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Difference Analysis (difference + analysis)

Distribution by Scientific Domains
Life Sciences27%
Earth and Environmental Science27%
Chemistry27%

Kinds of Difference Analysis

  • representational difference analysis
    		•

    Selected Abstracts

    Multiple molecular approaches yield no evidence for sex-determining genes in lake sturgeon (Acipenser fulvescens)

    JOURNAL OF APPLIED ICHTHYOLOGY, Issue 6 2008
    C. R. McCormick
    Summary Common DNA-based sexing assays have been widely used for the conservation and management of mammals and birds. However, many fishes do not have genetic sex determination and in those that do, the plasticity of the genes involved means that species-specific assays are normally required. Such DNA-sexing markers would be especially valuable in lake sturgeon (Acipenser fulvescens) because of their sexual monomorphism, delayed sexual maturity, and conservation status. We tried to identify genetic differences between male and female lake sturgeon using several different molecular genetic methods, including randomly amplified polymorphic DNA, representational difference analyses, subtractive hybridization, and a candidate gene approach. Ultimately, a number of genes were identified but none was sex-specific. Although the ultimate mechanism of sex determination is yet unknown, it is possible that sex determination is environmental in lake sturgeon, especially since recent studies have also failed to identify sex determination genes in other sturgeon species. [source]

    A new family of generalized-, time integration algorithms without overshoot for structural dynamics

    EARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 12 2008
    Yu KaiPing
    Abstract A new family of generalized-, (G-,) algorithm without overshoot is presented by introducing seven free parameters into the single-step three-stage formulation for solution of structural dynamic problems. It is proved through finite difference analysis that these algorithms are unconditionally stable, second-order accurate and numerical dissipation controllable. The comparison of the new G-, algorithms with the commonly used G-, algorithms shows that the newly developed algorithms have the advantage of eliminating the overshooting characteristics exhibited by the commonly used algorithms while their excellent property of dissipation is preserved. The numerical simulation results obtained using a single-degree-of-freedom system and a two-degree-of-freedom system to represent the character of typical large systems coincide well with the results of theoretical analyses. Copyright © 2008 John Wiley & Sons, Ltd. [source]

    Factors affecting fluid flow in strike,slip fault systems: coupled deformation and fluid flow modelling with application to the western Mount Isa Inlier, Australia

    GEOFLUIDS (ELECTRONIC), Issue 1 2009
    A. FORD
    Abstract Deformation and focused fluid flow within a mineralized system are critical in the genesis of hydrothermal ore deposits. Dilation and integrated fluid flux due to coupled deformation and fluid flow in simple strike,slip fault geometries were examined using finite difference analysis in three dimensions. A series of generic fault bend and fault jog geometries consistent with those seen in the western Mount Isa Inlier were modelled in order to understand how fault geometry parameters influence the dilation and integrated fluid flux. Fault dip, fault width, bend/jog angle, and length were varied, and a cross-cutting fault and contrasting rock types were included. The results demonstrate that low fault dips, the presence of contrasts in rock type, and wide faults produce highest dilation and integrated fluid flux values. Increasing fault bend lengths and angles increases dilation and integrated fluid flux, but increasing fault jog length or angle has the opposite effect. There is minimal difference between the outputs from the releasing and restraining fault bend and jog geometries. Model characteristics producing greater fluid flows and/or gradients can be used in a predictive capacity in order to focus exploration on regions with more favorable fault geometries, provided that the mineralized rocks had Mohr,Coulomb rheologies similar to the ones used in the models. [source]

    Stage-specific gene expression in early differentiating oligodendrocytes

    GLIA, Issue 2 2002
    Francesca Blasi
    Abstract The screening of a differential library from precursor and differentiated oligodendrocytes, obtained through the representational difference analysis (RDA) technique, has generated a number of cDNA recombinants corresponding to mRNA coding for known and unknown proteins: (1) mRNA coding for proteins involved in protein synthesis, (2) mRNA coding for proteins involved in the organization of the cytoskeleton, and (3) mRNA coding for proteins of unknown function. The expression profile of the mRNA was studied by Northern blot hybridization to the poly-A+ mRNA from primary rat progenitor and differentiated oligodendrocytes. In most cases, hybridization to the precursor was higher than hybridization to the differentiated mRNA, supporting the validity of the differential screening. Hybridization of the cDNA to rat cerebral hemisphere and brain stem poly-A+ mRNA, isolated from 1- to 90-day-old rats, confirms the results obtained with the mRNA from differentiating oligodendrocytes. The intensity of the hybridization bands decreases as differentiation proceeds. The pattern of expression observed in oligodendrocytes is different from that found in the brain only in the case of the nexin-1 mRNA, the level of which remains essentially constant throughout differentiation both in the brain stem and in the cerebral hemispheres, in agreement with the published data. In contrast, the intensity of hybridization to the oligodendrocyte mRNA is dramatically lower in the differentiated cells compared with the progenitor oligodendrocyte cells. Some of the recombinant cDNA represent mRNA sequences present at high frequency distribution in the cells, while others belong to the rare sequences group. Six recombinants code for proteins of the ribosomal family, suggesting that of approximately 70 known ribosomal proteins, only a few are upregulated during oligodendrocyte differentiation. The third category of open reading frame (ORF) is represented by rare messengers coding for proteins of unknown functions and includes six clones: RDA 279, 11, 95, 96, 254, and 288. GLIA 39:114,123, 2002. © 2002 Wiley-Liss, Inc. [source]

    Identification of differentially methylated CpG islands in prostate cancer

    INTERNATIONAL JOURNAL OF CANCER, Issue 5 2004
    Yasushi Yamada
    Abstract Epigenetic change such as DNA methylation is one important mechanism for regulating gene expression as genetic change, such as mutation or loss of heterozygosity. Methylation of cancer-related genes has been shown to play an important role in carcinogenesis and tumor progression. Using methylated CpG island amplification (MCA)/representational difference analysis (RDA), we identified four CpG islands in neurotrophin tyrosine kinase receptor type 2 (NTRK2), Protocadherine Flamingo1 and MFPC (Methylated Fragments in Prostate Cancer) 7 and 8. Bisulfite sequencing revealed that 2 regions of NTRK2 as well as MFPC7 and MFPC8 were aberrantly methylated in prostate cancer cell lines, and COBRA showed that 48 (76.24%), 37 (58.7%) and 14 (22.2%) of 63 prostate cancer tissues were methylated, respectively, for these sites. On the other hand, none of 13 benign prostate samples were methylated, except for 1 (7.7%) with NTRK2. For NTRK2, mRNA expression was negative in prostate cancer cell lines (LNCaP and DU145) but was recovered on a methyltransferase inhibitor (5-Aza-CdR) treatment. The role of NTRK2 within NTRK remains unclear. Our results suggest that these 3 hypermethylated DNA fragments also may be markers of prostate cancer detection. © 2004 Wiley-Liss, Inc. [source]

    Numerical Analysis of Survival of Listeria monocytogenes during In-Package Pasteurization of Frankfurters by Hot Water Immersion

    JOURNAL OF FOOD SCIENCE, Issue 5 2007
    Lihan Huang
    ABSTRACT:, The objective of this research was to develop and validate a more accurate method to analyze and calculate the inactivation of Listeria monocytogenes in frankfurter packages during postlethality hot water immersion heating and the subsequent cooling processes. Finite difference analysis with implicit scheme was used to simulate the heat transfer process during in-package pasteurization of frankfurters. A volumetrically distributed simulation method was developed to calculate the lethality of the thermal treatment. The simulation method was validated using frankfurter packages inoculated with a 4-strain cocktail of L. monocytogenes. Experimental results showed that the numerical analysis model could accurately simulate the heat transfer process during heating and cooling of frankfurter packages. The simulated temperatures on the surface or in the middle of the package matched very closely with the experimental observations. Using the simulated temperature distribution in the packages, the integrated lethality simulation method, based on the volumetric distribution of bacteria, could accurately predict the reduction in the bacterial counts. The calculation results were on average within 0.3 log(CFU/g) difference from the experimental observations, while the General Method systematically underestimated the bacterial reductions by approximately 0.9 log(CFU/g). The study shows that the integrated lethality method is more accurate than the General Method in calculating the lethality of thermal processes for conduction-heated foods. [source]

    The Salt-Inducible Kinase, SIK, Is Induced by Depolarization in Brain

    JOURNAL OF NEUROCHEMISTRY, Issue 6 2000
    Jonathan D. Feldman
    Abstract: Membrane depolarization of neurons is thought to lead to changes in gene expression that modulate neuronal plasticity. We used representational difference analysis to identify a group of cDNAs that are induced by membrane depolarization or by forskolin, but not by neurotrophins or growth factors, in PC12 pheochromocytoma cells. One of these genes, SIK (salt- inducible kinase), is a member of the sucrose-nonfermenting 1 protein kinase/AMP-activated protein kinase protein kinase family that was also recently identified from the adrenal gland of rats treated with high-salt diets. SIK mRNA is induced up to eightfold in specific regions of the hippocampus and cortex in rats, following systemic kainic acid administration and seizure induction. [source]

    Banana (Musa spp.) as a model to study the meristem proteome: Acclimation to osmotic stress

    PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 1 2007
    Sebastien C. Carpentier
    Abstract Banana (Musa spp.) multiple shoot meristems are an excellent model to study the meristem proteome. Using a 2-DE protocol developed for small amounts of tissue and MS-based cross species polypeptide identification, we have revealed the meristem proteome and investigated the influence of sucrose-mediated osmotic stress in a dehydration-tolerant variety. Proteins that were significantly up- or down-regulated due to the high-sucrose treatment were classified using non-parametric univariate statistics. Our results suggest that the maintenance of an osmoprotective intracellular sucrose concentration, the enhanced expression of particular genes of the energy-conserving glycolysis and the conservation of the cell wall integrity are essential to maintain homeostasis, to acclimate and to survive dehydration. By comparing the dehydration-tolerant variety with a dehydration-sensitive variety, we were able to distinguish several genotype-specific proteins (isoforms), and could associate the dehydration-tolerant variety with proteins involved in energy metabolism (e.g., phosphoglycerate kinase, phosphoglucomutase, UDP-glucose pyrophosphorylase) and proteins that are associated with stress adaptation (e.g., OSR40-like protein, abscisic stress ripening protein-like protein). This work shows that proteome analysis can be used successfully to perform quantitative difference analysis and to characterize genetic variations in a recalcitrant crop. [source]

    Field analyses of RDX and TCE in groundwater during a GCW pilot study

    REMEDIATION, Issue 1 2002
    Andrew C. Elmore
    Contaminant concentrations in groundwater are typically analyzed using traditional laboratory analytical procedures approved by the Environmental Protection Agency (EPA) or state regulatory agencies. The use of off-site laboratories provides very high-quality water quality data at a relatively high cost in terms of time and money. Yet there are many instances when it is desirable to have water quality data measured in the field. The field methods for measuring water quality typically cost much less than the corresponding laboratory methods. However, the usability of the field data may be uncertain when the results are qualitatively compared to duplicate laboratory results. Groundwater samples collected during a groundwater circulation well pilot study were analyzed using field kits to measure concentrations of trichloroethylene (TCE) and the explosive compound known as RDX. A subset of the samples was split for duplicate laboratory analysis. Linear regression analysis and relative percent difference analysis were performed on the duplicate results to evaluate the comparability of the field and laboratory data. The data analyses were also used to evaluate the concept that the field kits were more accurate for specific concentration ranges, as well as the concept the field kit results would improve as field personnel gained experience with the field analysis procedures. © 2002 Wiley Periodicals, Inc. [source]

    Identification and physical mapping of genes expressed in the corpus luteum in cattle,

    ANIMAL GENETICS, Issue 5 2003
    T. Bønsdorff
    Summary A representational difference analysis was performed to identify genes expressed in the corpus luteum of cattle. The corpus luteum is an ovarian structure that is essential for the establishment and maintenance of pregnancy. Knowledge of gene expression and function of corpus luteum will be important to improve fertility in humans and domestic animals. Housekeeping genes were removed from the corpus luteum representation (tester) using skeletal muscle as the subtracting agent (driver). A total of 80 clones of the final subtraction product were analysed by sequencing and 11 new bovine gene sequences were identified (pBTCL1,11). The sequences were mapped to segments of 10 different chromosomes using a somatic cell hybrid panel and a radiation hybrid panel. With one exception the locations are in agreement with published comparative maps of cattle and man. Expression in corpus luteum was verified by RT,PCR for all the 11 clones. [source]

    A Novel Heavy-Atom Label for Side-Specific Peptide Iodination: Synthesis, Membrane Incorporation and X-ray Reflectivity

    CHEMPHYSCHEM, Issue 9-10 2009
    Philipp E. Schneggenburger
    Abstract A novel iodine peptide label for X-ray analysis of membrane-active peptide structures is applied to solid-phase peptide synthesis. The resulting pore-structured labeled peptide as well as a non-labeled reference were reconstituted in lipid bilayer stacks (see scheme). The results indicate the exhibition of a membrane-spanning ,5.6 -double helical peptide structure and illustrate the quality of the new label. Structural parameters, such as conformation, orientation and penetration depth of membrane-bound peptides and proteins that may function as channels, pores or biocatalysts, are of persistent interest and have to be probed in the native fluid state of a membrane. X-ray scattering in combination with heavy-atom labeling is a powerful and highly appropriate method to reveal the position of a certain amino acid residue within a lipid bilayer with respect to the membrane normal axis up to a resolution of several Ångstrøm. Herein, we report the synthesis of a new iodine-labeled amino acid building block. This building block is intended for peptide incorporation to provide high intensities for electron density difference analysis of X-ray reflectivity data and improve the labeling potential for the lipid bilayer head-group and water region. The novel building block as well as the commercially available non-iodinated analogue, required for X-ray scattering, was implemented in a transmembrane peptide motif via manual solid-phase peptide synthesis (SPPS) following the fluorenylmethyloxycarbonyl (Fmoc)-strategy. The derived peptides were reconstituted in lipid vesicles as well as in highly aligned multilamellar lipid stacks and investigated via circular dichroism (CD) and X-ray reflectivity. Thereby, it has been revealed that the bulky iodine probe neither causes conformational change of the peptide structure nor lamellar disordering of the membrane complexes. [source]