Biomedical subjects

Nancy L Thompson

Publications and source records attributed to Nancy L Thompson.

13 recordsLinked to original sources

PubMed2006

Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis.

BACKGROUND: We have reported arginine-sensitive regulation of LAT1 amino acid transporter (SLC 7A5) in normal rodent hepatic cells with loss of arginine sensitivity and high level constitutive expression in tumor cells. We hypothesized that liver cell gene expression is highly sensitive to alterations in the amino acid microenvironment and that tumor cells may differ substantially in gene sets sensitive to amino acid availability. To assess the potential number and classes of hepatic genes sensitive to arginine availability at the RNA level and compare these between normal and tumor cells, we used an Affymetrix microarray approach, a paired in vitro model of normal rat hepatic cells and a tumorigenic derivative with triplicate independent replicates. Cells were exposed to arginine-deficient or control conditions for 18 hours in medium formulated to maintain differentiated function. RESULTS: Initial two-way analysis with a p-value of 0.05 identified 1419 genes in normal cells versus 2175 in tumor cells whose expression was altered in arginine-deficient conditions relative to controls, representing 9-14% of the rat genome. More stringent bioinformatic analysis with 9-way comparisons and a minimum of 2-fold variation narrowed this set to 56 arginine-responsive genes in normal liver cells and 162 in tumor cells. Approximately half the arginine-responsive genes in normal cells overlap with those in tumor cells. Of these, the majority was increased in expression and included multiple growth, survival, and stress-related genes. GADD45, TA1/LAT1, and caspases 11 and 12 were among this group. Previously known amino acid regulated genes were among the pool in both cell types. Available cDNA probes allowed independent validation of microarray data for multiple genes. Among genes downregulated under arginine-deficient conditions were multiple genes involved in cholesterol and fatty acid metabolism. Expression of low-density lipoprotein receptor was decreased in both normal and tumor cells. CONCLUSION: Arginine-sensitive regulation appears to be an important homeostatic mechanism to coordinate cell response and nutrient availability in hepatic cells. Genes predicted as arginine-responsive in stringent microarray data analysis were confirmed by Northern blot and RT-PCR. Although the profile of arginine-responsive genes is altered and increased, a considerable portion of the "arginome" is maintained upon neoplastic transformation.

Journal Article↗

PubMed2006

Analysis method for measuring submicroscopic distances with blinking quantum dots.

A method is described that takes advantage of the intermittency ("blinking") in the fluorescence of quantum dots (QDs) to measure absolute positions of closely spaced QDs. The concept is that even if two QDs are separated by only tens of nanometers, the position of each QD is resolvable if the point spread function of each can be imaged independently of the other. In the case of QDs, this is possible if each QD separately blinks completely on and off during a time-lapse sequence. To demonstrate the principle of this method, time-lapse sequences of single blinking QDs were acquired and the centroids of the point spread functions determined. Images of the blinking QDs were then overlapped in software, pixel by pixel, generating a range of submicroscopic distances between QD pairs. Methods were developed for analyzing the overlapped time sequences of the QD pairs so that the positions of the QDs and the distances between them could be determined without prior knowledge of the single QD positions. We subsequently used this method to measure the end-to-end length of a 122-basepair double-stranded DNA fragment.

Biotinylation↗

PubMed2006

Size dependence of protein diffusion very close to membrane surfaces: measurement by total internal reflection with fluorescence correlation spectroscopy.

The diffusion coefficients of nine fluorescently labeled antibodies, antibody fragments, and antibody complexes have been measured in solution very close to supported planar membranes by using total internal reflection with fluorescence correlation spectroscopy (TIR-FCS). The hydrodynamic radii (3-24 nm) of the nine antibody types were determined by comparing literature values with bulk diffusion coefficients measured by spot FCS. The diffusion coefficients very near membranes decreased significantly with molecular size, and the size dependence was greater than that predicted to occur in bulk solution. The observation that membrane surfaces slow the local diffusion coefficient of proteins in a size-dependent manner suggests that the primary effect is hydrodynamic as predicted for simple spheres diffusing close to planar walls. The TIR-FCS data are consistent with predictions derived from hydrodynamic theory. This work illustrates one factor that could contribute to previously observed nonideal ligand-receptor kinetics at model and natural cell membranes.

Antibodies↗

PubMed2006

Ligand binding by estrogen receptor beta attached to nanospheres measured by fluorescence correlation spectroscopy.

Although many indirect methods have been chosen to study the system of estrogen receptor ligand binding, an ideal method is fluorescence correlation spectroscopy (FCS). FCS is nondestructive to the sample, uses very small sample volumes, and operates well within physiological concentration ranges. The methodology was developed to biotinylate the estrogen receptor beta-ligand binding domain (ERbeta-LBD) using biotin with a very short spacer and to then attach this protein to a 40 nm neutravidin-coated bead (nanosphere). Diffusional FCS data were obtained for a fluorescently labeled coactivator peptide, steroid receptor coactivator peptide-1 (A-SRC-1(2)), in the absence and presence of bead-bound ERbeta-LBD. Data were also acquired in the presence of one of the endogenous ligands for ERbeta, 17beta-estradiol, and with tamoxifen. The bead strategy resulted in a decreased receptor diffusion coefficient and consequent increase in the decay time of the FCS autocorrelation functions for receptor-bound, labeled SRC-1(2). Thus, free and bound coactivators were much more readily distinguished by FCS. Discrimination between the fluorescently labeled unbound and bound species could be determined in autocorrelation functions obtained in as few as 30 s. The advantage of using FCS with the ERbeta-LBD: bead methodology is the ability to obtain reliable and reproducible data in a short time frame.

Avidin↗

PubMed2006

Tightly regulated induction of the adhesion molecule necl-5/CD155 during rat liver regeneration and acute liver injury.

TuAg1/TagE4, the rat ortholog of the human poliovirus receptor CD155, is expressed on a high percentage of rat hepatocellular carcinomas. Recent studies have shown that TuAg1/TagE4/CD155 is a member of the nectin family of immunoglobulin (Ig)-like cell adhesion molecules, designated necl-5. Necl-5 is present at exceedingly low levels in adult epithelial tissues but is upregulated in primary cultures of rat hepatocytes, suggesting that disruption of liver architecture triggers its expression. To explore this possibility, we examined expression of necl-5 after two-thirds partial hepatectomy or carbon tetrachloride (CCl4)-induced acute injury. Using quantitative real-time polymerase chain reaction (QPCR), we found that necl-5 mRNA levels increased 15-fold by 9 hours, and decreased to 4-fold above baseline by 24 hours after partial hepatectomy. Necl-5 mRNA levels increased over 100-fold 6 hours after treatment with CCl4, reaching a peak of 140-fold above baseline by 10 hours, and thereafter rapidly declining. Necl-5 was localized at the membrane of midlobular and centrilobular hepatocytes 10 to 48 hours after CCl4 exposure. Northern blot analysis demonstrated a close correlation between the kinetics of necl-5 expression and the immediate-early response gene c-myc. Subconfluent cultures of the non-transformed liver epithelial cell line WB-F344 expressed high levels of necl-5, which was down-regulated as cells approached confluence. The transformed WB-F344 line GP7TB did not demonstrate density-dependent regulation of necl-5 expression. In conclusion, we report the in vivo induction of necl-5 in rat hepatocytes and provide evidence that both necl-5 mRNA and protein are tightly regulated in adult epithelial cells and tissue.

Animals↗

PubMed2005

Adenoviral modulation of the tumor-associated system L amino acid transporter, LAT1, alters amino acid transport, cell growth and 4F2/CD98 expressionwith cell-type specific effects in cultured hepatic cells.

Altered expression of metabolite transporters is observed frequently in tumor cell lines and primary neoplasms. The extent to which these may to contribute to the growth autonomy associated with cancer is not clear. LAT1 is a major L-type amino acid transporter over-expressed in a variety of cancer types and a light chain component of the CD98 heterodimer. We utilized an adenoviral expression system to modulate the level of LAT1 in a hepatic in vitro model to examine phenotypic changes associated with short-term exogenous and blocked expression. LAT1 levels were increased three fold and resulted in increased L-type amino acid transport as a result of adenoviral expression in murine hepatocytes. The protein was expressed on the cell surface and complexed with the CD98 heavy chain known as 4F2. Surprisingly, levels of the total CD98 protein complex were increased 2.4-fold as a result of adenoviral expression of light chain only, suggesting coordinate regulation. Exogenous overexpression was less effective in normal rat liver cells relative to mouse. LAT1 antisense expression in hepatic tumor cells resulted in a modest though statistically significant decrease in cell number, viability and S-phase cells over a 5-day period relative to controls despite the absence of a significant decrease in L-type transport over this period. These studies are preparatory to in vivo efforts focusing on LAT1/CD98 as a potential therapeutic target.

Adenoviridae↗

PubMed2005

Detecting microdomains in intact cell membranes.

Current models for cellular plasma membranes focus on spatial heterogeneity and how this heterogeneity relates to cell function. In particular, putative lipid raft membrane domains have been postulated to exist based in large part on the results that a significant fraction of the membrane is detergent insoluble and that molecules facilitating key membrane processes like signal transduction are often found in the detergent-resistant membrane fraction. Yet, the in vivo existence of lipid rafts remains extremely controversial because, despite being sought for more than a decade, evidence for their presence in intact cell membranes is inconclusive. In this review, a variety of experimental techniques that have been or might be used to look for lipid microdomains in intact cell membranes are described. Experimental results are highlighted and the strengths and limitations of different techniques for microdomain identification and characterization are assessed.

Biomarkers↗

PubMed2004

Transcriptional regulation of the LAT-1/CD98 light chain.

LAT-1/CD98 amino acid transporter expression and activity are induced in hepatic cells deprived of arginine. The promoter dependency of this regulation was investigated. LAT-1 expression, in contrast to that of CD98 heavy chain 4F2, was actinomycin D sensitive in cells cultured without arginine. Transient transfection analysis with promoter reporter constructs including the 2 kbp LAT-1 promoter or a sub-sequence containing multiple potential amino acid response elements failed to show significant amino acid sensitivity in various cell types. Chromatin-dependency did not appear to account for this result as hepatic cell clones stably transfected with the promoter constructs showed little or no arginine or leucine responsive promoter activity. These studies suggest that while amino acid sensitivity of LAT-1 expression is transcriptionally regulated, cis elements within the proximal promoter do not directly mediate this regulation. Understanding mechanisms by which this gene responds to amino acid availability will contribute to our knowledge of how eukaryotic cells sense and respond to their environment.

Animals↗

PubMed2004

Total internal reflection with fluorescence correlation spectroscopy: nonfluorescent competitors.

Total internal reflection with fluorescence correlation spectroscopy is a method for measuring the surface association/dissociation rate constants and absolute densities of fluorescent molecules at the interface of a planar substrate and solution. This method can also report the apparent diffusion coefficient and absolute concentration of fluorescent molecules very close to the surface. Theoretical expressions for the fluorescence fluctuation autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave, in solution, contribute to the fluorescence fluctuations have been published previously. In the work described here, the nature of the autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave contribute to the fluorescence fluctuations, and when fluorescent and nonfluorescent molecules compete for surface binding sites, is described. The autocorrelation function depends in general on the kinetic association and dissociation rate constants of the fluorescent and nonfluorescent molecules, the surface site density, the concentrations of fluorescent and nonfluorescent molecules in solution, the solution diffusion coefficients of the two chemical species, the depth of the evanescent field, and the size of the observed area on the surface. Both general and approximate expressions are presented.

Algorithms↗

PubMed2003

Binding of NAP-22, a calmodulin-binding neuronal protein, to raft-like domains in model membranes.

The cholesterol-binding protein NAP-22 is a major component of the detergent-insoluble low-density fraction of rat brain. In this study, we found, using fluorescence microscopy, that native NAP-22, but not a demyristoylated form, binds to cholesterol-rich raft-like domains in planar-supported monolayers and remains bound after nonionic detergent extraction. NAP-22 also protects the cholesterol-rich domains during extraction by methyl-beta-cyclodextrin. The lateral mobility of this protein is much lower than that of other raft components in model membranes, suggesting that both cholesterol binding and inter-NAP-22 interactions markedly reduce its lateral diffusion. This study suggests that NAP-22 binding may be employed to image cholesterol-rich regions, such as caveolae/rafts, on the plasma membrane of cells, and preliminary efforts in that direction are presented.

3T3 Cells↗

PubMed2003

Ligand-receptor kinetics measured by total internal reflection with fluorescence correlation spectroscopy.

Total internal reflection excitation used in combination with fluorescence correlation spectroscopy (TIR-FCS) is a method for characterizing the dynamic behavior and absolute concentrations of fluorescent molecules near or at the interface of a planar substrate and a solution. In this work, we demonstrate for the first time the use of TIR-FCS for examining the interaction kinetics of fluorescent ligands in solution which specifically and reversibly associate with receptors in substrate-supported planar membranes. Fluorescence fluctuation autocorrelation functions were obtained for a fluorescently labeled IgG reversibly associating with the mouse receptor FcgammaRII, which was purified and reconstituted into substrate-supported planar membranes. Data were obtained as a function of the IgG solution concentration, the Fc receptor surface density, the observation area size, and the incident intensity. Best fits of the autocorrelation functions to appropriate theoretical forms gave measures of the average surface density of bound IgG, the local solution concentration of IgG, the kinetic rate constant for surface dissociation, and the rate of diffusion through the depth of the evanescent field. The average number of observed fluorescent molecules, both in solution and bound to the surface, scaled with the solution concentration of IgG, observation area size, and Fc receptor surface density as expected. The dissociation rate constant and rate of diffusion through the evanescent field agree with previous results, and all measured parameters were independent of the incident intensity.

Algorithms↗

PubMed2002

Fluorescence pattern photobleaching recovery for samples with multi-component diffusion.

The translational mobility of proteins and lipids in phospholipid bilayers is often not well described as ideal self diffusion. One of the best methods for characterizing such non-ideal diffusion is to use fluorescence pattern photobleaching recovery. In this method, the spatial gradient of the monitoring and bleaching intensity is created by using epi-fluorescence and an expanded Gaussian-shaped laser beam which passes though a Ronchi ruling placed at the back image plane of a microscope. A difficulty arises when the fluorescence recovery from the exchange of slowly diffusing molecules between illuminated and non-illuminated stripes temporally overlaps with the recovery from the exchange of more rapidly diffusing molecules through the gradient produced by the broad Gaussian shape of the illumination. In the work presented here, a general theory is developed that describes the shape of the resulting fluorescence recovery curve for these typical experimental conditions. Approximate expressions amenable to non-linear curve fitting are also given. The new theoretical formalism has been demonstrated on data for the translational mobility of a fluorescent lipid probe in phospholipid bilayers deposited on planar-fused silica substrates.

Biological Transport↗

PubMed2002

Recent advances in fluorescence correlation spectroscopy.

Fluorescence correlation spectroscopy is a method in which fluctuations in the fluorescence arising from a very small sample volume are correlated to obtain information about the processes giving rise to the fluctuations. Recent progress has been made in methodologies such as two-photon excitation, photon counting histogram analysis, cross-correlation, image correlation and evanescent excitation. Fluorescence correlation spectroscopy techniques have been applied to several biological processes, including fluorescent protein photodynamics, binding equilibria and kinetics, protein oligomerization, nucleic acid interactions, and membrane and intracellular dynamics.

Green Fluorescent Proteins↗