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Biomedical subjects

D L Tucker

Publications and source records attributed to D L Tucker.

7 recordsLinked to original sources
PubMed2002

DNA array analysis in a Microsoft Windows environment.

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.

Databases, Nucleic Acid↗
PubMed2001

The manganese stabilizing protein (MSP) and the control of O2 evolution in the unicellular, diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142.

The unicellular diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142 temporally separates N2 fixation from photosynthesis. To better understand the processes by which photosynthesis is regulated, we have analyzed Photosystem (PS) II O2 evolution and the PSII lumenal proteins, especially the Mn stabilizing protein (MSP). We describe a procedure using glycine betaine to isolate photosynthetic membranes from Cyanothece sp. that have high rates of PSI and PSII activity. Analysis with these membranes demonstrated similar patterns of O2 evolution in vivo and in vitro, with a trough at the time of maximal N2 fixation and with a peak in the late light period. The pattern of PSI activity was also similar in vivo and in vitro. We cloned the genes for MSP (psbO) and the 12 kDa protein (psbU) and analyzed their transcriptional properties throughout the diurnal cycle. We suggest that the changes in PSII activity in Cyanothece sp. were due to conformational changes in a highly flexible MSP, a suggestion which can now be studied in a chimera. The Cyanothece sp. psbO gene has been transformed into Synechocystis sp. PCC 6803; MSP and O2 evolution in the resulting transformant had properties that were similar to those in Cyanothece sp., providing additional confirmation for the properties of Cyanothece sp. MSP.

Amino Acid Sequence↗
PubMed2000

Analysis of chlorophyll-protein complexes from the cyanobacterium Cyanothece sp. ATCC 51142 by non-denaturing gel electrophoresis.

The unicellular diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142 temporally separates N(2) fixation from photosynthesis. We are analyzing the mechanism by which photosynthesis is down-regulated so that O(2) evolution is minimized during N(2) fixation. Previous results suggested changes in photosynthesis that are mediated through the redox poise of the plastoquinone pool (a process involving state transitions, in which the redistribution of excitation energy between the two photosystems helps to optimize photosynthetic yield) and the oligomerization state of the photosystems. Our working hypothesis was that the regulation of photosynthesis involved changes in the oligomerization of the photosystems. To analyze this hypothesis, we utilized a low-ionic strength, non-denaturing gel electrophoresis system to study the Chl-protein complexes. We determined that PSI is mostly trimeric, whereas PSII appears mainly as monomers. We demonstrated that most of the Chl-protein complexes in Cyanothece sp. remained constant throughout the diurnal cycle, except for the transient accumulation of a Chl-protein complex (band C) which appeared only during the late light period. Based on the size of this complex, band C represents either an interaction of PSI and PSII or a PSII dimer. These results provide support for the dynamic nature of the photosystems with respect to the diurnal cycle.

Blotting, Western↗
PubMed1999

Analysis of the nifHDK operon and structure of the NifH protein from the unicellular, diazotrophic cyanobacterium, Cyanothece strain sp. ATCC 51142(1).

Cyanothece sp. ATCC 51142 is a unicellular, diazotrophic cyanobacterium that demonstrates diurnal rhythms for photosynthesis and N(2) fixation, with peaks of O(2) evolution and nitrogenase activity approximately 12 h out of phase. We cloned and sequenced the nifHDK operon, and determined that the amino acid sequences of all three proteins were highly conserved relative to those of other cyanobacteria and bacteria. However, the Fe-protein, encoded by the nifH gene, demonstrated two differences from the related protein in Azotobacter vinelandii, for which a 3-D structure has been determined. First, the Cyanothece Fe-protein contained a 37 amino acid extension at the N-terminus. This approximately 4 kDa addition to the protein appeared to fold as a separate domain, but remained a part of the active protein, as was verified by migration on acrylamide gels. In addition, the Cyanothece Fe-protein had amino acid differences at positions involved in formation of the Fe-protein dimer-dimer contacts in A. vinelandii nitrogenase. There were also changes in residues involved with interaction between the Fe-protein and the MoFe-protein when compared with A. vinelandii. Since the Cyanothece Fe-protein is quickly degraded after activity, it is suggested that the extension and the amino acid alterations were somehow involved in this degradative process.

Amino Acid Sequence↗
PubMed1991

Changes in human tear protein levels with progressively increasing stimulus.

The levels of 13 proteins were measured in six tear samples collected atraumatically at progressively increasing flow rate from nonstimulated (less than 0.5 microliter/min) to highly stimulated (greater than 50 microliters/min) in ten subjects. Tears were fractionated initially by size-exclusion high-performance liquid chromatography (SE-HPLC). Enzyme-linked immunosorbent assays and kinetic assays were then applied to relevant SE-HPLC fractions to determine specific protein levels. Nine of the 13 proteins assayed showed significantly higher concentrations in nonstimulated tears than in any other tear sample. Immunoglobulin (Ig) M, secretory IgA, polymeric IgA1, and polymeric IgA2 all decreased progressively in concentration from nonstimulated tears to the higher flow-rate stimulated samples. The level of IgG, albumin, and transferrin showed a large drop in concentration between nonstimulated tears and the first (lowest flow-rate) stimulated sample, with relatively little decrease for any subsequent sample. Levels of lactoferrin, tear-specific prealbumin, lysozyme, and peroxidase were relatively constant throughout the series of tear samples. These results indicate that the mechanisms responsible for changes in concentration of constitutive, serum-derived, and regulated tear proteins with stimulus can be studied successfully using noninvasive methods to collect human tears. They also show that simply distinguishing between nonstimulated and stimulated tears is not sufficient to completely characterize the effect of stimulus conditions on tear protein composition.

Albumins↗
PubMed1990

Characterization of long-term cultured bovine CD4-positive and CD8-positive T-cell lines and clones.

Long-term cultured CD4+ or CD8+ bovine T-cell lines and clones were established. The CD8+ T-cell line and clones had a strong lectin-dependent cytotoxicity, whereas the CD4+ T-cell line did not. Both phenotype cell lines grew in an interleukin-2 (IL-2)-dependent manner and expressed 50,000-55,000 MW and 65,000-75,000 MW proteins associated with a putative IL-2 receptor (IL-2R), as demonstrated by the cross-linking of radioiodinated recombinant human IL-2 (rhIL-2). Additional molecules of 13,000 and 27,000 MW were also observed on CD8+ T cells. The binding of rhIL-2 was blocked by crude bovine IL-2, and Scatchard plot analysis of the binding data showed that both phenotype cells expressed two different affinity IL-2R that had equilibrium dissociation constants of 12-20 pm (3000-6000 sites/cell) and 146-490 pM (16,000-25,000 sites/well). Only IL-2 stimulated DNA synthesis in these cell lines, whereas mitochondrial enzymes activity, protein synthesis and protein secretion were enhanced by IL-2, mitogens and phorbol myristate acetate. The supernatant from mitogen-stimulated CD4+ cells was unable to enhance the DNA synthesis of either the CD4+ or CD8+ lines, whereas both freshly prepared Con A blasts and anti-immunoglobulin-treated bovine B cells showed elevated DNA synthesis under the same conditions.

Animals↗