proteomic analysis of type 2, inhibitory synaptic complexes isolated by affinity purification from the cerebral cortex. We show that these synaptic complexes contain a variety of neurotransmitter receptors, neural cell-scaffolding and adhesion molecules, but that they are entirely lacking in cell signaling proteins. This fundamental distinction between the functions of type 1 and type 2 synapses in the nervous system has far reaching implications for models of synaptic plasticity, rapid adaptations in neural circuits, and homeostatic mechanisms controlling the balance of excitation and inhibition in the mature brain.

  12. Synthesis of Biochemical Applications on Flow-Based Microfluidic Biochips using Constraint Programming

    DEFF Research Database (Denmark)

    Minhass, Wajid Hassan; Pop, Paul; Madsen, Jan

    2012-01-01

    Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. In this paper we are interested in flow-based biochips, in which the flow of liquid is manipulated using integrated microvalves. By combin...

  13. Strategies to overcome barriers to implementing osteoporosis and fracture prevention guidelines in long-term care: a qualitative analysis of action plans suggested by front line staff in Ontario, Canada.

    Science.gov (United States)

    Alamri, Sultan H; Kennedy, Courtney C; Marr, Sharon; Lohfeld, Lynne; Skidmore, Carly J; Papaioannou, Alexandra

    2015-08-01

    Osteoporosis is a major global health problem, especially among long-term care (LTC) facilities. Despite the availability of effective clinical guidelines to prevent osteoporosis and bone fractures, few LTC homes actually adhere to these practical recommendations. The purpose of this study was to identify barriers to the implementation of evidence-based practices for osteoporosis and fracture prevention in LTC facilities and elicit practical strategies to address these barriers. We performed a qualitative analysis of action plans formulated by Professional Advisory Committee (PAC) teams at 12 LTC homes in the intervention arm of the Vitamin D and Osteoporosis Study (ViDOS) in Ontario, Canada. PAC teams were comprised of medical directors, administrators, directors of care, pharmacists, dietitians, and other staff. Thematic content analysis was performed to identify the key themes emerging from the action plans. LTC teams identified several barriers, including lack of educational information and resources prior to the ViDOS intervention, difficulty obtaining required patient information for fracture risk assessment, and inconsistent prescribing of vitamin D and calcium at the time of admission. The most frequently suggested recommendations was to establish and adhere to standard admission orders regarding vitamin D, calcium, and osteoporosis therapies, improve the use of electronic medical records for osteoporosis and fracture risk assessment, and require bone health as a topic at quarterly reviews and multidisciplinary conferences. This qualitative study identified several important barriers and practical recommendations for improving the implementation of osteoporosis and fracture prevention guidelines in LTC settings.

  14. Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway.

    Directory of Open Access Journals (Sweden)

    Manpreet Randhawa

    Full Text Available Skin chronically exposed to sun results in phenotypic changes referred as photoaging. This aspect of aging has been studied extensively through genomic and proteomic tools. Metabolites, the end product are generated as a result of biochemical reactions are often studied as a culmination of complex interplay of gene and protein expression. In this study, we focused exclusively on the metabolome to study effects from sun-exposed and sun-protected skin sites from 25 human subjects. We generated a highly accurate metabolomic signature for the skin that is exposed to sun. Biochemical pathway analysis from this data set showed that sun-exposed skin resides under high oxidative stress and the chains of reactions to produce these metabolites are inclined toward catabolism rather than anabolism. These catabolic activities persuade the skin cells to generate metabolites through the salvage pathway instead of de novo synthesis pathways. Metabolomic profile suggests catabolic pathways and reactive oxygen species operate in a feed forward fashion to alter the biology of sun exposed skin.

  15. Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma

    Science.gov (United States)

    2013-01-01

    Background Differential gene expression (DGE) analysis is commonly used to reveal the deregulated molecular mechanisms of complex diseases. However, traditional DGE analysis (e.g., the t test or the rank sum test) tests each gene independently without considering interactions between them. Top-ranked differentially regulated genes prioritized by the analysis may not directly relate to the coherent molecular changes underlying complex diseases. Joint analyses of co-expression and DGE have been applied to reveal the deregulated molecular modules underlying complex diseases. Most of these methods consist of separate steps: first to identify gene-gene relationships under the studied phenotype then to integrate them with gene expression changes for prioritizing signature genes, or vice versa. It is warrant a method that can simultaneously consider gene-gene co-expression strength and corresponding expression level changes so that both types of information can be leveraged optimally. Results In this paper, we develop a gene module based method for differential gene expression analysis, named network-based differential gene expression (nDGE) analysis, a one-step integrative process for prioritizing deregulated genes and grouping them into gene modules. We demonstrate that nDGE outperforms existing methods in prioritizing deregulated genes and discovering deregulated gene modules using simulated data sets. When tested on a series of smoker and non-smoker lung adenocarcinoma data sets, we show that top differentially regulated genes identified by the rank sum test in different sets are not consistent while top ranked genes defined by nDGE in different data sets significantly overlap. nDGE results suggest that a differentially regulated gene module, which is enriched for cell cycle related genes and E2F1 targeted genes, plays a role in the molecular differences between smoker and non-smoker lung adenocarcinoma. Conclusions In this paper, we develop nDGE to prioritize

  16. Biochemical nature of Russell Bodies.

    Science.gov (United States)

    Mossuto, Maria Francesca; Ami, Diletta; Anelli, Tiziana; Fagioli, Claudio; Doglia, Silvia Maria; Sitia, Roberto

    2015-07-30

    Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.

  17. Biochemical parameters in chronic renal failure.

    Science.gov (United States)

    Hakim, R M; Lazarus, J M

    1988-03-01

    We analyzed biochemical data derived from 911 patients with renal insufficiency observed at our institution for periods up to 7 years. During early renal failure (RF) (creatinine less than 5 mg/dL), the rate of change of hematocrit, total CO2 (tCO2) and urea per unit change of creatinine was significantly higher than during moderate (creatinine between 5 and 10 mg/dL) or advanced (creatinine greater than 10 mg/dL) RF. For example, the rate of change of hematocrit (%, volume/volume [v/v]) was (mean +/- SEM) -2.15 +/- 0.15% for each 1 mg/dL increase in creatinine in the range of creatinine less than 5 mg/dL, whereas for the range of creatinine greater than 10 mg/dL, the rate of change was only -0.48 +/- 0.06% (P less than 0.001). Similarly, the rate of change of tCO2 was -1.68 +/- 0.09 mEq/L for each 1 mg/dL increment in creatinine concentration during early RF, and -0.19 +/- 0.09 mEq/L per unit increase in creatinine during advanced RF (P less than 0.001). Chloride concentration initially increased as a function of creatinine in early RF, but decreased in advanced RF, whereas the anion gap increased throughout the course of RF. Mean serum phosphate concentration also increased steadily, but remained below the upper range of normal (4.7 mg/dL) during early RF without the use of phosphate binders. These data suggest that different biochemical parameters change at different rates as a function of the severity of renal dysfunction, and that although phosphate retention may occur, hyperphosphatemia is not a hallmark of early RF.

  18. Gluconeogenesis: An ancient biochemical pathway with a new twist

    OpenAIRE

    Miyamoto, Tetsuya; Amrein, Hubert

    2017-01-01

    Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans...

  19. Modeling of uncertainties in biochemical reactions.

    Science.gov (United States)

    Mišković, Ljubiša; Hatzimanikatis, Vassily

    2011-02-01

    Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to

  20. The prevalence of autosomal dominant polycystic kidney disease (ADPKD: A meta-analysis of European literature and prevalence evaluation in the Italian province of Modena suggest that ADPKD is a rare and underdiagnosed condition.

    Directory of Open Access Journals (Sweden)

    Andrea Solazzo

    Full Text Available ADPKD is erroneously perceived as a not rare condition, which is mainly due to the repeated citation of a mistaken interpretation of old epidemiological data, as reported in the Dalgaard's work (1957. Even if ADPKD is not a common condition, the correct prevalence of ADPKD in the general population is uncertain, with a wide range of estimations reported by different authors. In this work, we have performed a meta-analysis of available epidemiological data in the European literature. Furthermore we collected the diagnosis and clinical data of ADPKD in a province in the north of Italy (Modena. We describe the point and predicted prevalence of ADPKD, as well as the main clinical characteristics of ADPKD in this region.We looked at the epidemiological data according to specific parameters and criteria in the Pubmed, CINAHL, Scopus and Web of Science databases. Data were summarized using linear regression analysis. We collected patients' diagnoses in the Province of Modena according to accepted clinical criteria and/or molecular analysis. Predicted prevalence has been calculated through a logistic regression prediction applied to the at-risk population.The average prevalence of ADPKD, as obtained from 8 epidemiological studies of sufficient quality, is 2.7: 10,000 (CI95 = 0.73-4.67. The point prevalence of ADPKD in the province of Modena is 3.63: 10,000 (CI95 = 3.010-3.758. On the basis of the collected pedigrees and identification of the at-risk subjects, the predicted prevalence in the Province of Modena is 4.76: 10,000 (CI 95% = 4.109-4.918.As identified in our study, point prevalence is comparable with the majority of the studies of literature, while predicted prevalence (4.76: 10,000 generally appears higher than in the previous estimates of the literature, with a few exceptions. Thus, this could suggest that undiagnosed ADPKD subjects, as predicted by our approach, could be relevant and will most likely require more clinical attention

  1. Biochemical phenotyping unravels novel metabolic abnormalities and potential biomarkers associated with treatment of GLUT1 deficiency with ketogenic diet.

    Science.gov (United States)

    Cappuccio, Gerarda; Pinelli, Michele; Alagia, Marianna; Donti, Taraka; Day-Salvatore, Debra-Lynn; Veggiotti, Pierangelo; De Giorgis, Valentina; Lunghi, Simona; Vari, Maria Stella; Striano, Pasquale; Brunetti-Pierri, Nicola; Kennedy, Adam D; Elsea, Sarah H

    2017-01-01

    Global metabolomic profiling offers novel opportunities for the discovery of biomarkers and for the elucidation of pathogenic mechanisms that might lead to the development of novel therapies. GLUT1 deficiency syndrome (GLUT1-DS) is an inborn error of metabolism due to reduced function of glucose transporter type 1. Clinical presentation of GLUT1-DS is heterogeneous and the disorder mirrors patients with epilepsy, movement disorders, or any paroxysmal events or unexplained neurological manifestation triggered by exercise or fasting. The diagnostic biochemical hallmark of the disease is a reduced cerebrospinal fluid (CSF)/blood glucose ratio and the only available treatment is ketogenic diet. This study aimed at advancing our understanding of the biochemical perturbations in GLUT1-DS pathogenesis through biochemical phenotyping and the treatment of GLUT1-DS with a ketogenic diet. Metabolomic analysis of three CSF samples from GLUT1-DS patients not on ketogenic diet was feasible inasmuch as CSF sampling was used for diagnosis before to start with ketogenic diet. The analysis of plasma and urine samples obtained from GLUT1-DS patients treated with a ketogenic diet showed alterations in lipid and amino acid profiles. While subtle, these were consistent findings across the patients with GLUT1-DS on ketogenic diet, suggesting impacts on mitochondrial physiology. Moreover, low levels of free carnitine were present suggesting its consumption in GLUT1-DS on ketogenic diet. 3-hydroxybutyrate, 3-hydroxybutyrylcarnitine, 3-methyladipate, and N-acetylglycine were identified as potential biomarkers of GLUT1-DS on ketogenic diet. This is the first study to identify CSF, plasma, and urine metabolites associated with GLUT1-DS, as well as biochemical changes impacted by a ketogenic diet. Potential biomarkers and metabolic insights deserve further investigation.

  2. Analysis on blood biochemical markers for risk factor of alcoholic avascular necrosis of the femoral head%酒精性股骨头坏死风险因素的血液生化指标分析

    Institute of Scientific and Technical Information of China (English)

    张颖; 孙瑞波; 张蕾蕾; 刘又文

    2017-01-01

    [Objective] To explore the risk factors of alcoholic osteonecrosis of the femoral head (ONFH) from blood biochemical markers by comparison of the patients with the healthy persons.[Methods] A retrospective study was conducted on 156 patients with alcoholic femoral head who were admitted to our hospital from March 2012 to October 2015.Of them,16 patients were excluded from this study for tumor or tuberculosis,and the remaining 140 patients were included.Other 140 normal patients were selected as the control from the Physical Examination Center database.One-way analysis of variance and Student's t test was used to screen the biochemical markers with significant difference to the health.The variables beyond the normal range were screened out and defined as potential risk factors.Finally,the risk factors were further evaluated by Stepwise logistic regression.[Results] The CO2CP (OR=19.36,P<0.001),CHOL (OR=66.56,P<0.001),TG (OR=97.66,P<0.001),HDL(OR=74.37,P<0.001) and LDL (OR=22.92,P<0.001) showed statistically significances in the regression equation,which indicated that CO2CP (down),CHOL (rise),TG (high),HDL (down),LDL (rise) were strong risk factors for alcoholic ONFH.[Conclusion]CO2CP (decreased),CHOL (elevated),TG (elevated),HDL (decreased),LDL (elevated) are strong risk factors for the occurrence of alcoholic ONFH.For alcohol abuse individual,blood biochemical tests can be carried out to screen out the risk of alcohol induced osteonecrosis of the femoral head.%[目的]通过比较酒精性股骨头坏死患者和健康人,探索酒精性股骨头坏死风险因素的血液生化指标.[方法]本研究经过回顾性筛选2012年3月~2015年10月本院收治的酒精性股骨头患者156例,其中16例因合并肿瘤或结核被排除,最终纳入140例作为坏死组.自本院检验中心数据库中抽取140例健康人作为对照组.对纳入的各组生化指标进行单因素方差分析并进行Student's t检验,筛选出有统计学意义的

  3. Prevalence of biochemical and immunological abnormalities in ...

    African Journals Online (AJOL)

    Tile prevalence of biochemical and immunological abnormalities was studied in a group of 256 patients with rheumatoid arthritis (104 coloureds, 100 whites and 52 blacks). The most common biochemical abnormalities detected were a reduction in the serum creatinine value (43,4%), raised globulins (39,7%), raised serum ...

  4. FEM effective suggestion of guitar construction

    Directory of Open Access Journals (Sweden)

    Vladimír Dániel

    2006-01-01

    Full Text Available Modal analysis of the whole guitar construction was performed. The results of eigenfrequencies were obtained. Stress in strings affects not only static loading of material, but also shift of eigenfrequencies. From obtained natural frequencies for solved spectrum such frequencies were used which coincides with assumed ribs new positions of ribs were suggested. Other ribs which do not carry out the mechanical function were removed. Also static reaction was evaluated and new position of ribs was adjusted. For final model new eigenfrequencies were computed and compared with previous ones. Significant changes were revealed in low frequencies (bellow 400 Hz where fewer amounts of natural shapes were obtained. Approximately 50% were lost by adding of ribs. For chosen frequencies of equal temperament the harmonic analysis was performed. The analysis proved ability of oscillation for frequencies far of natural frequencies. The final model satisfies the requirement of minimization of static stress in material due to strings and allows very effective oscillation of top the guitar resonance board. In comparison with literature good agreement in amplitude size of front board and amount of modes in appropriate frequencies were achieved. Suggested model even offers higher amount of natural shapes in comparison with literature, namely in high frequencies. From additional comparison of eigenfrequencies and natural shapes the influence of ribs position on natural shapes was approved.

  5. Organic and biochemical synthesis group

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Stable isotopes, because of their unique properties and non-radioactive nature, have great potential for many fields of science and technology. In particular, isotopes of carbon, nitrogen, oxygen, and sulfur (the basic building blocks of all biological molecules) would be widely used in biomedical and environmental research if they were economically available in sufficient quantities and in the required chemical forms. The major objective of our program continues to be stimulation of the widespread utilization of stable isotopes and commercial involvement through development and demonstration of applications which have potential requirements for large quantities of isotopes. Thus, demand will be created which is necessary for large-scale production of stable isotopes and labeled compounds and concomitant low unit costs. The program continues to produce a variety of labeled materials needed for clinical, biomedical, chemical, and environmental applications which serve as effective demonstrations of unique and advantageous utilization of stable isotopes. Future commercial involvement should benefit, and is a consideration in our research and development, from the technology transfer that can readily be made as a result of our organic and biochemical syntheses and also of various techniques involved in applications

  6. Consistent and significant improvement of nighttime voiding frequency (nocturia) with silodosin in men with LUTS suggestive of BPH: pooled analysis of three randomized, placebo-controlled, double-blind phase III studies.

    Science.gov (United States)

    Eisenhardt, Andreas; Schneider, Tim; Cruz, Francisco; Oelke, Matthias

    2014-10-01

    Nocturia is prevalent and bothersome in men with lower urinary tract symptoms suggestive of BPH (LUTS/BPH). α-Adrenoceptor antagonists without subtype selectivity have inconsistently shown significant effects on nocturia in these patients. We explored the effects of the α1A-adrenoceptor subtype-selective antagonist silodosin on nocturia by analyzing three placebo-controlled registration studies. Responses to question 7 of the IPSS questionnaire were analyzed for the entire study population and patients with ≥ 2 voids/night at baseline. Improvement/worsening rates for nocturia were calculated for once-daily silodosin 8 mg and placebo. Silodosin effects on the mean number of nocturnal voids were compared with placebo, and the number of patients in whom nocturia was reduced to silodosin or placebo; 1,266 men (85 %) had ≥ 2 voids/night at baseline. Compared to placebo, more men treated with silodosin reported about nocturia improvement (53.4 vs. 42.8 %, p Silodosin significantly reduced nocturia within each study and pooled cohort compared to placebo (p silodosin and placebo had reductions of ≥ 1 voids/night, respectively (p = 0.0003), and significantly more patients with silodosin had nocturia episodes at study end compared to placebo (29.3 vs. 19.0 %; p = 0.0002). Although a weak impact on nocturia is already known from α-adrenoceptor antagonists without subtype selectivity, the individual placebo-controlled studies and the pooled data analysis showed that the α1A-adrenoceptor subtype-selective antagonist silodosin consistently and significantly improves nocturia in men with LUTS/BPH.

  7. Whole transcriptome analysis of human erythropoietic cells during ontogenesis suggests a role of VEGFA gene as modulator of fetal hemoglobin and pharmacogenomic biomarker of treatment response to hydroxyurea in β-type hemoglobinopathy patients

    DEFF Research Database (Denmark)

    Chondrou, Vasiliki; Kolovos, Petros; Sgourou, Argyro

    2017-01-01

    from whole transcriptome analysis of erythroid cells, isolated from erythroid tissues at various developmental stages in an effort to identify distinct molecular signatures of each erythroid tissue. Results: From our in-depth data analysis, pathway analysis, and text mining, we opted to focus...

  8. Annona crassiflora Mart. fruit pulp effects on biochemical parameters and rat colon carcinogenesis

    Directory of Open Access Journals (Sweden)

    Vinícius Paula Venâncio

    2013-08-01

    Full Text Available A. crassiflora Mart. a Brazilian savannah fruit, is a source of phytochemical compounds that possess a wide array of biological activities, including free radical scavenging. This native fruit proved to potentialize the mutagenic process in previous in vivo investigations. The aim of the present study was to investigate the effects of A. crassiflora Mart. pulp intake on colonic cell proliferation and on the development of Aberrant Crypt Foci (ACF in male Wistar rats. The animals were fed with either a commercial diet or a diet supplemented with A. crassiflora Mart. pulp mixed in 1%, 10% or 20% (w/w for 4 weeks or 20 weeks. The carcinogen 1,2-dimethylhydrazine dihydrochloride (4 doses, 40 mg kg-1 each was used to induce colonic ACF. After euthanasia, the blood, liver and colon samples were collected for biochemical determinations, oxidative stress or ACF development analysis, respectively. Immunohistochemical analyses of the colonic mucosa were performed using antibodies against proliferating cell nuclear antigen (PCNA in normal-appearing colonic crypt and β-catenin in ACF. There was no ACF development in the colon from groups treated with A. crassiflora Mart. pulp. Also, the biochemical and oxidative stress analysis, PCNA labeling and ACF development (number, multiplicity or cellular localization of β-catenin were unchanged as a result of marolo pulp intake. Thus, the present results suggest that A. crassiflora Mart. pulp intake did not exert any protective effect in the colon carcinogenesis induced by DMH in rats.

  9. The emergence of mass spectrometry in biochemical research

    OpenAIRE

    1995-01-01

    The initial steps toward routinely applying mass spectrometry in the biochemical laboratory have been achieved. In the past, mass spectrometry was confined to the realm of small, relatively stable molecules; large or thermally labile molecules did not survive the desorption and ionization processes intact. Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allow for the analysis of both small and large biomolecules through "mild" desorption...

  10. Intermittency route to chaos in a biochemical system.

    Science.gov (United States)

    De la Fuente, I M; Martinez, L; Veguillas, J

    1996-01-01

    The numerical analysis of a glycolytic model performed through the construction of a system of three differential-delay equations reveals a phenomenon of intermittency route to chaos. In our biochemical system, the consideration of delay time variations under constant input flux as well as frequency variations of the periodic substrate input flux allows us, in both cases, to observe a type of transition to chaos different from the 'Feigenbaum route'.

  11. INVESTIGATIONS ON BIOCHEMICAL PURIFICATION OF GROUND WATER FROM HYDROGEN SULFIDE

    Directory of Open Access Journals (Sweden)

    Yu. P. Sedlukho

    2015-01-01

    Full Text Available The paper considers problems and features of biochemical removal of hydrogen sulfide from ground water. The analysis of existing methods for purification of ground water from hydrogen sulfide has been given in the paper. The paper has established shortcomings of physical and chemical purification of ground water. While using aeration methods for removal of hydrogen sulfide formation of colloidal sulfur that gives muddiness and opalescence to water occurs due to partial chemical air oxidation. In addition to this violation of sulfide-carbonate equilibrium taking place in the process of aeration due to desorption of H2S and CO2, often leads to clogging of degasifier nozzles with formed CaCO3 that causes serious operational problems. Chemical methods require relatively large flow of complex reagent facilities, storage facilities and transportation costs.In terms of hydrogen sulfide ground water purification the greatest interest is given to the biochemical method. Factors deterring widespread application of the biochemical method is its insufficient previous investigation and necessity to execute special research in order to determine optimal process parameters while purifying groundwater of a particular water supply source. Biochemical methods for oxidation of sulfur compounds are based on natural biological processes that ensure natural sulfur cycle. S. Vinogradsky has established a two-stage mechanism for oxidation of hydrogen sulfide with sulfur bacteria (Beggiatoa. The first stage presupposes oxidation of hydrogen sulphide to elemental sulfur which is accumulating in the cytoplasm in the form of globules. During the second stage sulfur bacteria begin to oxidize intracellular sulfur to sulfuric acid due to shortage of hydrogen sulfide.The paper provides the results of technological tests of large-scale pilot plants for biochemical purification of groundwater from hydrogen sulfide in semi-industrial conditions. Dependences of water quality

  12. A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.

    Science.gov (United States)

    Fleming, R M T; Maes, C M; Saunders, M A; Ye, Y; Palsson, B Ø

    2012-01-07

    We derive a convex optimization problem on a steady-state nonequilibrium network of biochemical reactions, with the property that energy conservation and the second law of thermodynamics both hold at the problem solution. This suggests a new variational principle for biochemical networks that can be implemented in a computationally tractable manner. We derive the Lagrange dual of the optimization problem and use strong duality to demonstrate that a biochemical analogue of Tellegen's theorem holds at optimality. Each optimal flux is dependent on a free parameter that we relate to an elementary kinetic parameter when mass action kinetics is assumed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Studies on some biochemical parameters in viral hepatitis patients

    International Nuclear Information System (INIS)

    El-Sherbiny, E.M.

    2002-01-01

    The present investigation deals with studying liver amino transferases (ALT. AST). Cholesterol and triglycerides. As well as testosterone and protection hormones in blood of Egyptian men infected with hepatitis C virus.hepatitis B virus and mixed B and C viruses. These biochemical parameters were evaluated to be used in diagnosis and prognosis of viral hepatitis. Which considered the most important health problem in Egypt and developing countries. Biochemical analysis were performed using spectrophotometric and radioimmunoassay techniques. All data will be subjected to statistical analysis in order to detect the most suitable biochemical analysis that can be used as specific tests for early diagnosis of viral hepatitis and to detect the parameters that show abnormalities among the different groups of infected patients. The data revealed that AST and ALT levels were increased in all patient groups. Concerning the level of triglycerides, it was increased only in the group of mixed viral hepatitis B and C, while cholesterol showed non-significant changes in all viral hepatitis groups. The sex hormone testosterone was decreased in all infected patients while the prolactin level was increased only in case of patients infected with mixed B and C viruses. However, these abnormal values in such sex hormones play a serious role in male sterility

  14. Biochemical thermodynamics: applications of Mathematica.

    Science.gov (United States)

    Alberty, Robert A

    2006-01-01

    reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

  15. Morphological, physiological and biochemical studies on Pyricularia ...

    African Journals Online (AJOL)

    SARAH

    2014-02-28

    Feb 28, 2014 ... compounds seem to reflect inherent biochemical and physiological differences among P. grisea isolates .... solutions for imaging and microscopy, soft image system .... characteristics among 12 P. grisea isolates from rice were.

  16. Biochemical changes in blood caused by radioisotopes

    International Nuclear Information System (INIS)

    Zapol'skaya, N.A.; Fedorova, A.V.

    1975-01-01

    The changes were studied occurring in some biochemical indicators in blood at chronic peroral administration of strontium-90, cesium-137 and iodine-131 in amounts resulting in accumulation of commensurable doses in critical organs corresponding to each isotope

  17. Biochemical and kinetic characterization of geranylgeraniol 18 ...

    African Journals Online (AJOL)

    Suchart

    2015-07-22

    Jul 22, 2015 ... biochemical characterization of GGOH 18-hydroxylase activity in the microsomal fraction from C. .... method as previously described (Chanama et al., 2009). Briefly, 30 g of frozen ..... Catalytic properties of the plant cytochrome.

  18. Short Report Biochemical derangements prior to emergency ...

    African Journals Online (AJOL)

    MMJ VOL 29 (1): March 2017. Biochemical derangements prior to emergency laparotomy at QECH 55. Malawi Medical Journal 29 (1): March 2017 ... Venepuncture was performed preoperatively for urgent cases, defined as those requiring.

  19. A Program on Biochemical and Biomedical Engineering.

    Science.gov (United States)

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  20. Ultrasonographic findings of early abortion: suggested predictors

    International Nuclear Information System (INIS)

    Jun, Soon Ae; Ahn, Myoung Ock; Cha, Kwang Yul; Lee, Young Doo

    1992-01-01

    To investigate predictable ultrasonographic findings of early abortion. To investigate objective rules for the screening of abortion. Ultrasonographic examination of 111 early pregnancies between the sixth and ninth week in women who had regular 28 day menstrual cycles was performed. Ultrasonographic measurements of the gestational sac, crown rump length and fetal heart rate were performed using a linear array real time transducer with doppler ultrasonogram. All measurements of 17 early abortions were compared to those of 94 normal pregnancies. Most of early aborted pregnancies were classified correctly by discriminant analysis with G-SAC and CRL (G-SAC=0.5 CRL + 15, sensitivity 76.5%, specificity 96.8%). With the addition of FHR, 94.1% of early abortions could be predicted. In conclusion, ultrasonographic findings of early intrauterine growth retardation, small gestational sac and bradycardia can be predictable signs suggestive of poor prognosis of early pregnancies

  1. [Biochemical diagnostics of fatal opium intoxication].

    Science.gov (United States)

    Papyshev, I P; Astashkina, O G; Tuchik, E S; Nikolaev, B S; Cherniaev, A L

    2013-01-01

    Biochemical diagnostics of fatal opium intoxication remains a topical problem in forensic medical science and practice. We investigated materials obtained in the course of forensic medical expertise of the cases of fatal opium intoxication. The study revealed significant differences between myoglobin levels in blood, urine, myocardium, and skeletal muscles. The proposed approach to biochemical diagnostics of fatal opium intoxication enhances the accuracy and the level of evidence of expert conclusions.

  2. Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer’s disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids

    Directory of Open Access Journals (Sweden)

    Bautista-Aguilera OM

    2014-10-01

    Full Text Available Oscar M Bautista-Aguilera,1,* Gerard Esteban,2,* Mourad Chioua,1 Katarina Nikolic,3 Danica Agbaba,3 Ignacio Moraleda,4 Isabel Iriepa,4 Elena Soriano,5 Abdelouahid Samadi,1 Mercedes Unzeta,2 José Marco-Contelles1 1Laboratory of Medicinal Chemistry (Institute of General Organic Chemistry [IQOG], National Research Council [CSIC], Madrid, Spain; 2Department of Biochemistry and Molecular Biology, Institute of Neurosciences, Autonomous Barcelona University, Barcelona, Spain; 3Institute of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia; 4Department of Organic Chemistry, Faculty of Pharmacy, University of Alcalá, Ctra Barcelona, Alcalá de Henares, Spain; 5Synthesis, and Structure of Organic Compounds (SEPCO (IQOG, CSIC, Madrid, Spain *These authors have equally contributed to this work Abstract: The design, synthesis, and biochemical evaluation of donepezil-pyridyl hybrids (DPHs as multipotent cholinesterase (ChE and monoamine oxidase (MAO inhibitors for the potential treatment of Alzheimer’s disease (AD is reported. The 3D-quantitative structure-activity relationship study was used to define 3D-pharmacophores for inhibition of MAO A/B, acetylcholinesterase (AChE, and butyrylcholinesterase (BuChE enzymes and to design DPHs as novel multi-target drug candidates with potential impact in the therapy of AD. DPH14 (­Electrophorus electricus AChE [EeAChE]: half maximal inhibitory concentration [IC50] =1.1±0.3 nM; equine butyrylcholinesterase [eqBuChE]: IC50 =600±80 nM was 318-fold more potent for the inhibition of AChE, and 1.3-fold less potent for the inhibition of BuChE than the reference compound ASS234. DPH14 is a potent human recombinant BuChE (hBuChE inhibitor, in the same range as DPH12 or DPH16, but 13.1-fold less potent than DPH15 for the inhibition of human recombinant AChE (hAChE. Compared with donepezil, DPH14 is almost equipotent for the inhibition of hAChE, and 8.8-fold more potent for h

  3. Serum antioxidant capacity, biochemical profile and body composition of breast cancer survivors in a randomized Mediterranean dietary intervention study.

    Science.gov (United States)

    Skouroliakou, Maria; Grosomanidis, D; Massara, P; Kostara, C; Papandreou, P; Ntountaniotis, D; Xepapadakis, G

    2017-06-20

    Increasing evidence suggests that Mediterranean Diet (MD) is correlated with reduced risk of breast cancer (BC) and cancer mortality, since it modifies patients' serum antioxidant capacity, body composition and biochemical parameters. The aim of the study was to investigate whether a dietary intervention based on MD has a beneficial effect on these factors. In this intervention study, seventy female BC survivors were randomly assigned to (1) the intervention group (personalized dietary intervention based on MD) and (2) the control group (received the updated American Cancer Society Guidelines on Nutrition and Physical Activity for Cancer Prevention and ad libitum diet). Both groups were assessed twice [beginning, end of study (after 6 months)] regarding their anthropometric and biochemical parameters, serum vitamin C, vitamin A, a-tocopherol and CoQ10 levels, dietary intake and adherence to MD. An additional intermediate analysis was conducted on participants' body composition and biochemical profile. Concerning the intervention group, body weight, body fat mass, waist circumference, body mass index as well as HDL-cholesterol were significantly decreased (P body weight, body fat mass and serum total cholesterol rose (P body composition, adherence to MD and glycemic profile of postmenopausal BC survivors.

  4. Pin count-aware biochemical application compilation for mVLSI biochips

    DEFF Research Database (Denmark)

    Lander Raagaard, Michael; Pop, Paul

    2015-01-01

    Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. In this paper we are interested in flow-based biochips, in which the fluidic flow manipulated using integrated microvalves, which are cont...... a biochemical application. We focus on the compilation task, where the strategy is to delay operations, without missing their deadlines, such that the sharing of control signals is maximized. The evaluation shows a significant reduction in the number of control pins required....

  5. Re-analysis of clinical and treatment related prognostic factors on outcome using biochemical control as an end-point in patients with prostate cancer treated with external beam irradiation

    International Nuclear Information System (INIS)

    Ziaja, Ellen L.; Horwitz, Eric M.; Vicini, Frank A.; Dmuchowski, Carl F.; Brabbins, Donald S.; Gustafson, Gary S.; Hollander, Jay; Matter, Richard C.; Stromberg, Jannifer S.; Martinez, Alvaro A.

    1996-01-01

    Purpose: Prostate specific antigen (PSA) has been established as the most important prognostic factor for prostate cancer. We reviewed our experience treating patients with clinically localized prostate cancer with external beam irradiation (RT) to evaluate if previously defined clinical and treatment related prognostic factors remain valid when biochemical control was used as an end-point to evaluate results. Methods and Materials: Between 1/87 and 12/91, 480 patients with clinically localized prostate cancer received external beam irradiation (RT) using localized prostate fields at William Beaumont Hospital. The median dose to the prostate was 66.6 Gy (range 58 - 70.4 Gy) using a 4 field or arc technique. Pre- and post-treatment serum PSA levels were recorded. Biochemical control was defined as PSA nadir ≤ 1.5 ng/ml within 1 year of treatment completion. After achieving nadir, if 2 consecutive increases of PSA were noted, the patient was scored a failure at the time of the first increase. Patients (pts) were divided into 3 groups according to total number of days on treatment: ≤ 49 days (≤ 7 weeks)- 21 pts; 50-63 days (8-9 weeks)- 429 pts; and ≥ 64 days (≥ 9 weeks)- 15 pts. Patients were also divided into groups with respect to the method of diagnosis: TURP (81 pts), or other means (399 pts). Patients were further divided into 2 groups: 1) if they had ever had a pre-treatment TURP (170 pts) or 2) if they had not (310 pts). Patients were divided into 2 groups according to boost technique: bilateral arcs (459 pts) or 4 field box (21 pts). Patients were also divided into groups according to total RT dose: ≤ 70 Gy (421 pts) or > 70 Gy (59 pts). Patients were further subdivided into 3 dose groups: 70 Gy (59 pts). Results: Median follow-up is 48 months (range 3 - 112 months). No statistically significant difference in rates of biochemical control were noted for treatment time, overall time (date of biopsy to completion of RT), or treatment time divided into

  6. Biochemical study of leaf browning in minimally processed leaves of lettuce (Lactuca sativa L. var. acephala).

    Science.gov (United States)

    Degl'Innocenti, E; Guidi, L; Pardossi, A; Tognoni, F

    2005-12-28

    A series of biochemical parameters, including the concentration of total ascorbic acid (ASA(tot)) and the activities of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), and peroxidases (PODs), was investigated during cold storage (72 h at 4 degrees C in the dark) in fresh-cut (minimally processed) leaves of two lettuce (Lactuca sativa L. var. acephala) cultivars differing in the susceptibility to tissue browning: Green Salade Bowl (GSB), susceptible, and Red Salade Bowl (RSB), resistant. The two cultivars showed differences also at the biochemical level. The content in ASA(tot) increased in RSB, as a consequence of increased DHA concentration; conversely, ASA(tot) diminished in GSB, in which ASA was not detectable after 72 h of storage, thus suggesting a disappearance of ascorbate (both ASA and DHA) into nonactive forms. The antioxidant capacity (as determined by using FRAP analysis) decreased significantly during storage in RSB, while a strong increase was observed in GSB. PAL activity increased soon after processing reaching a maximum by 3 h, then it declined to a relatively constant value in RSB, while in GSB it showed a tendency to decrease in the first few hours from harvest and processing. POD activity, at least for chlorogenic acid, increased significantly during storage only in GSB.

  7. Biochemical characterization of the plasma membrane H+ - ATPase from red beet (Beta vulgaris) hypocotyl tissue

    International Nuclear Information System (INIS)

    Oleski, N.A.

    1986-01-01

    Several biochemical techniques including selective solubilization followed by gel filtration or various types of affinity chromatography, and antibody production were employed in an attempt to purify the plasma membrane H + - ATPase from red beet hypocotyl tissue. While the enzyme could not be purified using any of these methods, it was possible to successfully conduct a more detailed biochemical analysis of the H + - ATPase. The molecular weight and isoelectric point of the enzyme were determined using N,N'dicyclohexylcarbodiimide (DCCD) and a H + - ATPase antibody. When plasma membrane vesicles were incubated with 20 μM [ 14 C]-DCCD at 0 C, a single 97,000 dalton protein was apparent on a fluorograph. A close correlation between [ 14 C]-DCCD labelling of the 97,000 dalton protein and the extent of ATPase inhibition over a range of DCCD concentrations suggests that this 97,000 dalton protein is a component of the plasma membrane H + - ATPase. An antibody raised against the plasma membrane H + - ATPase of Neurospora crassa cross-reacted with the 97,000 dalton DCCD-binding protein, further supporting the identity of this protein. Immunoblots of two dimensional gels of red beet plasma membrane vesicles indicated the isoelectric point of the enzyme to be pH 6.5

  8. Conformational analysis of gramicidin-gramicidin interactions at the air/water interface suggests that gramicidin aggregates into tube-like structures similar as found in the gramicidin-induced hexagonal HII phase

    NARCIS (Netherlands)

    Brasserua, R.; Killian, J.A.; Kruijff, B. de; Ruysschaert, J.M.

    1987-01-01

    The energetics of interaction and the type of aggregate structure in lateral assemblies of up to five gramicidin molecules in the β6.3 helical conformation at the air/water interface was calculated using conformational analysis procedures. It was found that within the aggregate two types of

  9. Polyphenol Oxidase as a Biochemical Seed Defense Mechanism

    Directory of Open Access Journals (Sweden)

    E. Patrick Fuerst

    2014-12-01

    Full Text Available Seed dormancy and resistance to decay are fundamental survival strategies, which allow a population of seeds to germinate over long periods of time. Seeds have physical, chemical, and biological defense mechanisms that protect their food reserves from decay-inducing organisms and herbivores. Here, we hypothesize that seeds also possess enzyme-based biochemical defenses, based on induction of the plant defense enzyme, polyphenol oxidase (PPO, when wild oat (Avena fatua L. caryopses and seeds were challenged with seed-decaying Fusarium fungi. These studies suggest that dormant seeds are capable of mounting a defense response to pathogens. The pathogen-induced PPO activity from wild oat was attributed to a soluble isoform of the enzyme that appeared to result, at least in part, from proteolytic activation of a latent PPO isoform. PPO activity was also induced in wild oat hulls (lemma and palea, non-living tissues that cover and protect the caryopsis. These results are consistent with the hypothesis that seeds possess inducible enzyme-based biochemical defenses arrayed on the exterior of seeds and these defenses represent a fundamental mechanism of seed survival and longevity in the soil. Enzyme-based biochemical defenses may have broader implications since they may apply to other defense enzymes as well as to a diversity of plant species and ecosystems.

  10. Economic evaluation of diagnostic localization following biochemical prostate cancer recurrence.

    Science.gov (United States)

    Barocas, Daniel A; Bensink, Mark E; Berry, Kristin; Musa, Zahra; Bodnar, Carolyn; Dann, Robert; Ramsey, Scott D

    2014-10-01

    The aim of this study was to assess potential cost-effectiveness of using a prostate cancer specific functional imaging technology capable of identifying residual localized disease versus small volume metastatic disease for asymptomatic men with low but detectable prostate specific antigen (PSA) elevation following radical prostatectomy. Markov modeling was used to estimate the incremental impact on healthcare system costs (2012 USD) and quality-adjusted life-years (QALYs) of two alternative strategies: (i) using the new diagnostic to guide therapy versus (ii) current usual care-using a combination of computed tomography, magnetic resonance imaging, and bone scan to guide therapy. Costs were based on estimates from literature and Medicare reimbursement. Prostate cancer progression, survival, utilities, and background risk of all-cause mortality were obtained from literature. Base-case diagnostic sensitivity (75 percent), specificity (90 percent), and cost (USD 2,500) were provided by our industry partner GE Healthcare. The new diagnostic strategy provided an average gain of 1.83 (95 percent uncertainty interval [UI]: 1.24-2.64) QALYs with added costs of USD 15,595 (95 percent UI: USD -6,330-44,402) over 35 years. The resulting incremental cost-effectiveness ratio was USD 8,516/QALY (95 percent UI: USD -2,947-22,372). RESULTS were most influenced by the utility discounting rate and test performance characteristics; however, the new diagnostic provided clinical benefits over a wide range of sensitivity and specificity. This analysis suggests a diagnostic technology capable of identifying whether men with biochemical recurrence after radical prostatectomy have localized versus metastatic disease would be a cost-effective alternative to current standard work-up. The results support additional investment in development and validation of such a diagnostic.

  11. Industrial dust sulphate and its effects on biochemical and morphological characteristics of Morus (Morus alba) plant in NCR Delhi.

    Science.gov (United States)

    Gupta, Gyan Prakash; Singh, Sudha; Kumar, Bablu; Kulshrestha, U C

    2015-03-01

    Abundance of CaCO3 rich soil dust is a typical feature of atmospheric environment in the Indian region. During prevailing dry weather conditions, dustfall is deposited onto the foliar surfaces of plant affecting their morphology, stomata and the levels of biochemical constituents. This study reports the chemical characteristics of dustfall, its effect on foliar morphology and biochemical constituents of a medicinal plant (Morus alba) at two sites which are differentiated on the basis of landuse pattern, viz., (i) residential, Jawaharlal Nehru University (JNU), and (ii) industrial, Sahibabad (SB), located in the National Capital Region (NCR) of Delhi. Dustfall was characterized for major anions (F(-), Cl(-), NO3 (-) and SO4 (--)) and cations (Na(+), NH4 (+), K(+), Mg(++) and Ca(++)). Biochemical parameters such as chlorophyll a, chlorophyll b, total chlorophyll, carotenoid, proline and ascorbic acid were determined in foliar samples. The results showed that the dustfall fluxes of all the major ions were found to be higher at the industrial site (SB) as compared to the residential site (JNU). Foliar analysis revealed that the levels of biochemical parameters were more affected at SB site due to higher levels of dust SO4 (--) contributed by various anthropogenic sources resulting in more stressful conditions affecting the biochemistry of the plant. The possible entry pathways for dust SO4 (--) into foliar cells are also discussed in the paper. It was noticed that the deposition of urban dust was responsible for the damage of trichome, epidermis, cuticle and stomatal guard cells significantly affecting foliar morphology. SB exhibited more damage to these morphological parts suggesting that industrial dust is harmful to the plants.

  12. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

    Directory of Open Access Journals (Sweden)

    Daigle Bernie J

    2012-05-01

    . Conclusions This work provides a novel, accelerated version of a likelihood-based parameter estimation method that can be readily applied to stochastic biochemical systems. In addition, our results suggest opportunities for added efficiency improvements that will further enhance our ability to mechanistically simulate biological processes.

  13. Biochemical and biomechanical characterisation of equine cervical facet joint cartilage.

    Science.gov (United States)

    O'Leary, S A; White, J L; Hu, J C; Athanasiou, K A

    2018-04-15

    The equine cervical facet joint is a site of significant pathology. Located bilaterally on the dorsal spine, these diarthrodial joints work in conjunction with the intervertebral disc to facilitate appropriate spinal motion. Despite the high prevalence of pathology in this joint, the facet joint is understudied and thus lacking in viable treatment options. The goal of this study was to characterise equine facet joint cartilage and provide a comprehensive database describing the morphological, histological, biochemical and biomechanical properties of this tissue. Descriptive cadaver studies. A total of 132 facet joint surfaces were harvested from the cervical spines of six skeletally mature horses (11 surfaces per animal) for compiling biomechanical and biochemical properties of hyaline cartilage of the equine cervical facet joints. Gross morphometric measurements and histological staining were performed on facet joint cartilage. Creep indentation and uniaxial strain-to-failure testing were used to determine the biomechanical compressive and tensile properties. Biochemical assays included quantification of total collagen, sulfated glycosaminoglycan and DNA content. The facet joint surfaces were ovoid in shape with a flat articular surface. Histological analyses highlighted structures akin to articular cartilage of other synovial joints. In general, biomechanical and biochemical properties did not differ significantly between the inferior and superior joint surfaces as well as among spinal levels. Interestingly, compressive and tensile properties of cervical facet articular cartilage were lower than those of articular cartilage from other previously characterised equine joints. Removal of the superficial zone reduced the tissue's tensile strength, suggesting that this zone is important for the tensile integrity of the tissue. Facet surfaces were sampled at a single, central location and do not capture the potential topographic variation in cartilage properties. This

  14. Craniometaphyseal dysplasia with obvious biochemical abnormality and rickets-like features.

    Science.gov (United States)

    Wu, Bo; Jiang, Yan; Wang, Ou; Li, Mei; Xing, Xiao-Ping; Xia, Wei-Bo

    2016-05-01

    Craniometaphyseal dysplasia (CMD) is a rare genetic disorder that is characterized by progressive sclerosis of the craniofacial bones and metaphyseal widening of long bones, and biochemical indexes were mostly normal. To further the understanding of the disease from a biochemical perspective, we reported a CMD case with obviously abnormal biochemical indexes. A 1-year-old boy was referred to our clinic. Biochemical test showed obviously increased alkaline phosphatase (ALP) and parathyroid hormone (PTH), mild hypocalcemia and hypophosphatemia. Moreover, significant elevated receptor activator of nuclear factor kappa-B ligand (RANKL) level, but normal β-C-terminal telopeptide of type I collagen (β-CTX) concentration were revealed. He was initially suspected of rickets, because the radiological examination also showed broadened epiphysis in his long bones. Supplementation with calcium and calcitriol alleviated biochemical abnormality. However, the patient gradually developed osteosclerosis which was inconformity with rickets. Considering that he was also presented with facial paralysis and nasal obstruction symptom, the diagnosis of craniometaphyseal dysplasia was suspected, and then was confirmed by the mutation analysis of ANKH of the proband and his family, which showed a de novo heterozygous mutation (C1124-1126delCCT) on exon 9. Our study revealed that obvious biochemical abnormality and rickets-like features might present as uncommon characteristics in CMD patients, and the calcium and calcitriol supplementation could alleviate biochemical abnormalities. Furthermore, although early osteoclast differentiation factor was excited in CMD patient, activity of osteoclast was still inert. Copyright © 2016. Published by Elsevier B.V.

  15. Causal correlation of foliar biochemical concentrations with AVIRIS spectra using forced entry linear regression

    Science.gov (United States)

    Dawson, Terence P.; Curran, Paul J.; Kupiec, John A.

    1995-01-01

    link between wavelengths chosen by stepwise regression and the biochemical of interest, and this in turn has cast doubts on the use of imaging spectrometry for the estimation of foliar biochemical concentrations at sites distant from the training sites. To investigate this problem, an analysis was conducted on the variation in canopy biochemical concentrations and reflectance spectra using forced entry linear regression.

  16. Phytochemical, Toxicological, Biochemical and Haematological ...

    African Journals Online (AJOL)

    The avocado tree belongs to the family lauraceae and is classified as Persea americana. The analysis of the fruits extract revealed the presence of considerable amounts of vitamins A, B2, C, K, folic acid, lutein, zeaxanthin, coenzyme Q10 and beta-carotene. When administered to wistar rats for acute toxicity studies, the ...

  17. Suggestibility and negative priming: two replication studies.

    Science.gov (United States)

    David, Daniel; Brown, Richard J

    2002-07-01

    Research suggests that inhibiting the effect of irrelevant stimuli on subsequent thought and action (cognitive inhibition) may be an important component of suggestibility. Two small correlation studies were conducted to address the relationship between different aspects of suggestibility and individual differences in cognitive inhibition, operationalized as the degree of negative priming generated by to-be-ignored stimuli in a semantic categorization task. The first study found significant positive correlations between negative priming, hypnotic suggestibility, and creative imagination; a significant negative correlation was obtained between negative priming and interrogative suggestibility, demonstrating the discriminant validity of the study results. The second study replicated the correlation between negative priming and hypnotic suggestibility, using a different suggestibility measurement procedure that assessed subjective experience and hypnotic involuntariness as well as objective responses to suggestions. These studies support the notion that the ability to engage in cognitive inhibition may be an important component of hypnotic responsivity and maybe of other forms of suggestibility.

  18. Scrutiny of the ASTRO consensus definition of biochemical failure in irradiated prostate cancer patients demonstrates its usefulness and robustness

    International Nuclear Information System (INIS)

    Hanlon, Alexandra L.; Hanks, Gerald E.

    2000-01-01

    immediately following treatment under the ASTRO definition. Modifying the censoring pattern had little effect on failure estimates in any patient group, regardless of definition used. The exclusion of patients with slow prostate-specific antigen (PSA) doubling time did not result in biochemical estimates that differed significantly from those for all patients. The analysis of patients with agreement in failure status continued to demonstrate significant differences in estimates between the two definitions, and thus differences may be attributed to the specification of time to failure. For all patient groups, hazard rates were dependent upon failure definition: under the FCCC failure definition, patients were at constant risk of failure over the observation period; under the ASTRO failure definition, patients were at risk of failure during the first 4 years following treatment, and then at low risk of failure beyond 5 years. Conclusions: Both FCCC and ASTRO failure definitions were robust to modifications in censoring and the inclusion of patients with long doubling times. The ASTRO failure definition was robust to specifying the time to failure at first rise, as opposed to midway between nadir and first rise. Similarities in estimates for all patients versus patients with agreeing failure status suggest that differences in failure definition lie in the specification of time to failure. The ASTRO definition of failure is more appropriate because it does not impose an empirical failure marker but is based on the initiation of biochemical rise. The use of the ASTRO consensus definition demonstrated little risk of biochemical failure 4 years beyond treatment. The ASTRO failure definition should be adopted in all research involving biochemical failure analysis of men treated with radiation therapy

  19. Biochemical composition of amniotic fluid in normal puppies at term of pregnancy: preliminary data

    Directory of Open Access Journals (Sweden)

    Barbara Bolis

    2017-05-01

    Full Text Available The full knowledge of the normal fetal fluids composition could be useful in the dog for the better management of newborns. The aim of the present study was to define the biochemical composition of amniotic fluid of puppies born by elective Caesarean section (CS at term of pregnancy. The study enrolled 24 purebred bitches, classified into small size (20kg. All the bitches were healthy and clinically monitored from mating until parturition. For all the bitches an elective CS at term of pregnancy was performed [1]. For each puppy, the amniotic fluid was collected, immediately centrifuged and frozen at – 20° C until analysis for ALB, AMY, TB, CHOL, CK, ALP, GGT, AST, ALT, LDH, Mg, Ca, K, Na, Trig, BUN, Glc, TP, CREA, LIP, Cl, and GLOB. Data were analyzed by ANCOVA to verify the possible effects of parity, breed body size and newborn gender on amniotic biochemical composition. A total of 69 amniotic fluid samples were collected. The amniotic mean±SD and min-max values for each parameter were defined. LDH (p<0.01 and CK activity (p<0.05, as well as Glc concentrations (p<0.0001 were negatively influenced by the parity. AMY activity was significantly (p<0.05 higher in large sized (44.2±20.87 U/L respect to small sized dogs (30.3±19.89 U/L, while lower (p<0.05 CHOL amniotic concentrations were found in small sized (3.0±2.71 mg/dl as compared to large sized (3.9±2.93 mg/dl dogs. Gender of the newborn did not influence the amniotic biochemical composition. The preliminary results of this study showed some similarities as well as some differences concerning the biochemical composition of the amniotic fluid in dogs at term of pregnancy if compared to data reported for the cat [2]. Furthermore, the results suggested that, in dogs, some amniotic parameters could be influenced by breed body size and by parity.

  20. Relationship between obesity and biochemical markers in Brazilian adolescents

    Directory of Open Access Journals (Sweden)

    Alexandre Romero

    2014-03-01

    The aim of this study was to describe the prevalence of biochemical markers and associate with obesity in Brazilian adolescents enrolled in public schools in a rural area. The sample consisted of 199 adolescents between 10 to 14 years old from Piracicaba, Brazil. The obesity was measured by body mass index (BMI and according to the World Health Organization curves. We collected blood for biochemical markers analysis (total cholesterol, high density lipoprotein, low density lipoprotein, triacylglycerol, insulin and glycemia. Mann Whitney test was used to compare continuous variables between sexes. Chi-square test was used to compare proportions. To investigate the association between the independent variables and biochemical markers a multiple logistic regression model was performed. Among 199 adolescents, 23.1% was obese and 65.8% were insufficiently active. A high prevalence of dyslipidemia (71.4% was observed, whereas the low levels of high density lipoprotein (40.7% were the most prevalent. An association between obesity and undesirable values for high density lipoprotein, triacylglycerol and insulin resistance was found. Obese adolescents were less likely to present a desirable value for high density lipoprotein. It is understood that obesity is detrimental to metabolic profile and should be prevented and treated even in adolescence.

  1. Considerations on the biochemical composition of some freshwater zooplankton species.

    Directory of Open Access Journals (Sweden)

    Nicoletta RICCARDI

    1999-02-01

    Full Text Available The mean elemental (C, H, N and biochemical composition (lipids, carbohydrates and proteins of some abundant crustacean zooplankton species of Italian insubric lakes has been estimated by the analysis of samples collected at different seasons from various environments (Lake Maggiore, Lake Varese, Lake Comabbio, Lake Monate. From each sample an adequate number of specimens of each abundant species was sorted and analyzed by a CHN elemental analyzer. The percentage of lipids, carbohydrates and proteins and the calorific content were calculated from the elemental composition according to Gnaiger & Bitterlich (1984. Inter- and intraspecific variability of biochemical composition was quite high, while elemental composition and calorific content were less variable. An estimate of the mean elemental and biochemical composition of each species was obtained by pooling the data. These mean values have been used to estimate the pools of elements and compounds in the crustacean zooplankton of Lake Comabbio to provide an example of the importance of a multiple approach in zooplankton studies.

  2. Improved biochemical preservation of heart slices during cold storage.

    Science.gov (United States)

    Bull, D A; Reid, B B; Connors, R C; Albanil, A; Stringham, J C; Karwande, S V

    2000-01-01

    Development of myocardial preservation solutions requires the use of whole organ models which are animal and labor intensive. These models rely on physiologic rather than biochemical endpoints, making accurate comparison of the relative efficacy of individual solution components difficult. We hypothesized that myocardial slices could be used to assess preservation of biochemical function during cold storage. Whole rat hearts were precision cut into slices with a thickness of 200 microm and preserved at 4 degrees C in one of the following solutions: Columbia University (CU), University of Wisconsin (UW), D5 0.2% normal saline with 20 meq/l KCL (QNS), normal saline (NS), or a novel cardiac preservation solution (NPS) developed using this model. Myocardial biochemical function was assessed by ATP content (etamoles ATP/mg wet weight) and capacity for protein synthesis (counts per minute (cpm)/mg protein) immediately following slicing (0 hours), and at 6, 12, 18, and 24 hours of cold storage. Six slices were assayed at each time point for each solution. The data were analyzed using analysis of variance and are presented as the mean +/- standard deviation. ATP content was higher in the heart slices stored in the NPS compared to all other solutions at 6, 12, 18 and 24 hours of cold storage (p cold storage (p cold storage.

  3. Improved biochemical preservation of lung slices during cold storage.

    Science.gov (United States)

    Bull, D A; Connors, R C; Reid, B B; Albanil, A; Stringham, J C; Karwande, S V

    2000-05-15

    Development of lung preservation solutions typically requires whole-organ models which are animal and labor intensive. These models rely on physiologic rather than biochemical endpoints, making accurate comparison of the relative efficacy of individual solution components difficult. We hypothesized that lung slices could be used to assess preservation of biochemical function during cold storage. Whole rat lungs were precision cut into slices with a thickness of 500 microm and preserved at 4 degrees C in the following solutions: University of Wisconsin (UW), Euro-Collins (EC), low-potassium-dextran (LPD), Kyoto (K), normal saline (NS), or a novel lung preservation solution (NPS) developed using this model. Lung biochemical function was assessed by ATP content (etamol ATP/mg wet wt) and capacity for protein synthesis (cpm/mg protein) immediately following slicing (0 h) and at 6, 12, 18, and 24 h of cold storage. Six slices were assayed at each time point for each solution. The data were analyzed using analysis of variance and are presented as means +/- SD. ATP content was significantly higher in the lung slices stored in NPS compared with all other solutions at each time point (P cold storage. Copyright 2000 Academic Press.

  4. Suggestibility and Expectancy in a Counseling Analogue

    Science.gov (United States)

    Kaul, Theodore J.; Parker, Clyde A.

    1971-01-01

    The data indicated that (a) subjectively experienced suggestibility was more closely related to attitude change than was objective suggestibility, and (b) the generalized expectancy treatments were ineffective in influencing different criterion scores. (Author)

  5. Biochemical Removal of HAP Precursors From Coal

    International Nuclear Information System (INIS)

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE's interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals

  6. Biochemical Removal of HAP Precursors From Coal

    Energy Technology Data Exchange (ETDEWEB)

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE`s interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals.

  7. eQuilibrator--the biochemical thermodynamics calculator.

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

  8. eQuilibrator—the biochemical thermodynamics calculator

    Science.gov (United States)

    Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

  9. Evidentiality and Suggestibility: A New Research Venue

    Science.gov (United States)

    Aydin, Cagla; Ceci, Stephen J.

    2009-01-01

    Recent research suggests that acquisition of mental-state language may influence conceptual development. We examine this possibility by investigating the conceptual links between evidentiality in language and suggestibility. Young children are disproportionately suggestible and tend to change their reports or memories when questioned. The authors…

  10. The Effects of Suggestibility on Relaxation.

    Science.gov (United States)

    Rickard, Henry C.; And Others

    1985-01-01

    Selected undergraduates (N=32) on the basis of Creative Imagination Scale scores and randomly assigned high and low suggestibility subjects to progressive relaxation (PR) and suggestions of relaxation (SR) training modes. Results revealed a significant pre-post relaxation effect, and main efffects for both suggestibility and training mode. (NRB)

  11. Reinventing suggestion systems for continuous improvement

    NARCIS (Netherlands)

    Schuring, R.W.; Luijten, Harald

    2001-01-01

    This article reports an experiment to increase the effectiveness of a suggestion system by deliberately applying principles of the kaizen and performance management. Design rules for suggestion systems are derived from these theories. The suggestion system that resulted differs from traditional

  12. Radiation effects on biochemical systems

    International Nuclear Information System (INIS)

    Seddon, G.M.

    2000-04-01

    Xanthine oxidase catalyses the oxidative hydroxylation of hypoxanthine, xanthine and a wide range of carbonyl compounds. The enzyme exists as an oxidase and a dehydrogenase; both catalyze the oxidation of the same substrates. Steady state radiolysis and pulse radiolysis were used to generate oxidative and reductive free radicals. Their effects on the enzymatic activity of xanthine oxidase were determined. Initially inactivation studies were carried out to evaluate the extent to which radiolysis in aqueous solution affects the enzyme activity. Values of D 37 and G inactivation were calculated following irradiation in the presence of free radical scavengers and in the presence of catalase and superoxide dismutase. The kinetic constants Vmax and Km were also determined following radiolysis. The effect of ionising radiation on the iron content of xanthine oxidase was measured using atomic absorption spectrometry. Native gel electrophoresis and iso-electric focussing were performed in an attempt to demonstrate changes in the overall structure of the enzyme. The binding of xanthine oxidase to heparin was carried out by measuring, (1) the displacement of methylene blue (MB + ) from a heparin-MB + complex, (2) affinity chromatography and, (3) pulse radiolysis. The effect of irradiation on the binding process was investigated using techniques (1) and (2). Finally the radiation-induced conversion of xanthine oxidase to dehydrogenase was established. The results indicate that xanthine oxidase is inactivated greatest in the presence of air and irradiation causes Vmax to he reduced and Km to increase. The iron content of irradiated xanthine oxidase is unaffected. Electrophoresis shows the enzyme becomes fragmented and the isoelectric points of the fragments vary over a wide range of pH. Binding of xanthine oxidase to heparin as measured by displacement of MB + from a heparin-MB + complex suggests that irradiation increases the affinity of the enzyme for the polyanion, whereas

  13. A neurological and biochemical study of early lead poisoning

    Energy Technology Data Exchange (ETDEWEB)

    Ashby, J A.S.

    1980-05-01

    Motor nerve conduction velocities in 194 workers exposed to lead in a battery factory were compared with those of 94 age-matched controls. Changes in nerve conduction velocities of the 94 lead workers were found to have occurred. All mean maximum motor nerve conducting velocities measured were significantly lower in the lead-exposed group than in the control group. There was no statistically significant correlation to indicate that progressive slowing of nerve conduction was associated with increasing exposure to lead or with the commonly measured biochemical changes associated with disturbed haemopoiesis in lead exposure. Results suggest that the onset of nerve conduction changes occurs within two years.

  14. Lignin biodegradation: experimental evidence, molecular, biochemical and physiological mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Monties, B

    1985-01-01

    A critical review is presented of English, French and some German language literature, mainly from 1983 onwards. It examines experimental evidence on the behaviour as barriers to biodegradation of lignins and phenolic polymers such as tannins and suberins. The different molecular mechanisms of lignolysis by fungi (mainly), actinomycetes and bacteria are examined. A new biochemical approach to the physiological mechanism of regulation of lignolytic activities is suggested based on the discoveries of ligniolytic enzymes: effects of nitrogen, oxygen and substrate are discussed. It is concluded that a better knowledge of the structure and reactivity of phenolic barriers is needed in order to control the process of lignolysis.

  15. Biochemical activity of fullerenes and related derivatives

    International Nuclear Information System (INIS)

    Huczko, A.; Lange, H.; Calko, E.

    1999-01-01

    An astonishing scientific interest, embodied in over 15000 research articles so far, has been encountered since 1985 when fullerenes were discovered. From new superconductors to a rich electrochemistry and reaction chemistry, fullerene nanostructures continue to excite the scientific world, and new findings continue at record pace. This review presents many examples of the biochemical activities of fullerenes and derivatives, e. g. cytotoxic activity, selective DNA cleavage and antiviral activity against HIV. We also present some results of our testing which show that, despite its chemical and biochemical activity, fullerene matter does not present any health hazard directly related to skin irritation and allergic risks. (author)

  16. The influence of suggestibility on memory.

    Science.gov (United States)

    Nicolas, Serge; Collins, Thérèse; Gounden, Yannick; Roediger, Henry L

    2011-06-01

    We provide a translation of Binet and Henri's pioneering 1894 paper on the influence of suggestibility on memory. Alfred Binet (1857-1911) is famous as the author who created the IQ test that bears his name, but he is almost unknown as the psychological investigator who generated numerous original experiments and fascinating results in the study of memory. His experiments published in 1894 manipulated suggestibility in several ways to determine effects on remembering. Three particular modes of suggestion were employed to induce false recognitions: (1) indirect suggestion by a preconceived idea; (2) direct suggestion; and (3) collective suggestion. In the commentary we suggest that Binet and Henri's (1894) paper written over 115 years ago is still highly relevant even today. In particular, Binet's legacy lives on in modern research on misinformation effects in memory, in studies of conformity, and in experiments on the social contagion of memory. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. The relationships between suggestibility, influenceability, and relaxability.

    Science.gov (United States)

    Polczyk, Romuald; Frey, Olga; Szpitalak, Malwina

    2013-01-01

    This research explores the relationships between relaxability and various aspects of suggestibility and influenceability. The Jacobson Progressive Muscle Relaxation procedure was used to induce relaxation. Tests of direct suggestibility, relating to the susceptibility of overt suggestions, and indirect suggestibility, referring to indirect hidden influence, as well as self-description questionnaires on suggestibility and the tendency to comply were used. Thayer's Activation-Deactivation Adjective Check List, measuring various kinds of activation and used as a pre- and posttest, determined the efficacy of the relaxation procedure. Indirect, direct, and self-measured suggestibility proved to be positively related to the ability to relax, measured by Thayer's subscales relating to emotions. Compliance was not related to relaxability. The results are discussed in terms of the aspects of relaxation training connected with suggestibility.

  18. Pathological and 3 Tesla Volumetric Magnetic Resonance Imaging Predictors of Biochemical Recurrence after Robotic Assisted Radical Prostatectomy: Correlation with Whole Mount Histopathology.

    Science.gov (United States)

    Tan, Nelly; Shen, Luyao; Khoshnoodi, Pooria; Alcalá, Héctor E; Yu, Weixia; Hsu, William; Reiter, Robert E; Lu, David Y; Raman, Steven S

    2018-05-01

    We sought to identify the clinical and magnetic resonance imaging variables predictive of biochemical recurrence after robotic assisted radical prostatectomy in patients who underwent multiparametric 3 Tesla prostate magnetic resonance imaging. We performed an institutional review board approved, HIPAA (Health Insurance Portability and Accountability Act) compliant, single arm observational study of 3 Tesla multiparametric magnetic resonance imaging prior to robotic assisted radical prostatectomy from December 2009 to March 2016. Clinical, magnetic resonance imaging and pathological information, and clinical outcomes were compiled. Biochemical recurrence was defined as prostate specific antigen 0.2 ng/cc or greater. Univariate and multivariate regression analysis was performed. Biochemical recurrence had developed in 62 of the 255 men (24.3%) included in the study at a median followup of 23.5 months. Compared to the subcohort without biochemical recurrence the subcohort with biochemical recurrence had a greater proportion of patients with a high grade biopsy Gleason score, higher preoperative prostate specific antigen (7.4 vs 5.6 ng/ml), intermediate and high D'Amico classifications, larger tumor volume on magnetic resonance imaging (0.66 vs 0.30 ml), higher PI-RADS® (Prostate Imaging-Reporting and Data System) version 2 category lesions, a greater proportion of intermediate and high grade radical prostatectomy Gleason score lesions, higher pathological T3 stage (all p <0.01) and a higher positive surgical margin rate (19.3% vs 7.8%, p = 0.016). On multivariable analysis only tumor volume on magnetic resonance imaging (adjusted OR 1.57, p = 0.016), pathological T stage (adjusted OR 2.26, p = 0.02), positive surgical margin (adjusted OR 5.0, p = 0.004) and radical prostatectomy Gleason score (adjusted OR 2.29, p = 0.004) predicted biochemical recurrence. In this cohort tumor volume on magnetic resonance imaging and pathological variables, including Gleason score

  19. Correlates of the Gudjonsson Suggestibility Scale in delinquent adolescents.

    Science.gov (United States)

    Muris, Peter; Meesters, Cor; Merckelbach, Harald

    2004-02-01

    Correlations between scores on the Gudjonsson Suggestibility Scale and a number of relevant personality characteristics, i.e., intelligence, memory, social inadequacy, social desirability, and fantasy proneness, were examined in a sample of 71 delinquent boys. Analysis showed that intelligence and memory were negatively related to suggestibility scores. That is, lower memory and intelligence were associated with higher suggestibility. No significant correlations were found between suggestibility and other personality characteristics.

  20. SABIO-RK: A data warehouse for biochemical reactions and their kinetics

    Directory of Open Access Journals (Sweden)

    Krebs Olga

    2007-03-01

    Full Text Available Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics, a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

  1. Variations in biochemical values for common laboratory tests: a comparison among multi-ethnic Israeli women cohort.

    Science.gov (United States)

    Birk, Ruth; Heifetz, Eliyahu M

    2018-04-28

    Biochemical laboratory values are an essential tool in medical diagnosis, treatment, and follow-up; however, they are known to vary between populations. Establishment of ethnicity-adjusted reference values is recommended by health organizations. To investigate the ethnicity element in biochemical lab values studying women of different ethnic groups. Biochemical lab values (n = 27) of 503 adult Israeli women of three ethnicities (Jewish Ashkenazi, Jewish Sephardic, and Bedouin Arab) attending a single medical center were analyzed. Biochemical data were extracted from medical center re