DNA ploidy and markovian analysis of neoplastic progression in experimental pancreatic cancer.

Computer-assisted analysis of DNA ploidy and nuclear morphology were used to elucidate changes in the cell nucleus that occur during the development of experimental pancreatic cancer. Ductal pancreatic adenocarcinoma was induced in 49 Syrian hamsters by SC injection of N-nitrosobis (2-oxopropyl) amine; twenty hamsters served as controls. Groups of animals were sacrificed every 4 weeks for 20 weeks and adjacent sections of pancreatic tissue were H&E and Feulgen-stained for light microscopy and computer assisted cytometry. Pancreatic ductal cells were classified as normal, atypical, or malignant; tissue inflammation (pancreatitis) was also noted when present. DNA ploidy and nuclear morphology evaluation (Markovian analysis) identified an atypical cell stage clearly distinguishable from either normal or malignant cells; pancreatitis preceded this atypia. The DNA ploidy histogram of these atypical cells revealed a major diploid peak and a minor aneuploid peak. The receiver operator characteristic curve areas for a logistic regression model of normal vs atypical cells was 0.94 and for atypical vs malignant was 0.98, numbers indicative of near-perfect discrimination among these three cell types. The ability to identify an atypical cell population should be useful in establishing the role of these cells in the progression of human pancreatic adenocarcinoma.     

SILAC zebrafish for quantitative analysis of protein turnover and tissue regeneration

Defective tissue regeneration is thought to contribute to several human diseases, including neurodegenerative disorders, heart failure and various lung diseases. Boosting the regenerative capacity has been suggested a possible therapeutic approach. Methods to metabolically label newly synthesized proteins in vivo with stable isotopic forms of amino acids holds promise for the study of protein turnover and tissue regeneration that are fundamental to the sustained life of all organisms. Here, we used the "stable isotope labeling with amino acids in cell culture" (SILAC) approach to explore normal protein turnover and tissue regeneration in adult zebrafish. The ratio of labeled and unlabeled proteins/peptides in specific organs of zebrafish fed a SILAC diet containing (13)C(6)-labeled lysine was determined by liquid chromatography and tandem mass spectrometry. Labeling was highest in tissues with high regenerative capacity, including intestine, liver, and fin, whereas brain and heart displayed the lowest labeling. Proteins with high degree of labeling were mainly involved in catalytic or transport activity pathways. The technique also verified increased protein synthesis during regeneration of the caudal fin following amputation. This newly developed SILAC zebrafish model constitutes a novel tool to analyze tissue regeneration in an animal model amenable to genetic and pharmacologic manipulation.     

Three-dimensional ultrastructure and quantitative analysis of the human Sertoli cell nucleolus

The nucleolus of the human Sertoli cell displays a spontaneous segregation of its components and has only one or 2 large fibrillar centers. The 3-dimensional reconstruction and quantitative analysis of its components was undertaken using a Quantimet 900 image analysis system in order to define the spatial relationships between the dense fibrillar component and the fibrillar center and especially to investigate whether threads of dense fibrillar component exist independently, without being linked to a fibrillar center. Our 3D reconstructions demonstrated that the dense fibrillar threads or sheets were never independent of fibrillar centers. These structures belonged to a continuous network that joined the layer of dense fibrils surrounding the fibrillar center. When the nucleolus contained 2 different-sized fibrillar centers, quantitative analysis showed that there was a proportional relationship between the volume of the dense fibrillar component and the volume of the fibrillar center. These data, compared with those previously obtained by means of autoradiographic techniques, suggest that the rDNA-containing chromatin passes through the fibrillar center and unwinds from there into the dense fibrillar component.     

Validation of rat reference genes for improved quantitative gene expression analysis using low density arrays

Real-time PCR has become increasingly important in gene expression profiling research, and it is widely agreed that normalized data are required for accurate estimates of messenger RNA (mRNA) expression. With increased gene expression profiling in preclinical research and toxicogenomics, a need for reference genes in the rat has emerged, and the studies in this area have not yet been thoroughly evaluated. The purpose of our study was to evaluate a panel of rat reference genes for variation of gene expression in different tissue types. We selected 48 known target genes based on their putative invariability. The gene expression of all targets was examined in 11 types of rat tissues using TaqMan low density array (LDA) technology. The variability of each gene was assessed using a two-step statistical model. The analysis of mean expression using multiple reference genes was shown to provide accurate and reliable normalized expression data. The least five variable genes from each specific tissue were recommended for future tissue-specific studies. Finally, a subset of investigated rat reference genes showing the least variation is recommended for further evaluation using the LDA platform. Our work should considerably enhance a researcher's ability to simply and efficiently identify appropriate reference genes for given experiments.     

Plant phenolics regulate neoplastic cell growth and survival: a quantitative structure-activity and biochemical analysis

The anti-tumour activities of many plant phenolics at high concentrations (>100 micromol/L) suggest their potential use as dietary supplements in cancer chemoprevention and cancer chemotherapy. However, it is not clear what impact phenolic compounds have at the physiological concentrations obtained through consumption of high phenolic diets on neoplastic cells. In the present study, 54 naturally occurring phenolics were evaluated at physiologically relevant concentrations for their capacity to alter PC12 cell viability in response to serum deprivation, the chemotherepeutic agent etoposide, and the apoptogen C2-ceramide. Surprisingly, novel mitogenic, cytoprotective, and antiapoptotic activities were detected. Quantitative structure-activity relationship modelling indicated that many of these activities could be predicted by compound lipophilicity, steric bulk, and (or) antioxidant capacity, with the exception of inhibition of ceramide-induced apoptosis. Where quantitative structure-activity relationship analysis was insufficient, biochemical assessment demonstrated that the benzoate orsellinic acid blocked downstream caspase-12 activation following ceramide challenge. These findings demonstrate substantive mitogenic, cytoprotective, and antiapoptotic biological activities of plant phenolics on neoplastic cells at physiologically relevant dietary concentrations that should be considered in chemopreventive and chemotherapeutic strategies.     

An interactive microcomputer-based system for the quantitative analysis of stratified tissue sections

This paper describes a microcomputer-based system that allows diagnostically relevant properties of stratified tissue sections to be objectively measured. The results of detailed nuclear image analyses are examined in the broader context of the position of nuclei within the tissue section and relative to histologic structures and each other. Quantitative measures are obtained for important morphometric and densitometric properties of individual nuclei and mitotic figures and especially for their distribution and orientation within the tissue section relative to the stratum germinativum and each other. Recorded karyometric and histometric parameters include measures of nuclear DNA content (based on optical density measurements), size, roundness, texture, shape, distance to the basal layer, angle with the stratum germinativum, epithelial height and proximate nuclear distance. Statistics generated describe normalized mitotic density as a function of depth in the epithelium, and a composite mitotic index is produced based upon weighting of these densities relative to their distance from the stratum germinativum. These properties and derived statistics may be examined as a function of epithelial depth and nuclear type and may be plotted as a function of other diagnostic features in addition to the observed stratum. The system is one part of microTICAS-STRATEX, an expert diagnostic system for the clinical evaluation of stratified tissue sections, now under development as an outgrowth of the microTICAS system. Results of measurements made with this system will be compared with site-specific and diagnosis-specific reference profiles and used in conjunction with clinical data derived from a data base at the University of Chicago of over 1.5 million patients to generate diagnostic and prognostic evaluations.     

The mechanics of development: Models and methods for tissue morphogenesis

Embryonic development is a physical process during which groups of cells are sculpted into functional organs. The mechanical properties of tissues and the forces exerted on them serve as epigenetic regulators of morphogenesis. Understanding these mechanobiological effects in the embryo requires new experimental approaches. Here we focus on branching of the lung airways and bending of the heart tube to describe examples of mechanical and physical cues that guide cell fate decisions and organogenesis. We highlight recent technological advances to measure tissue elasticity and endogenous mechanical stresses in real time during organ development. We also discuss recent progress in manipulating forces in intact embryos. Birth Defects Research (Part C) 90:193–202, 2010. © 2010 Wiley‐Liss, Inc.     

Three-dimensional imaging and morphometric analysis of alveolar tissue from microfocal X-ray-computed tomography

We evaluated microfocal X-ray-computed tomography (micro-CT) as a method to visualize lung architecture two and three dimensionally and to obtain morphometric data. Inflated porcine lungs were fixed by formaldehyde ventilation. Tissue samples (8-mm diameter, 10-mm height) were stained with osmium tetroxide, and 400 projection images (1,024 x 1,024 pixel) were obtained. Continuous isometric micro-CT scans (voxel size 9 microm) were acquired to reconstruct two- and three-dimensional images. Tissue samples were sectioned (8-microm thickness) for histological analysis. Alveolar surface density and mean linear intercept were assessed by stereology-based morphometry in micro-CT scans and corresponding histological sections. Furthermore, stereology-based morphometry was compared with morphometric semi-automated micro-CT analysis within the same micro-CT scan. Agreement of methods was assessed by regression and Bland-Altman analysis. Comparing histology with micro-CT, alveolar surface densities (35.4 +/- 2.4 vs. 33.4 +/- 1.9/mm, P < 0.05) showed a correlation (r = 0.72; P = 0.018) with an agreement of 2 +/- 1.6/mm; the mean linear intercept (135.7 +/- 14.5 vs. 135.8 +/- 15 microm) correlated well (r = 0.97; P < 0.0001) with an agreement of -0.1 +/- 3.4 microm. Semi-automated micro-CT analysis resulted in smaller alveolar surface densities (33.4 +/- 1.9 vs. 30.5 +/- 1/mm; P < 0.01) with a correlation (r = 0.70; P = 0.023) and agreement of 2.9 +/- 1.4/mm. Non-destructive micro-CT scanning offers the advantage to visualize the spatial tissue architecture of small lung samples two and three dimensionally.     

A novel method for the generation of reaggregated organotypic cultures that permits juxtaposition of defined cell populations

Cellular reaggregation methods have been used to generate in vitro organotypic cultures as a means to elucidate the cellular and molecular requirements of organogenesis. However, reproducibility from experiment to experiment has remained problematic and furthermore, current protocols do not support reaggregation of many important tissues. Here, using the thymus as a model organ, we present a novel reaggregation method termed “compaction reaggregation” that offers improved kinetics of reaggregation and greatly improved efficiency. Using compaction reaggregation we have been able to reaggregate the aorta‐gonad‐ mesonephros region, a tissue that previously proved refractory to commonly used reaggregation methods, enabling the study of hematopoietic stem cell emergence and expansion. Additionally, compaction reaggregation permits the juxtaposition of different cell layers within the aggregated structure thus providing the means to study inductive interactions between different cell populations in vitro. genesis 47:346–351, 2009. © 2009 Wiley‐Liss, Inc.     

Three-dimensional visualization and quantitative analysis of cervical cell nuclei with confocal laser scanning microscopy

OBJECTIVE: To develop a method for the acquisition and processing of 3-dimensional images based on confocal laser scanning microscopy for the purpose of 3-dimensional visualization and quantitative analysis of cell nuclei. STUDY DESIGN: A contour-based surface rendering method was used, and volume rendering was implemented according to the basic volume rendering pipeline. To extract quantitative features, a 3-dimensional labeling method based on slice information was used. After applying the labeling algorithm, the measurements for 3-dimensional quantitative analysis of nuclei were extracted: nuclear volume, surface area and spherical shape factor. We compared the 3-dimensional features of normal and abnormal cervical cell nuclei. RESULTS: Comparison of the size of 3-dimensional cervical cell nuclei between normal and abnormal revealed a statistically significant difference. The proposed method could overcome the limitation inherent in 2-dimensional analysis and could become a way of improving the accuracy and reproducibility of quantification of cell nuclei. CONCLUSION: Three-dimensional visualization and quantification of cell nuclei provide valuable medical information that can lead to a more objective diagnosis.     

Chromosomal axis formation and meiotic progression in chicken oocytes: a quantitative analysis

The assembly and disassembly of the synaptonemal complexes (SCs) correlate with the progression of meiotic prophase I. Using immunostaining of the cohesin component SMC3, which is present in the axial elements of the SC, we characterized the synaptic process in chicken oocytes and quantified the frequency of the different prophase stages at hatching and at 3 different ages after hatching. The analysis provides detailed quantitative data regarding the meiotic stages in the chicken ovary showing that the maximum amount of pachytene oocytes is found around hatching and that oocytes reach the diplotene stage 5 days after entering into meiosis. We confirmed the asynchrony of the meiotic development in the female chicken gonad showing that the ovary has a composite population of cells at different stages from day 17 before hatching and for several days after hatching. The significance of these results is discussed in relationship to functional experimental procedures that involve avian oocytes.     

Effect of methionine on the growth and morphogenesis ofSaccharomycopsis fibuligera in defined medium

Summary The growth ofSaccharomycopsis fibuligera on defined media has been investigated. Growth on a minimal medium was stimulated by the addition of methionine but not by the addition of norleucine or other amino acids including cysteine. Growth in the presence of methionine produced pseudomycelium rather than the true mycelium which is produced during growth on complex media A requirement for methionine for growth and pseudomycelium formation inS. fibuligera has been demonstrated.