Proteomic analysis of nuclei dissected from fixed rat brain tissue using expression microdissection.

Expression microdissection (xMD) is a high-throughput, operator-independent technology that enables the procurement of specific cell populations from tissue specimens. In this method, histological sections are first stained for cellular markers via either chemical or immuno-guided methods, placed in close contact with an ethylene vinyl acetate (EVA) film, and exposed to a light source. The focal, transient heating of the stained cells or subcellular structures melts the EVA film selectively to the targets for procurement. In this report, we introduce a custom-designed flashcube system that permits consistent and reproducible microdissection of nuclei across an FFPE rat brain tissue section in milliseconds. In addition, we present a method to efficiently recover and combine captured proteins from multiple xMD films. Both light and scanning electron microscopy demonstrated captured nuclear structures. Shotgun proteomic analysis of the samples showed a significant enrichment in nuclear localized proteins, with an average 25% of recovered proteins localized to the nucleus, versus 15% for whole tissue controls (p < 0.001). Targeted mass spectrometry using multiple reaction monitoring (MRM) showed more impressive data, with a 3-fold enrichment in histones, and a concurrent depletion of proteins localized to the cytoplasm, cytoskeleton, and mitochondria. These data demonstrate that the flashcube-xMD technology is applicable to the proteomic study of a broad range of targets in molecular pathology.

Utility of multivariate analysis in support of in vitro metabolite identification studies: retrospective analysis using the antidepressant drug nefazodone.

The utility of multivariate analysis in in vitro metabolite identification studies was examined with nefazodone, an antidepressant drug with a well-established metabolic profile. The chromatographic conditions were purposefully chosen to reflect those utilized in high-throughput screening for microsomal stability of new chemical entities. Molecular ion, retention time information on groups of human liver microsomal samples with/without nefazodone was evaluated by principal component analysis (PCA). Resultant scores and loadings plots from the PCA revealed the segregation and the ions of interest that designated the drug and its corresponding metabolites. Subsequent acquisition of tandem mass spectrometry (MS/MS) spectra for targeted ions permitted the interrogation and interpretation of spectra to identify nefazodone and its metabolites. A comparison of nefazodone metabolites identified by PCA versus those found by traditional metabolite identification approaches resulted in very good correlation when utilizing similar analytical methods. Fifteen metabolites of nefazodone were identified in beta-nicotinamide adenine dinucleotide phosphate (NADPH)-supplemented human liver microsomal incubations, representing nearly all primary metabolites previously reported. Of the 15 metabolites, eight were derived from the N-dealkylation and N-dephenylation of the N-substituted 3-chlorophenylpiperazine motif in nefazodone, six were derived from mono- and bis-hydroxylation, and one was derived from the Baeyer Villiger oxidation of the ethyltriazolone moiety in nefazodone.

The Clementine bistatic radar experiment.

During the Clementine 1 mission, a bistatic radar experiment measured the magnitude and polarization of the radar echo versus bistatic angle, beta, for selected lunar areas. Observations of the lunar south pole yield a same-sense polarization enhancement around beta = 0. Analysis shows that the observed enhancement is localized to the permanently shadowed regions of the lunar south pole. Radar observations of periodically solar-illuminated lunar surfaces, including the north pole, yielded no such enhancement. A probable explanation for these differences is the presence of low-loss volume scatterers, such as water ice, in the permanently shadowed region at the south pole.

Laser capture microdissection.

Laser capture microdissection (LCM) under direct microscopic visualization permits rapid one-step procurement of selected human cell populations from a section of complex, heterogeneous tissue. In this technique, a transparent thermoplastic film (ethylene vinyl acetate polymer) is applied to the surface of the tissue section on a standard glass histopathology slide; a carbon dioxide laser pulse then specifically activates the film above the cells of interest. Strong focal adhesion allows selective procurement of the targeted cells. Multiple examples of LCM transfer and tissue analysis, including polymerase chain reaction amplification of DNA and RNA, and enzyme recovery from transferred tissue are demonstrated.

[Eye fundus autofluorescence technique in the early diagnosis of age-related macular degeneration].

Autofluorescence (AF) of the eye fundus is one of the most promising studies. AF provides specific molecular information on the retinal pigment epithelium and enables one to diagnose early phenotypic changes that are predictors for progression of age-related macular degeneration. Many investigations have demonstrated that AF is a valuable clinical technique that should be improved in order to have information accessible to a patient on the diagnosis and prediction of age-related macular degeneration.

Laser-capture microdissection: opening the microscopic frontier to molecular analysis.

As the list of expressed human genes expands, a major scientific challenge is to understand the molecular events that drive normal tissue morphogenesis and the evolution of pathological lesions in actual tissue. Laser capture microdissection (LCM) has been developed to provide a reliable method to procure pure populations of cells from specific microscopic regions of tissue sections, in one step, under direct visualization. The cells of interest are transferred to a polymer film that is activated by laser pulses. The exact morphology of the procured cells (with intact DNA, RNA and proteins) is retained and held on the transfer film. With the advent of LCM, cDNA libraries can be developed from pure cells obtained directly from stained tissue, and microhybridization arrays of thousands of genes can now be used to examine gene expression in microdissected human tissue biopsies. The fluctuation of expressed genes or alterations in the cellular DNA that correlate with a particular disease stage can ultimately be compared within or between individual patients. Such a fingerprint of gene-expression patterns can provide crucial clues for etiology and might, ultimately, contribute to diagnostic decisions and therapies tailored to the individual patient. Molecules found to be associated with a defined pathological lesion might serve as imaging ot therapeutic targets.

Biomarker risk assessment and bladder cancer detection in a cohort exposed to benzidine.

BACKGROUND: Cancer screening with highly sensitive, specific biomarkers that reflect molecular phenotypic alterations is an attractive strategy for cancer control. We examined whether biomarker profiles could be used for risk assessment and cancer detection in a cohort of Chinese workers occupationally exposed to benzidine and at risk for bladder cancer. METHODS: The cohort consisted of 1788 exposed and 373 nonexposed workers, followed from 1991 through 1997. We assayed urothelial cells from voided urine samples for DNA ploidy (expressed as the 5C-exceeding rate [DNA 5CER]), the bladder tumor-associated antigen p300, and a cytoskeletal protein (G-actin). Workers were stratified into different risk groups (high, moderate, and low risk) at each examination based on a predefined biomarker profile. For workers who developed bladder cancer, tumor risk assessment was analyzed from samples collected 6-12 months before the cancer diagnosis. The associations between risk group and subsequent development of bladder cancer were analyzed by Cox proportional hazards regression analysis and logistic analysis, after adjustment. All statistical tests were two-sided. RESULTS: Twenty-eight bladder cancers were diagnosed in exposed workers and two in nonexposed workers. For risk assessment, DNA 5CER had 87.5% sensitivity, 86.5% specificity, an odds ratio (OR) of 46.2 (95% confidence interval [CI] = 8.1 to 867.0), and a risk ratio (RR) of 16.2 (95% CI = 7.1 to 37.0); p300 had 50.0% sensitivity, 97.9% specificity, an OR of 40.0 (95% CI = 9.0 to 177.8), and an RR of 37.9 (95% CI = 16.8 to 85.3). The risk of developing bladder cancer was 19.6 (95% CI = 8.0 to 47.9) times higher in workers positive for either the DNA 5CER or p300 biomarkers than in workers negative for both biomarkers and 81.4 (95% CI = 33.3 to 199.3) times higher in workers positive for both biomarkers. G-actin was a poor marker of individual risk. CONCLUSIONS: Occupationally exposed workers at risk for bladder cancer can be individually stratified, screened, monitored, and diagnosed based on predefined molecular biomarker profiles.

Cellular F-actin levels as a marker for cellular transformation: correlation with bladder cancer risk.

Previous findings in cultured cells that differentiated cells had markedly higher F-actin levels than undifferentiated cells (Cancer Res., 50: 2215-2220, 1990) suggested that quantitative F-actin measurements in urinary cells might provide diagnostic or prognostic information by identifying those individuals with cells tending towards a lower degree of differentiation. The feasibility of such an approach was investigated using a risk stratification schema. Bladder wash samples were obtained from 163 symptomatic patients being evaluated for bladder cancer and 41 asymptomatic controls without hematuria or other symptoms consistent with bladder cancer. F-actin levels were evaluated by flow cytometry using a fluorescent phalloidin probe. The risk of bladder cancer was stratified according to biopsy, either DNA ploidy by flow cytometry or quantitative fluorescence image analysis cytology, previous bladder cancer history, and hematuria. A strong correlation between the presence of cells with abnormally low F-actin content in cells obtained by bladder wash from 38 patients and biopsy-proved bladder transitional cell carcinoma (P less than 0.001) was observed. A strong correlation was also observed between the presence of cells with low F-actin content and risk of bladder cancer assessed by either stratification schema (P less than 0.0001). The correlation was more consistent with the stratification by quantitative fluorescence image analysis cytology because of the 37% false-positive rate of ploidy analysis by flow cytometry among the control patients. Further evidence that low F-actin was correlated with cellular abnormality was obtained from simultaneously labeling cells for F-actin and with M344 antibody, a monoclonal antibody against a low-grade bladder tumor-related antigen. These studies showed that the F-actin content of the M344-positive cells was lower than that of the M344-negative cells. These results suggest that F-actin could be an early and sensitive marker for bladder cancer detection and risk prognostication.

Microvascular blood flow, volume, and velocity measured by laser Doppler techniques in IDDM.

A laser Doppler device with the capability to simultaneously measure skin blood flow, microvascular volume, and erythrocyte velocity was used to assess blood flow changes in 35 insulin-dependent diabetes mellitus (IDDM) subjects, mean age 33 +/- 1 yr, with average duration of diabetes 14 +/- 1 yr, and in a nondiabetic control group. Blood flow was determined at 35 and 44 degree C at several sites on the upper and lower extremities with a temperature-regulated probe. Blood flow was highest at both temperatures on the pulps of the index finger and the first toe, regions of high density of arteriovenous anastomoses. There was significantly greater blood flow at most locations for the nondiabetic than the diabetic group at 35 degree C, and the differences between the two groups were substantially larger at 44 degree C. At 44 degree C, blood flow in the control group was approximately 40% greater in the upper extremity and 50% greater in the lower extremity than it was in the diabetic subjects. The differences were attributed to decreases of both microvascular volume and velocity in the diabetic group. In the upper extremity, volumes in the diabetic patients were 10-15% lower and velocities 10-40% lower than in the nondiabetic subjects. In the lower extremity, volumes were 20-25% lower and velocities 40-50% lower. We conclude that laser Doppler techniques can be used to assess microvascular changes in the skin of diabetic patients. This approach may be useful to evaluate and model diabetic microangiopathy.

Structural dynamics of frog muscle during isometric contraction.

Intensity fluctuation autocorrelation functions of laser light scattered by actively contracting muscle were measured at points in the scattered field. They were reproducible and showed characteristics which depended on the physiological state of the muscle and the parameters of the scattering geometry. The autocorrelation functions had large amplitudes and decay rates that varied significantly with the phase of the contraction-relaxation cycle. The dependence of the autocorrelation function on scattering geometry indicated many elements with diameters on the order of 0.5 mum (presumed to be myofibrillar sarcomeres or their A bands or I bands) undergo independent random changes in their axial positions and their internal distribution of optical polarizability during the plateau of an isometric tetanus. The experimental results are interpreted in terms of a model in which most of the scattering elements in isometrically contracting muscle have random fluctuating axial velocities of average magnitude 20 nm/ms that persist for a few milliseconds at least. In addition to these axial motions there are local fluctuations in polarizability. Similar intensity fluctuation autocorrelation functions were observed throughout the active state on two muscle preparations, whole sartorius muscle and small bundles of single fibers (three to eight) of semitendinosus muscle. These results imply that the tension developed during an isometric tetanus contains a fluctuating component as well as a constant component.

In vivo human atherosclerotic plaque recognition by laser-excited fluorescence spectroscopy.

Arterial wall perforation and chronic restenosis represent important factors limiting the clinical application of laser angioplasty. Discrimination of normal and atherosclerotic vessels by laser-excited fluorescence spectroscopy may offer a means of targeting plaque ablation, thereby reducing the frequency of restenosis and transmural perforation. In this study, with use of a 325 nm low power helium-cadmium laser, in vivo endogenous surface fluorescence was excited through a flexible 200 microns optical fiber within a 0.018 in. (0.046 cm) guide wire in contact with the intima of 268 vascular interrogation sites from 48 patients either during open heart surgery or during percutaneous catheterization procedures. Fluorescence spectra could be recorded in all patients in bloodless and blood-filled arteries. Endogenous surface fluorescence was analyzed measuring peak intensity, peak position and shape index of the spectra. Compared with normal wall, noncalcified and calcified coronary atheroma showed a 42% (p less than 0.001) and a 58% (p less than 0.001) decrease of peak intensity, and higher shape index (p less than 0.001 and p less than 0.01, respectively). In addition, peak position was shifted to longer wavelengths for noncalcified coronary atheroma (p less than 0.001). Compared with normal aorta sites, aortic plaques demonstrated a 46% decrease of peak intensity, longer peak position wavelengths (p less than 0.05) and a higher shape index (p less than 0.001). Using an atheroma detection algorithm, prospective analysis of aorta and coronary spectra showed a specificity of 100% for identifying normal sites and a sensitivity of 73% for recognizing atherosclerotic sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Human arterial surface fluorescence: atherosclerotic plaque identification and effects of laser atheroma ablation.

In vivo plaque recognition may be important for safe and precise intra-arterial atheroma ablation during laser coronary angioplasty. This study examined the feasibility and sensitivity of utilizing quantitative fluorescence spectroscopy and video-enhanced fluorescence imaging for plaque identification in atherosclerotic human necropsy arterial wall before and after laser atheroma ablation. With wide-band (450 to 490 nm) blue light excitation, the 540 nm fluorescence intensity ratio of normal to diseased sites (n = 13) was 2.09 +/- 0.82 (p less than 0.001) and video fluorescence imaging provided enhanced delineation of atheroma surface characteristics. Continuous argon and pulsed excimer (308 nm) laser ablation of atheroma decreased fluorescence intensity ratios by 42 and 20% (p less than 0.001), respectively (that is, from abnormal to nearly normal). Low power 325 nm laser-excited fluorescence spectroscopy from normal (n = 115) and abnormal (n = 146) necropsy sites revealed an average 45% decrease in atheroma fluorescence intensity (p less than 0.0001) and changes in fluorescence spectra appearance that corresponded to plaque morphologic subtypes. Studies using a dual laser system combining 325 nm laser-excited fluorescence plaque recognition and a 480 nm pulsed dye laser for tissue ablation with common optical fibers demonstrated normalization of both fluorescence intensity and spectra appearance after laser atheroma ablation. Thus, in vitro analysis of surface arterial fluorescence by quantitative spectroscopy and video fluorescence imaging reliably differentiate plaque from normal tissue and may provide the feedback signal needed to activate a laser source for selective plaque removal.

Pulsed laser and thermal ablation of atherosclerotic plaque: morphometrically defined surface thrombogenicity in studies using an annular perfusion chamber.

Although clinical trials using laser and thermal angioplasty devices have been underway, the effects of pulsed laser and thermal ablation of atherosclerotic plaque on surface thrombogenicity are poorly understood. This study examined the changes in platelet adherence and thrombus formation on freshly harvested atherosclerotic aorta segments from Watanabe-heritable hyperlipidemic rabbits after ablation by two pulsed laser sources (308-nm xenon chloride excimer and 2,940-nm erbium:yttrium-aluminum-garnet [YAG] lasers) and a prototype catalytic hot-tip catheter. Specimens were placed in a modified Baumgartner annular chamber and perfused with citrated whole human blood, followed by quantitative morphometric analysis to determine the percent surface coverage by adherent platelets and thrombi in the treated and contiguous control areas. Pulsed excimer laser ablation of plaque did not change platelet adherence or thrombus formation in the treated versus control zones. However, photothermal plaque ablation with a pulsed erbium:YAG laser resulted in a 67% reduction in platelet adherence, compared with levels in control areas (from 16.7 +/- 2.2% to 5.5 +/- 1.8%; p less than 0.005). Similarly, after plaque ablation using a catalytic thermal angioplasty device, there was a 74% reduction in platelet adherence (from 29.2 +/- 5.1% to 7.7 +/- 1.6%; p less than 0.005) and a virtual absence of platelet thrombi (from 8.6 +/- 2.3% to 0.03 +/- 0.03%; p less than 0.005). This reduced surface thrombogenicity after plaque ablation with either an erbium:YAG laser or a catalytic hot-tip catheter suggests that thermal modifications in the arterial surface ultrastructure or thermal denaturation of surface proteins, or both, may be responsible for reduced platelet adherence. These in vitro findings indicate that controlled thermal plaque ablation by catheter-based techniques may elicit endovascular responses that can reduce early thrombus formation during angioplasty procedures.

General statistics of stochastic process of gene expression in eukaryotic cells.

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations.

Eradication of Helicobacter spp. from a rat breeding colony.

Although Helicobacter spp. have been viewed as bacteria with low pathogenicity, many investigators have shown that these low-grade pathogens have the potential to become a severe threat in immunocompromised, inbred, and transgenic animals. Therefore the presence of Helicobacter spp. in experimental animals is considered to be an unacceptable variable. In this study a formulation of medicated feed was designed and tested in an attempt to eradicate Helicobacter spp. from an infected rat breeding colony. Two feeding protocols were used: 1) treating Helicobacter-infected pregnant dams to produce clean offspring and 2) treating infected adult animals long enough to eliminate the organisms. Bacterial DNA was extracted from feces and amplified using primers that recognized the Helicobacter spp.-specific region of the 16S rRNA gene. Fecal samples from the weanlings from protocol 1 tested negative for Helicobacter spp. at 1 week before and 2 and 12 weeks after weaning. Infected adult rats from protocol 2 tested negative after three cycles of 2 weeks on and 2 weeks off the medicated feed. Animals from both protocols have remained Helicobacter-free for 8 months.

Glucagon administration decreases hepatic nuclear triiodothyronine binding capacity.

The maximal binding capacity (MBC) of nuclear triiodothyronine (T3) receptor sites in rat liver decreases markedly after glucagon administration. Administration of serial doses of glucagon (2.5 microgram/100 g BW) resulted in a 33% decrease in MBC in 3.5 h and MBC was reduced by 45% in 6.25 h. The individual doses used were in the same order of magnitude as those used in the treatment of hypoglycemic human subjects (1.5 microgram/100 g BW). This report presents the first evidence that a peptide hormone can change the number of nuclear T3 receptor sites. The physiological significance of these findings remains to be clarified.

Characterization of the DD23 tumor-associated antigen for bladder cancer detection and recurrence monitoring. Marker Network for Bladder Cancer.

Bladder cancer detection, monitoring, and prevention represent major problems that could be addressed with sensitive and specific biomarkers. The antigen recognized by the DD23 antibody, previously developed against a tumor-related antigen, was partially biochemically characterized, and its sensitivity and specificity in cancer detection and recurrence monitoring was evaluated. Quantitative fluorescence image analysis was used to quantify antigen content in exfoliated urothelial cells in a cross-section of patients with bladder cancers of all grades and stages and control populations. The antigen was found in tumor cells as well as normal-appearing urothelial cells, suggesting it represents a marker induced by the altered growth factor environment of a cancer-containing bladder. When used as a quantitative marker, the sensitivity for bladder cancer detection was 85%, and the specificity was 95%. No significant difference was seen between symptomatic and asymptomatic control populations, including patients with previous bladder cancers in the absence of a recurrence. In bladder cancer recurrence monitoring, results were consistently negative until just before detection of a recurrence. The biomarker reflects a "field effect" that occurs very late in tumorigenesis and seems to represent events common to most cancers involving the genitourinary tract. Western blotting showed the antibody recognized a dimeric protein. DD23 quantification in single cells may be particularly useful in targeting cystoscopic intervention for recurrence monitoring and, because of its high specificity, could be a tool for bladder cancer screening in high-risk groups.

Microdissection, microchip arrays, and molecular analysis of tumor cells (primary and metastases).

Advances in biotechnology and bioinformatics are offering promise for new breakthroughs in gene discovery and elucidation of gene function. At present, many candidate genes related to cancer pathogenesis have been identified in several types of human cancer, yet frequently their function remains elusive. This is particularly true as it relates to the progression of human cancer. This landscape could change dramatically, however, as technological innovations and improvements continue to revolutionize these fields. High-throughput molecular approaches are emerging, which may become accurate, automated, and cost-effective. For example, DNA arrays on microchips are under development with numerous applications, including the ability to screen genes rapidly for mutations and to study patterns of gene expression on a large scale. Automated systems for microdissection and sequencing are also in their implementation stages. Commensurate with their integration and evolution, these information and technological tools have the potential to offer a more comprehensive understanding of multiple genetic and cellular alterations occurring during cancer initiation, development, and progression. Ultimately, this fundamental knowledge can provide strategies for intervention, prevention, and early diagnosis. This is a US government work. There are no restrictions on its use.

Laser Doppler blood flow studies during open muscle biopsy in patients with neuromuscular diseases.

Laser Doppler measurements of skeletal muscle blood flow were performed in 12 patients with neuromuscular disorders and 6 controls. The mean resting blood flows and postocclusive reactive hyperemias were similar for the patients with neuropathic disorders and for controls. The patients with myopathic disorders had higher resting muscle blood flows and reactive hyperemias. Correlation of blood flow results and muscle biopsy characteristics suggested that muscle type grouping was not associated with a change in skeletal muscle blood flow, whereas muscle fiber degeneration was associated with an increased blood flow.

Matching- and delayed matching-to-sample performance as measures of visual processing, selective attention, and memory in aging and alcoholic individuals.

Visual processing time, selective attention to visual cues, and memory for those cues were measured in groups of normal and alcoholic research participants within three different age ranges: young (35-45 yr), middle (46-59 yr) and older (60-70 yr). Performance across groups also was compared to that of alcoholic Korsakoff patients, known to have processing and attentional abnormalities. The matching-to-sample task was employed in which participants are required to match one of two laterally located response choices with a stimulus displayed in the center between them. Duration of the center sample stimulus varied between 20 and 500 msec, and delay between sample offset and response-choice (match) onset varied between 0 and 30 sec. Complexity of the sample stimulus also was varied, containing one or two dimensions (color and/or form). Levels of performance for all groups improved with increased sample stimulus durations, and were negatively related to a stimulus complexity and length of delay. Significant group differences in accuracy were evident with short stimulus exposures; the Korsakoff and older groups made more errors than the younger groups. Similarly, response times were influenced differentially by stimulus duration, stimulus complexity, and the delay between sample and matching stimuli, with young participants (alcoholics and controls) responding fastest. Results emphasize the contribution of processing deficits to other cognitive impairments in aging and alcoholic individuals, as well as the relative independence of aging and alcoholism.