Sample records for biochemical analysis

  1. Biochemical Analysis of Microbial Rhodopsins. (United States)

    Maresca, Julia A; Keffer, Jessica L; Miller, Kelsey J


    Ion-pumping rhodopsins transfer ions across the microbial cell membrane in a light-dependent fashion. As the rate of biochemical characterization of microbial rhodopsins begins to catch up to the rate of microbial rhodopsin identification in environmental and genomic sequence data sets, in vitro analysis of their light-absorbing properties and in vivo analysis of ion pumping will remain critical to characterizing these proteins. As we learn more about the variety of physiological roles performed by microbial rhodopsins in different cell types and environments, observing the localization patterns of the rhodopsins and/or quantifying the number of rhodopsin-bearing cells in natural environments will become more important. Here, we provide protocols for purification of rhodopsin-containing membranes, detection of ion pumping, and observation of functional rhodopsins in laboratory and environmental samples using total internal reflection fluorescence microscopy. © 2016 by John Wiley & Sons, Inc. PMID:27153387

  2. Probabilistic sensitivity analysis of biochemical reaction systems


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


    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. ...

  3. Category analysis: from biochemical mechanics to astrophysics

    International Nuclear Information System (INIS)

    Full text: One of the main goals of this report is to bridge the gap between computer modelling and group analysis of nonlinear partial differential equations. But we can work with a category of groups rather than a Lie group. In view of the experience of the past development of the relation between mathematics, mechanics and physics, the categorical extension may be justified that one day categoric structures will be as important as groups are today. Also our aim is the application of the same category-theoretic methods in biochemical mechanics and astrophysics. As examples we consider the category analysis of material models for concrete, wood and reinforcing or prestressing steel, on the one hand, and process of the linear and circular polarization of the cosmic microwave background radiation due to the quantum effects of electromagnetic field in anisotropic Bianchi-type cosmological models, on the other hand. (author)

  4. Skin biochemical composition analysis by Raman spectroscopy

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    Oliveira, Patricia Karen; Tosato, Maira Gaspar; Alves, Rani de Souza; Martin, Airton Abrahao; Favero, Priscila Pereira; Raniero, Leandro, E-mail: [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)


    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. Sensitivity analysis for computational models of biochemical systems




    Systems biology is an integrated area of science which aims at the analysis of biochemical systems using an holistic perspective. In this context, sensitivity analysis, a technique studying how the output variation of a computational model can be associated to its input state plays a pivotal role. In the thesis it is described how to properly apply the different sensitivity analysis techniques according to the specific case study (i.e., continuous deterministic rather than discrete stochastic...

  6. Study on color difference estimation method of medicine biochemical analysis (United States)

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


    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.

  7. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

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    Goutsias John


    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 Conclusions Our approach provides an attractive statistical methodology for

  8. Dynamic analysis of biochemical network using complex network method


    Wang Shuqiang; Shen Yanyan; Hu Jinxing; Li Ning; Zeng Dewei


    In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger ...

  9. Dynamic analysis of biochemical network using complex network method

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    Wang Shuqiang


    Full Text Available In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger information capacity and is more efficient in information transmission. This is consistent with theory of evolution.

  10. Imminent Cardiac Risk Assessment via Optical Intravascular Biochemical Analysis

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


    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

  11. Automatising the analysis of stochastic biochemical time-series


    Caravagna, Giulio; De Sano, Luca; Antoniotti, Marco


    Background Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these frameworks it is possible to analyse complex models under a variety of configurations, eventually selecting the best setting of, e.g., parameters for a target system. Motivation This operational pipeline relies on the ability to interpret the predictions of a model, often represented...

  12. An integrated microfluidic biochemical detection system for protein analysis with magnetic bead-based sampling capabilities. (United States)

    Choi, Jin-Woo; Oh, Kwang W; Thomas, Jennifer H; Heineman, William R; Halsall, H Brian; Nevin, Joseph H; Helmicki, Arthur J; Henderson, H Thurman; Ahn, Chong H


    This paper presents the development and characterization of an integrated microfluidic biochemical detection system for fast and low-volume immunoassays using magnetic beads, which are used as both immobilization surfaces and bio-molecule carriers. Microfluidic components have been developed and integrated to construct a microfluidic biochemical detection system. Magnetic bead-based immunoassay, as a typical example of biochemical detection and analysis, has been successfully performed on the integrated microfluidic biochemical analysis system that includes a surface-mounted biofilter and electrochemical sensor on a glass microfluidic motherboard. Total time required for an immunoassay was less than 20 min including sample incubation time, and sample volume wasted was less than 50 microl during five repeated assays. Fast and low-volume biochemical analysis has been successfully achieved with the developed biofilter and immunosensor, which is integrated to the microfluidic system. Such a magnetic bead-based biochemical detection system, described in this paper, can be applied to protein analysis systems. PMID:15100857

  13. 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


    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.

  14. Biochemical analysis of the crude extract of Momordica charantia (L.). (United States)

    Dar, Ume Kalsoom; Owais, Farah; Ahmad, Manzoor; Rizwani, Ghazala H


    Momordica charantia (L.) commonly referred as bitter gourd, karela and balsam pear. Its fruit is used for the treatment of diabetes and related conditions amongst the indigenous populations of Asia, South America, India and East Africa. The study was conducted to find out the biochemical aspects of crude extract of whole fruit of M. charantia including seeds which includes blood test (Hemoglobin, RBC, Total leukocyte count, platelets count, HbA1C (Glycocylated heamoglobin Type A1C)), Lipid profile test and electrolyte balance. Hemoglobin (7.1±0.14), platelets count (827 ×109±1.95), Cholesterol level (111±2), HDL (high density lipoproteins) (20±1.22) at 10mg shows marked increase in values as compared to control. While 25 mg dose shows insignificant result. Electrolyte balance are found significant at 10mg and 25mg except bicarbonates (Na(+¬)=143±1.87, K-=3.45±0.35, Cl(-) =108±1.48). Another important property of M. charantia is the elevation of platelet counts, heamoglobin and specifically high-density lipoproteins (HDL). It also controls cholesterol, triglycerides, HDL, LDL and VLDL at low dosage (10mg). Further studies can be conducted to find out which phytochemical components acts on specific biochemical activity. PMID:26045386

  15. A feedback approach to bifurcation analysis in biochemical networks with many parameters


    Waldherr, Steffen; Allgower, Frank


    Feedback circuits in biochemical networks which underly cellular signaling pathways are important elements in creating complex behavior. A specific aspect thereof is how stability of equilibrium points depends on model parameters. For biochemical networks, which are modelled using many parameters, it is typically very difficult to estimate the influence of parameters on stability. Finding parameters which result in a change in stability is a key step for a meaningful bifurcation analysis. We ...

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

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    Qian Hong


    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.

  17. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis. (United States)

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


    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 together with an instruction. PMID:24623466

  18. Investigating modularity in the analysis of process algebra models of biochemical systems

    CERN Document Server

    Ciocchetta, Federica; Hillston, Jane; 10.4204/EPTCS.19.4


    Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in a formalism which allows the problem to be tackled compositionally. In this paper we consider the extent to which the compositional structure which is inherent in process algebra models of biochemical systems can be exploited during model solution. In essence this means using the compositional structure to guide decomposed solution and analysis. Unfortunately the dynamic behaviour of biochemical systems exhibits strong interdependencies between the components of the model making decomposed solution a difficult task. Nevertheless we believe that if such decomposition based on process algebras could be established it would demonstrate substantial benefits for systems biology modelling. In this paper we present our preliminary investigations based on a case study of the phero...

  19. Ultrastructural and biochemical analysis of fibrinogen receptors on activated thrombocytes

    International Nuclear Information System (INIS)

    The present studies have been concerned with the role of fibrinogen and its receptor, GP IIb/IIIa, during the activation and early aggregation of pigeon thrombocytes. Thrombocytes were surface labeled with 125I then separated on SDS-PAGE. Analysis by gel autoradiography revealed major bands at MW 145 kd and 98 kd, which corresponded to human GPIIb and GPIIIa. Immunologic similarity of the pigeon and human receptor components was established by dot blot analysis using polyclonal antibodies directed against human GPIIb and GPIIIa. Pigeon fibrinogen, isolated by plasma precipitation with PEG-1000 and purified over Sepharose 4B, was used to study receptor-ligand interaction. Separation of pigeon fibrinogen on SDS-PAGE resulted in three peptides having apparent MW of 62kd, 55kd, and 47kd which are comparable to human fibrinogen. Further similarity of human and pigeon fibrinogen was verified by immonodiffusion against an antibody specific for the human protein. The role of fibrinogen and its receptor in thrombocyte function was established by turbidimetric aggregation using thrombin as an agonist under conditions requiring Ca++ and fibrinogen

  20. Biochemical and computational analysis of LNX1 interacting proteins.

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    Cheryl D Wolting

    Full Text Available PDZ (Post-synaptic density, 95 kDa, Discs large, Zona Occludens-1 domains are protein interaction domains that bind to the carboxy-terminal amino acids of binding partners, heterodimerize with other PDZ domains, and also bind phosphoinositides. PDZ domain containing proteins are frequently involved in the assembly of multi-protein complexes and clustering of transmembrane proteins. LNX1 (Ligand of Numb, protein X 1 is a RING (Really Interesting New Gene domain-containing E3 ubiquitin ligase that also includes four PDZ domains suggesting it functions as a scaffold for a multi-protein complex. Here we use a human protein array to identify direct LNX1 PDZ domain binding partners. Screening of 8,000 human proteins with isolated PDZ domains identified 53 potential LNX1 binding partners. We combined this set with LNX1 interacting proteins identified by other methods to assemble a list of 220 LNX1 interacting proteins. Bioinformatic analysis of this protein list was used to select interactions of interest for future studies. Using this approach we identify and confirm six novel LNX1 binding partners: KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2 and PBK, and suggest that LNX1 functions as a signalling scaffold.

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

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    Robin Donaldson


    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.

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

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    Cook, Douglas R; Riely, Brendan K


    -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.

  3. The role of lipids in Plasmodium falciparum invasion of erythrocytes: a coordinated biochemical and microscopic analysis.



    The role of lipids in Plasmodium falciparum invasion of erythrocytes was investigated by biochemical and fluorescent microscopic analysis. Metabolic incorporation of radioactive oleate or palmitate and fractionation of radiolabeled phospholipids by thin-layer chromatography revealed no difference in the major phospholipid classes of schizonts and early ring forms after merozoite invasion. Fluorescent anthroyloxy derivatives of oleate and palmitate were also metabolically incorporated into par...

  4. On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking


    Brim, Lubos; Ceska, Milan; Drazan, Sven; Safranek, David


    This report proposes a novel framework for a rigorous robustness analysis of stochastic biochemical systems. The technique is based on probabilistic model checking. We adapt the general definition of robustness introduced by Kitano to the class of stochastic systems modelled as continuous time Markov Chains in order to extensively analyse and compare robustness of biological models with uncertain parameters. The framework utilises novel computational methods that enable to effectively evaluat...

  5. Bioimpedance spectroscopy as technique of hematological and biochemical analysis of blood (United States)

    Malahov, M. V.; Smirnov, A. V.; Nikolaev, D. V.; Melnikov, A. A.; Vikulov, A. D.


    Bioimpedance spectroscopy may become a useful method for the express analysis and monitoring of blood parameters. The aim of this study was to identify biochemical and hematological parameters of blood that can be accurately predicted by means of bioimpedance technique. Hematological (red blood cell and white blood cell parameters) and biochemical (total proteins, albumins, fibrinogen, sodium, potassium, chloride ion concentrations in plasma) parameters were measured with a hematological analyzer and routine methods. Bioimpedance spectroscopy of the whole blood (1.5 ml) in frequency range 5-500 kHz (31 frequencies) was performed using BIA analyzer ABC-01 "Medass". Frequency relationships of resistance and reactance of the whole blood and the parameters of the Cole model were investigated. Close simple and multiple correlations of bioimpedance indices were observed only with erythrocyte parameters (Ht, Hb, RBC). Thus bioimpedance analysis of the whole blood can accurately predict red cell parameters but it is less effective for estimation of plasma biochemical and white cell parameters.

  6. Techno-Economic Analysis of Bioconversion of Methane into Biofuel and Biochemical (Poster)

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    Fei, Q.; Tao, L.; Pienkos, P .T.; Guarnieri, M.; Palou-Rivera, I.


    In light of the relatively low price of natural gas and increasing demands of liquid transportation fuels and high-value chemicals, attention has begun to turn to novel biocatalyst for conversion of methane (CH4) into biofuels and biochemicals [1]. A techno-economic analysis (TEA) was performed for an integrated biorefinery process using biological conversion of methane, such as carbon yield, process efficiency, productivity (both lipid and acid), natural gas and other raw material prices, etc. This analysis is aimed to identify research challenges as well provide guidance for technology development.

  7. Molecular and biochemical analysis of aroma in CSR10 x Taraori basmati derived Recombinant Inbred Lines

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    Pummy Kumari, Uma Ahuja , Sunita Jain and R.K. Jain


    Full Text Available The aroma or fragrance of Basmati rice is associated with the presence and content of chemical compound, 2-acetyl-1-pyrrolineand the trait is monogenic recessive. Several PCR-based co-dominant marker based on RG28 locus were developed, which can differentiate between fragrant and non-fragrant rice cultivars. 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 SSD method was used. RILs are among the best mapping populations, which provide a novel material for linkage mapping of genes/QTLs marker for various traits. 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 amplified aroma specific alleles having 256 bp in 72 lines, BADEX7-5 with 95 bp in 74 lines and SCUSSR1 with 129 bp in 79 lines. Mentel test of significance detected by biochemical analysis of RILs (with 1.7 % KOH and molecular marker study revealed high degree (>90 % of association of aroma with the above mentioned markers, respectively. Some of the F10 lines amplified the heterozygous alleles for two sets of specific markers (BAD2 and SCUSSR-1 but did not show the presence of aroma as analyzed by chemical test. Aromatic and non-aromatic lines were almost common in three markers indicating association of markers with the trait and chromosome 8. The results revealed that these markers could be used for marker assisted selection and RIL population for mapping of aroma QTLs/genes.

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

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal


    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 be much more widely applied, although it was originally based on linearized kinetics. The methodology of determining elasticity coefficients directly from pool levels is illustrated with an analysis of the first two steps of the biosynthetic pathway of penicillin. The results compare well...

  9. Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks (United States)

    Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)


    Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

  10. A moment-convergence method for stochastic analysis of biochemical reaction networks (United States)

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou


    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.

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

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    Bennett Hayley J


    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

  12. Microarray and Biochemical Analysis of Lovastatin-induced Apoptosis of Squamous Cell Carcinomas

    Directory of Open Access Journals (Sweden)

    Jim Dimitroulakos


    Full Text Available We recently identified 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA reductase, the rate-limiting enzyme of the mevalonate pathway, as a potential therapeutic target of the head and neck squamous cell carcinomas (HNSCC and cervical carcinomas (CC. The products of this complex biochemical pathway, including de novo cholesterol, are vital for a variety of key cellular functions affecting membrane integrity, cell signaling, protein synthesis, and cell cycle progression. Lovastatin, a specific inhibitor of HMG-CoA reductase, induces a pronounced apoptotic response in a specific subset of tumor types, including HNSCC and CC. The mediators of this response are not well established. Identification of differentially expressed genes represents a feasible approach to delineate these mediators as lovastatin has the potential to modulate transcription indirectly by perturbing levels of sterols and other mevalonate metabolites. Expression analysis following treatment of the HNSCC cell lines SCC9 or SCC25 with 10 μM lovastatin for 1 day showed that less than 2% (9 cDNAs of the 588 cDNAs on this microarray were affected in both cell lines. These included diazepam-binding inhibitor/acyl-CoA-binding protein, the activated transcription factor 4 and rhoA. Because the biosynthesis of mevalonate leads to its incorporation into more than a dozen classes of end products, their role in lovastatin-induced apoptosis was also evaluated. Addition of the metabolites of all the major branches of the mevalonate pathway indicated that only the nonsterol moiety, geranylgeranyl pyrophosphate (GGPP, significantly inhibited the apoptotic effects of lovastatin in HNSCC and CC cells. Because rhoA requires GGPP for its function, this links the microarray and biochemical data and identifies rhoA as a potential mediator of the anticancer properties of lovastatin. Our data suggest that the depletion of nonsterol mevalonate metabolites, particularly GGPP, can be potential mediators of

  13. Early effects of radiotherapy in small cell lung cancer xenografts monitored by 31P magnetic resonance spectroscopy and biochemical analysis

    DEFF Research Database (Denmark)

    Kristjansen, P E; Pedersen, E J; Quistorff, B;


    31P magnetic resonance spectroscopy (31P MRS) and biochemical analysis of extracts were applied to study the metabolic response to X-irradiation of small cell lung cancer in nude mice. Two small cell lung cancer xenografts, CPH SCCL 54A and 54B, with different radiosensitivity, although derived...

  14. 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.

  15. Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel (United States)

    Qin, Huibin; Sun, Qinghui; Pan, Xuewei; Qiao, Zhijun; Yang, Hongjiang


    Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely.

  16. Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel. (United States)

    Qin, Huibin; Sun, Qinghui; Pan, Xuewei; Qiao, Zhijun; Yang, Hongjiang


    Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely. PMID:27610102

  17. Biofilm reactor based real-time analysis of biochemical oxygen demand. (United States)

    Liu, Changyu; Jia, Jianbo; Dong, Shaojun


    We reported a biofilm reactor (BFR) based analytical system for real-time biochemical oxygen demand (BOD) monitoring. It does not need a blank solution and other chemical reagents to operate. The initial dissolved oxygen (DO) in sample solution was measured as blank, while DO in the BFR effluent was measured as response. The DO difference obtained before and after the sample solution flowed through the BFR was regarded as an indicator of real-time BOD. The analytical performance of this reagent-free BFR system was equal to the previous BFR system operated using phosphate buffer saline (PBS) and high purity deionized water in reproducibility, accuracy and long-term stability. Besides, this method embraces many notable advantages, such as no secondary pollution. Additionally, the sample solutions are free from temperature controlling and air-saturation before injection. Significantly, this is a real-time BOD analysis method. This method was successfully carried out in a simulated emergency, and the obtained results agreed well with conventional BOD₅. These advantages, coupled with simplicity in device, convenience in operation and minimal maintenance, make such a reagent-free BFR analytical system promising for practical BOD real-time warning. PMID:23228491

  18. Mutational and Biochemical Analysis of the DNA-entry Nuclease EndA from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    M Midon; P Schafer; A Pingoud; M Ghosh; A Moon; M Cuneo; R London; G Meiss


    EndA is a membrane-attached surface-exposed DNA-entry nuclease previously known to be required for genetic transformation of Streptococcus pneumoniae. More recent studies have shown that the enzyme also plays an important role during the establishment of invasive infections by degrading extracellular chromatin in the form of neutrophil extracellular traps (NETs), enabling streptococci to overcome the innate immune system in mammals. As a virulence factor, EndA has become an interesting target for future drug design. Here we present the first mutational and biochemical analysis of recombinant forms of EndA produced either in a cell-free expression system or in Escherichia coli. We identify His160 and Asn191 to be essential for catalysis and Asn182 to be required for stability of EndA. The role of His160 as the putative general base in the catalytic mechanism is supported by chemical rescue of the H160A variant of EndA with imidazole added in excess. Our study paves the way for the identification and development of protein or low-molecular-weight inhibitors for EndA in future high-throughput screening assays.

  19. Expression, Purification, and Biochemical Analysis of the LSD1/KDM1A Histone Demethylase. (United States)

    Laurent, B; Shi, Y


    Posttranslational modifications (PTMs) of histones play important roles in the regulation of chromatin architecture and gene transcription. A decade ago, it was still believed that methyl groups could not be removed from histones, until the first histone demethylase LSD1 (lysine-specific demethylase 1; also known as KDM1A) was identified. This discovery initiated an era in the understanding of chromatin dynamic regulation by active histone demethylation. Since then, the repertoire of histone demethylases has expanded, and our understanding of the molecular mechanisms, structures, and macromolecular complexes of the demethylases has grown significantly. Histone demethylases have emerged as important players in developmental processes and have been linked to human diseases and cancer. Studies highlighting the functions of LSD1 have significantly increased our understanding of chromatin biology and have revealed that new facets of histone demethylases remain to be discovered. In vitro methods have been developed to assess the biochemistry, structure, and enzymology of lysine demethylases. Here, we describe the methods of expression, purification, and biochemical analysis that we have successfully used in characterizing the functions of LSD1. PMID:27372756

  20. Structural and biochemical analysis of Bcl-2 interaction with the hepatitis B virus protein HBx. (United States)

    Jiang, Tianyu; Liu, Minhao; Wu, Jianping; Shi, Yigong


    HBx is a hepatitis B virus protein that is required for viral infectivity and replication. Anti-apoptotic Bcl-2 family members are thought to be among the important host targets of HBx. However, the structure and function of HBx are poorly understood and the molecular mechanism of HBx-induced carcinogenesis remains unknown. In this study, we report biochemical and structural characterization of HBx. The recombinant HBx protein contains metal ions, in particular iron and zinc. A BH3-like motif in HBx (residues 110-135) binds Bcl-2 with a dissociation constant of ∼193 μM, which is drastically lower than that for a canonical BH3 motif from Bim or Bad. Structural analysis reveals that, similar to other BH3 motifs, the BH3-like motif of HBx adopts an amphipathic α-helix and binds the conserved BH3-binding groove on Bcl-2. Unlike the helical Bim or Bad BH3 motif, the C-terminal portion of the bound HBx BH3-like motif has an extended conformation and makes considerably fewer interactions with Bcl-2. These observations suggest that HBx may modulate Bcl-2 function in a way that is different from that of the classical BH3-only proteins. PMID:26858413

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

    International Nuclear Information System (INIS)

    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

  2. Modeling and Robustness Analysis of Biochemical Networks of Glycerol Metabolism by Klebsiella Pneumoniae (United States)

    Ye, Jianxiong; Feng, Enmin; Wang, Lei; Xiu, Zhilong; Sun, Yaqin

    Glycerol bioconversion to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae (K. pneumoniae) can be characterized by an intricate network of interactions among biochemical fluxes, metabolic compounds, key enzymes and genetic regulatory. To date, there still exist some uncertain factors in this complex network because of the limitation in bio-techniques, especially in measuring techniques for intracellular substances. In this paper, among these uncertain factors, we aim to infer the transport mechanisms of glycerol and 1,3-PD across the cell membrane, which have received intensive interest in recent years. On the basis of different inferences of the transport mechanisms, we reconstruct various metabolic networks correspondingly and subsequently develop their dynamical systems (S-systems). To determine the most reasonable metabolic network from all possible ones, we establish a quantitative definition of biological robustness and undertake parameter identification and robustness analysis for each system. Numerical results show that it is most possible that both glycerol and 1,3-PD pass the cell membrane by active transport and passive diffusion.

  3. Combining flux and energy balance analysis to model large-scale biochemical networks. (United States)

    Heuett, William J; Qian, Hong


    Stoichiometric Network Theory is a constraints-based, optimization approach for quantitative analysis of the phenotypes of large-scale biochemical networks that avoids the use of detailed kinetics. This approach uses the reaction stoichiometric matrix in conjunction with constraints provided by flux balance and energy balance to guarantee mass conserved and thermodynamically allowable predictions. However, the flux and energy balance constraints have not been effectively applied simultaneously on the genome scale because optimization under the combined constraints is non-linear. In this paper, a sequential quadratic programming algorithm that solves the non-linear optimization problem is introduced. A simple example and the system of fermentation in Saccharomyces cerevisiae are used to illustrate the new method. The algorithm allows the use of non-linear objective functions. As a result, we suggest a novel optimization with respect to the heat dissipation rate of a system. We also emphasize the importance of incorporating interactions between a model network and its surroundings. PMID:17245812

  4. Clinical, biochemical and molecular analysis of two infants with familial chylomicronemia syndrome. (United States)

    Zhang, Yonghong; Zhou, Jing; Zheng, Wenxin; Lan, Zhangzhang; Huang, Zhiwei; Yang, Qingnan; Liu, Chengbo; Gao, Rui; Zhang, Yongjun


    Familial chylomicronemia syndrome (FCS) is a rare autosomal recessive disease due mainly to inherited deficiencies in the proteins or enzymes involved in the clearance of triglycerides from circulation. It usually happens in late childhood and adolescence, which can have serious consequences if misdiagnosed or untreated. In the present study, we investigated two Chinese male babies (A and B), 30d and 48d in age, respectively, who have milky plasma. Clinical, biochemical, and radiological assessments were performed, while samples from the patients were referred for molecular diagnosis, including genetic testing and subsequent analysis of related genes. The fasting serum lipids of the two patients showed extreme lipid abnormalities. Through a low-lipid formula diet including skimmed milk and dietary advice, their plasma lipid levels were significantly lower and more stable at the time of hospital discharge. The genetic testing revealed compound heterozygote mutations in the lipoprotein lipase (LPL) gene for patient A and two known compound heterozygote LPL gene mutations for the patient B. FCS is the most dramatic example of severe hypertriglyceridemia. Early diagnosis and timely dietary intervention is very important for affected children. PMID:27153815

  5. Estrogen and progesterone receptors in endometrial carcinoma: comparison of immunohistochemical and biochemical analysis

    DEFF Research Database (Denmark)

    Nyholm, H C; Nielsen, Anette Lynge; Lyndrup, J;


    In 159 endometrial carcinomas, estrogen (ER) and progesterone receptors (PR) were determined biochemically by dextran-coated charcoal (DCC) assay and immunohistochemically (ICA) on frozen sections. ICA receptor content was estimated by a total histologic score (HSCORE), including all tissue...

  6. The use of Fourier transform (FT) surface-enhanced Raman scattering for biochemical analysis (United States)

    Jeffers, Robert Butler

    Surface-enhanced Raman scattering (SERS) is a powerful spectroscopic technique that has created exciting opportunities in the field of bioanalytical chemistry, where it combines ultrasensitive detection of biologically relevant molecules with vibrational spectroscopy. Due to the difficulties in preparing reproducible SERS active substrates, SERS has been mainly used as a qualitative tool. In order for SERS to be utilized as a viable tool for quantitative analysis, simple, facile SERS substrates which generate clean, highly reproducible signals must be developed. This dissertation deals with the evaluation of three different methods of SERS that led to the development of a novel substrate for the analysis of biological molecules. In this dissertation, I demonstrated the generation of a SERS signal from pyridine adsorbed to the surface of a roughened silver electrode. The Raman signal was detected utilizing a remote fiber optic probe dispersive Raman instrument. The necessary parameters for generating the optimal SERS signal were established. The SERS spectrum of pyridine was successfully characterized. The synthesis of silver colloid solutions for use as a SERS active substrate was demonstrated. Two different synthetic methods were utilized and the conditions for optimal SERS signal strength were established. SERS signals from solutions of tryptophan were successfully generated and detected using an FT-Raman spectrometer. In this dissertation. I report the successful chemical deposition of a thin silver film on the surface of a quartz/glass fiber filter for use as a SERS active substrate. The successful detection of the SERS signal of solutions of phenylalanine and tryptophan utilizing the silver-coated filters and a FT-Raman instrument was demonstrated. Significant progress was made to develop a quantifiable SERS method utilizing the silver-coated filters. The silver-coated filter SERS method presented here is a novel and promising method for biochemical analysis

  7. Examination of the relationships between environmental exposures to volatile organic compounds and biochemical liver tests: application of canonical correlation analysis


    Jing LIU; Drane, Wanzer; Liu, Xuefeng; Wu, Tiejian


    This study was to explore the relationships between personal exposure to ten volatile organic compounds (VOCs) and biochemical liver tests with the application of canonical correlation analysis. Data from a subsample of the 1999–2000 National Health and Nutrition Examination Survey were used. Serum albumin, total bilirubin (TB), alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), alkaline phosphatase (ALP), and γ-glutamyl transferase (GGT) served as ...

  8. Metabolomic profiling and genomic analysis of wheat aneuploid lines to identify genes controlling biochemical pathways in mature grain. (United States)

    Francki, Michael G; Hayton, Sarah; Gummer, Joel P A; Rawlinson, Catherine; Trengove, Robert D


    Metabolomics is becoming an increasingly important tool in plant genomics to decipher the function of genes controlling biochemical pathways responsible for trait variation. Although theoretical models can integrate genes and metabolites for trait variation, biological networks require validation using appropriate experimental genetic systems. In this study, we applied an untargeted metabolite analysis to mature grain of wheat homoeologous group 3 ditelosomic lines, selected compounds that showed significant variation between wheat lines Chinese Spring and at least one ditelosomic line, tracked the genes encoding enzymes of their biochemical pathway using the wheat genome survey sequence and determined the genetic components underlying metabolite variation. A total of 412 analytes were resolved in the wheat grain metabolome, and principal component analysis indicated significant differences in metabolite profiles between Chinese Spring and each ditelosomic lines. The grain metabolome identified 55 compounds positively matched against a mass spectral library where the majority showed significant differences between Chinese Spring and at least one ditelosomic line. Trehalose and branched-chain amino acids were selected for detailed investigation, and it was expected that if genes encoding enzymes directly related to their biochemical pathways were located on homoeologous group 3 chromosomes, then corresponding ditelosomic lines would have a significant reduction in metabolites compared with Chinese Spring. Although a proportion showed a reduction, some lines showed significant increases in metabolites, indicating that genes directly and indirectly involved in biosynthetic pathways likely regulate the metabolome. Therefore, this study demonstrated that wheat aneuploid lines are suitable experimental genetic system to validate metabolomics-genomics networks. PMID:26032167

  9. DNA methylation and physio-biochemical analysis of chickpea in response to cold stress. (United States)

    Rakei, Aida; Maali-Amiri, Reza; Zeinali, Hassan; Ranjbar, Mojtaba


    Cold stress (CS) signals are translated into physiological changes as products of direct and/or indirect of gene expression regulated by different factors like DNA methylation. In this study, some of these factors were comparatively studied in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold-tolerant genotype, and ILC533, cold susceptible one) under control (23 °C) and days 1, 3, and 6 after exposing the seedlings to CS (4 °C). Under CS, tolerant genotype prevented H2O2 accumulation which led to a decrease in damage indices (malondialdehyde and electrolyte leakage index) compared to susceptible one. The significant activities of antioxidant enzymes (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and polyphenol oxidase) along with a significant proportion of change in DNA methylation/demethylation patterns were often effective factors in preserving cell against cold-induced oxidative stress. Chickpea cells in response to CS changed access to their genome as the number of bands without change from day 1 to day 6 of exposure to CS particularly in tolerant genotype was decreased. During CS, the methylation level was higher compared to demethylation (29.05 vs 19.79 %) in tolerant genotype and (27.92 vs 22.09 %) in susceptible one. However, for prolonged periods of CS, changes in demethylated bands in tolerant genotype were higher than that of in susceptible one (9.24 vs 4.13 %), indicating higher potential for activation of CS responsive genes. Such a status along with higher activity of antioxidants and less damage indices could be related to cold tolerance (CT) mechanisms in chickpea. Sequencing analysis confirmed the important role of some specific DNA sequences in creating CT with possible responsive components involved in CS. Thus, dynamic assessment using multi-dimensional approaches allows us to progressively fill in the gaps between physio-biochemical and molecular events in creating CT, to comprehend better the

  10. S-system-based analysis of the robust properties common to many biochemical network models. (United States)

    Matsuoka, Yu; Jahan, Nusrat; Kurata, Hiroyuki


    Robustness is a key feature to characterize the adaptation of organisms to changes in their internal and external environments. A broad range of kinetic or dynamic models of biochemical systems have been developed. Robustness analyses are attractive for exploring some common properties of many biochemical models. To reveal such features, we transform different types of mathematical equations into a standard or intelligible formula and use the multiple parameter sensitivity (MPS) to identify some factors critically responsible for the total robustness to many perturbations. The MPS would be determined by the top quarter of the highly sensitive parameters rather than the single parameter with the maximum sensitivity. The MPS did not show any correlation to the network size. The MPS is closely related to the standard deviation of the sensitivity profile. A decrease in the standard deviation enhanced the total robustness, which shows the hallmark of distributed robustness that many factors (pathways) involve the total robustness. PMID:26861555

  11. Biochemical and physiological analysis in carrot seeds from different orders of umbels


    Patrícia Pereira da Silva; Marcelo Coelho Sekita; Denise Cunha Fernandes dos Santos Dias; Warley Marcos Nascimento


    ABSTRACT In carrot seed production, harvesting of the umbels is generally staggered, or sometimes the whole plant is harvested with the umbels at different stages of maturation; in that case, there is a risk of harvesting immature seeds and of losses due to natural dehiscent, or to physiological deterioration as a result of unfavourable environmental factors. The present study aimed to evaluate the physiological and biochemical changes related to the maturation of 'Planalto' carrot seeds from...

  12. Physiochemical, Biochemical, Minerals Content Analysis, and Antioxidant Potential of National and International Honeys in Pakistan


    Mahmood Ahmed; Muhammad Imtiaz Shafiq; Anum Khaleeq; Rahila Huma; Muhammad Abdul Qadir; Ayesha Khalid; Amir Ali; Abdul Samad


    16 honey samples from Pakistan and two other countries were investigated for their physiochemical, biochemical, minerals, and antioxidant potential. Antioxidant activities of all honey samples were performed by using percentage inhibition of DPPH free radical, AEAC, and FRAP. 5-HMF and mineral contents were determined by HPLC and AAS, respectively. The obtained values of respective parameters, namely, pH, EC, TDS, total acidity, moisture, ash, color intensity, sugars, proline, and protein wer...

  13. Evaluation of Biochemical Changes in Skin-Derived Mesenchymal Stem Cells during In Vitro Neurodifferentiation by FT-IR Analysis


    Parfejevs, V.; Gavare, M.; Cappiello, L.; Grube, M.; Muceniece, R.; Riekstina, U.


    Recently FT-IR analysis has been employed to study changes in molecular signatures during embryonic stem cell differentiation. We were interested to find out whether FT-IR spectroscopy could be applied to analyze changes in human skin mesenchymal stem cell (S-MSC) biochemical profile during in vitro neurodifferentiation. S-MSCs were propagated in serum-free medium with EGF and FGF-2 during six weeks. Neural progenitor cell line ReNcell CX (Millipore) was used as a reference cell line. Samples...

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


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


    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 six Dickeya species which included the type strains. A group of twenty-two potato strains isolated between 2005-2007 in the Netherlands, Poland, Finland and Israel were characterised as belonging t...

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

    International Nuclear Information System (INIS)

    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)

  16. Metabolomics analysis reveals insights into biochemical mechanisms of mental stress-induced left ventricular dysfunction (United States)

    Boyle, Stephen H.; Matson, Wayne R.; Velazquez, Eric J.; Samad, Zainab; Williams, Redford B.; Sharma, Swati; Thomas, Beena; Wilson, Jennifer L.; O'Connor, Christopher


    Mental stress induced left ventricular dysfunction (LVD) has been associated with a greater risk of adverse events in coronary heart disease (CHD) patients independent of conventional risk indicators. The underlying biochemical mechanisms of this cardiovascular condition are poorly understood. Our objective was to use metabolomics technology to identify biochemical changes that co-occur with mental stress-induced LVD in patients with clinically stable CHD. Participants were adult CHD patients who were recruited for mental stress-induced myocardial ischemia screening. For this study, we randomly selected 30 patients representing the extremes of the mental stress-induced left ventricular ejection fraction (LVEF) change distribution; 15 who showed LVD (i.e. LVEF reduction ≥5) and 15 who showed a normal left ventricular response (NLVR; i.e. a LVEF increase of ≥5) to three mental stressors. An electrochemistry based metabolomics platform was used to profile pre- and post-stress serum samples yielding data for 22 known compounds, primarily within the tyrosine, tryptophan, purine and methionine pathways. There were significant stress-induced changes in several compounds. A comparison between the NLVR and LVD groups showed significant effects for kynurenine (p = .036, N-acetylserotonin (p = .054), uric acid (p = .015), tyrosine (p = .019) and a trend for methionine (p = .065); the NLVR group showed a significantly greater stress-induced reduction in all of those compounds compared to the LVD group. Many of these biochemicals have been implicated in other stress-related phenomena and are plausible candidates for mechanisms underlying LVD in response to mental stress. PMID:25983674

  17. Role of nitric oxide, angiogenic growth factors and biochemical analysis in preeclampsia. (United States)

    Saha, Tanmay; Halder, Mrityunjoy; Das, Amitabha; Das, Subir Kumar


    Preeclampsia, a pregnancy-related hypertensive disorder, is one of the leading causes of fetal and maternal mortality and morbidity globally. Angiogenic growth factors, including vascular endothelial growth factor (VEGF) and placental growth factor (P1GF) are involved in the generation of new blood vessels required for placental development and physiological functions, while nitric oxide (NO) acts as vasodilator and also plays a role in angiogenesis. The objective of this study was to evaluate the role of NO, angiogenic growth factors (VEGF and PIGF) and other biochemical parameters in the development of preeclampsia among pregnant mothers. A complete clinical history, including anthropometric measurements and biochemical investigations, including renal function tests, liver function tests and lipid profile were performed among twenty preeclampsia patients aged 19 to 32 yrs. Results were compared with age-matched normotensive pregnant mothers. The body weight, body mass index (BMI), blood pressure, concentrations of urea, uric acid and triglyceride and activities of transaminase enzymes (aspartate transaminase, AST and alanine transaminase, ALT) in serum were significantly higher (p preeclampsia development. PMID:24772969

  18. Clinical Relevance of the Advanced Microbiologic and Biochemical Investigations in Periodontal Diagnosis: A Critical Analysis

    Directory of Open Access Journals (Sweden)

    Vishakha Grover


    Full Text Available New approaches to periodontal diagnosis, including advanced microbiologic, biochemical, and genetic tests, have been shown to provide the clinician with the information not available by traditional means. The purpose of a diagnostic test is to confirm, exclude, classify, or monitor disease to guide treatment. Their clinical value depends on whether the information they provide leads to improved patient outcomes. This can be assessed by randomized trials, which compare patient outcomes from the new diagnostic test versus the old test strategy. Being nonmandatory for marketing approval, such trials are not always feasible because of large sample sizes requirements. So, many diagnostic tests enter the practice without being critically analysed for any additional benefits. Effective diagnosis is just as essential as the selection of effective treatments for the success of periodontal therapy. So, the current paper aims to focus on the practical utility of this rapidly emerging plethora of periodontal diagnostic tools, emphasizing the critical issues surrounding the clinical application of microbiologic and biochemical investigations, employed for periodontal diagnosis.

  19. Integrated Physiological, Biochemical, and Molecular Analysis Identifies Important Traits and Mechanisms Associated with Differential Response of Rice Genotypes to Elevated Temperature


    Sailaja, Boghireddy; Subrahmanyam, Desiraju; Neelamraju, Sarla; Vishnukiran, Turaga; Rao, Yadavalli Venkateswara; Vijayalakshmi, Pujarula; Voleti, Sitapati R.; Bhadana, Vijai P.; Mangrauthia, Satendra K.


    In changing climatic conditions, heat stress caused by high temperature poses a serious threat to rice cultivation. A multiple organizational analysis at physiological, biochemical, and molecular levels is required to fully understand the impact of elevated temperature in rice. This study was aimed at deciphering the elevated temperature response in 11 popular and mega rice cultivars widely grown in India. Physiological and biochemical traits specifically membrane thermostability (MTS), antio...

  20. Comparative biochemical analysis of recombinant reverse transcriptase enzymes of HIV-1 subtype B and subtype C

    Directory of Open Access Journals (Sweden)

    Moisi Daniella


    Full Text Available Abstract Background HIV-1 subtype C infections account for over half of global HIV infections, yet the vast focus of HIV-1 research has been on subtype B viruses which represent less than 12% of the global pandemic. Since HIV-1 reverse transcriptase (RT is a major target of antiviral therapy, and since differential drug resistance pathways have been observed among different HIV subtypes, it is important to study and compare the enzymatic activities of HIV-1 RT derived from each of subtypes B and C as well as to determine the susceptibilities of these enzymes to various RT inhibitors in biochemical assays. Methods Recombinant subtype B and C HIV-1 RTs in heterodimeric form were purified from Escherichia coli and enzyme activities were compared in cell-free assays. The efficiency of (- ssDNA synthesis was measured using gel-based assays with HIV-1 PBS RNA template and tRNA3Lys as primer. Processivity was assayed under single-cycle conditions using both homopolymeric and heteropolymeric RNA templates. Intrinsic RNase H activity was compared using 5'-end labeled RNA template annealed to 3'-end recessed DNA primer in a time course study in the presence and absence of a heparin trap. A mis-incorporation assay was used to assess the fidelity of the two RT enzymes. Drug susceptibility assays were performed both in cell-free assays using recombinant enzymes and in cell culture phenotyping assays. Results The comparative biochemical analyses of recombinant subtype B and subtype C HIV-1 reverse transcriptase indicate that the two enzymes are very similar biochemically in efficiency of tRNA-primed (- ssDNA synthesis, processivity, fidelity and RNase H activity, and that both enzymes show similar susceptibilities to commonly used NRTIs and NNRTIs. Cell culture phenotyping assays confirmed these results. Conclusions Overall enzyme activity and drug susceptibility of HIV-1 subtype C RT are comparable to those of subtype B RT. The use of RT inhibitors (RTIs

  1. Physiochemical, Biochemical, Minerals Content Analysis, and Antioxidant Potential of National and International Honeys in Pakistan

    Directory of Open Access Journals (Sweden)

    Mahmood Ahmed


    Full Text Available 16 honey samples from Pakistan and two other countries were investigated for their physiochemical, biochemical, minerals, and antioxidant potential. Antioxidant activities of all honey samples were performed by using percentage inhibition of DPPH free radical, AEAC, and FRAP. 5-HMF and mineral contents were determined by HPLC and AAS, respectively. The obtained values of respective parameters, namely, pH, EC, TDS, total acidity, moisture, ash, color intensity, sugars, proline, and protein were in compliance with codex standard and recommendation of council directive by European Union. The total phenolics contents in acacia honey from Germany and jujube honey from Pakistan are similar to monofloral honey from Saudi Arabia and Yemen, respectively. The mineral contents in tested honey samples are comparable with honey from Brazil and Romania. Dark color honeys contained higher phenolic contents than light color ones and attributed to higher oxidation potential and have strong positive correlation with DPPH and FRAP.

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


    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 (power of 5mW for 1, 5 and 10minutes, respectively); 45, 230, and (7.5mW for 1, 5 and 10 minutes); and 60, 300 and (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.

  3. Histological and biochemical analysis of DNA damage after BNCT in rat model

    International Nuclear Information System (INIS)

    To understand the mechanism of tumor cell death induced by boron neutron capture therapy (BNCT) and to optimize BNCT condition, we used rat tumor graft models and histological and biochemical analyses were carried out focusing on DNA damage response. Rat lymphosarcoma cells were grafted subcutaneously into male Wister rats. The rats with developed tumors were then treated with neutron beam irradiation 45 min after injection of 330 mg/kg bodyweight boronophenylalanine (10BPA) (+BPA) or saline control (–BPA). BNCT was carried out in the National Nuclear Center of the Republic of Kazakhstan (neutron flux: 1×109 nvt/s, fluence: 6×1011 nvt) with the presence of background γ-irradiation of 33 Gy. 6 and 20 h after BNCT treatment, tumors were resected, fixed and subjected to immunohistochemistry and biochemical analyses. Immunostaining of nuclei showed that double strand break (DSB) marker gamma H2AX staining was high in 20 h/+BPA sample but not in 20 h/–BPA samples. Poly(ADP-ribose), DSB and single strand break markers of DNA, also demonstrated this tendency. These two markers were observed at low levels in unirradiated tissues or 6 h after BNCT either under −BPA and +BPA conditions. HMGB1 level increased in 6 h/+BPA but not in 6 h/−BPA or 20 h/+BPA samples. The persistent staining of γH2AX and poly(ADP-ribose) in +BPA group suggests accumulated DSB damage after BNCT. The early HMGB1 upregulation and γH2AX and poly(ADP-ribose) observed later might be the markers for monitoring the DNA damage induced by BNCT. - Highlights: • We used rat tumor graft models and DNA damage response in BNCT was analyzed. • HMGB1 upregulation was suggested to be an early marker for BNCT. • The persistent presence of γH2AX and PAR in the nuclei might serve as late markers

  4. 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


    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.

  5. Tissue microarrays compared with whole sections and biochemical analyses. A subgroup analysis of DBCG 82 b&c

    DEFF Research Database (Denmark)

    Kyndi, M; Sørensen, Flemming Brandt; Knudsen, H;


    with by increasing the size and number of cores punched from each tumor. No consensus exists on the most optimal size, number, and position of TMA cores in the donor paraffin block and no information exist regarding agreement between TMA cores from two different paraffin blocks from the same tumor or...... between TMA cores and biochemical analyses. PATIENTS AND METHODS: A central and a peripheral 1mm core and a whole section from each of 54 paraffin blocks from 27 breast cancers included in a one-institution cohort, and a single 1mm central TMA core, from each breast tumor from 1000 patients included in...... the DBCG82 b&c trials, were IHC stained for ER, PgR and HER2. In addition, ER and PgR were measured in the DBCG82 b&c trials by a biochemical analysis. Statistical analyses included Kappa statistics, Kaplan-Meier survival curves, Log-rank tests, and Cox regression hazards analyses. RESULTS AND...

  6. Dynamic Analysis of Changes of Protein Levels and Selected Biochemical Indices in Rat Serum in the Course of Experimental Pleurisy. (United States)

    Całkosiński, Ireneusz; Majda, Jacek; Terlecki, Grzegorz; Gostomska-Pampuch, Kinga; Małolepsza-Jarmołowska, Katarzyna; Sobolewska, Sylwia; Całkosińska, Aleksandra; Kumala, Aleksandra; Gamian, Andrzej


    A significant role is played in inflammation by the liver, which, stimulated by inflammatory mediators, synthetizes plasma proteins with various dynamics. The purpose of these studies is to generate a detailed dynamic analysis of changes to concentrations of plasma and serum protein fractions and selected acute-phase proteins as well as nonspecific biochemical indices during the course of an induced pleurisy. The studies were conducted on female inbred Buffalo rats, which were divided into two groups: a control group (C) and an experimental group (IP) in which pleurisy was induced. In the IP group, significant changes in biochemical indices were observed between the 48th and 96th hours of pleurisy. A reduction of albumin, transferrin, urea, and creatinine concentrations was observed, while concentrations of the complement components C3 and C4, haptoglobin, and fibrinogen increased. An early increase of IL-1 was observed, while increases of IL-6 and TNF were noted in the later period. The maximum intensity of the processes described above occurred between the 72nd and 96th hours of pleurisy. PMID:27083876

  7. Supervised Regularized Canonical Correlation Analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery

    Directory of Open Access Journals (Sweden)

    Golugula Abhishek


    Full Text Available Abstract Background Multimodal data, especially imaging and non-imaging data, is being routinely acquired in the context of disease diagnostics; however, computational challenges have limited the ability to quantitatively integrate imaging and non-imaging data channels with different dimensionalities and scales. To the best of our knowledge relatively few attempts have been made to quantitatively fuse such data to construct classifiers and none have attempted to quantitatively combine histology (imaging and proteomic (non-imaging measurements for making diagnostic and prognostic predictions. The objective of this work is to create a common subspace to simultaneously accommodate both the imaging and non-imaging data (and hence data corresponding to different scales and dimensionalities, called a metaspace. This metaspace can be used to build a meta-classifier that produces better classification results than a classifier that is based on a single modality alone. Canonical Correlation Analysis (CCA and Regularized CCA (RCCA are statistical techniques that extract correlations between two modes of data to construct a homogeneous, uniform representation of heterogeneous data channels. In this paper, we present a novel modification to CCA and RCCA, Supervised Regularized Canonical Correlation Analysis (SRCCA, that (1 enables the quantitative integration of data from multiple modalities using a feature selection scheme, (2 is regularized, and (3 is computationally cheap. We leverage this SRCCA framework towards the fusion of proteomic and histologic image signatures for identifying prostate cancer patients at the risk of 5 year biochemical recurrence following radical prostatectomy. Results A cohort of 19 grade, stage matched prostate cancer patients, all of whom had radical prostatectomy, including 10 of whom had biochemical recurrence within 5 years of surgery and 9 of whom did not, were considered in this study. The aim was to construct a lower

  8. Biochemical analysis of whole wheat (triticum aestivum) flour of different wheat cultivars commonly grown in NWFP

    International Nuclear Information System (INIS)

    Whole wheat (Triticum aestivum) flour of six different NWFP wheat (Triticum aestivum) cultivars named as Ghaznavi-98, Auqab, Fakhr-e-sarhad Saleem-2000, Khyber-87 and Pirsabak-2005 were evaluated for Biochemical, Physical and Sensory characteristics in order to highlight their nutritional significance. The maximum level of Protein content (16.11%) was found in wheat cultivar Pirsabak-2005 where as minimum protein content was found in Auqab (11.73%). Crude fat content of whole-wheat flour was found lower in Khyber-87 (1.74%)and higher in Fakhr-e-sarhad (2.21%), Ghaznavi-98 was found to have maximum crude fiber value (0.74%) while Saleem-2000 was found to have minimum value (0.40%). Maximum ash content was found for Fakhr-e-sarhad (2.12%) and minimum was found for Saleem-2000 (1.05%). Wheat cultivars Ghaznavi-98 was found to have maximum moisture content (14%), while Pirsabak-2005 was found to have lower moisture content (13.11%). The wet gluten content was recorded in the range of 8.7 to 5.2% while dry gluten content was found in the ranged of 2.82 to 2.03% and The falling number was recorded in the range of 64 to 214 and significantly higher in saleem-2000 (214). For Sensory Evaluation, it is evidence that maximum overall acceptability were found both for Ghaznavi-98 and Pirsabak-2000 and Minimum for Saleem-2000 (6.4). (author)

  9. 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)


    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.

  10. Design and construction of an equibiaxial cell stretching system that is improved for biochemical analysis. (United States)

    Ursekar, Chaitanya Prashant; Teo, Soo-Kng; Hirata, Hiroaki; Harada, Ichiro; Chiam, Keng-Hwee; Sawada, Yasuhiro


    We describe the design and validation of an equibiaxial stretching device in which cells are confined to regions of homogeneous strain. Using this device, we seek to overcome a significant limitation of existing equibiaxial stretching devices, in which strains are not homogeneous over the entire region of cell culture. We cast PDMS in a mold to produce a membrane with a cylindrical wall incorporated in the center, which was used to confine cell monolayers to the central membrane region subjected to homogeneous equibiaxial strain. We demonstrated that the presence of the wall to hold the culture medium did not affect strain homogeneity over the majority of the culture surface and also showed that cells adhered well onto the PDMS membranes. We used our device in cyclic strain experiments and demonstrated strain-dependent changes in extracellular signal-regulated kinase (ERK) and tyrosine phosphorylation upon cell stretching. Furthermore, we examined cell responses to very small magnitudes of strain ranging from 1% to 6% and were able to observe a graduated increase in ERK phosphorylation in response to these strains. Collectively, we were able to study cellular biochemical response with a high degree of accuracy and sensitivity to fine changes in substrate strain. Because we have designed our device along the lines of existing equibiaxial stretching technologies, we believe that our innovations can be incorporated into existing systems. This device would provide a useful addition to the set of tools applied for in vitro studies of cell mechanobiology. PMID:24626190

  11. Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics (United States)

    Naruemon, Rueangkham; Charin, Modchang


    Most biochemical processes in cells are usually modeled by reaction–diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations. Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

  12. Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae). (United States)

    Casimiro-Soriguer, Inés; Narbona, Eduardo; Buide, M L; Del Valle, José C; Whittall, Justen B


    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 (ABP). 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 paralogs for the 15 candidate genes in the ABP. We assembled complete coding sequences for 16 structural loci and nine of ten regulatory loci. Among these 29 putative paralogs, 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 by downregulation of Myb1a. PMID:26973662

  13. Biochemical analysis of SV40 small t mediated theophylline resistance in CV-1 cells

    International Nuclear Information System (INIS)

    The papovavirus SV40 encodes for the two tumor antigens, large T and small t. While much is known about large T, little information is available about the role of small t in the viral life cycle. The authors have developed a system for studying small t antigen based on its ability to overcome the G0 growth arrest induced by the methylxanthine, theophylline. Uninfected CV-1 cells, the permissive host for SV40, are arrested by 1-2mM theophylline. In contrast, Wt-infected cells are not arrested by the same concentrations of this drug. Biochemical studies were designed to analyze the effects of theophylline and the means by which small t can overcome the growth arrest of CV-1 cells. Theophylline, a cyclic AMP analogue, does not appear to arrest CV-1 cells by a cAMP-dependent mechanism. Theophylline appears to arrest CV-1 cells by inhibiting sodium influx. Both 86Rb+ and 22Na+ uptake were inhibited by theophylline. Amiloride and TMB-8, drugs which are known to inhibit the plasma membrane Na+/H+ antiporter, decreased 86Rb+ and 22Na+ uptake to the same degree as theophylline. Because these drugs also arrested mock and D1- but not Wt-infected cells it is possible that theophylline inhibits sodium uptake by inhibiting this antiporter. Furthermore, because Wt-infected cells are resistant to the growth arrest induced by these drugs, it is possible that small t acts either by directly altering this antiporter or by bypassing the step which requires the activity of the antiporter

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

    Institute of Scientific and Technical Information of China (English)

    Constanza Liggieri; Walter Obregòn; Sebastian Trejo; Nora Priolo


    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 iso-lated 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 character-istics, 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 inhib-ited by cysteine proteases inhibitors like E-64, but not by any other protease inhibitors such as 1,10-phenantroline, phenylmethanesulfonyl fluoride, and pepstatine. The N-terminal sequence (LPSFVDWRQKGVVFPIRNQGQ CGSCWTFSA) showed a high similarity with those of other plant cysteine proteinases. When assayed on N-α-CBZ-amino acid-p-nitrophenyl esters, the enzyme exhibited higher preference for the glutamine derivative. Determinations of kinetic parameters were performed with N-α-CBZ-L-Gln-p-nitrophenyl ester as substrate: Km=0.1634 mM, kcat=121.48 s-1, and kcat/Km =7.4×105 s-1/mM.

  15. Acromegaly Clinical Trial Methodology Impact on Reported Biochemical Efficacy Rates of Somatostatin Receptor Ligand Treatments: A Meta-Analysis


    CARMICHAEL, JOHN D.; Bonert, Vivien S.; Nuño, Miriam; Ly, Diana; Melmed, Shlomo


    Introduction: Biochemical efficacy of somatostatin receptor ligand (SRL) treatment in acromegaly is defined by metrics for GH and IGF-1 control. Since the earliest therapeutic trials, biochemical control criteria, medical formulations, and assay techniques have evolved. Materials and Methods: We searched PubMed for English-language trials published from 1974 to 2012 evaluating 10 or more patients, with a duration of more than 3 months and biochemical control as a key objective. We used a rand...

  16. Some Genetic, Biochemical and Morphological Analysis of Selected Powdery Mildew Strains at the Beginning of Sporulation on Barley

    Directory of Open Access Journals (Sweden)



    Full Text Available The present work analyzes some characteristics of four powdery mildew pathotypes, RU-3, Sk-5/11, Sk-12/1 and A-4/0, selected from the wild strains of BGH from Central European regions. Our results showed that the studied BGH strains differ in the virulence and avirulence genes in their genomes, in prolongation of their asexual phase of the growth and also in morphological and biochemical characteristics. Protein analysis confirmed the genetic differences between the studied powdery mildew pathotypes. Abundant acid glucanases in all studied BHG pathotypes were found between molecular weights Mr ? 25-35 kDa and 11-22kDa. Races RU-3 and A-4/0 also contained low molecular weight glucanases with Mr ? 9-14kDa. Immunological analyses showed higher specificity of pathogen chitinases to plant antibody compared to barley cultivars carrying different dominant/semidominant resistance genes. Rabbit antibody prepared against the plant interacellular acid chitinase Chi 14.4 (PR-4 gave the positive signal for two powdery mildew races, Sk-5/11 and A-4/0. These pathotypes were more aggressive compared to races Sk-12/1 and RU-3. Their genomes contained more virulence genes and asexual phase of the growth was shorter. Ultrastructural analyses of BGH body in the sensitive barley cultivar cells, showed presence of virus like particles, which probably play role by the synthesis of some PR-proteins with hydrolytic function. Genetic and biochemical analyses indicate that some powdery mildew pathotypes contain genes in their genome which are orthological to those in their hosts, which makes them suitable subjects for the future as a source of new resistance genes for plant breeding.

  17. A sensitive ferricyanide-mediated biochemical oxygen demand assay for analysis of wastewater treatment plant influents and treated effluents. (United States)

    Jordan, Mark A; Welsh, David T; John, Richard; Catterall, Kylie; Teasdale, Peter R


    Representative and fast monitoring of wastewater influent and effluent biochemical oxygen demand (BOD) is an elusive goal for the wastewater industry and regulatory bodies alike. The present study describes a suitable assay, which incorporates activated sludge as the biocatalyst and ferricyanide as the terminal electron acceptor for respiration. A number of different sludges and sludge treatments were investigated, primarily to improve the sensitivity of the assay. A limit of detection (LOD) (2.1 mg BOD₅ L⁻¹) very similar to that of the standard 5-day BOD₅ method was achieved in 4 h using raw influent sludge that had been cultured overnight as the biocatalyst. Reducing the microbial concentration was the most effective means to improve sensitivity and reduce the contribution of the sludge's endogenous respiration to total ferricyanide-mediated (FM) respiration. A strong and highly significant relationship was found (n = 33; R = 0.96; p treatment plant (WWTP) influent and treated effluent, as well as several grey water samples. The activated sludge FM-BOD assay presented here is an exceptional surrogate method to the standard BOD₅ assay, providing representative, same-day BOD analysis of WWTP samples with a comparable detection limit, a 4-fold greater analytical range and much faster analysis time. The industry appeal of such an assay is tremendous given that ~90% of all BOD₅ analysis is dedicated to measurement of WWTP samples, for which this assay is specifically designed. PMID:23200506

  18. Attention-deficit hyperactivity disorder in adults: A systematic review and meta-analysis of genetic, pharmacogenetic and biochemical studies. (United States)

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


    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

  19. 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.


    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.

  20. 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.

  1. Biochemical Analysis of Autophagy in Algae and Plants by Monitoring the Electrophoretic Mobility of ATG8. (United States)

    Pérez-Pérez, María Esther; Andrés-Garrido, Ascensión; Crespo, José L


    Identification of specific autophagy markers has been fundamental to investigate autophagy as catabolic process. Among them, the ATG8 protein turned out to be one of the most widely used and specific molecular markers of autophagy both in higher and lower eukaryotes. Here, we describe how ATG8 can be used to monitor autophagy in Chlamydomonas and Arabidopsis by western blot analysis. PMID:27424752

  2. 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


    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.

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

    International Nuclear Information System (INIS)

    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

  4. Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways. (United States)

    Hudson, André O; Harkness, Taylor C M; Savka, Michael A


    Functional complementation assay (FCA) is an in vivo assay that is widely used to elucidate the function/role of genes/enzymes. This technique is very common in biochemistry, genetics and many other disciplines. A comprehensive overview of the technique to supplement the teaching of biochemical pathways pertaining to amino acids, peptidoglycan and the bacterial stringent response is reported in this manuscript. Two cDNAs from the model plant organism Arabidopsis thaliana that are involved in the metabolism of lysine (L,L-diaminopimelate aminotransferase (dapL) and tyrosine aminotransferase (tyrB) involved in the metabolism of tyrosine and phenylalanine are highlighted. In addition, the bacterial peptidoglycan anabolic pathway is highlighted through the analysis of the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-meso-2,6-diaminopimelate ligase (murE) gene from the bacterium Verrucomicrobium spinosum involved in the cross-linking of peptidoglycan. The bacterial stringent response is also reported through the analysis of the rsh (relA/spoT homolog) bifunctional gene responsible for a hyper-mucoid phenotype in the bacterium Novosphingobium sp. Four examples of FCA are presented. The video will focus on three of them, namely lysine, peptidoglycan and the stringent response. PMID:27403640

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

    DEFF Research Database (Denmark)

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


    -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 to be...

  6. Biochemical and molecular characterization of thyroid tissue by micro-Raman spectroscopy and gene expression analysis (United States)

    Neto, Lázaro P. M.; Martin, Aírton A.; Soto, Claudio A. T.; Santos, André B. O.; Mello, Evandro S.; Pereira, Marina A.; Cernea, Cláudio R.; Brandão, Lenine G.; Canevari, Renata A.


    Thyroid carcinomas represent the main endocrine malignancy and their diagnosis may produce inconclusive results. Raman spectroscopy and gene expression analysis have shown excellent results on the differentiation of carcinomas. This study aimed to improve the discrimination between different thyroid pathologies combining of both analyses. A total of 35 thyroid tissues samples including normal tissue (n=10), goiter (n=10), papillary (n=10) and follicular carcinomas (n=5) were analyzed. Confocal Raman spectra was obtain by using a Rivers Diagnostic System, 785 nm laser excitation and CCD detector. The data was processed by the software Labspec5 and Origin 8.5 and analyzed by Minitab® program. The gene expression analysis was performed by qRT-PCR technique for TG, TPO, PDGFB, SERPINA1, LGALS3 and TFF3 genes and statistically analyzed by Mann-Whitney test. The confocal Raman spectroscopy allowed a maximum discrimination of 91.1% between normal and tumor tissues, 84.8% between benign and malignant pathologies and 84.6% among carcinomas analyzed. Significant differences was observed for TG, LGALS3, SERPINA1 and TFF3 genes between benign lesions and carcinomas, and SERPINA1 and TFF3 genes between papillary and follicular carcinomas. Principal component analysis was performed using PC1 and PC2 in the papillary carcinoma samples that showed over gene expression when compared with normal sample, where 90% of discrimination was observed at the Amide 1 (1655 cm-1), and at the tyrosine spectra region (856 cm-1). The discrimination of tissues thyroid carried out by confocal Raman spectroscopy and gene expression analysis indicate that these techniques are promising tools to be used in the diagnosis of thyroid lesions.

  7. Recent advances in biochemical and molecular analysis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency (United States)

    Kim, Gu-Hwan; Yoo, Han-Wook


    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. PMID:27104172

  8. Recent advances in biochemical and molecular analysis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency. (United States)

    Choi, Jin-Ho; Kim, Gu-Hwan; Yoo, Han-Wook


    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. PMID:27104172

  9. Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis. (United States)

    Lenka, Sangram K; Carbonaro, Nicole; Park, Rudolph; Miller, Stephen M; Thorpe, Ian; Li, Yantao


    Triacylglycerols (TAGs) are highly reduced energy storage molecules ideal for biodiesel production. Microalgal TAG biosynthesis has been studied extensively in recent years, both at the molecular level and systems level through experimental studies and computational modeling. However, discussions of the strategies and products of the experimental and modeling approaches are rarely integrated and summarized together in a way that promotes collaboration among modelers and biologists in this field. In this review, we outline advances toward understanding the cellular and molecular factors regulating TAG biosynthesis in unicellular microalgae with an emphasis on recent studies on rate-limiting steps in fatty acid and TAG synthesis, while also highlighting new insights obtained from the integration of multi-omics datasets with mathematical models. Computational methodologies such as kinetic modeling, metabolic flux analysis, and new variants of flux balance analysis are explained in detail. We discuss how these methods have been used to simulate algae growth and lipid metabolism in response to changing culture conditions and how they have been used in conjunction with experimental validations. Since emerging evidence indicates that TAG synthesis in microalgae operates through coordinated crosstalk between multiple pathways in diverse subcellular destinations including the endoplasmic reticulum and plastids, we discuss new experimental studies and models that incorporate these findings for discovering key regulatory checkpoints. Finally, we describe tools for genetic manipulation of microalgae and their potential for future rational algal strain design. This comprehensive review explores the potential synergistic impact of pathway analysis, computational approaches, and molecular genetic manipulation strategies on improving TAG production in microalgae. PMID:27321475

  10. Sequential analysis of biochemical markers of bone resorption and bone densitometry in multiple myeloma

    DEFF Research Database (Denmark)

    Abildgaard, Niels; Brixen, Kim; Eriksen, Erik Fink; Kristensen, Jens Erik; Nielsen, Johan Lanng; Heickendorff, Lene


    less informative. In Cox analysis, ICTP showed the highest predictive value, but should be replaced with NTx in patients with nephropathy. Pretreatment low lumbar BMD was predictive of early vertebral fractures. INTERPRETATION AND CONCLUSIONS: Sequential DEXA-scans showed heterogeneous local BMD...... changes, and our data do not support routine use of sequential DEXA-scans. However, lumbar DEXA-scans at diagnosis can identify patients with increased risk of early vertebral collapses. Sequential analyses of serum ICTP and urinary NTx are useful for monitoring bone damage....

  11. Enzyme and biochemical producing fungi

    DEFF Research Database (Denmark)

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


    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....

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

    International Nuclear Information System (INIS)

    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

  13. Physical activity and lifestyle effects on bone mineral density among young adults: sociodemographic and biochemical analysis. (United States)

    Alghadir, Ahmad H; Gabr, Sami A; Al-Eisa, Einas


    [Purpose] The purpose of this study was to assess the possible role of physical activities, calcium consumption and lifestyle factors in both bone mineral density and bone metabolism indices in 350 young adult volunteers. [Subjects and Methods] All volunteers were recruited for the assessment of lifestyle behaviors and physical activity traits using validated questioners, and bone mineral density (BMD), serum osteocalcin (s-OC), bone-specific alkaline phosphatase (BAP), and calcium were estimated using dual-energy X-ray absorptiometry analysis, and immunoassay techniques. [Results] Male participants showed a significant increase in BMD along with an increase in bone metabolism markers compared with females in all groups. However, younger subjects showed a significant increase in BMD, OC, BAP, and calcium compared with older subjects. Osteoporosis was more common in older subjects linked with abnormal body mass index and waist circumference. Bone metabolism markers correlated positively with BMD, physically activity and negatively with osteoporosis in all stages. Also, moderate to higher calcium and milk intake correlated positively with higher BMD. However, low calcium and milk intake along with higher caffeine, and carbonated beverage consumption, and heavy cigarette smoking showed a negative effect on the status of bone mineral density. Stepwise regression analysis showed that life style factors including physical activity and demographic parameters explained around 58-69.8% of the bone mineral density variation in young adults especially females. [Conclusion] body mass index, physical activity, low calcium consumption, and abnormal lifestyle have role in bone mineral density and prognosis of osteoporosis in young adults. PMID:26311965

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

    Directory of Open Access Journals (Sweden)

    Eleni Ntokou

    Full Text Available 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 homology and may be evolutionarily linked to a common ancestor. To explore their individual specificity and similarity we performed two sets of experiments. We created a homology model of Cfr and explored the C2/C8 specificity using docking and binding energy calculations on the Cfr homology model and an X-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 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 to be responsible for the C2/C8 specificity and most of the combinations involve interchanging segments at this site. Almost all replacements showed no function in the primer extension assay, apart from a few that had a weak effect. Thus Cfr and RlmN appear to be much less similar than expected from their sequence similarity and common target.

  15. Genome-Wide Analysis of the Glutathione S-Transferase Gene Family in Capsella rubella: Identification, Expression, and Biochemical Functions (United States)

    He, Gang; Guan, Chao-Nan; Chen, Qiang-Xin; Gou, Xiao-Jun; Liu, Wei; Zeng, Qing-Yin; Lan, Ting


    Extensive subfunctionalization might explain why so many genes have been maintained after gene duplication, which provides the engine for gene family expansion. However, it is still a particular challenge to trace the evolutionary dynamics and features of functional divergences in a supergene family over the course of evolution. In this study, we identified 49 Glutathione S-transferase (GST) genes from the Capsella rubella, a close relative of Arabidopsis thaliana and a member of the mustard family. Capsella GSTs can be categorized into eight classes, with tau and phi GSTs being the most numerous. The expansion of the two classes mainly occurs through tandem gene duplication, which results in tandem-arrayed gene clusters on chromosomes. By integrating phylogenetic analysis, expression patterns, and biochemical functions of Capsella and Arabidopsis GSTs, functional divergence, both in gene expression and enzymatic properties, were clearly observed in paralogous gene pairs in Capsella (even the most recent duplicates), and orthologous GSTs in Arabidopsis/Capsella. This study provides functional evidence for the expansion and organization of a large gene family in closely related species.

  16. Morphological, Biochemical and Genetic Analysis of a Brittle Stalk Mutant of Maize Inserted by Mutator

    Institute of Scientific and Technical Information of China (English)

    FU Xue-qian; FENG Jing; YU Bin; GAO You-jun; ZHENG Yong-lian; YUE Bing


    Mutants on stalk strength are essential materials for the studies on the formation of plant cell wall. In this study, a brittle stalk mutant of maize, designated as Bk-x, was screened from a Mutator inserted mutant library. At the germination and early seedling stage, the mutant plants were indistinguishable from the normal ones. However, all of the plant organs were brittle after the 5th-leaf stage and remained brittle throughout the rest of the growing period. Microstructure observation showed that the cell wall in vascular bundle sheath of Bk-x was thinner than that in normal plants. The leaf mechanical strength in Bk-x was 77.9%of that in normal plants growing at Xishuangbanna (BN), Yunnan province and that was 61.7%in Wuhan (WH), Hubei Province, China. The proportion of cellulose was 12.3%in Bk-x, which was significantly lower than that in normal plants (26.7%), while the soluble sugar content was 36.1%in Bk-x, which is significantly higher than that in normal plants (12.4%). Genetic analysis using two F2 populations and one F2:3 families demonstrated that the trait of brittle stalk is controlled by a single recessive gene.

  17. Somaclonal variation: a morphogenetic and biochemical analysis of Mandevilla velutina cultured cells

    Directory of Open Access Journals (Sweden)

    M. Maraschin


    Full Text Available Cell cultures of Mandevilla velutina have proved to be an interesting production system for biomass and secondary metabolites able to inhibit the hypotensive activity of bradykinin, a nonapeptide generated in plasma during tissue trauma. The crude ethyl acetate extract of cultured cells contains about 31- to 79-fold more potent anti-bradykinin compounds (e.g., velutinol A than that obtained with equivalent extracts of tubers. Somaclonal variation may be an explanation for the wide range of inhibitor activity found in the cell cultures. The heterogeneity concerning morphology, differentiation, carbon dissimilation, and velutinol A production in M. velutina cell cultures is reported. Cell cultures showed an asynchronous growth and cells in distinct developmental stages. Meristematic cells were found as the major type, with several morphological variations. Cell aggregates consisting only of meristematic cells, differentiated cells containing specialized cell structures such as functional chloroplasts (cytodifferentiation and cells with embryogenetic characteristics were observed. The time course for sucrose metabolism indicated cell populations with significant differences in growth and metabolic rates, with the highest biomass-producing cell line showing a cell cycle 60% shorter and a metabolic rate 33.6% higher than the control (F2 cell population. MALDI-TOF mass spectrometric analysis of velutinol A in selected cell lines demonstrated the existence of velutinol A producing and nonproducing somaclones. These results point to a high genetic heterogeneity in general and also in terms of secondary metabolite content.

  18. Biochemical analysis of myeloid antigens and cDNA expression of gp55 (CD14)

    International Nuclear Information System (INIS)

    The authors have analyzed the reactivity patterns of the myeloid panel of mAbs by immunoprecipitation and SDS-PAGE analysis of 125I-labelled membrane extracts and surface binding to transfected COS7 and L-cells expressing specific gene products. Forty-seven of the 150 myeloid antibodies precipitated recognizable protein products. Fifteen mAbs reacted with molecules of 160-170kDa, four reacted with molecules of 220kDa, two reacted with molecules of 43kDa, and five reacted with molecules of 130- 140kDa. Several others reacted with protein products that did not fall into any of these categories. By surface binding to COS7 cells transfected with a specific gp55 (CD14) cDNA clone, 20 mAbs were shown to have reactivity with the gp55 molecule. Similarly, surface binding to transfected L-cells expressing a 130-140kDa (CD31) product demonstrated that two mAbs had a unique specificity

  19. The qualitative analysis of biochemical content in textbooks of elementary school

    Directory of Open Access Journals (Sweden)

    K. W.M. Etcheverria et al


    Full Text Available Introduction: Biochemistry is the science that deals with the metabolic functions of living beings. In its concepts, it uses chemistry and biology to study the interactions of organisms with the environment. For basic education students is often complex the association of biochemistry with their daily lives, especially in elementary school where they have their first contact with science in school and the didactic book will serve as an important tool for research. Thus, this work aims to analyze qualitatively content related to biochemistry in science books of the final years of elementary school. Methods: We analyzed six science books used in elementary school, and the following criteria were examined: clarity and language presented on the inserted content; resolutions and images shown subtitles, and interdisciplinarity of matters. Results and discussion: The books of the sixth and fifth years were those who achieved the expected learning goals. The first of then made a very good presentation of the content and the images, addressing the subject in an interdisciplinary way. However, the second one is well below in the analyzed criteria, bringing the matter in a vague writing, and failing in associate the content with other assumptions themes. The images had a very low quality and their explanations were difficult to associate. Conclusion: We can say that the biochemistry content are complex, however its development from the beginning of primary education contributes to overcoming the complexity of their understanding. The analysis of the books brought a result that was expected. Only one book had significantly positive results in all analyzed characteristics, the other books had some very good aspects, but in several details, they were vague and poorly contextualized. Approaching the school sciences to the student every day we can demystify scientific knowledge and its production.

  20. Energy status of dairy cows determined by biochemical analysis of organic components of milk

    Directory of Open Access Journals (Sweden)

    Šamanc Horea


    Full Text Available Valid indicators of the energy status of cows are the body condition, parameters of the metabolic profile, hormonal status, and organic components of milk. The energy status of cows of the Holstein-Friesian breed from four farms was estimated on the grounds of urea, protein and fat concentration in milk. Investigations covered 62 samples of milk (11 from farm A, 16 from farm B, 15 from farm C, and 20 from farm D. All cows were in the first stage of lactation and fed rations recommended for that category of animal. The average fat concentration in all milk samples was 23±13 g/l, the average protein concentration was 29±3 g/l, while the average urea concentration was 4.6±1.3 mmol/l. It could be concluded on the basis of the value for the milk fat concentration alone that a decreased milk fat syndrome was present. In addition, graphic presentations are given for the relation between urea concentration and protein concentration, as well as protein and fat concentrations in the individual milk samples. Such an analysis provided a more detailed picture of the energy status of the examined cows. It was established that cows on farm A had a deficiency of energy and protein, and cows on farms B and C a deficiency of energy with a relative surplus of proteins. It was established that cows from farm D had a deficiency of energy, and there was an equal number of cows with a deficiency and with a relative surplus of proteins. The obtained results provide grounds for making recommendations for correcting the feed rations and improving the health of the cows. It stems from the obtained results that the determination of urea, fat and protein concentrations in milk is a reliable indicator of the energy status of cows, that it is rational and financially acceptable for every producer, regardless of whether it is implemented in small or large cattle farms. The diagnostic procedures used so far have been implemented in a limited form in daily practice because of

  1. Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant. (United States)

    Wang, Yue-zhi; Zhang, Shujun; Dai, Mei-song; Shi, Ze-bin


    Exocarp color of sand pear is an important trait for the fruit production and has caused our concern for a long time. Our previous study explored the different expression genes between the two genotypes contrasting for exocarp color, which indicated the different suberin, cutin, wax and lignin biosynthesis between the russet- and green-exocarp. In this study, we carried out microscopic observation and Fourier transform infrared spectroscopy analysis to detect the differences of tissue structure and biochemical composition between the russet- and green-exocarp of sand pear. The green exocarp was covered with epidermis and cuticle which was replaced by a cork layer on the surface of russet exocarp, and the chemicals of the russet exocarp were characterized by lignin, cellulose and hemicellulose. We explored differential gene expression between the russet exocarp of 'Niitaka' and its green exocarp mutant cv. 'Suisho' using Illumina RNA-sequencing. A total of 559 unigenes showed different expression between the two types of exocarp, and 123 of them were common to the previous study. The quantitative real time-PCR analysis supports the RNA-seq-derived gene with different expression between the two types of exocarp and revealed the preferential expression of these genes in exocarp than in mesocarp and fruit core. Gene ontology enrichment analysis revealed divorced expression of lipid metabolic process genes, transport genes, stress responsive genes and other biological process genes in the two types of exocarp. Expression changes in lignin metabolism-related genes were consistent with the different pigmentation of russet and green exocarp. Increased transcripts of putative genes involved the suberin, cutin and wax biosynthesis in 'Suisho' exocarp could facilitate deposition of the chemicals and take a role in the mutant trait responsible for the green exocarp. In addition, the divorced expression of ATP-binding cassette transporters involved in the trans

  2. Impact of glutathione-S-transferases (GST polymorphisms and hypermethylation of relevant genes on risk of prostate cancer biochemical recurrence: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Rui Chen

    Full Text Available INTRODUCTION: Accurate prediction of the biochemical recurrence (BCR is critical for patients after intended curative therapy like radical prostatectomy (RP or definitive radiotherapy for prostate cancer. Glutathione-S-transferases polymorphisms as well as hypermethylation of GSTP1 and functional genes in carcinogenesis, including tumor suppression gene (APC, hormone receptor that regulates cell growth and differentiation gene (RARbeta were reported to be associated with BCR. Nevertheless, the reported results are inconsistent. To evaluate the relationship between glutathione-S-transferases polymorphisms and hypermethylation of these genes and the risk of prostate cancer BCR, we carried out a meta-analysis of the published studies. METHODS AND MATERIALS: We performed a search in Medline, Embase and CNKI database with GST, APC, RARbeta in combination with single nucleotide polymorphism, hypermethylation, prostate cancer and recurrence. Languages were restricted to English and Chinese. RESULTS: Our study included 4 case-control studies and 7 cohort studies including 12 data sets and 3,037 prostate cancer patients. We confirmed that APC hypermethylation is associated with a modest hazard for biochemical recurrence after RP (HR = 1.85, 95%CI = 1.12-3.06. We also suggest GSTP1 polymorphism and CpG hypermethylation tested in serum are associated with BCR (HR = 1.94, 95%CI = 1.13-3.34. We also identified a possible association between GSTM1 null polymorphism and prostate cancer biochemical recurrence risk with borderline significance (HR = 1.29, 95%CI = 0.97-1.71. CONCLUSION: To our knowledge, this is the first meta-analysis evaluating the relationship of polymorphisms and hypermethylation in GSTs and biochemical recurrence. GSTM1, GSTP1 polymorphisms and hypermethylation of GSTP1, APC may be potential biomarkers for the evaluation of the probability of BCR. Further studies are warranted to validate these findings in larger cohorts with longer follow-up.

  3. 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


    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

  4. 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


    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.

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

    International Nuclear Information System (INIS)

    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)

  6. Comparative biochemical analysis of three members of the Schistosoma mansoni TAL family: Differences in ion and drug binding properties


    Thomas, Charlotte M.; Fitzsimmons, Colin M; Dunne, David W.; Timson, David J


    The tegumental allergen-like (TAL) proteins from Schistosoma mansoni are part of a family of calcium binding proteins found only in parasitic flatworms. These proteins have attracted interest as potential drug or vaccine targets, yet comparatively little is known about their biochemistry. Here, we compared the biochemical properties of three members of this family: SmTAL1 (Sm22.6), SmTAL2 (Sm21.7) and SmTAL3 (Sm20.8). Molecular modelling suggested that, despite similarities in domain organisa...

  7. A Novel Three Domains Glycoside Hydrolase Family 3 from Sclerotinia sclerotiorum Exhibits β-Glucosidase and Exoglucanase Activities: Molecular, Biochemical, and Transglycosylation Potential Analysis. (United States)

    Chahed, Haifa; Ezzine, Aymen; Mlouka, Mohamed Amine Ben; Rihouey, Christophe; Hardouin, Julie; Jouenne, Thierry; Marzouki, M Nejib


    The filamentous fungus Sclerotinia sclerotiorum produces a complete set of cellulolytic enzymes. We report here the purification and the biochemical characterization of a new β-glucosidase from S. sclerotiorum which belongs to the family 3 of glycoside hydrolases and that was named as SsBgl3. After two size-exclusion chromatography steps, purified protein bands of 80 and 90 kDa from SDS-PAGE were subjected to a mass spectrometry analysis. The results displayed four peptides from the upper band belonging to a polypeptide of 777 amino acids having a calculated molecular weight of 83.7 kDa. Biochemical analysis has been carried out to determine some properties. We showed that this SsBgl3 protein displayed both β-glucosidase and exoglucanase activities with optimal activity at 55 °C and at pH 5. The transglycosylation activity was investigated using gluco-oligosaccharides TLC analysis. The molecular modeling and comparison with different crystal structures of β-glucosidases showed that SsBgl3 putative protein present three domains. They correspond to an (α/β)8 domain TIM barrel, a five-stranded α/β sandwich domain (both of which are important for active-site organization), and a C-terminal fibronectin type III domain. Enzyme engineering will be soon investigated to identify the key residues for the catalytic reactions. PMID:26385478

  8. Rapid Biochemical Analysis on the International Space Station (ISS): Preparing for Human Exploration of the Moon and Mars (United States)

    Maule, J.; Morris, Heather; Monaco, L.; Steele, A.; Wainwright, N.


    The Lab-on-a-Chip Application Development - Portable Test System, known as LOCAD-PTS, was launched to the International Space Station (ISS) aboard Space Shuttle Discovery (STS-116) on December 9th,2006. Since that time, it has remained onboard ISS and has been operated by the crew on 10 separate occasions LOCAD-PTS is a handheld device for rapid biochemical analysis; it consists of a spectrophotometer, a series of interchangeable cartridges, a pipette and several clean/sterilized swabbing kits to obtain samples from ISS surfaces. Sampling, quantitative analysis and data retrieval is performed onboard, therefore reducing the need to return samples to Earth. Less than 20 minutes are required from sampling to data, significantly faster than existing culture-based methods on ISS, which require 3-5 days. Different cartridges are available for the detection of different target molecules (simply by changing the formulation within each cartridge), thereby maximizing the benefit and applications addressed by a single instrument. Initial tests on ISS have focused on the detection of the bact.erial macromolecule endotoxin, a component of bacterial cell walls. LOCAD-PTS detects endotoxin with a cartridge that contains a formulation known as Limulus Amebocyte Lysate (LAL) assay. LAL is derived from blood of the horseshoe crab, Limulus polyphemus, and detects enodotoxin with an enzyme cascade that triggers generation Of a yellow colored dye, p-nitroanaline. The more p-nitroanaline product, the more endotoxin is in the original sample. To enable quantitative analysis, the absorbance of this color is measured by LOCAD-PTS through a 395 nm filter and compared with an internal calibration curve, to provide a reading on the LED display that ranges from 0.05 Endotoxin Units (EU)/ml to 5 EU/ml. Several surface sites were analyzed within ISS between March 2007 and February 2008, including multiple locations in the US Laboratory Destiny, Node 1 Unity, AMock, and Service Module Zvezda

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

    International Nuclear Information System (INIS)

    Purpose: To define the optimal dose for 125I 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 125I 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

  10. 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: [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)


    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.

  11. Serum Biochemical Phenotypes in the Domestic Dog (United States)

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.


    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  12. 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


    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.

  13. Biochemical analysis of PIFTC3, the Trypanosoma brucei orthologue of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components. (United States)

    Franklin, Joseph B; Ullu, Elisabetta


    DYF-13, originally identified in Caenorhabditis elegans within a collection of dye-filling chemosensory mutants, is one of several proteins that have been classified as putatively involved in intraflagellar transport (IFT), the bidirectional movement of protein complexes along cilia and flagella and specifically in anterograde IFT. Although genetic studies have highlighted a fundamental role of DYF-13 in nematode sensory cilium and trypanosome flagellum biogenesis, biochemical studies on DYF-13 have lagged behind. Here, we show that in Trypanosoma brucei the orthologue to DYF-13, PIFTC3, participates in a macromolecular complex of approximately 660 kDa. Mass spectroscopy of affinity-purified PIFTC3 revealed several components of IFT complex B as well as orthologues of putative IFT factors DYF-1, DYF-3, DYF-11/Elipsa and IFTA-2. DYF-11 was further analysed and shown to be concentrated near the basal bodies and in the flagellum, and to be required for flagellum elongation. In addition, by coimmunoprecipitation we detected an interaction between DYF-13 and IFT122, a component of IFT complex A, which is required for retrograde transport. Thus, our biochemical analysis supports the model, proposed by genetic analysis in C. elegans, that the trypanosome orthologue of DYF-13 plays a central role in the IFT mechanism. PMID:20923419

  14. Quantitative Raman spectral changes of the differentiation of mesenchymal stem cells into islet-like cells by biochemical component analysis and multiple peak fitting (United States)

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


    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.

  15. A monoclonal antibody against a canine CD45 homologue: analysis of tissue distribution, biochemical properties and in vitro immunological activity. (United States)

    Aguiar, Paulo Henrique Palis; Barrouin-Melo, Stella Maria; Franke, Carlos Roberto; dos Santos, Roberto Robson Borges; Silva, Tânia Maria Correia; Mengel, José O; dos-Santos, Washington Luis Conrado; Pontes-de-Carvalho, Lain


    This report describes the characterisation of a monoclonal antibody (mAb), AB6, which recognises specifically a cluster of canine leukocyte surface molecules. The immunogen used for obtaining the AB6 mAb was a lysate of canine peripheral blood mononuclear cells (PBMC). This novel mAb belongs to the IgG2a isotype, and reacted in Western blot with four different canine leukocyte glycoproteins with apparent molecular weights of 180, 190, 205 and 220 kDa. The AB6 mAb recognised the majority of canine peripheral blood leukocytes as determined by flow cytometry (97%). It also exhibited a broad reactivity pattern against lymphoid and myeloid cells, inhibited the proliferation of mitogen-stimulated canine PBMC and did not recognise human PBMC and murine splenocytes. The biochemical properties, cell and tissue specificity, and in vitro biological activity of the AB6 mAb indicate that it recognises a canine CD45 homologue. The mAb could become a valuable diagnostic and research tool for the evaluation of immune functions in dogs. PMID:16249107

  16. Oligomerization of the human immunodeficiency virus type 1 (HIV-1 Vpu protein – a genetic, biochemical and biophysical analysis

    Directory of Open Access Journals (Sweden)

    Tanwar Charu


    Full Text Available Abstract Background The human immunodeficiency virus type 1(HIV-1 is a complex retrovirus and the causative agent of acquired immunodeficiency syndrome (AIDS. The HIV-1 Vpu protein is an oligomeric integral membrane protein essential for particle release, viral load and CD4 degradation. In silico models show Vpu to form pentamers with an ion channel activity. Results Using Vpu proteins from a primary subtype C and the pNL4-3 subtype B isolates of HIV-1, we show oligomerization of the full-length protein as well as its transmembrane (TM domain by genetic, biochemical and biophysical methods. We also provide direct evidence of the presence of Vpu pentamers in a stable equilibrium with its monomers in vitro. This was also true for the TM domain of Vpu. Confocal microscopy localized Vpu to the endoplasmic reticulum and Golgi regions of the cell, as well as to post-Golgi vesicles. In fluorescence resonance energy transfer (FRET experiments in live cells we show that Vpu oligomerizes in what appears to be either the Golgi region or intracellular vesicles, but not in the ER. Conclusion We provide here direct evidence that the TM domain, is critical for Vpu oligomerization and the most favourable channel assembly is a pentamer. The Vpu oligomerization appears to be either the Golgi region or intracellular vesicles, but not in the ER.

  17. 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.

  18. Biochemical analysis of the interaction of calcium with toposome: a major protein component of the sea urchin egg and embryo. (United States)

    Hayley, Michael; Sun, Ming; Merschrod, Erika F; Davis, Philip J; Robinson, John J


    We have investigated the biochemical and functional properties of toposome, a major protein component of sea urchin eggs and embryos. Atomic force microscopy was utilized to demonstrate that a Ca(2+)-driven change in secondary structure facilitated toposome binding to a lipid bilayer. Thermal denaturation studies showed that toposome was dependent upon calcium in a manner paralleling the effect of this cation on secondary and tertiary structure. The calcium-induced, secondary, and tertiary structural changes had no effect on the chymotryptic cleavage pattern. However, the digestion pattern of toposome bound to phosphatidyl serine liposomes did vary as a function of calcium concentration. We also investigated the interaction of this protein with various metal ions. Calcium, Mg(2+), Ba(2+), Cd(2+), Mn(2+), and Fe(3+) all bound to toposome. In addition, Cd(2+) and Mn(2+) displaced Ca(2+), prebound to toposome, while Mg(2+), Ba(2+), and Fe(3+) had no effect. Collectively, these results further enhance our understanding of the role of Ca(2+) in modulating the biological activity of toposome. PMID:17786928

  19. Tryptophan as key biomarker to detect gastrointestinal tract cancer using non-negative biochemical analysis of native fluorescence and Stokes Shift spectroscopy (United States)

    Wang, Leana; Zhou, Yan; Liu, Cheng-hui; Zhou, Lixin; He, Yong; Pu, Yang; Nguyen, Thien An; Alfano, Robert R.


    The objective of this study was to find out the emission spectral fingerprints for discrimination of human colorectal and gastric cancer from normal tissue in vitro by applying native fluorescence. The native fluorescence (NFL) and Stokes shift spectra of seventy-two human cancerous and normal colorectal (colon, rectum) and gastric tissues were analyzed using three selected excitation wavelengths (e.g. 300 nm, 320 nm and 340 nm). Three distinct biomarkers, tryptophan, collagen and reduced nicotinamide adenine dinucleotide hydrate (NADH), were found in the samples of cancerous and normal tissues from eighteen subjects. The spectral profiles of tryptophan exhibited a sharp peak in cancerous colon tissues under a 300 nm excitation when compared with normal tissues. The changes in compositions of tryptophan, collagen, and NADH were found between colon cancer and normal tissues under an excitation of 300 nm by the non-negative basic biochemical component analysis (BBCA) model.

  20. Analysis and assessment of the nutrients, biochemical indexes and heavy metals in the Three Gorges Reservoir, China, from 2008 to 2013. (United States)

    Gao, Qiang; Li, Yi; Cheng, Qingyuan; Yu, Mingxia; Hu, Bo; Wang, Zhigang; Yu, Zhiqiang


    The Three Gorges Reservoir, the world's largest hydropower project, has operated stably for more than five years. To understand its water quality status, the nutrient and biochemical indexes, the total nitrogen (TN), the total phosphorus (TP), the potassium permanganate index (CODMn), the five-day biochemical oxygen demand (BOD5) and fecal coliform (F. coli), as well as the heavy metals (Cu, Hg, As, Cd, Zn and Pb) of samples collected from 10 sites during the time period of 2008-2013 were studied via using multiple analysis approaches. For each parameter, pictures of the spatial and temporal distributions were presented, and the reasons behind their variation trends were elaborated. Principal component analysis (PCA) was applied to identify the types of pollution. The Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI) was calculated to concisely mark the water quality. In addition, a human health risk assessment of the heavy metals in a representative site was conducted. The results showed that the water quality state in the Three Gorges Reservoir was intricate but stable and acceptable from 2008 to 2013. The TN, TP and Pb were considered to be the key pollution indexes. Enforcements to alleviate industrial and urban pollution, along with ship management, have worked. The decrease in heavy metal concentrations from upstream to downstream was associated with the self-purification of the reservoir. However, rural pollution became worse in those years. Improper agricultural activity was an important reason for this trend. For local residents, drinking water was generally safe, but cancer caused by As and Pb is a potential issue. PMID:26874779

  1. Biochemical and functional characterisation of casein and whey protein hydrolysates.


    Ven, van de, P.M.


    Whey protein and sodium caseinate were hydrolysed with commercially available enzyme preparations. The resulting hydrolysates were characterised using several analytical characterisation methods and by determination of several functional properties. Subsequently, correlations between the biochemical characteristics themselves and between biochemical and functional properties were studied using multivariate regression analysis.Biochemical characteristics of hydrolysates were determined using u...

  2. 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


    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.

  3. Recent abstracts in biochemical technology


    R R Siva Kiran; Brijesh P


    “Recent abstracts in biochemical technology” is a collection of interesting research articles published in “List of biochemical technology journals” (Table 1). The abstracts are most likely to report significant results in biochemical technology.

  4. Qualitative, Biochemical and Nanoparticle-Antimicrobial Analysis of Lactobacillus SPS screened from the various milk and curd samples of southern Tamilnadu

    Directory of Open Access Journals (Sweden)

    U. Malathi


    Full Text Available To study probiotic microbes like lactobacillus species were isolated from various milk and curd samples was collected from different places such as vellore , kannamangalam , gudiyatham. Which were subjected to screening and characterized and examined for the presence of probiotic properties of lactobacillus. Lactobacillus is a genus of lactic acid bacteria and It’s a group of regular,non-sporing, gram positive bacteria,rod shaped,non-motile and absence of catalase enzyme. Milk and curd samples is an important culture media for lactobacillus. Analysis for quality of milk and curd samples by mbrt test. To detect various adulterants present in milk by using specific biochemical test. The main aim of this study to isolates were obtained by growing on de man rogosa and sharpe[MRS] Agar medium. Lactobacillus was isolated for the production of silver nanoparticles was monitered by UV-spectroscopic analysis.The peak was observed between 400-450nm indicating this presence. Finally the antibacterial activity of nanoparticles were checked against lactobacillus.

  5. Observability analysis of biochemical process models as a valuable tool for the development of mechanistic soft sensors. (United States)

    Golabgir, Aydin; Hoch, Thomas; Zhariy, Mariya; Herwig, Christoph


    By enabling the estimation of difficult-to-measure target variables using available indirect measurements, mechanistic soft sensors have become important tools for various bioprocess monitoring and control scenarios. Despite promising higher process efficiencies and increased process understanding, widespread application of soft sensors has been stalled by uncertainty about the feasibility and reliability of their estimations given present process analytical constraints. Observability analysis can provide an indication of the possibility and reliability of soft sensor estimations by analyzing the structural properties of first-principle (mechanistic) models. In addition, it can provide a criteria for selection of suitable measurement methods with respect to their information content; thereby leading to successful implementation of soft sensors in bioprocess development and manufacturing environments. We demonstrate the utility of observability analysis for two classes of upstream bioprocesses: the processes involving growth and ethanol formation by Saccharomyces cerevisiae and the process of penicillin production by Penicillium chrysogenum. Results obtained from laboratory-scale cultivations in addition to in-silico experiments enable a comparison of theoretical aspects of observability analysis and the real-life performance of soft sensors. By taking the expected error of measurements provided to the soft sensor into account, an innovative scaling approach facilitates a higher degree of comparability of observability results among various measurement configurations and process conditions. PMID:26404038

  6. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari


    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.

  7. Biochemical analysis of a multifunctional cytochrome P450 (CYP51) enzyme required for synthesis of antimicrobial triterpenes in plants


    Geisler, Katrin; Hughes, Richard K; Sainsbury, Frank; Lomonossoff, George P.; Rejzek, Martin; Fairhurst, Shirley; Olsen, Carl-Erik; Motawia, Mohammed Saddik; Melton, Rachel E.; Hemmings, Andrew M; Bak, Søren; Osbourn, Anne


    We carried out functional analysis of the oat enzyme AsCYP51H10, which is a divergent member of the CYP51 cytochrome P450 family and showed that this enzyme is able to catalyze both hydroxylation and epoxidation of the simple triterpene β-amyrin to give 12,13β-epoxy-3β,16β-dihydroxy-oleanane (12,13β-epoxy-16β-hydroxy-β-amyrin). In contrast, the canonical CYP51 enzymes are highly conserved and catalyze only sterol demethylation. We further show that the C12,13 epoxy group is critical for antif...

  8. Transcriptome and biochemical analysis reveals that suppression of GPI-anchor synthesis leads to autophagy and possible necroptosis in Aspergillus fumigatus.

    Directory of Open Access Journals (Sweden)

    Jianghong Yan

    Full Text Available Previously, it has been shown that GPI proteins are required for cell wall synthesis and organization in Aspergillus fumigatus, a human opportunistic pathogen causing life-threatening invasive aspergillosis (IA in immunocompromised patients. Blocking GPI anchor synthesis leads to severe phenotypes such as cell wall defects, increased cell death, and attenuated virulence. However, the mechanism by which these phenotypes are induced is unclear. To gain insight into global effects of GPI anchoring in A. fumigatus, in this study a conditional expression mutant was constructed and a genome wide transcriptome analysis was carried out. Our results suggested that suppression of GPI anchor synthesis mainly led to activation of phosphatidylinositol (PtdIns signaling and ER stress. Biochemical and morphological evidence showed that autophagy was induced in response to suppression of the GPI anchor synthesis, and also an increased necroptosis was observed. Based on our results, we propose that activation of PtdIns3K and increased cytosolic Ca(2+, which was induced by both ER stress and PtdIns signaling, acted as the main effectors to induce autophagy and possible necroptosis.

  9. Association between High Serum Homocysteine Levels and Biochemical Characteristics in Women with Polycystic Ovarian Syndrome: A Systematic Review and Meta-Analysis (United States)

    Peng, Zheng; Liu, Xuexiang; Sun, Yifan; Dai, Shengming


    Background Elevated homocysteine levels have been observed in previous studies of PCOS; however, the nature of the associations between high homocysteine levels and the biochemical characteristics of polycystic ovarian syndrome (PCOS)—such as obesity, insulin resistance (IR), and androgen levels—is still uncertain. Methods A systematic search was conducted electronically up to December 28, 2015 using specific eligibility criteria. Standardized mean difference (SMD) and the corresponding 95% confidence intervals (95% CIs) were used as a measure of effect size. Results A total of 34 studies (with 1,718 cases and 1,399 controls) of homocysteine levels in PCOS were pooled in this meta-analysis. Significantly lower homocysteine levels were found in controls than in PCOS patients (SMD = 0.895, 95% CI = 0.643–1.146, PPCOS patients were significantly lower than those of PCOS patients with IR (SMD = 0.69, 95% CI = 0.37–1.01, PPCOS patients (SMD = –0.17, 95% CI = –1.10–0.75, P = 0.71; I2 = 92% and PPCOS are not related to degree of obesity, IR, or androgen levels. Metformin treatment cannot decrease the homocysteine levels in PCOS patients. PMID:27281026

  10. 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)

    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

  11. Biochemical and biological analysis of Philodryas baroni (Baron's green racer; Dipsadidae) venom: relevance to the findings of human risk assessment. (United States)

    Sánchez, M N; Timoniuk, A; Maruñak, S; Teibler, P; Acosta, O; Peichoto, M E


    Philodryas baroni--an attractively colored snake--has become readily available through the exotic pet trade. Most people consider this species harmless; however, it has already caused human envenomation. As little is known about the venom from this South American opisthoglyphous "colubrid" snake, herein, we studied its protein composition by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), as well as its effects on the hemostatic system. Both reducing and nonreducing SDS-PAGE analysis demonstrated that the venom exhibits greatest complexity in the range of 50-80 kDa. The venom displayed proteolytic activity toward azocollagen, with a specific activity of 75.5 U mg⁻¹, and rapidly hydrolyzed the Aα-chain of fibrinogen, exhibiting lower activity toward the Bβ- and γ-chains. The venom from P. baroni showed no platelet proaggregating activity per se, but it inhibited collagen- and thrombin-induced platelet aggregation. Prominent hemorrhage developed in mouse skin after intradermal injection of the crude venom, and its minimum hemorrhagic dose was 13.9 μg. When injected intramuscularly into the gastrocnemius of mice, the venom induced local effects such as hemorrhage, myonecrosis, edema, and leucocyte infiltration. Due to its venom toxicity shown herein, P. baroni should be considered dangerous to humans and any medically significant bite should be promptly reviewed by a qualified health professional. PMID:23800999

  12. Proteomic analysis of the venom from the scorpion Tityus stigmurus: biochemical and physiological comparison with other Tityus species. (United States)

    Batista, C V F; Román-González, S A; Salas-Castillo, S P; Zamudio, F Z; Gómez-Lagunas, F; Possani, L D


    The venom from the Brazilian scorpion Tityus stigmurus was fractionated by high performance liquid chromatography (HPLC) and the corresponding components were used for molecular mass determination using electrospray ion trap mass spectrometry. One hundred distinct components were clearly assigned showing molecular masses from 216.5 to 44,800.0 Da. Fifteen new components were isolated and sequenced, four of them to completion: Tst-3 (similar to Na(+) channel specific scorpion toxins), Tst-17 (a K(+) channel blocking peptide similar to Tc1), Tst beta KTx (a peptide with identical sequence as that of TsTX-K beta toxin earlier described to exist in T. serrulatus venom) and finally a novel proline-rich peptide of unknown function. Among the eleven components partially sequenced were two enzymes: hyaluronidase and lysozyme. The first enzyme has a molecular mass of 44,800.0 Da. This enzyme showed high activity against the substrate hyaluronan in vitro. Amino acid sequence of the second enzyme showed that it is similar to other known lysozymes, with similar molecular mass and sequence to that of bona fide lysozymes reported in public protein data banks. Finally, this communication reports a correlation among HPLC retention times and molecular masses of folded scorpion toxins as well as a comparative structural and physiological analysis of components from the venom of several species of the genus Tityus. PMID:17270501

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

    Directory of Open Access Journals (Sweden)



    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.

  14. LIB spectroscopic and biochemical analysis to characterize lead toxicity alleviative nature of silicon in wheat (Triticum aestivum L.) seedlings. (United States)

    Tripathi, Durgesh Kumar; Singh, Vijay Pratap; Prasad, Sheo Mohan; Dubey, Nawal Kishore; Chauhan, Devendra Kumar; Rai, Awadesh Kumar


    The responses of wheat seedling treated with silicon (Si; 10 μM) and lead (Pb; 100 μM) for 7 days have been investigated by analyzing growth, Pb uptake, chlorophyll fluorescence, oxidative stress, antioxidants and nutrients regulation. Results indicated that, Pb significantly (PSi addition alleviated Pb-induced decrease in growth and alterations in photosynthesis, and also significantly (PSi addition improved the status of antioxidants. The non-protein thiols (NP-SH) showed enhanced level under Pb stress. Pb stress considerably disturbed status of the nutrients as decrease in Ca, P, Mg, Zn and Ni contents while an increase in K, S, B, Cu, Fe, Mn and Na contents were noticed. Si addition maintained status of all the nutrients remarkably. The quickest method of element analysis: LIBS spectra revealed significantly lower uptake of Pb in seedlings grown under Si and Pb combination and same was correlated with the data of AAS. Overall results pointed out that excess Pb uptake disturbed status of nutrients, photosynthetic performance, antioxidant capacity, hence severe oxidative damage to lipids occurred. Further, Si supplementation successfully regulated these parameters by inhibiting Pb uptake hence maintained growth of wheat seedlings. Similar pattern of data recorded by the LIBS, AAS and ICAP-AES confirmed that LIBS may be one of the promising and authentic tools to monitor the mineral and metal distribution in the plants without hampering or disturbing the environment due to its eco-friendly and non-invasive nature. PMID:26700425

  15. 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)


    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

  16. Biochemical analysis and structure determination of bacterial acetyltransferases responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine. (United States)

    Morrison, Michael J; Imperiali, Barbara


    UDP-N,N'-diacetylbacillosamine (UDP-diNAcBac) is a unique carbohydrate produced by a number of bacterial species and has been implicated in pathogenesis. The terminal step in the formation of this important bacterial sugar is catalyzed by an acetyl-CoA (AcCoA)-dependent acetyltransferase in both N- and O-linked protein glycosylation pathways. This bacterial acetyltransferase is a member of the left-handed β-helix family and forms a homotrimer as the functional unit. Whereas previous endeavors have focused on the Campylobacter jejuni acetyltransferase (PglD) from the N-linked glycosylation pathway, structural characterization of the homologous enzymes in the O-linked glycosylation pathways is lacking. Herein, we present the apo-crystal structures of the acetyltransferase domain (ATD) from the bifunctional enzyme PglB (Neisseria gonorrhoeae) and the full-length acetyltransferase WeeI (Acinetobacter baumannii). Additionally, a PglB-ATD structure was solved in complex with AcCoA. Surprisingly, this structure reveals a contrasting binding mechanism for this substrate when compared with the AcCoA-bound PglD structure. A comparison between these findings and the previously solved PglD crystal structures illustrates a dichotomy among N- and O-linked glycosylation pathway enzymes. Based upon these structures, key residues in the UDP-4-amino and AcCoA binding pockets were mutated to determine their effect on binding and catalysis in PglD, PglB-ATD, and WeeI. Last, a phylogenetic analysis of the aforementioned acetyltransferases was employed to illuminate the diversity among N- and O-linked glycosylation pathway enzymes. PMID:24064219

  17. Biochemical and functional analysis of CTR1, a protein kinase that negatively regulates ethylene signaling in Arabidopsis (United States)

    Huang, Yafan; Li, Hui; Hutchison, Claire E.; Laskey, James; Kieber, Joseph J.


    CTR1 encodes a negative regulator of the ethylene response pathway in Arabidopsis thaliana. The C-terminal domain of CTR1 is similar to the Raf family of protein kinases, but its first two-thirds encodes a novel protein domain. We used a variety of approaches to investigate the function of these two CTR1 domains. Recombinant CTR1 protein was purified from a baculoviral expression system, and shown to possess intrinsic Ser/Thr protein kinase activity with enzymatic properties similar to Raf-1. Deletion of the N-terminal domain did not elevate the kinase activity of CTR1, indicating that, at least in vitro, this domain does not autoinhibit kinase function. Molecular analysis of loss-of-function ctr1 alleles indicated that several mutations disrupt the kinase catalytic domain, and in vitro studies confirmed that at least one of these eliminates kinase activity, which indicates that kinase activity is required for CTR1 function. One missense mutation, ctr1-8, was found to result from an amino acid substitution within a new conserved motif within the N-terminal domain. Ctr1-8 has no detectable effect on the kinase activity of CTR1 in vitro, but rather disrupts the interaction with the ethylene receptor ETR1. This mutation also disrupts the dominant negative effect that results from overexpression of the CTR1 amino-terminal domain in transgenic Arabidopsis. These results suggest that CTR1 interacts with ETR1 in vivo, and that this association is required to turn off the ethylene-signaling pathway.

  18. Biochemical characterization and functional analysis of the POU transcription factor POU-M2 of Bombyx mori. (United States)

    Liu, Lina; Li, Yu; Wang, Yejing; Zhao, Peng; Wei, Shuguang; Li, Zhenzhen; Chang, Huaipu; He, Huawei


    POU-M2 is a homeodomain transcription factor which plays important roles in the development and silk synthesis of Bombyx mori. In this study, we expressed, purified and characterized POU-M2 and studied its transcription regulation on fibroin heavy chain gene of Bombyx mori. Gel filtration showed POU-M2 existed as a dimer in solution. Far-UV circular dichroism spectra indicated POU-M2 had a well-defined α-helix structure and the α-helix content was about 26.4%. The thermal unfolding transition of POU-M2 was a cooperative process. Tm, ΔH and ΔS were 45.15±0.2°C, 138.4±0.5KJ/mol and 0.4349±0.04KJ/(mol·K), respectively. Western blotting analysis indicated the expression level of POU-M2 increased slightly from day 3 to day 7 of the fifth instar larvae in the posterior silk gland. POU-M2 was positioned in the nucleus of cells. The luciferase reporter assay demonstrated POU-M2 could stimulate the promoter activity of fibroin heavy chain gene, and the activation effect was dependent on the amount of POU-M2. Our study suggested POU-M2 may be involved in the transcriptional regulation of fibroin heavy chain gene. These findings expand toward a better understanding of the structure of POU-M2 and its function in silk synthesis of Bombyx mori. PMID:26854886

  19. Integrated chemical/biochemical sample collection, pre-concentration, and analysis on a digital microfluidic lab-on-a-chip platform (United States)

    Fair, Richard B.; Khlystov, A.; Srinivasan, Vijay; Pamula, Vamsee K.; Weaver, Kathryn N.


    An ideal on-site chemical/biochemical analysis system must be inexpensive, sensitive, fully automated and integrated, reliable, and compatible with a broad range of samples. The advent of digital microfluidic lab-on-a-chip (LoC) technology offers such a detection system due to the advantages in portability, reduction of the volumes of the sample and reagents, faster analysis times, increased automation, low power consumption, compatibility with mass manufacturing, and high throughput. We describe progress towards integrating sample collection onto a digital microfluidic LoC that is a component of a cascade impactor device. The sample collection is performed by impacting airborne particles directly onto the surface of the chip. After the collection phase, the surface of the chip is washed with a micro-droplet of solvent. The droplet will be digitally directed across the impaction surface, dissolving sample constituents. Because of the very small droplet volume used for extraction of the sample from a wide colection area, the resulting solution is realatively concentrated and the analytes can be detected after a very short sampling time (1 min) due to such pre-concentration. After the washing phase, the droplet is mixed with specific reagents that produce colored reaction products. The concentration of the analyte is quantitatively determined by measuring absorption at target wavelengths using a simple light emitting diode and photodiode setup. Specific applications include automatic measurements of major inorganic ions in aerosols, such as sulfate, nitrate and ammonium, with a time resolution of 1 min and a detection limit of 30 nm/m3. We have already demonstrated the detection and quantification of nitroaromatic explosives without integrating the sample collection. Other applications being developed include airborne bioagent detection.

  20. Measures of Biochemical Sociology (United States)

    Snell, Joel; Marsh, Mitchell


    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…

  1. Biochemical Education in Brazil. (United States)

    Vella, F.


    Described are discussions held concerning the problems of biochemical education in Brazil at a meeting of the Sociedade Brazileira de Bioquimica in April 1988. Also discussed are other visits that were made to universities in Brazil. Three major recommendations to improve the state of biochemistry education in Brazil are presented. (CW)

  2. Stochastic analysis of biochemical systems

    CERN Document Server

    Anderson, David F


    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...

  3. Ouroboros - Playing A Biochemical

    Directory of Open Access Journals (Sweden)

    D. T. Rodrigues


    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

  4. 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

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Graham D. [University of Western Ontario, London, Ontario (Canada); Pickles, Tom [Department of Radiation Oncology, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Crook, Juanita [Department of Radiation Oncology, Kelowna General Hospital, Kelowna, British Columbia (Canada); Martin, Andre-Guy; Vigneault, Eric [Department of Radiation Oncology, L' Hotel Dieu de Quebec, Quebec City, Quebec (Canada); Cury, Fabio L. [Department of Radiation Oncology, Montreal General Hospital, Montreal, Quebec (Canada); Morris, Jim [Department of Radiation Oncology, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Catton, Charles [Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Lukka, Himu [Department of Radiation Oncology, Juravinski Cancer Centre, Hamilton, Ontario (Canada); Warner, Andrew [Department of Radiation Oncology, London Health Sciences Center, London, Ontario (Canada); Yang, Ying [University of Waterloo, Waterloo, Ontario (Canada); Rodrigues, George, E-mail: [University of Western Ontario, London, Ontario (Canada); Department of Radiation Oncology, London Health Sciences Center, London, Ontario (Canada)


    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

  5. Conceptual Aspects of Theory Appraisal: Some Biochemical Examples

    Directory of Open Access Journals (Sweden)

    F. Michael Akeroyd


    Full Text Available This paper considers papers on conceptual analysis by Laudan (1981 and Whitt (1989 and relates them to three biochemical episodes: (1 the modern 'biochemical explanation' of acupuncture; (2 the chemio-osmotic hypothesis of oxidative phosphorylation; (3 the theory of the complete digestion of proteins in the gut. The advantages of including philosophical debate in chemical/biochemical undergraduate courses is then discussed.

  6. Multiplexing oscillatory biochemical signals. (United States)

    de Ronde, Wiet; ten Wolde, Pieter Rein


    In recent years it has been increasingly recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that the protein signaling network of living cells has a bow-tie structure and that components are often shared between different signaling pathways. Here we show by mathematical modeling that living cells can multiplex a constant and an oscillatory signal: they can transmit these two signals simultaneously through a common signaling pathway, and yet respond to them specifically and reliably. We find that information transmission is reduced not only by noise arising from the intrinsic stochasticity of biochemical reactions, but also by crosstalk between the different channels. Yet, under biologically relevant conditions more than 2 bits of information can be transmitted per channel, even when the two signals are transmitted simultaneously. These observations suggest that oscillatory signals are ideal for multiplexing signals. PMID:24685537

  7. 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)

    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

  8. Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding (United States)

    Me´ndez, Eduardo; Cerda´, María F.


    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…

  9. Genomic and Biochemical Analysis of Lipid Biosynthesis in the Unicellular Rhodophyte Cyanidioschyzon merolae: Lack of a Plastidic Desaturation Pathway Results in the Coupled Pathway of Galactolipid Synthesis▿ †


    Sato, Naoki; Moriyama, Takashi


    The acyl lipids making up the plastid membranes in plants and algae are highly enriched in polyunsaturated fatty acids and are synthesized by two distinct pathways, known as the prokaryotic and eukaryotic pathways, which are located within the plastids and the endoplasmic reticulum, respectively. Here we report the results of biochemical as well as genomic analyses of lipids and fatty acids in the unicellular rhodophyte Cyanidioschyzon merolae. All of the glycerolipids usually found in photos...

  10. Biochemical analysis of PIFTC3, the Trypanosoma brucei ortholog of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components


    Franklin, Joseph B.; Ullu, Elisabetta


    DYF-13, originally identified in C. elegans within a collection of dye-filling chemosensory mutants, is one of several proteins that have been classified as putatively involved in intraflagellar transport (IFT), the bidirectional movement of protein complexes along cilia and flagella, and specifically in anterograde IFT. Although genetic studies have highlighted a fundamental role of DYF-13 in nematode sensory cilium and trypanosome flagellum biogenesis, biochemical studies on DYF-13 have lag...

  11. 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: [Department of Animal Morphology and Physiology, Universidade Federal Rural de Pernambuco, Recife (Brazil)


    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.

  12. 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)

    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

  13. Analysis on the relationship between renal osteodystrophy and the biochemical marker of bone turnover and other related factors in patients with chronic kidney diseases

    International Nuclear Information System (INIS)

    Objective: To investigate the relationship between renal osteodystrophy and the biochemical marker of bone turnover in patients with chronic kidney diseases. Methods: A total of 102 patients with chronic kidney diseases (CKD) and 52 healthy subjects (normal control) were included in this study. The level of total procollagen type Ⅰ amino-terminal propeptide of (TP Ⅰ NP), β-isomerized carboxyterminal propeptide (β-CTx), intact parathyroid hormone (iPTH), serum calcium (Ca2+), serum phosphorus (P), alkaline phosphatase (ALP) were detected. The correlations between renal osteodystrophy in the patients with chronic kidney diseases and other related factors were analyzed. Results: Compared with the normal control group, there were higher TP Ⅰ NP, β-CTx, iPTH, P, ALP, Cr, Bun and β2-MG, in the CKD group which were significantly different according to Mann-Whitney U test (P<0.05 or <0.01). The Ca2+ and 1, 25-OH Vitamin d3 [1, 25 (OH)2D3] in the CKD group were significantly decreased compared with the normal control group (P<0.05). Correlation analysis showed TP Ⅰ NP was positively correlated with β-CTx, iPTH, P, CaxP, ALP, Cr, Bun, β2-MG (r was 0.790, 0.681, 0.573, 0.541, 0.550, 0.598, 0.793 respectively, P<0.01), Correlation analysis showed β-CTx was positively correlated with iPTH, P, CaxP, ALP, Cr, Bun, β2-MG (r was 0.803, 0.527, 0.449, 0.659, 0.672, 0.565, 0.624 respectively, P<0.01). TP Ⅰ NP was negatively correlated with Ca2+ and 1, 25 (OH)2D3 (r was -0.302, -0.582 respectively, P<0.01). β-CTx was negatively correlated with Ca2+ and 1, 25 (OH)2D3 (r was -0.265, -0.595 respectively, P<0.01). The iPTH was positively correlated with age, TP Ⅰ NP, β-CTx, P, CaxP, ALP, Cr, Bun and β2-MG (r was 0.485, 0.681, 0.803, 0.630, 0.541, 0.486, 0.690, 0.648, 0.531 respectively, P<0.05 or <0.01), but was negatively correlated with Ca2+ and 1, 25 (OH)2D3 (r was -0.318, -0.621 respectively, P<0.05). Conclusion: The application of total procollagen type

  14. Biochemical Hypermedia: Galactose Metabolism.

    Directory of Open Access Journals (Sweden)

    J.K. Sugai


    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.


    Institute of Scientific and Technical Information of China (English)

    徐成; 王可玲; 尤锋; 吴谡琦; 张培军


    During Sep. 1994-Dec. 1995, 37 sea bass (Lateolabrax japonicus) samples were collected from coastal water of Qingdao, Shandong Province. Starch gel electrophoresis and polyacrylamide gel electropho resis were used to detect expression of isozymes in seven organs or tissues: eye , muscle, heart, liver, kidney, gill and pectoral fin. LDH, MDH, MEP, IDHP, PGM, G3PDH, AK, CK were analyzed in Tris-citric acid buffer system (TC, pH=6.9); AD H , SDH, G6PDH, GDH, PGDH, CAT and MPI were analyzed in EDTA-boric acid-Tris buf fe r system (EBT, pH=8.9); SOD and EST in Tris-gly buffer system (TG, pH=8.3). Bio c hemical genetic analysis showed 17 isozymes were coded by 31 gene loci, 8 of whi ch were found polymorphic. Of the polymorphic loci, Mep-1, Gdh, Pgdh, Est-1 an d Est-4 each had two alleles and three phenotypes; Pgm-1, Sdh and Mpi each had thr ee alleles, all six phenotypes of Mpi were observed, but only four of Pgm-1 and three of Sdh were observed, low frequency phenotypes were absent. Mean proportio n of polymorphic loci was 25.8%.%于1994年9月—1995年12月,在青岛近海采集37尾 鲈鱼的生化样品,采用淀粉胶和聚丙烯酰胺凝胶2种电泳方法,分析了LDH、MDH、MEP、IDHP 、PGM、G3PDH、AK、CK、ADH、SDH、G6PDH、GDH、PGDH、CAT、MPI、EST、SOD等同工酶在鲈 鱼眼睛、肌肉、心脏、肝脏、肾脏、鳃、胸鳍等7种组织或器官中的表达情况,并对同工酶 表型进行了生化遗传分析,以期为其种质资源保护和开发,以及遗传育种等方面的研究提供 基础资料。结果表明,17种同工酶由31个基因座位编码,其中Mep-1、Pgm-1、Sdh、Gdh、Pg dh、Mpi、Est-1、Est-4等8个基因座位为多态。多态座位比例为25.8%。

  16. Variability of expression and arrangement of cytokeratin and neurofilaments in cutaneous neuroendocrine carcinomas (Merkel cell tumors): immunocytochemical and biochemical analysis of twelve cases. (United States)

    Moll, R; Osborn, M; Hartschuh, W; Moll, I; Mahrle, G; Weber, K


    Twelve specimens of cutaneous neuroendocrine carcinomas (Merkel cell tumors) available as fresh tissue were analyzed for intermediate filament (IF) expression by immunocytochemical and biochemical methods. In immunofluorescence microscopy, most cases were positive for both simple-epithelium-type cytokeratins and the neurofilament L- and M-polypeptides. Several different IF staining patterns ranging from presence of plaque-like structures (fibrous bodies) only to nearly exclusive expression of delicate cytokeratin fibrils could be distinguished. In immunoelectron microscopy the labeling for both cytokeratin and neurofilament polypeptides seemed evenly distributed among the IFs of the fibrous bodies. In primary culture, tumor cells maintained the coexpression of both IF types. Desmoplakin-positive true desmosomes were found in 5 specimens. Biochemically, cytokeratins nos. 8, 18 and, variably, 19, as well as IT protein and, in many specimens, the neurofilament L-protein and a putative neurofilament M-protein were detected. Only traces of the neurofilament H-polypeptide were found. Our results show that a coexpression of cytokeratin IFs and neurofilaments in variable patterns is a characteristic feature of cutaneous neoendocrine carcinomas; occasionally, however, neurofilaments may be very scarce. The biological, histogenetic and diagnostic implications are discussed. PMID:2435039

  17. 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)

    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)

  18. Biochemical synthesis with stable isotopes

    International Nuclear Information System (INIS)

    Descriptions of the biochemical synthesis of glucose-13C6 from Agmenellum quadruplication; the biochemical labelling of [13C, 15N] Chlorella and [13C] E. coli, [15N] E. coli, and the production of lactic-13C3 acid utilizing Lactobacillus casei are discussed


    Directory of Open Access Journals (Sweden)

    R.M. Lima


    Full Text Available Many people fail to properly evaluate INTERNET information. This is often due to alack of understanding of the issues, by responsible authorities, and, morespecifically, a lack of understanding of the structure and modis operandi of theINTERNET tool. The aim of this project was to analyze biochemical issuesavailable in WEB pages, evaluating contents quality, coverage, accuracy, authorityand currency. Twenty three sites were analyzed for their contents, presence ofbibliographical references, authorship, titles responsibility and adequacy to targetpublic. The great majority (95% did not mention bibliographic references andtarget public. Less than half divulged names and/or graduation status ofresponsibles. Some sites contained critical conceptual errors, such as: oxygen isessential for anaerobic respiration; presence of H2O in photosynthesis dark phase;yeast is a pluricellular fungal; the overall equation of photosynthesis with errors;NADH2 instead NAD+; etc. None of the analyzed sites was thus consideredexcellent. Although the use of the internet is expanding rapidly on collegecampuses, little is known about students usage; how they perceive the reality ofinternet information and how successful they are in searching through it. Our datastrenghthen the need for rigorous evaluation concerning to educational research ofbiochemical themes on the WEB.

  20. The Biochemical Anatomy of Cortical Inhibitory Synapses


    Heller, E.A.; Zhang, W.; Selimi, F.; Earnheart, J.C.; Slimak, M.A.; Santos-Torres, J.; Ibanez-Tallon, I.; Aoki, C; Chait, B. T.; Heintz, N


    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 th...

  1. Biochemical Neuroscience Laboratory (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...

  2. Reconstructing biochemical pathways from time course data. (United States)

    Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago


    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. PMID:17370261

  3. Biological dosimetry: biochemical and cellular parameters

    International Nuclear Information System (INIS)

    Early after the beginning of radiobiology studies, biochemistry has led to research of a biological dosimeter. From an extensive literature review, methods were selected that might be suitable for dose assessment via biochemical indicators. By now, research both in laboratory animals and in therapeutic or accidental human exposures, do not allow to retain a biochemical parameter alone for the purpose of diagnosis or prognosis. Several enzymatic activities have been precociously studied after irradiation: from these studies, it seems that analysis of four enzymatic activities in serum (serum glutamic oxaloacetic transaminase, amylase, lactic dehydrogenase, alkaline phosphatase) could be the most useful dosimetry system for mass sorting. Detection of DNA damage or methods for measuring somatic mutations are currently advancing and provide important new opportunities for biological dosimetry of low doses

  4. Advancement in biochemical assays in andrology

    Institute of Scientific and Technical Information of China (English)

    Wolf-BernhardSchill; RaftHenkel


    Determination of maikers of sperm function, accessory sex gland secretion and silent male genital tract inflammation is of considerable diagnostic value in the evaluation of male infertility. The introduction of biochemical tests into the analysis of male factor has the advantage that standardized assays with a coefficient of variafion characteristic of clinical chemistry are performed, in contrast to biological test systems with a large variability .Biochemical parameters may be used in clinical practice to evaluate the sperm fertitizing capacity (acrosin, aniline blue,ROS), to characterize male accessory sex gland secretinns (fructose, a-glucosidase, PSA), and to identify men with silent genital tract inflammation (elastase, C'3 complement component, coeruloplasmin, IgA, IgG, ROS). (As/an J Androl 1999 Jun; 1: 45-51)

  5. Evidence that nerve growth factor promotes the recovery of peripheral neuropathy induced in mice by cisplatin: behavioral, structural and biochemical analysis. (United States)

    Aloe, L; Manni, L; Properzi, F; De Santis, S; Fiore, M


    In this study we investigate the neurotoxic action of Cisplatin (6 micrograms/g body weight for 5 treatment cycles during 15 weeks with a total dose of 30 micrograms/g), an antitumor drug, and its effect on the level of nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) in peripheral tissues. We found that Cisplatin in adult rodents impairs peripheral sensory function and both sympathetic and sensory peripheral innervation as shown by the hot-plate response, catecholamine distribution and substance P immunoreactivity respectively. These changes are associated with decreased NGF in intestine, paws, and bladder while NGF increased in the spinal cord. Also BDNF decreased in bladder and paws and increased in spinal cord and intestine. To further investigate the role of NGF in the pathogenesis of Cisplatin-induced peripheral neuropathies a group of animals was injected with NGF (1 microgram/g every 4 days for 4 times) following Cisplatin treatment and evaluated for sensory function, sympathetic and sensory innervation and BDNF levels. Data demonstrated that exogenous NGF administration is able to restore biochemical, structural and functional changes induced by Cisplatin. These findings suggest that the reduction of NGF availability could be a cause of Cisplatin-induced peripheral neuropathies and that NGF exogenous administration could prevent or reduce Cisplatin neurotoxicity also in cancer patients, reducing the side effects of chemotherapy. PMID:11269929

  6. Multi-level stressor analysis from the DNA/biochemical level to community levels in an urban stream and integrative health response (IHR) assessments. (United States)

    Lee, Jae Hoon; Kim, Joon Ha; Oh, Hee-Mock; An, Kwang-Guk


    The objectives of this study were to identify multi-level stressors at the DNA/biochemical level to the community level in fish in an urban stream and to develop an integrative health response (IHR) model for ecological health diagnosis. A pristine control site (S (c) ) and an impacted site (S (i) ) were selected from among seven pre-screened sites studied over seven years. Various chemical analyses indicated that nutrient enrichment (Nitrogen, Phosphorus) and organic pollution were significantly greater (t > 8.783, p platypus showed that the regression coefficient (b) was 3.012 for the S (i) site and 2.915 for the S (c) site, indicating population skewness in the downstream reach. Community-level health was impaired at the S (i) site based on an index of biological integrity (IBI), and physical habitat modifications were identified by a qualitative habitat evaluation index (QHEI). Overall, the model values for the integrative health response (IHR), developed using the star plot approach, were 3.22 (80.5%) at the S (c) site and 0.74 (18.5%) at the S (i) site, indicating that, overall, ecological health impairments were evident in the urban reach. Our study was based on multi-level approaches using biological organization and the results suggest that there is a pivotal point of linkage between mechanistic understanding and real ecological consequences of environmental stressors. PMID:23043344

  7. Biochemical genetic analysis of isozymes in Plecoglossus altivelis population in Fuxi%凫溪香鱼群体同工酶的生化遗传分析

    Institute of Scientific and Technical Information of China (English)

    黄福勇; 李明云


    30 ayu(Plecoglossus altivelis) samples were collected from the cultural net in Fuxi Town, Ninghai County, Zhejiang Province. Polyarylamide gel electrophoresis was used to detect the expression of isozymes in 8 organs or tissues: eye, liver, kidney, muscle, spleen, heart, gill and pectroral fin. ADH,CAT,POD,ACP,ALP,EST,LDH,MDH,ME,GcDH,SCD,GDH,SDH,SOD,ATP were analyzed and the biochemical genetic results showed that 15 isozymes were coded by 55 gene loci, 12 of which (ADH-1, ADH-4, CAT-2, POD-3,ALP-2, EST-3, EST-4, LDH-5, ME-4, GcDH-4, GDH, SDH-2) were found polymorphic. The population of ayu (Plecoglossus altivelis) in Fuxi town showed the higher genetic diversity when compared with other freshwater fishes, with 21.8% of the proportion of polymorphic loci and 0.0459 of the average heterozygosity per loci. And we think the expression of CAT, POD and SOD of ayu (Plecoglossus altivelis) can be used to evaluate the influence to body-protecting system of the fish when environmental factors were changed. The expression of isozymes in pectroral fin can be used as genetic marker in breeding of ayu (Plecoglossus altivelis)

  8. Serum Biochemical Profile of Post Partum Metritic Cow


    Magnus P. K.; Lali F. A.


    Present study was conducted to find out the relationship between serum biochemical profile and postpartum metritis. Mainly serum glucose, total protein, albumin, albumin globulin ratio, blood urea nitrogen (BUN), creatinine and calcium were studied. Colorimetric method was used for quantitative estimation of biochemical profile. Twenty-seven animals with recent history of calving and subsequent metritis were included in the study. On analysis, serum glucose was found to be 22.3 ± 2.1...

  9. Homogenous demineralized dentin matrix and platelet-rich plasma for bone tissue engineering in cranioplasty of diabetic rabbits: biochemical, radiographic, and histological analysis. (United States)

    Gomes, M F; Valva, V N; Vieira, E M M; Giannasi, L C; Salgado, M A C; Vilela-Goulart, M G


    This study evaluated the effects of homogenous demineralized dentin matrix (HDDM) slices and platelet-rich plasma (PRP) in surgical defects created in the parietal bones of alloxan-induced diabetic rabbits, treated with a guided bone regeneration technique. Biochemical, radiographic, and histological analyses were performed. Sixty adult New Zealand rabbits were divided into five groups of 12: normoglycaemic (control, C), diabetic (D), diabetic with a PTFE membrane (DM), diabetic with a PTFE membrane and HDDM slices (DM-HDDM), and diabetic with PTFE membrane and PRP (DM-PRP). The quantity and quality of bone mass was greatest in the DM-HDDM group (respective radiographic and histological analyses: at 15 days, 71.70 ± 16.50 and 50.80 ± 1.52; 30 days, 62.73 ± 16.51 and 54.20 ± 1.23; 60 days, 63.03 ± 11.04 and 59.91 ± 3.32; 90 days, 103.60 ± 24.86 and 78.99 ± 1.34), followed by the DM-PRP group (respective radiographic and histological analyses: at 15 days 23.00 ± 2.74 and 20.66 ± 7.45; 30 days 31.92 ± 6.06 and 25.31 ± 5.59; 60 days 25.29 ± 16.30 and 46.73 ± 2.07; 90 days 38.10 ± 14.04 and 53.38 ± 9.20). PRP greatly enhanced vascularization during the bone repair process. Abnormal calcium metabolism was statistically significant in the DM-PRP group (PAlkaline phosphatase activity was significantly higher in the DM-HDDM group (P<0.001) in comparison to the C, D, and DM-PRP groups, confirming the findings of intense osteoblastic activity and increased bone mineralization. Thus, HDDM promoted superior bone architectural microstructure in bone defects in diabetic rabbits due to its effective osteoinductive and osteoconductive activity, whereas PRP stimulated angiogenesis and red bone marrow formation. PMID:26482638

  10. 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.


    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 h

  11. Utility of the discriminant analysis to categorize untrained Spanish Pure Bred horses on the basis of biochemical and muscle variables before and after a standardized exercise test. (United States)

    Escribano, B M; Agüera, E I; Rubio, M D; Santisteban, R; Vivo, R; Agüera, S; Tovar, P


    We hypothesized that the information obtained from a discriminant analysis could be used to objectively discriminate horses untrained from early ages, in agreement with certain physiological characteristics. In the biopsies of 24 Spanish Pure Bred horses (1.5-3 years old) before and after a standardized exercise test (SET; 4-7 m/s with a change of velocity of 1m/s every 2 min) muscle enzymes, substrate and metabolites were determined. Also, diverse plasma and blood parameters were considered. Three pre-exercise groups (A1: six horses; A2: seven horses and A3: eleven horses) and two post-exercise groups (B1: sixteen horses; B2: eight horses) were defined from a correspondence analysis. Forward stepwise discriminant analysis selected 11 variables which differentiated the groups between each other both pre- and post-exercise. The results of the present study suggested the utility of a discriminant analysis to categorize horses in agreement with certain physiological variables. It could be used for establishing different types of training in each group by expert trainers. PMID:21458835

  12. 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


    Ming-Zhi Zhu; Wei Wu; Li-Li Jiao; Ping-Fang Yang; Ming-Quan Guo


    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 bio...

  13. Development of Amplified 16S Ribosomal DNA Restriction Analysis for Identification of Actinomyces Species and Comparison with Pyrolysis-Mass Spectrometry and Conventional Biochemical Tests


    Hall, Val; O’Neill, G. L.; Magee, J T; Duerden, B I


    Identification of Actinomyces spp. by conventional phenotypic methods is notoriously difficult and unreliable. Recently, the application of chemotaxonomic and molecular methods has clarified the taxonomy of the group and has led to the recognition of several new species. A practical and discriminatory identification method is now needed for routine identification of clinical isolates. Amplified 16S ribosomal DNA restriction analysis (ARDRA) was applied to reference strains (n = 27) and clinic...

  14. Analysis of Changes in Biochemical Composition Under Free-Air CO2 enrichment by 13C Nuclear Magnetic Resonance: Leaf Litter, Roots, and Soils From Oak Ridge (United States)

    Hockaday, W. C.; Masiello, C. A.; Baldock, J. A.; Iversen, C. M.; Norby, R. J.


    Changes in plant biochemistry as a result of increasing atmospheric carbon dioxide concentration [CO2] influence the cycling of the terrestrial carbon pool and thereby constitute a climate feedback. We have investigated molecular-level changes in the chemical composition of the organic carbon pool of a deciduous forest in Oak Ridge, Tennessee, after 9 years of free-air CO2 enrichment. We employ a novel approach based upon solid-state 13C nuclear magnetic resonance (NMR) analysis and application of a molecular mixing model. This method generates quantitative estimates of total lipids, proteins, carbohydrates, and lignin. 13C NMR spectra were acquired for acid-insoluble soil organic matter from depths of 0 - 5 cm and 5 - 15 cm in two ambient and two elevated [CO2] treatments. In the upper 5 cm, elevated [CO2] soils show a 7% increase in lignin, while lipids and proteins decrease by approximately 10%. Below 5 cm, soil lipid content decreased by 15% relative to ambient [CO2] soils. Changes in the composition of the SOM pool may be attributed to changes in plant biochemistry under elevated [CO2]. Therefore we have performed 13C NMR analysis of major aboveground and belowground biomass inputs: senesced leaves and fine roots (<1 mm diameter). Significant [CO2] effects on root chemistry are observed. Based upon these data, we are able to make a preliminary assessment of the contributions of leaf C and root C to changes in the molecular composition of the SOM pool.

  15. BNDB – The Biochemical Network Database

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael


    Full Text Available Abstract Background Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. Description We present the Biochemical Network Database (BNDB, a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. Conclusion BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at

  16. 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


    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.

  17. Biochemical analysis and immunohistochemical examination of a GnRH-like immunoreactive peptide in the central nervous system of a decapod crustacean, the kuruma prawn (Marsupenaeus japonicus). (United States)

    Amano, Masafumi; Okumura, Takuji; Okubo, Kataaki; Amiya, Noriko; Takahashi, Akiyoshi; Oka, Yoshitaka


    We examined whether a gonadotropin-releasing hormone (GnRH)-like peptide exists in the central nervous system (CNS) of the kuruma prawn, Marsupenaeus japonicus, by reverse-phase high performance liquid chromatography (rpHPLC) combined with time-resolved fluoroimmunoassay (TR-FIA) analysis and by immunohistochemistry. The displacement curve obtained for serially diluted extracts of the kuruma prawn brain paralleled the chicken GnRH-II (cGnRH-II) standard curve obtained by cGnRH-II TR-FIA using the anti-cGnRH-II antibody, which cross-reacts not only with cGnRH-II but also with lamprey GnRH-II (lGnRH-II) and octopus GnRH (octGnRH). Extracts of kuruma prawn brains and eyestalks showed a similar retention time to synthetic lGnRH-II and octGnRH in rpHPLC combined with TR-FIA analysis. Using this antibody, we detected GnRH-like-immunoreactive (ir) cell bodies in the anterior-most part of the supraesophageal ganglion (brain), the protocerebrum. Furthermore, GnRH-like-ir fibers were observed in the protocerebrum and deutocerebrum. In the eyestalk, GnRH-like-ir cell bodies were detected in the medulla interna, and GnRH-like-ir fibers were distributed in the medulla interna, medulla externa, and lamina ganglionalis. In the thoracic ganglion, GnRH-like-ir fibers, but not GnRH-like-ir cell bodies, were detected. No GnRH-like-ir cell bodies or fibers were detected in the abdominal ganglion or ovary. Thus, we have shown the existence and distribution of a GnRH-like peptide in the CNS of the kuruma prawn. PMID:19968471

  18. Hyponatraemia: biochemical and clinical perspectives.


    Gill, G; Leese, G


    Hyponatraemia is a common bio-chemical abnormality, occurring in about 15% of hospital inpatients. It is often associated with severe illness and relatively poor outcome. Pathophysiologically, hyponatraemia may be spurious, dilutional, depletional or redistributional. Particularly difficult causes and concepts of hyponatraemia are the syndrome of inappropriate antidiuresis and the sick cell syndrome, which are discussed here in detail. Therapy should always be targeted at the underlying disea...

  19. Biochemical markers of bone turnover

    International Nuclear Information System (INIS)

    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

  20. Salt stress induced lipid accumulation in heterotrophic culture cells of Chlorella protothecoides: Mechanisms based on the multi-level analysis of oxidative response, key enzyme activity and biochemical alteration. (United States)

    Wang, Tao; Ge, Haiyan; Liu, Tingting; Tian, Xiwei; Wang, Zejian; Guo, Meijin; Chu, Ju; Zhuang, Yingping


    Salt stress as an effective stress factor that could improve the lipid content and lipid yield of glucose in the heterotrophic culture cells of Chlorella protothecoides was demonstrated in this study. The highest lipid content of 41.2% and lipid yield of 185.8mg/g were obtained when C. protothecoides was stressed under 30g/L NaCl condition at its late logarithmic growth phase. Moreover, the effects of salt and osmotic stress on lipid accumulation were comparatively analyzed, and it was found that the effects of NaCl and KCl stress had no significant differences at the same osmolarity level of 1150mOsm/kg with lipid contents of 41.7 and 40.8% as well as lipid yields of 192.9 and 186.8mg/g, respectively, whereas these results were obviously higher than those obtained under the iso-osmotic glycerol and sorbitol stresses. Furthermore, basing on the multi-level analysis of oxidative response, key enzyme activity and biochemical alteration, the superior performance of salt stress driving lipid over-synthesis was probably ascribed to the more ROS production as a result of additional ion effect besides the osmotic effect, subsequently mediating the alteration from carbohydrate storage to lipid accumulation in signal transduction process of C. protothecoides. PMID:27085889

  1. Individual and combined toxic effect of nickel and chromium on biochemical constituents in E. coli using FTIR spectroscopy and Principle component analysis. (United States)

    Gupta, Annika Durve; Karthikeyan, Sivakumaran


    Ni and Cr are ubiquitous pollutants in the aquatic environments. These heavy metals elicit toxicities to aquatic organisms including microbes. In this study, interaction of the two heavy metals on the toxicity in Escherichia coli (E. coli) was studied using FTIR spectroscopy. The binding of Ni(II) to E. coli was stronger than that for Cr(VI). Cr exhibited antagonistic effects in the presence of Ni in E. coli. FTIR analysis showed a decrease in lipid content in the presence of Ni and not for Cr. Further, a decrease in band area was observed in the region of 3000-2800cm(-1) and at ~1455cm(-1) due to a decrease in fatty acids and lipid molecules. The band area ratio of lipid was used to monitor the changes in fatty acids due to metal toxicity. Principle component method helps to discriminates the results between control and metal toxicities in E. coli from the FTIR data. The study shows the importance of metal interaction and its toxicity on E. coli. PMID:27152659

  2. Biochemical mechanisms of laser vascular tissue fusion. (United States)

    Guthrie, C R; Murray, L W; Kopchok, G E; Rosenbaum, D; White, R A


    This study examines the biochemical changes that occur in argon laser-fused canine veins compared with control segments of vein. Laser fusions were formed using 0.5 W argon laser energy (1100-1500 J/cm2). Immediately following tissue fusion, blood flow was reestablished to test the integrity of the welds. 1-mm3 sections of the anastomoses and control sections were minced and protein extraction was performed by solubilizing the tissue in hot SDS Laemmli gel sample buffer. The proteins were separated electrophoretically on 5 and 10% polyacylamide SDS gels and silver stained. The analysis demonstrated significant biochemical differences between control and lased veins. We noted increases in several proteins after laser welding: the putative beta chain of type V collagen (5/5 gels), the putative gamma chain of type I collagen (4/5 gels), a 156-kDa protein (based on collagen molecular weight standards) 7/7 gels), an 82-kDa protein (8/9 gels), and several proteins of lower molecular weight (3/8 gels). The increases may be due to crosslinking of lower molecular weight proteins, degradation of higher molecular weight proteins, or increased solubility of certain proteins. These findings suggest that laser welding may occur by formation of crosslinks or by denaturation and reannealment of structural proteins. PMID:1863584

  3. Profile of biochemical traits influencing tenderness of muscles from the beef round. (United States)

    Anderson, M J; Lonergan, S M; Fedler, C A; Prusa, K J; Binning, J M; Huff-Lonergan, E


    The objective of this study was to define the biochemical differences that govern tenderness and palatability of economically important muscles from the beef round using cuts with known tenderness differences. At 24h postmortem, the longissimus dorsi (LD), gracillus (GR), adductor (AD), semimembranosus (SM), sartorius (SAR), vastus lateralis (VL), and vastus intermedius (VI) muscles were removed from ten market weight beef cattle. Sensory and biochemical characteristics were determined in each cut and compared with the LD. The GR, SAR and VI had sensory traits similar to the LD while the SM, AD and VL differed. The GR, SAR, AD, and SM all had multiple biochemical characteristics similar to the LD, while the VI and AD had numerous biochemical differences. While no one biochemical characteristic can be used to predict tenderness across all muscles, analysis of the biochemical characteristics revealed that in most beef round cuts postmortem proteolysis provided a good indication of the tenderization occurring during aging. PMID:22386323

  4. Biochemical analysis of extracting fermented coconut oil




    Vegetable oil can be produced from a perennial plant such as coconut (Cocos nucifera L.). There are few techniques for coconut oil extraction, such as physical, chemical, and fermentative processes. The fermentation process uses microbial inoculum as starter. Ground coconut meat was soaked in warm water, than squeezed several times to get coconut milk. After being allowed to stand for 4-5 hours, it separated into two layers, cream and skim. Starter was prepared from a mixture of milk and coco...

  5. Behavior and biochemical analysis of phencyclidine

    International Nuclear Information System (INIS)

    The objectives of this research were: (1) to develop the radial maze as a tool for the study of phencyclidine (PCP) and related drugs; (2) to evaluate verapamil and colonidine, two proposed treatments for PCP intoxication, as potential antagonists of PCP in the radial maze; and (3) to evaluate the functionality of two distinct types of PCP binding sites as receptors by comparing, for a series of drugs, activity in competitive binding experiments with behavioral activity. The radial maze proved to be a useful tool for the study of PCP and related drugs. With training, rats became highly efficient at obtaining the 8 food pellets placed in the maze. However, PCP and related drugs disrupted this performance, causing numerous reentries into previously visited arms. Results of correlation analyses comparing rank-order affinities with rank-order potencies of (+)SKF-10,047 (the prototypical sigma-opioid agonist), PCP, and several PCP analogs support the involvement of [3H]-1-(2-thienyl)cyclohexyl piperidine binding sites (TCP sites) in mediating both the discriminative stimulus properties of PCP and disruption of performance in a 4-arm radial maze

  6. Comparative Analysis of Glucose Determination Results Using POCT Glucose Meter and Automatic Biochemical Analyzer%POCT血糖仪与全自动生化分析仪血糖测定结果的比对分析

    Institute of Scientific and Technical Information of China (English)

    王宾; 张剑平; 李耀军


    Objective To study test results of using the Johnson &johnson glucose meter and BS - 420 ful y automatic biochemical analyzer. Methods 81 cases patients who needed blood glucose detection in our hospital outpatient service were selected, Johnson &johnson glucose meter was used to determine peripheral blood glucose, the BS - 420 analyzer to detect serum glucose, analysis of the dif erences in test results. Results Johnson &johnson glucose meter and BS - 420 analyzer determination results were 9.45±4.28,9.26±4.12mmol/L respectively, there is no statistical dif erence (> 0.05). Conclusion Johnson &johnson glucose meter has smal volume, simple operation and fast inspection speed, can be used in the screening of outpatient emergency treatment in patients with diabetes.%目的:探讨强生血糖仪和BS-420全自动生化分析仪检测结果。方法选择我院门诊需进行血糖检测的患者81例,采用强生血糖仪测定末梢血血糖,采用BS-420分析仪检测血清血糖,分析二者检测结果的差异。结果强生血糖仪及BS-420分析仪测定结果分别为(9.45±4.28)、(9.26±4.12)mmol/L,二者无统计学差异(跃0.05)。结论强生血糖仪具有体积小、操作简单、检测速度快等优点,可用于门诊急诊患者糖尿病的筛查。

  7. Biochemical bases of mineral waters genesis

    Directory of Open Access Journals (Sweden)

    D. D. Zhernosekov


    Full Text Available This work directs data about mineral water genesis. The accent on balneological sense is done. We suggest the criteria of biochemical processes estimation which take part in mineral water compounds creation. These criteria can be used for illustration of dependence between waters medical properties and biochemical processes of their genesis.

  8. Biochemical disease-free survival following adjuvant and salvage irradiation after radical prostatectomy

    International Nuclear Information System (INIS)

    Purpose: To present the biochemical cure rates (biochemically no evidence of disease) after external irradiation (RT) in patients with high-risk prostate cancer after radical prostatectomy. Methods and Materials: Seventy-six patients who underwent radical prostatectomy and subsequent RT were included in this analysis. No patient received hormonal therapy. Adjuvant RT was administered in 35 patients (46%), and 41 patients (54%) underwent salvage RT. After prostatectomy, the Gleason score was <7 in 87%, and 24% had seminal vesicle invasion. The median RT dose in the adjuvant RT and salvage RT groups was 60 Gy and 65 Gy, respectively. The biochemical cure rate was defined as a serum prostate-specific antigen of ≤0.2 ng/mL. Results: The overall 5-year Kaplan-Meier biochemical control rate from the end of RT was 70%. The 5-year biochemical cure rate for adjuvant RT was significantly superior to that after salvage RT (86% vs. 57%). The significant predictors of biochemical failure were seminal vesicle invasion in the adjuvant RT group and the presence of Gleason grade 4 or 5 in the salvage RT group. The clinical local control rate in the prostate bed was 100%. Conclusion: This report demonstrates the efficacy of RT in achieving high biochemical cure rates after radical prostatectomy. Additional clinical studies are required to determine the optimal treatment of patients at high risk of biochemical failure after postprostatectomy RT



    Ali Hafez El-Far


    Blood samples from diseased and clinically healthy Balady sheep of both sexes were collected and subjected for biochemical analysis of serum glucose, fructosamine, lactate, growth hormone, insulin, creatine phosphokinase, Lactate dehydrogenase and aldolase. The obtained results revealed a significant decrease in serum zinc and growth hormone were stated. In contrary, serum glucose and lactate, insulin, CPK, LDH and aldolase were significantly increased statically. While, fructosamine levels w...


    Directory of Open Access Journals (Sweden)

    Yu. P. Sedlukho


    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

  11. Studies on some biochemical parameters in viral hepatitis patients

    International Nuclear Information System (INIS)

    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

  12. High-dose rate brachytherapy in the treatment of prostate cancer: acute toxicity and biochemical behavior analysis; Braquiterapia de alta taxa de dose no tratamento do carcinoma da prostata: analise da toxicidade aguda e do comportamento bioquimico

    Energy Technology Data Exchange (ETDEWEB)

    Esteves, Sergio Carlos Barros; Oliveira, Antonio Carlos Zuliani de; Cardoso, Herbeni; Tagawa, Eduardo Komai; Castelo, Roberto [Beneficencia Portuguesa de Sao Paulo, SP (Brazil). Hospital Sao Joaquim. Servico de Radioterapia]. E-mail:; D' Imperio, Marcio [Beneficencia Portuguesa de Sao Paulo, SP (Brazil). Hospital Sao Joaquim. Servico de Urologia


    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)


    Directory of Open Access Journals (Sweden)



    Full Text Available Diabetic nephropathy is a clinical syndrome characterized by the following- Persistent albuminuria (>300mg/d or >200μg/min, that is confirmed on at least 2 occasions 3-6 months apart diabetic, progressive decline in the Glomerular Filtration Rate (GFR, elevated arterial blood pressure. The earliest biochemical criteria for the diagnosis of diabetic nephropathy is the presence of micro-albumin in the urine, which if left untreated will eventually lead to End-Stage Renal Disease (ESRD. Micro-albuminuria refers to the excretion of albumin in the urine at a rate that exceeds normal limits. The current study was conducted to establish the prevalence of micro-albuminuria in a sequential sample of diabetic patients attending hospital and OPD Clinic to determine its relationship with known and putative risk factors to identify micro- and normo-albuminuric patients in their sample for subsequent comparison in different age, sex, weight and creatinine clearance of the micro- and normo-albuminuric patients. This cross-sectional analytical study was conducted in one hundred patients at Saraswathi Institute of Medical Sciences, Anwarpur, Hapur, U. P. Patients having diabetes mellitus in different age group ranging from 30 to 70 years were selected. Data was analysed by SPSS software. Micro-albuminuria was observed in 35% in patients with type 2 diabetes mellitus. It was observed that 65% patients were free from any type of albuminuria. Also micro-albuminuria was present in 10% of the patients less than 50 yrs. of age, while 15% of the patients more than 50 yrs. of age were having micro-albuminuria. There was a statistically significant correlation of micro-albuminuria with duration of diabetes. Incidence of micro-albuminuria increases with age as well as increased duration of diabetes mellitus. Our study shows that only 5% patients developed macro-albuminuria. Glycosylated haemoglobin and fasting plasma glucose was significantly raised among all these

  14. The Development of a Biochemical Profile of Acacia Honey by Identifying Biochemical Determinants of its Quality

    Directory of Open Access Journals (Sweden)

    Liviu Alexandru MARGHITAS


    Full Text Available Codex Alimentarius Standard, EU Legislation and National Standards state honey authenticity. Authenticity in respect of production (to prevent adulteration and authenticity in respect of geographical and botanical origin are the two main aspects of general honey authenticity. Quality of honey depends on the plant source, the chemical composition of these plants as well, as on the climatic conditions and soil mineral composition. Romanian acacia (Robinia pseudoacacia honey that came from the most important Transylvanian massif (Valea lui Mihai, Bihor County, Romania was evaluated for authenticity by pollen-analysis, several physico-chemical analyses, including sugar profile and mineral content. As polyphenolic content could be also an important factor for botanical authentification, HPLC-DAD-MS analyses were performed to assess the fingerprint of this important secondary plant metabolite. Statistical data were processed in order to develop a biochemical profile of this type of honey and the main quality categories identification. The results of physico-chemical analysis demonstrated that the tested honey samples could be framed into monofloral type of acacia honeys. The analysis of acacia honeys originating from Valea lui Mihai, Romania, showed that polyphenolic profile (phenolic acids and flavonoids could be used as a complementary method for authenticity determination together with pollen analysis and other physico-chemical analysis.

  15. Correlation analysis on results of blood sugar tested by terumo glucome-ter and Hitachi 7180 biochemical analyzer%泰尔茂血糖仪与日立7180生化分析仪检测血糖结果相关性分析

    Institute of Scientific and Technical Information of China (English)

    刘斌; 刘伟红; 康玉国


    Objective To compare and analyze the results of patients' blood sugar value tested by Terumo glucometer and Hitachi 7180 biochemical analyzer, and to analyze their correlation. Methods Fifty blood samples with different blood sugar values. Terumo glucometer was used to test blood sugar for three times and an average value was calculat-ed;full-automatic Hitachi 7180 biochemical analyzer was used to test blood sugar for three times by serum centrifuga-tion of 3000 rpm, and an average value was calculated. SPSS software was used for analysis. Results Precision of Teru-mo glucometer CV% was less than 5%, and the relative bias accorded with related requirements. Compared with the test results by Hitachi 7180 full-automatic biochemical analyzer, results of blood sugar by Terumo glucometer were all within the allowed range. Standard deviation of sample average of 50 samples tested by Terumo glucometer was (7.51±0.69), and the standard deviation of sample average of samples tested by Hitachi 7180 biochemical analyzer was (7.37±0.66). Results of blood sugar tested by Terumo glucometer and Hitachi 7180 biochemical analyzer were not statistically different (t=0.15, P>0.05); correlation coefficient R2 of Terumo glucometer and Hitachi 7180 biochemical analyzer was 0.9739. Conclusion Correlation between glucometer and full-automatic biochemical analyzer in testing blood sugar is favorable, which can be used for blood sugar testing for diabetic patients, but the blood sugar value tested by biochemi-cal analyzer must be taken as diagnostic basis.%目的:对我院在用的泰尔茂血糖测定仪检测患者血糖结果与全自动日立7180生化仪检测血糖值分析比较,分析其相关性。方法采用血糖值不同的50份血液标本,使用泰尔茂血糖测定仪测3次,取均值;3000转/min离心取血清在全自动日立7180生化分析仪上测定3次,取均值,用SPSS软件进行分析。结果泰尔茂血糖测定仪检测精密度CV%小于5%,


    Directory of Open Access Journals (Sweden)

    A.A.G. Bianco


    Full Text Available This work presents a course dedicated to the pedagogical instruction of graduate students (Ensino deBioqumica - QBQ 5711 in which they have to plan and teach a 30 hour-discipline for undergraduatestudents. The graduate students have to choose a subject for the discipline and, in 2003, the cho-sen subject was Nutrition and Sports: a Biochemical Approach, which is not specically broached inregular disciplines. The discipline was structured in the basis of collaborative learning, thus, the 75 en-rolled undergraduate students (from dierent courses as Nutrition, Sports, Pharmacy, Chemistry andBiology were organized in small working groups. The students were given a study guide produced bythe graduate teachers (available in Portuguese at,in which the following contents were covered: muscle contraction, O2 up-take, oxidative stress andanti-oxidant response, cramp, hydration, doping and nutritional supplies. In the nal activity thestudents had to evaluate critically myths and true facts in 80 statements usually associated to physi-cal activities and sports. The discipline was evaluated through questionnaires. From the analysis ofthe answers of both undergraduate and graduate/teachers students it is possible to conclude that thediscipline was well conduced and succeeded. These results emphasize the relevance and contribution ofthis kind of discipline to the pedagogical instruction of the graduate students and also to the increaseof undergraduate students interests in Biochemistry.

  17. Biochemical and proteomic characterization of alkaptonuric chondrocytes. (United States)

    Braconi, Daniela; Bernardini, Giulia; Bianchini, Claretta; Laschi, Marcella; Millucci, Lia; Amato, Loredana; Tinti, Laura; Serchi, Tommaso; Chellini, Federico; Spreafico, Adriano; Santucci, Annalisa


    Alkaptonuria (AKU) is a rare genetic disease associated with the accumulation of homogentisic acid (HGA) and its oxidized/polymerized products which leads to the deposition of melanin-like pigments (ochronosis) in connective tissues. Although numerous case reports have described ochronosis in joints, little is known on the molecular mechanisms leading to such a phenomenon. For this reason, we characterized biochemically chondrocytes isolated from the ochronotic cartilage of AKU patients. Based on the macroscopic appearance of the ochronotic cartilage, two sub-populations were identified: cells coming from the black portion of the cartilage were referred to as "black" AKU chondrocytes, while those coming from the white portion were referred to as "white" AKU chondrocytes. Notably, both AKU chondrocytic types were characterized by increased apoptosis, NO release, and levels of pro-inflammatory cytokines. Transmission electron microscopy also revealed that intracellular ochronotic pigment deposition was common to both "white" and "black" AKU cells. We then undertook a proteomic and redox-proteomic analysis of AKU chondrocytes which revealed profound alterations in the levels of proteins involved in cell defence, protein folding, and cell organization. An increased post-translational oxidation of proteins, which also involved high molecular weight protein aggregates, was found to be particularly relevant in "black" AKU chondrocytes. PMID:22213341

  18. Biochemical genetics of some Indian fishes

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Qasim, S.Z.

    Studies on biochemical genetics of fishes, using electrophoretic methods, are relatively of recent origin. Earlier serum and eye lens protein were used to identify marine populations. This technique showed that closely related species have...

  19. Physics and Electro-Biochemical Technology

    Directory of Open Access Journals (Sweden)

    Conrad P Pritscher


    Full Text Available Not Available Keywords: Biochemical technology, physics Received: 22 October 2008 / Received in revised form: 23 October 2008, Accepted: 24 October 2008 Published online: 07 January 2009

  20. 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


    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

  1. Research on SWOT analysis and countermeasure for biochemical laboratory safety and environmental sprotection management in colleges and universities%高校生化类实验室安全与环保管理的SW OT分析与对策研究

    Institute of Scientific and Technical Information of China (English)

    宋玉厚; 乔威; 朱榜芹


    以实验室安全与环保典型事故为例,阐述了高校实验室安全与环保管理工作对于师生员工的生命及财产安全的重要性。运用SWOT分析法对高校生化类实验室安全与环保管理工作的内外部环境因素进行了分析,指出高校生化类实验室安全与环保管理工作存在的优势和劣势、面临的机遇和威胁。以山东大学(威海)为例,基于该分析开展了卓有成效的研究和实践,提出了高校生化类实验室安全与环保管理工作的若干对策建议。%Taking typical accidents about laboratory safety and environmental protection as an example ,this paper elaborates on the importance of laboratory safety and environmental protection management in colleges and universities to the safety of the faculty’s and students’ life and property .With the SWOT analysis method defined , this paper by using the SWOT analysis method analyzes in detail the internal and external environmental factors about biochemical laboratory safety and environmental protection management in colleges and universities , and points out the advantages , disadvantages , opportunities and threats in biochemical laboratory safety and environmental protection management in colleges and universities . Taking Shandong University ( Weihai) as an example and based on the analysis ,the authors have conducted a very fruitful practice exploration ,and proposes several countermeasures for biochemical laboratory safety and environmental protection management in colleges and universities .

  2. Free energy simulations of important biochemical processes


    Yang LIU; 刘洋


    Free energy simulations have been widely employed to compute the thermodynamic properties of many important biochemical processes. In the first part of this dissertation, two important biochemical processes, protonation/deprotonation of acid in solution and solvation of small organic molecules, are investigated using free energy simulations. Accurate computation of the pKa value of a compound in solution is important and challenging. To efficiently simulate the free energy change associat...

  3. Mode of inheritance for biochemical traits in genetically engineered cotton under water stress. (United States)

    Abid, Muhammad Ali; Malik, Waqas; Yasmeen, Azra; Qayyum, Abdul; Zhang, Rui; Liang, Chengzhen; Guo, Sandui; Ashraf, Javaria


    Drought is an abiotic environmental stress that can significantly reduce crop productivity. We examined the mode of inheritance for different biochemical traits including total soluble proteins, chlorophyll a, chlorophyll b, total chlorophyll, carotenoids, total phenolic contents and enzymatic antioxidants (superoxide dismutase, peroxidase and catalase), and their relationship with Bacillus thuringiensis (Bt) toxin under control and drought conditions. Eight genetically diverse cotton genotypes were selfed for two generations to ensure homozygosity. Fifteen F1 hybrids were developed by crossing five non-Bt female lines with three Bt male testers. The F1 hybrids and eight parents were finally evaluated under control (100 % field capacity (FC)) and drought (50 % FC) conditions in 2013. The biochemical traits appeared to be controlled by non-additive gene action with low narrow sense heritability estimates. The estimates of general combining ability and specific combining ability for all biochemical traits were significant under control and drought conditions. The genotype-by-trait biplot analysis showed the better performance of Bt cotton hybrids when compared with their parental genotypes for various biochemical traits under control and drought conditions. The biplot and path coefficient analyses revealed the prevalence of different relationships between Cry1Ac toxin and biochemical traits in the control and drought conditions. In conclusion, biochemical traits could serve as potential biochemical markers for breeding Bt cotton genotypes without compromising the optimal level of Bt toxin. PMID:26839284

  4. 40 CFR 158.2010 - Biochemical pesticides data requirements. (United States)


    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides... required to support registration of biochemical pesticides. Sections 158.2080 through 158.2084 identify...

  5. 40 CFR 158.2000 - Biochemical pesticides definition and applicability. (United States)


    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  6. Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori.

    Directory of Open Access Journals (Sweden)

    Han-Pil Choi

    Full Text Available The functional characterization of Open Reading Frames (ORFs from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In particular, the functional characterization of proteins with only remote sequence homology to known proteins can be challenging, as there may be few clues to guide initial experiments. Affinity enrichment of proteins from cell lysates, and a global perspective of protein function as provided by COMBREX, affords an approach to this problem. We present here the biochemical analysis of six proteins from Helicobacter pylori ATCC 26695, a focus organism in COMBREX. Initial hypotheses were based upon affinity capture of proteins from total cellular lysate using derivatized nano-particles, and subsequent identification by mass spectrometry. Candidate genes encoding these proteins were cloned and expressed in Escherichia coli, and the recombinant proteins were purified and characterized biochemically and their biochemical parameters compared with the native ones. These proteins include a guanosine triphosphate (GTP cyclohydrolase (HP0959, an ATPase (HP1079, an adenosine deaminase (HP0267, a phosphodiesterase (HP1042, an aminopeptidase (HP1037, and new substrates were characterized for a peptidoglycan deacetylase (HP0310. Generally, characterized enzymes were active at acidic to neutral pH (4.0-7.5 with temperature optima ranging from 35 to 55°C, although some exhibited outstanding characteristics.

  7. Considerations on the biochemical composition of some freshwater zooplankton species.

    Directory of Open Access Journals (Sweden)

    Nicoletta RICCARDI


    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.

  8. Molecular and biochemical studies on bovine ephemeral fever

    Directory of Open Access Journals (Sweden)

    Nahed S. Thabet; Emad W. Ghazy; Mohamed A. Nayel; Mohamed Abo-Elkhair


    Full Text Available Bovine ephemeral fever (BEF in cattle has been reported to be associated with a range of biochemical changes which are similar to those seen in milk fever. This study aimed to clarify the biochemical alterations that associate infection of cattle with BEF with special references to the mechanisms involved in the development of hypocalcemia. The study was conducted on 30 cases of cattle infected with BEF based on the characteristic clinical signs which were confirmed by isolation of virus and RT-PCR. Another 6 healthy cows were used in the study as control. The evaluated parameters included biochemical variables such as serum values of total protein (TP, albumin (Alb, glucose (Glu, total calcium (tCa, ionized calcium (iCa, inorganic phosphorus (P, magnesium (Mg, sodium (Na, potassium (K, chloride (Cl, creatinine (Cr, blood urea nitrogen (BUN and serum activity of alkaline phosphatase (ALP. Hormonal profile included parathyroid hormone (PTH, insulin (Ins, and cortisol (Cor. The results showed that BEF-infected animals demonstrated a significant decrease (P<0.05 in serum concentrations of TP, Glo, iCa, P, Na, K, BUN and ALP while the mean values of serum levels of Glu and Cl were significantly increased (P<0.05. The mean values of serum levels of PTH were significantly decreased (P<0.05 while serum concentrations of Ins and Cor showed a significant increase. It was concluded that the clinical signs of bovine ephemeral fever are related to the hypocalcemia resulting from suppression of parathyroid hormone which seems to be mediated by respiratory alkalosis caused by the disease. This explanation needs future studies to provide a direct link between measurement of blood indicators of acid-base status, blood biochemical parameters and urine analysis. However, this work can provide a good knowledge about the pathogenesis of the disease that can lead to better management and proper treatment.

  9. Blood glucose meter with biochemical analyzer blood glucose than on analysis%血糖仪与生化分析仪测定血糖的比对分析

    Institute of Scientific and Technical Information of China (English)

    秦亚军; 张保龙; 杨笑琼


      目的:探讨血糖仪与生化分析仪测定血糖的比对情况,为合理选择血糖检测方法提供参考。方法:选择2009年2月~2012年8月在我院门诊住院患者糖尿病人员共120例,上肢肘静脉和手指末端分别采血进行生化分析仪与血糖仪检测。结果:经过检测,生化分析仪检测的血糖值为(6.30±0.22)mmol/L,血糖仪检测的血糖值为(6.25±1.89)mmol/L,两种方法检测值对比无明显差异(P>0.05)。但是血糖仪检测的重复性不强,导致s值比较大。结论:血糖仪在糖尿病患者的血糖监测中有很大的局限性,在临床中要将血糖仪的监测和医院血糖检测结合使用,才能达到良好的血糖控制目的。%Objective:To investigate the blood glucose meter and biochemical analyzer than on blood sugar, and provide a reference for the reasonable choice of blood glucose testing method. Methods:From February 2009 to August 2012, a total of 120 cases of staff in our hospital hospitalized patients with diabetes, venous and finger blood samples were collected at the end of the upper limb elbow biochemical analyzer and blood glucose meter testing. Results:After testing, the the biochemical analyzer blood sugar value of (6.30± 0.22)mmol/L, blood glucose meter testing blood sugar value of (6.25±1.89)mmol/L, two methods for detecting the value of contrast was no significant difference(P>0.05). However, the reproducibility of the blood glucose meter detecting is not strong, resulting in the value of s is relatively large. Conclusion: The blood glucose meter glucose monitoring in diabetes has many limitations, combined To glucometer monitoring and hospital blood glucose testing in clinical use, in order to achieve good glycemic control purposes.

  10. Reconfigurable neuromorphic computation in biochemical systems. (United States)

    Chiang, Hui-Ju Katherine; Jiang, Jie-Hong R; Fages, Francois


    Implementing application-specific computation and control tasks within a biochemical system has been an important pursuit in synthetic biology. Most synthetic designs to date have focused on realizing systems of fixed functions using specifically engineered components, thus lacking flexibility to adapt to uncertain and dynamically-changing environments. To remedy this limitation, an analog and modularized approach to realize reconfigurable neuromorphic computation with biochemical reactions is presented. We propose a biochemical neural network consisting of neuronal modules and interconnects that are both reconfigurable through external or internal control over the concentrations of certain molecular species. Case studies on classification and machine learning applications using the DNA strain displacement technology demonstrate the effectiveness of our design in both reconfiguration and autonomous adaptation. PMID:26736417

  11. Analysis of the consistency of the detection results of glycosylated hemoglobin (HbA1c) by SMART POCT and hitachi 7180 biochemical analyzers%SM ART POCT 与日立7180生化仪检测糖化血红蛋白的一致性分析

    Institute of Scientific and Technical Information of China (English)

    田建红; 汪屹; 贾江花; 章玉胜


    目的:探讨SMART POCT和日立7180检测糖化血红蛋白(HbA1c)的结果相关性。方法首先分别对SMART POCT和日立7180生化仪检测 HbA1c进行精密度评价,再随机选取20份样本在两台仪器上分别进行测定,对测定结果进行相关性分析。结果两台仪器的精密度高,所测结果的相关性好,相关系数(r2)为0.9811。结论 SMART POCT 和日立7180检测HbA1c具有很高的一致性。%Objective To analyze the consistency of the detection results of glycosylated hemoglobin (HbA1c) by SMART POCT and Hitachi 7180 biochemical analyzers .Methods Firstly the accuracy of HbA1c detected by the SMART POCT and Hita‐chi 7180 biochemical analyzers were evaluated .And then 20 randomly selected samples were tested by both equipments .A relevance analysis between detected data from two equipments was conducted .Results There was a good correlation between the results of the HbA1c detected by two detecting systems ,with the correlation coefficient of r2 =0 .981 1 .Conclusion There is a good consis‐tency in detection results of glycosylated hemoglobin (HbA1c) detected by SM ART POCT and Hitachi 7180 biochemical analyzer .

  12. Comparative analysis on blood glucose results detected by portable glucose meter and Olympus AU2700 automatic biochemical analyzer%便携式血糖仪与 Olympus AU2700血糖测定结果的比对分析

    Institute of Scientific and Technical Information of China (English)

    吴立春; 张莉; 刘明炎; 王左


    Objective To perform the comparative analysis on the blood glucose results detected by the portable glucose meter and the Olympus AU2700 biochemical analyzer.Methods 20 fresh whole blood samples with sodium fluoride and potassium oxalate anticoagulation were the Olympus AU2700 biochemical analyzer biochemical analyzer.Results In these 27 portable glucose meters, the comparison results in only 1 portable glucose meter was unqualified,which in the other 26 portable glucose meters were passed, the passing rate was 96.3%,which in 2 glucose meters were clinically acceptable and which in the other 24 glucose meters were completely acceptable and the clinical completely acceptable rate was 88.9%.Conclusion There are some biases of blood glucose results detected by the portable glucose meter and the fully automatic biochemical analyzer,but the overall correlation is well.The comparison and calibration of the blood glucose meters should be performed at the regular intervals for improving the consistency and accuracy of blood glucose detection results.%目的:对血糖仪和全自动生化分析仪测定血糖结果进行比对,评估其测定结果的偏倚及相关性。方法选择20份氟化钠-草酸钾抗凝全血对全院27台血糖仪和 Olympus AU2700全自动生化分析仪进行同时检测,对检测结果进行分析。结果27台血糖仪中1台血糖仪比对结果未通过,其余26台血糖仪均通过,通过率96.3%;2台血糖仪比对结果属于临床尚可接受水平,24台血糖仪属于临床完全可接受水平,临床完全可接受率为88.9%。结论血糖仪与全自动生化分析仪血糖测定结果虽然存在一定的偏差,但总体相关性较好,应定期对血糖仪进行比对和校准以提高检测结果的一致性和准确性。

  13. Murine interleukin 2 receptor. IV. Biochemical characterization

    International Nuclear Information System (INIS)

    The IL 2 receptor isolated from the IL 2-dependent CTL-L cell line was subjected to biochemical analysis. Pulse-chase and tunicamycin studies, as well as digestion with the endoglycosidases, Endo-F and Endo-H, of 35S-methionine-labeled IL 2 receptors suggested a single protein pecursor of 32,000 (p32) daltons. The p32 precursor was rapidly processed by addition of high-mannose-containing core N-linked sugars to intracytoplasmic precursor intermediates of 38,000 (p38) and 40,000 (p40) daltons, which undergo further processing to yield a mature surface receptor with heterogeneous apparent m.w. of 52,000 to 65,000 (p58). Two-dimensional gel studies indicated that p58 exhibited broad charge heterogeneity between pH 4.6 and 6.3. Endo-F digestions of p58 shifted the isoelectric focus point to a more basic 5.5 to 7.4. This considerable charge heterogeneity is consistent with the possibility that other post-translational modifications to the mouse IL 2 receptor occur besides addition of complex N-linked glycans. Immunoprecipitations of the IL 2 receptor from surface iodinated cells also revealed an additional band at 110,000 (p110) daltons. IEF vs SDS-PAGE two-dimensional gel studies demonstrated that p110 also had an isoelectric focus point identical to p58. Western blot studies with an anti-IL 2 receptor monoclonal antibody (7D4) demonstrates that p38, p40, p58, and p110 each expressed the epitope recognized by this antibody. Thus, it is likely that p110 is not a unique molecule that coprecipitates with IL 2 receptor. Western blot analysis of mitogen-stimulated T and B lymphocytes also revealed bands similar to p58 and p110, although these bands had an average apparent m.w. 3000 and 6000 less than those seen for CTL-L cells

  14. Predictive biochemical assays for late radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    Rubin, P.; Finkelstein, J.N.; Siemann, D.W.; Shapiro, D.L.; Van Houtte, P.; Penney, D.P.


    Surfactant precursors or other products of Type II pneumocytes have the potential to be the first biochemical marker for late radiation effects. This is particularly clinically important in the combined modality era because of the frequent occurrence of pneumonitis and pulmonary fibrosis secondary to radiation or chemotherapy. Accordingly, correlative studies have been pursued with the Type II pneumocyte as a beginning point to understand the complex pathophysiology of radiation pneumonitis and fibrosis. From our ultrastructural and biochemical studies, it is evident that Type II pneumocytes are an early target of radiation and the release of surfactant into the alveolus shortly after exposure persists for days and weeks. Through the use of lavaging techniques, alveolar surfactant has been elevated after pulmonary irradiation. In three murine strains and in the rabbit, there is a strong correlation with surfactant release at 7 and/or 28 days in vivo with later lethality in months. In vitro studies using cultures of type II pneumocytes also demonstrate dose response and tolerance factors that are comparable to the in vivo small and large animal diagnostic models. New markers are being developed to serve as a predictive index for later lethal pneumonopathies. With the development of these techniques, the search for early biochemical markers in man has been undertaken. Through the use of biochemical, histological, and ultrastructural techniques, a causal relationship between radiation effects on type II pneumocytes, pulmonary cells, endothelial cells of blood vessels, and their roles in the production of pneumonitis and fibrosis will evolve.

  15. Biochemical Applications in the Analytical Chemistry Lab (United States)

    Strong, Cynthia; Ruttencutter, Jeffrey


    An HPLC and a UV-visible spectrophotometer are identified as instruments that helps to incorporate more biologically-relevant experiments into the course, in order to increase the students understanding of selected biochemistry topics and enhances their ability to apply an analytical approach to biochemical problems. The experiment teaches…

  16. Survey of Biochemical Education in Japanese Universities. (United States)

    Kagawa, Yasuo


    Reports findings of questionnaires sent to faculty in charge of biochemical education in medical schools and other programs from dentistry to agriculture. Total class hours have declined since 1984. New trends include bioethics and computer-assisted learning. Tables show trends in lecture hours, lecture content, laboratory hours, core subject…

  17. Predictive biochemical assays for late radiation effects

    International Nuclear Information System (INIS)

    Surfactant precursors or other products of Type II pneumocytes have the potential to be the first biochemical marker for late radiation effects. This is particularly clinically important in the combined modality era because of the frequent occurrence of pneumonitis and pulmonary fibrosis secondary to radiation or chemotherapy. Accordingly, correlative studies have been pursued with the Type II pneumocyte as a beginning point to understand the complex pathophysiology of radiation pneumonitis and fibrosis. From our ultrastructural and biochemical studies, it is evident that Type II pneumocytes are an early target of radiation and the release of surfactant into the alveolus shortly after exposure persists for days and weeks. Through the use of lavaging techniques, alveolar surfactant has been elevated after pulmonary irradiation. In three murine strains and in the rabbit, there is a strong correlation with surfactant release at 7 and/or 28 days in vivo with later lethality in months. In vitro studies using cultures of type II pneumocytes also demonstrate dose response and tolerance factors that are comparable to the in vivo small and large animal diagnostic models. New markers are being developed to serve as a predictive index for later lethal pneumonopathies. With the development of these techniques, the search for early biochemical markers in man has been undertaken. Through the use of biochemical, histological, and ultrastructural techniques, a causal relationship between radiation effects on type II pneumocytes, pulmonary cells, endothelial cells of blood vessels, and their roles in the production of pneumonitis and fibrosis will evolve

  18. 2009 Biochemical Conversion Platform Review Report

    Energy Technology Data Exchange (ETDEWEB)

    Ferrell, John [Office of Energy Efficiency and Renewable Energy (EERE), Washington, DC (United States)


    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

  19. Biochemical Thermodynamics under near Physiological Conditions (United States)

    Mendez, Eduardo


    The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables…

  20. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L


    Full Text Available Abstract Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology

  1. Multivariate modeling of chromium-induced oxidative stress and biochemical changes in plants of Pistia stratiotes L.


    Sinha, Sarita; Basant, Ankita; Malik, Amrita; Singh, Kunwar P.


    Biochemical changes in the plants of Pistia stratiotes L., a free floating macrophyte exposed to different concentrations of hexavalent chromium (0, 10, 40, 60, 80 and 160 μM) for 48, 96 and 144 h were studied. Chromium-induced oxidative stress in macrophyte was investigated using the multivariate modeling approaches. Cluster analysis rendered two fairly distinct clusters (roots and shoots) of similar characteristics in terms of their biochemical responses. Discriminant analysis identified as...

  2. Classification and fingerprinting of different berries based on biochemical profiling and antioxidant capacity

    Directory of Open Access Journals (Sweden)

    Jasminka Milivojević


    Full Text Available The objective of this work was to evaluate the biochemical composition of six berry types belonging to Fragaria, Rubus, Vaccinium and Ribes genus. Fruit samples were collected in triplicate (50 fruit each from 18 different species or cultivars of the mentioned genera, during three years (2008 to 2010. Content of individual sugars, organic acids, flavonols, and phenolic acids were determined by high performance liquid chromatography (HPLC analysis, while total phenolics (TPC and total antioxidant capacity (TAC, by using spectrophotometry. Principal component analysis (PCA and hierarchical cluster analysis (CA were performed to evaluate the differences in fruit biochemical profile. The highest contents of bioactive components were found in Ribes nigrum and in Fragaria vesca, Rubus plicatus, and Vaccinium myrtillus. PCA and CA were able to partially discriminate between berries on the basis of their biochemical composition. Individual and total sugars, myricetin, ellagic acid, TPC and TAC showed the highest impact on biochemical composition of the berry fruits. CA separated blackberry, raspberry, and blueberry as isolate groups, while classification of strawberry, black and red currant in a specific group has not occurred. There is a large variability both between and within the different types of berries. Metabolite fingerprinting of the evaluated berries showed unique biochemical profiles and specific combination of bioactive compound contents.

  3. Clinical and pathologic factors predictive of biochemical control following post-prostatectomy irradiation

    International Nuclear Information System (INIS)

    Purpose/Objective: Indications for post-prostatectomy radiation therapy are not well defined. We reviewed our experience treating post-prostatectomy patients with external beam irradiation to assess clinical and pathologic factors predictive of biochemical control. Materials and Methods: Between 1/87 and 3/93, 61 patients received post-operative tumor bed irradiation with a median dose of 59.4 Gy (50.4 - 68 Gy). Median follow-up was 4.1 years (7.6 months - 8.3 years) from irradiation. Patients were treated for the following reasons: 1) adjuvantly, within 6 months of surgery for extracapsular extension, seminal vesicle involvement, or positive surgical margins (n=38); 2) persistently elevated PSA post-operatively (n=2); 3) rising PSA >6 months after surgery (n=9); and 4) biopsy proven local recurrence (n=12). No patients had known nodal or metastatic disease. All patients had post-radiation PSA data available. Biochemical control was the endpoint studied using Kaplan-Meier life table analysis. Biochemical control was defined as the ability to maintain an undetectable PSA (4 and ≤1 0, >10 and ≤20, and > 20 ng/ml. The 3 year actuarial rates of biochemical control were 100% for group 1, 66.7% for group 2, 61.5% for group 3, and 28.6% for group 4. Pre-RT PSA values were also evaluated. Univariate Cox models indicated lower presurgical and pre-RT PSA values were predictive of biochemical control (p=0.017, p6 months after surgery (group 3), the 3 year actuarial rate of biochemical control was 55.6%. The 3 year actuarial rate of biochemical control for patients treated for a biopsy proven recurrence (group 4) was 8.3%. By pair-wise log rank test, the rates of biochemical control were significantly different between groups 1 and 3 (p=0.036), groups 1 and 4 (p<0.001), and groups 3 and 4 (p=0.009). Conclusion: Biochemical control was achieved in approximately half of the patients treated with post-operative prostatic fossa irradiation. Elevated presurgical and pre-RT PSA


    Directory of Open Access Journals (Sweden)

    Ekeanyanwu Raphael Chukwuma


    Full Text Available The nutritive constituents of the seeds of Monodora tenuifolia were analyzed to augment the available information on Monodora tenuifolia research. Blood glucose and lipid profile were investigated on the flavonoid rich fraction of M. tenuifolia in rats. The composition (gkg-1 of alkaloids, cyanogenic glycosides, tannins and flavonoids were 13.3±0.1, 21.2×10-2±0.6, 1.3±0.1, 1.7±0.1 and 11.7±1.1 respectively. The proximate composition (gkg-1 of M. tenuifolia seed were crude fibre (262.3±1.2, crude protein (82.6±1.0, crude fat (349.9±1.9, ash (49.9±0.6, moisture (190.0±0.00 and carbohydrate (65.5±4.7. Analysis of the minerals content (gkg-1 yielded calcium (864.0±29.38, sodium (2752.0±140.35, iron (3.34±0.06, zinc (5.26±0.08, potassium (326.4±13.06, magnesium (342.9±13.71 and phosphorus (9.52±0.17, while vitamin analysis yielded vitamin A (10.05±0.17 iu/100 g, C (56.40±0.14 gkg-1 and E (11.71±0.87 iu /100 g, thiamine (0.11±0.01 gkg-1, niacin (0.46±0.32 gkg-1 and riboflavin (0.04±0.01 gkg-1. The results of amino acid analysis showed the total amino acid of M. tenuifolia seed was 71.78 of crude protein. The total essential amino acid with Histidine was calculated to be 29.24 of the crude protein. The antinutrient analysis of M. tenuifolia shows it contained total phenol (0.8±0.0 gkg-1, oxalates (4.09±1.17 gkg-1, phytates (0.012±0.42 gkg-1 and trypsin inhibitor (0.230±0.42 iu/g. The main fatty acids of the seed oil are linoleic acid (401.7 g kg-1, oleic acid (346.1 g kg-1 and palmitic acid (122.61 g kg-1. The LD50 of the flavonoid-rich fraction was found to be above 5000 mg kg-1 b.w. After the day 14 study, biochemical markers such as triacylglycerol, very low density lipoprotein increased significantly (p0.05 effect was observed on the blood glucose and lipid profile of wistar albino rats compared with the control. The result shows that M. tenuifolia seed is rich

  5. Kombucha tea fermentation: Microbial and biochemical dynamics. (United States)

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan


    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  6. Stoichiometric estimates of the biochemical conversion efficiencies in tsetse metabolism

    Directory of Open Access Journals (Sweden)

    Custer Adrian V


    published experimental measurements. Conclusion This biochemical analysis provides reasonable first estimates of the conversion efficiencies for the major pathways used by tsetse metabolism. These results now enable a deeper analysis of tsetse ecology based on the construction of a dynamic mass-energy budget for tsetse and their populations.

  7. 病毒性肝炎患者的相关生化检验指标分析%Analysis of related biochemical indicators for patients with viral hepatitis

    Institute of Scientific and Technical Information of China (English)



    目的:评价分析病毒性肝炎患者的相关生化检验指标。方法:选取120例病毒性肝炎患者的临床资料,具体按照病毒感染类别分为慢性乙肝组及慢性丙肝组,选取同期80例健康人群为对照组,对比分析3组检测对象的生化检验指标。结果:慢性乙肝组和慢性丙肝组患者血液中白细胞、中性粒细胞及血小板计数均明显低于对照组健康人群,淋巴细胞则高于对照组(P0.05;慢性乙肝组和慢性丙肝组患者A/G及ALB指标水平明显低于对照组健康人群,ALT及TBIL指标检测水平明显高于对照组健康人群,P0. 05). The A/G and ALB index levels of chronic hepatitis B group and chronic hepatitis C group were significant-ly lower than those of control group, while ALT levels and TBIL indicators were significantly higher than those of control group (P<0. 05). The A/G and ALB levels of chronic hepatitis B group were significantly higher than those of chronic hepatitis C group (P<0. 05). Conclusions:The routine biochemical tests for the patients with viral hepatitis are simple and cheap, can contribute to the clini-cal diagnosis and treatment of patients, and deserves to be promoted in clinical practice.

  8. Biochemical considerations in the design of radiopharmaceuticals

    International Nuclear Information System (INIS)

    The goal of radiopharmaceutical chemistry is to design and develop radiotracers targeted to an organ or function whose activity kinetics in tissue can be detected externally by a gamma or a positron device. Radiopharmaceuticals are divided into the general categories of specific and non-specific agents. The specific radiopharmaceuticals are the tracers that follow a biochemical pathway or are involved in a particular interaction, for example metabolic substrates, drugs or analogs, and antibodies. This paper will focus on trends in the design of specific agents. The best radionuclides for the development of specific tracers are the positron emitting nuclides: carbon-11, nitrogen-13, oxygen-15 and fluorine-18. First the design of radiopharmaceuticals are considered in general (labeling strategies, stereochemical effects, specific activity). Next, a brief summary of the use of several radiopharmaceuticals is presented on the basis of their biochemical rationale. (orig./G.J.P.)

  9. Cytologic-Biochemical Radiation Dosimeters in Man

    International Nuclear Information System (INIS)

    The result of radiation interacting with living tissue is the deposition of energy therein. This energy triggers numerous chemical reactions within the molecules of the target tissues. We have measured in man the results of some of these reactions at doses up to 300 rads: chromosome aberrations; alterations in the kinetics of specific human cell populations; changes in 37 biochemical constituents of serum and/or urine. The utilization of chromosomes as a biological dosimeter is partially perfected but there are numerous discrepancies in data between different laboratories. Etiocholanolone can be used to evaluate marrow injury before the white-cell count falls below 5000/mm3. Most biochemical dosimeters evaluated gave negative or inconsistent results. However, salivary amylase is a promising indicator of human radiation injury from doses as low as 100 rads. (author)

  10. Optical Biochemical Platforms for Nanoparticles Detection

    CERN Document Server

    Campanella, Clarissa Martina


    In the biochemical sensing field, a fervent research activity related to the development of real time, low cost, compact and high throughput devices for the detection and characterization of natural or synthetic nanoparticles NPs actually exists. In this research scenario, different platforms for biosensing purposes have been developed according to the huge amount of physical effects involved in the transduction of the biochemical-signal into a measurable output signal. In the present work two different optical platforms for NP detection have been investigated, one based on integrated optics and the other based on microscopy. Both the approaches rely on the study of the interaction of an electromagnetic wave with a small particle in the hypothesis of dealing with a Rayleigh scatterer, i.e. a nanoparticle having a size really smaller than the one of the wavelength of the incident light and scattering light elastically.

  11. Biochemical changes in ginger after gamma irradiation

    International Nuclear Information System (INIS)

    Ginger (Zingiber officinate) was irradiated with gamma rays (0.1Kgy, 1.0Kgy). Biochemical changes during storage at room temperature (23-28 degree centigrade), in sand (23-28 degree centigrade) and at cold (8 degree centigrade) temperature were observed. Changes in starch, soluble protein, fixed oil and volatile oil contents showed that treatment of ginger at 0.1Kgy radiation level was most appropriate for storage upto 45 days

  12. Prions: the danger of biochemical weapons


    Eric Almeida Xavier


    The knowledge of biotechnology increases the risk of using biochemical weapons for mass destruction. Prions are unprecedented infectious pathogens that cause a group of fatal neurodegenerative diseases by a novel mechanism. They are transmissible particles that are devoid of nucleic acid. Due to their singular characteristics, Prions emerge as potential danger since they can be used in the development of such weapons. Prions cause fatal infectious diseases, and to date there is no therapeutic...

  13. The stochastic dynamics of biochemical systems


    Challenger, Joseph Daniel


    The topic of this thesis is the stochastic dynamics of biochemical reaction systems. The importance of the intrinsic fluctuations in these systems has become more widely appreciated in recent years, and should be accounted for when modelling such systems mathematically. These models are described as continuous time Markov processes and their dynamics defined by a master equation. Analytical progress is made possible by the use of the van Kampen system-size expansion, which splits the dynamics...

  14. [Biochemical antenatal screening for fetal anomalies.]. (United States)

    Torfadóttir, G; Jónsson, J J


    Biochemical antenatal screening started 30 years ago. Initially, the goal was to detect neural tube defects by measuring a-fetoprotein in maternal serum (MS-AFP) and amniotic fluid (AF-AFP). The serendipitous discovery of an association between low AFP maternal serum concentration and chromosomal anomalies resulted in increased research interest in biochemical screening in pregnancy. Subsequently double, triple or quadruple tests in 2nd trimester of pregnancy became widely used in combination with fetal chromosome determination in at risk individuals. In Iceland, antenatal screening for chromosomal anomalies has essentially been based on fetal chromosome studies offered to pregnant women 35 years or older. This strategy needs to be revised. Recently first trimester biochemical screening based on maternal serum pregnancy associated plasma protein A (MS-PAPP-A) and free b-human chorionic gonadotropin (MS-free b-hCG) and multivariate risk assessment has been developed. This screening test can be improved if done in conjunction with nuchal translucency measurements in an early sonography scan. PMID:17018982

  15. Electronic modulation of biochemical signal generation (United States)

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F.; Bentley, William E.


    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  16. Hydrogel-based piezoresistive biochemical microsensors (United States)

    Guenther, Margarita; Schulz, Volker; Gerlach, Gerald; Wallmersperger, Thomas; Solzbacher, Florian; Magda, Jules J.; Tathireddy, Prashant; Lin, Genyao; Orthner, Michael P.


    This work is motivated by a demand for inexpensive, robust and reliable biochemical sensors with high signal reproducibility and long-term-stable sensitivity, especially for medical applications. Micro-fabricated sensors can provide continuous monitoring and on-line control of analyte concentrations in ambient aqueous solutions. The piezoresistive biochemical sensor containing a special biocompatible polymer (hydrogel) with a sharp volume phase transition in the neutral physiological pH range near 7.4 can detect a specific analyte, for example glucose. Thereby the hydrogel-based biochemical sensors are useful for the diagnosis and monitoring of diabetes. The response of the glucosesensitive hydrogel was studied at different regimes of the glucose concentration change and of the solution supply. Sensor response time and accuracy with which a sensor can track gradual changes in glucose was estimated. Additionally, the influence of various recommended sterilization methods on the gel swelling properties and on the mechano-electrical transducer of the pH-sensors has been evaluated in order to choose the most optimal sterilization method for the implantable sensors. It has been shown that there is no negative effect of gamma irradiation with a dose of 25.7 kGy on the hydrogel sensitivity. In order to achieve an optimum between sensor signal amplitude and sensor response time, corresponding calibration and measurement procedures have been proposed and evaluated for the chemical sensors.

  17. Salvage Hypofractionated Radiotherapy for Biochemically Recurrent Prostate Cancer After Radical Prostatectomy

    International Nuclear Information System (INIS)

    Purpose: To evaluate whether hypofractionation is well tolerated and to preliminarily assess biochemical control of this regimen in a postprostatectomy, salvage setting. Methods and Materials: A retrospective analysis was performed in 50 patients treated between May 2003 and December 2005 with hypofractionated radiotherapy for biochemical recurrence after radical prostatectomy. Radiotherapy was prescribed to the prostatic fossa to 65-70 Gy in 26-28 fractions of 2.5 Gy each, using intensity-modulated radiotherapy with daily image localization. Toxicities were scored using a modified Radiation Therapy Oncology Group scale and the Fox Chase modification of Late Effects Normal Tissue scale. The median follow-up was 18.9 months (range, 5.3-35.9). Results: No Grade 3 or greater acute or late toxicities were observed. Grade 2 toxicities included four acute genitourinary, one acute gastrointestinal, two late genitourinary, and two late gastrointestinal toxicities. Of the 50 patients, 39 demonstrated a continuous biochemical response after salvage therapy, 3 had an initial response before prostate-specific antigen failure, and 7 had prostate-specific antigen progression, 1 of whom died of progressive metastatic disease. Finally, 1 patient discontinued therapy because of the diagnosis of a metachronous pancreatic cancer and died without additional prostate cancer follow-up. All remaining patients were alive at the last follow-up visit. A lower presalvage prostate-specific antigen level was the only significant prognostic factor for improved biochemical control. The estimated actuarial biochemical control rate at 2 years was 72.9%. Conclusions: The toxicity and early biochemical response rates were consistent with expectations from conventional fractionation. Additional follow-up is required to better document the biochemical control, but these results suggest that hypofractionation is a well-tolerated approach for salvage radiotherapy

  18. The application of information theory to biochemical signaling systems

    International Nuclear Information System (INIS)

    Cell signaling can be thought of fundamentally as an information transmission problem in which chemical messengers relay information about the external environment to the decision centers within a cell. Due to the biochemical nature of cellular signal transduction networks, molecular noise will inevitably limit the fidelity of any messages received and processed by a cell's signal transduction networks, leaving it with an imperfect impression of its environment. Fortunately, Shannon's information theory provides a mathematical framework independent of network complexity that can quantify the amount of information that can be transmitted despite biochemical noise. In particular, the channel capacity can be used to measure the maximum number of stimuli a cell can distinguish based upon the noisy responses of its signaling systems. Here, we provide a primer for quantitative biologists that covers fundamental concepts of information theory, highlights several key considerations when experimentally measuring channel capacity, and describes successful examples of the application of information theoretic analysis to biological signaling. (paper)

  19. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory


    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  20. Transient amplification limits noise suppression in biochemical networks (United States)

    Dixon, John; Lindemann, Anika; McCoy, Jonathan H.


    Cell physiology is orchestrated, on a molecular level, through complex networks of biochemical reactions. The propagation of random fluctuations through these networks can significantly impact cell behavior, raising challenging questions about how network design shapes the cell's ability to suppress or exploit these fluctuations. Here, drawing on insights from statistical physics, fluid dynamics, and systems biology, we explore how transient amplification phenomena arising from network connectivity naturally limit a biochemical system's ability to suppress small fluctuations around steady-state behaviors. We find that even a simple system consisting of two variables linked by a single interaction is capable of amplifying small fluctuations orders of magnitude beyond the levels predicted by linear stability theory. We also find that adding additional interactions can promote further amplification, even when these interactions implement classic design strategies known to suppress fluctuations. These results establish that transient amplification is an essential factor determining baseline noise levels in stable intracellular networks. Significantly, our analysis is not bound to specific systems or interaction mechanisms: we find that noise amplification is an emergent phenomenon found near steady states in any network containing sufficiently strong interactions, regardless of its form or function.

  1. Serum Biochemical Profile of Post Partum Metritic Cow

    Directory of Open Access Journals (Sweden)

    Magnus P. K.


    Full Text Available Present study was conducted to find out the relationship between serum biochemical profile and postpartum metritis. Mainly serum glucose, total protein, albumin, albumin globulin ratio, blood urea nitrogen (BUN, creatinine and calcium were studied. Colorimetric method was used for quantitative estimation of biochemical profile. Twenty-seven animals with recent history of calving and subsequent metritis were included in the study. On analysis, serum glucose was found to be 22.3 ± 2.18 mg/dl, total protein 6.1 ± 0.51 g/dl, albumin 2.8 ± 0.29 g/dl, BUN 27 ± 0.19 mg/dl, creatinine 1.8 ± 0.13 mg/dl and calcium was 7.0 ± 0.43 mg/dl. On comparison of this result with normal values it was found that glucose and calcium was below the normal level and albumin fraction was less than the globulin. It was concluded that in postpartum metritis, cattle exhibit hypocalcaemia, hypoglycaemia and reduced globulin fraction, whereas total protein, albumin, BUN and creatinine did not exhibit much variation. Ketone bodies were present in urine of 90% of tested animals. [Vet. World 2009; 2(1.000: 27-28

  2. The Cytochrome P450 Engineering Database: integration of biochemical properties

    Directory of Open Access Journals (Sweden)

    Lisitsa Andrey


    Full Text Available Abstract Background Cytochrome P450 monooxygenases (CYPs form a vast and diverse enzyme class of particular interest in drug development and a high biotechnological potential. Although very diverse in sequence, they share a common structural fold. For the comprehensive and systematic comparison of protein sequences and structures the Cytochrome P450 Engineering Database (CYPED was established. It was built up based on an extensible data model that enables its functions readily enhanced. Description The new version of the CYPED contains information on sequences and structures of 8613 and 47 proteins, respectively, which strictly follow Nelson's classification rules for homologous families and superfamilies. To gain biochemical information on substrates and inhibitors, the CYPED was linked to the Cytochrome P450 Knowledgebase (CPK. To overcome differences in the data model and inconsistencies in the content of CYPED and CPK, a metric was established based on sequence similarity to link protein sequences as primary keys. In addition, the annotation of structurally and functionally relevant residues was extended by a reliable prediction of conserved secondary structure elements and by information on the effect of single nucleotide polymorphisms. Conclusion The online accessible version of the CYPED at provides a valuable tool for the analysis of sequences, structures and their relationships to biochemical properties.

  3. Activators of Biochemical and Physiological Processes in Plants Based on Fine Humic Acids (United States)

    Churilov, G.; Polishuk, S.; Kutskir, M.; Churilov, D.; Borychev, S.


    This article describes the application of ultrafine humic acids as growth promoters and development of crops, for example corn. During the study we determined the optimal concentration of humic acids in ultrafine state for presowing treatment of seeds of maize. An analysis of laboratory and field tests was presented. We showed the relationship between physiological changes and biochemical processes.

  4. Towards droplet size-aware biochemical application compilation for AM-EWOD biochips

    DEFF Research Database (Denmark)

    Pop, Paul; Alistar, Mirela


    droplet size-aware compilation by proposing a routing algorithm that considers the droplet size. Our routing algorithm is developed for a novel digital microfluidic biochip architecture based on Active Matrix Electrowetting on Dielectric, which uses a thin film transistor array for the electrodes. We also......Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate onchip all the necessary functions for biochemical analysis using microfluidics. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as...

  5. Seasonal variation of serum biochemical values of Amazonian snakes (Boa constrictor constrictor) kept in captivity


    Dennis José da Silva Lima; Renata Kelly Gonzaga Bastos; Larissa dos Santos Seixas; Monique Araújo Luz; Erika Renata Branco; Nazaré Fonseca de Souza; Carla Cristina Guimarães de Moraes; Andre Marcelo Conceição Meneses


    In northern Brazil, the seasons are not well defined compared to the South and Southeast regions, due to a hot and humid equatorial climate with a rainy season, known as the Amazonian winter, and a period with less rain, known as the Amazonian summer. The goal of this study was to evaluate the biochemical variation of serum from the Amazon Boa constrictor by correlating the values with the seasons of the region. A biochemical analysis of the serum was performed (AST, ALT, LDH, ALP, calcium, u...

  6. Correlation between yield and biochemical parameters in the mulberry silkworm,Bombyx mori L. (United States)

    Chatterjee, S N; Rao, C G; Chatterjee, G K; Ashwath, S K; Patnaik, A K


    A detailed study was carried out on six biochemical parameters and four yield attributes using multiple regression analysis to investigate their relationship in the mulberry silkworm,Bombyx mori. The study generated new information on the importance of digestive amylase activity for the survival of the silkworm and revealed the inability of other enzymes to affect this relationship. Data also substantiate the observations made earlier on the genetic variability of amylase in the mulberry silkworm. Analyses extend the positive role of alkaline phosphatase and invertase in the expression of the other yield traits studied and indicate the definite possibility of using biochemical markers for silkworm breeding. PMID:24190267

  7. Biochemical and histological characterization of tomato mutants

    Directory of Open Access Journals (Sweden)

    Carolina C. Monteiro


    Full Text Available Biochemical responses inherent to antioxidant systems as well morphological and anatomical properties of photomorphogenic, hormonal and developmental tomato mutants were investigated. Compared to the non-mutant Micro-Tom (MT, we observed that the malondialdehyde (MDA content was enhanced in the diageotropica (dgt and lutescent (l mutants, whilst the highest levels of hydrogen peroxide (H2O2 were observed in high pigment 1 (hp1 and aurea (au mutants. The analyses of antioxidant enzymes revealed that all mutants exhibited reduced catalase (CAT activity when compared to MT. Guaiacol peroxidase (GPOX was enhanced in both sitiens (sit and notabilis (not mutants, whereas in not mutant there was an increase in ascorbate peroxidase (APX. Based on PAGE analysis, the activities of glutathione reductase (GR isoforms III, IV, V and VI were increased in l leaves, while the activity of superoxide dismutase (SOD isoform III was reduced in leaves of sit, epi, Never ripe (Nr and green flesh (gf mutants. Microscopic analyses revealed that hp1 and au showed an increase in leaf intercellular spaces, whereas sit exhibited a decrease. The au and hp1 mutants also exhibited a decreased in the number of leaf trichomes. The characterization of these mutants is essential for their future use in plant development and ecophysiology studies, such as abiotic and biotic stresses on the oxidative metabolism.Neste trabalho, analisamos as respostas bioquímicas inerentes ao sistema antioxidante, assim como propriedades morfológicas e anatômicas de mutantes fotomorfogenéticos e hormonais de tomateiro. Comparados ao não mutante Micro-Tom (MT, observamos que o conteúdo de malondialdeído (MDA aumentou nos mutantes diageotropica (dgt e lutescent (l, enquanto os maiores níveis de H2O2 foram encontrados nos mutantes high pigment 1 (hp1 e aurea (au. Análises de enzimas antioxidantes mostraram que todos os mutantes reduziram a atividade de catalase (CAT quando comparado a MT. A

  8. Histochemical diagnosis of Hirschsprung's disease and a comparison of the histochemical and biochemical activity of acetylcholinesterase in rectal mucosal biopsies.


    Patrick, W. J.; Besley, G T; Smith, I. I.


    Three hundred and seventy-two rectal mucosal biopsies, taken from 150 children and young adults with chronic constipation, were subjected to histochemical and biochemical analysis of acetylcholinesterase to excude Hirschsprung's disease. The relative merits of the procedures were compared. The histochemical method was considered to be the most practical for laboratories handling small numbers of biopsies but the biochemical estimation of acetylcholinesterase activity was found to be a useful ...

  9. Biochemical Changes in Orange Fruit Due to Plant – Penicillium italicum – Antagonism Interactions

    Directory of Open Access Journals (Sweden)

    Rahil GHASEMI


    Full Text Available One of the most important orange fruit diseases is blue mold which cause by Penicillium italicum that is responsible for important economic losses. This study investigated biochemical changes in exo-mesocarp layers of orange fruits related to host- pathogen- yeast interactions. Initial result showed that among eight strains isolated, the most effective antagonist were belonged to two species of Pichia kluyveri (M45 and Rhodotorula mucilaginosa (M61. These isolates were selected for biochemical evaluation. In order to assessment of biochemical changes, the orange fruits were inoculated with 40 µl of yeast cell suspension and after 24 h, the wounds were inoculated with 20 µl of conidial suspension of P. italicum. The analysis of variance showed that all of the measured biochemical characterises were significant in both layers by treatments (yeast isolates; pathogen; yeast isolates + pathogen and control (P ≤ 0.01, including POD, CAT and β-1, 3-glucanase activities and total phenolic compounds. Also result showed that when the yeast isolates (M45 or M54 were inoculated into wounds with the pathogen, it stimulated the orange to increase produce of total phenol and enzymes activity (POD, CAT and β-1, 3-glucanase and these changes were related to incubation time. The result showed that understanding biochemical mechanism derived from plant-pathogen-antagonist interactions is essential for investigating the dynamics of infectious processes.

  10. Biochemical Network Stochastic Simulator (BioNetS: software for stochastic modeling of biochemical networks

    Directory of Open Access Journals (Sweden)

    Elston Timothy C


    Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from BioNetS also can be run as a stand alone package. All the required files are accessible from Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.