Testing different 3D techniques using geometric morphometrics: Implications for cranial fluctuating asymmetry in humans

This study aimed to test the performance of 3D digitizer, CT scanner, and surface scanner in detecting cranial fluctuating asymmetry. Sets of 32 landmarks (6 in the midline and 13 bilateral) were acquired from 14 archeological crania using a 3D digitizer, and from 3D models generated from a CT scanner and surface scanner using Viewbox 4. Levels of shape variation were analyzed in MorphoJ using Procrustes analysis of variance and Principal component analysis. Intra-observer error accounted for 1.7%, 1.8%, and 4.5% of total shape variation for 3D digitizer, CT scanner, and surface scanner respectively. Fluctuating asymmetry accounted for 15%–16% of total shape variation. Variation between techniques accounted for 18% of total shape variation. We found a higher level of missing landmarks in our surface scan data than for both 3D digitizer and CT scanner data, and both 3D model-based techniques sometimes obscured taphonomic damage. All three 3D techniques are appropriate for measuring cranial fluctuating asymmetry. We advise against combining data collected with different techniques.     

Movement characteristics of ejaculated sperm from cynomolgus monkeys (Macaca fascicularis) analyzed by manual and automated computerized image analysis

Sperm motility is an important indicator of male reproductive function. An automated computerized system was used to measure the movement characteristics of cynomolgus monkey sperm. Swimming velocities were in good agreement with data derived from tracking sperm heads manually with a digitizer, but sperm counting by the system was erroneous. In some ejaculates, there were two subpopulations of sperm with different curvilinear velocities, linearities of swim-paths, and lateral movements of the heads.     

Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding

Formalin‐fixed paraffin‐embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study formalin‐induced alternations on a proteome‐wide level. We compared LC‐MS/MS data of FFPE and frozen human kidney tissues by two methods. First, clustering analysis revealed that the biological variation is higher than the variation introduced by the two sample processing techniques and clusters formed in accordance with the biological tissue origin and not with the sample preservation method. Second, we combined open modification search and spectral counting to find modifications that are more abundant in FFPE samples compared to frozen samples. This analysis revealed lysine methylation (+14 Da) as the most frequent modification induced by FFPE preservation. We also detected a slight increase in methylene (+12 Da) and methylol (+30 Da) adducts as well as a putative modification of +58 Da, but they contribute less to the overall modification count. Subsequent SEQUEST analysis and X!Tandem searches of different datasets confirmed these trends. However, the modifications due to FFPE sample processing are a minor disturbance affecting 2–6% of all peptide‐spectrum matches and the peptides lists identified in FFPE and frozen tissues are still highly similar.     

Proliferation patterns in the canine endometrium during the estrous cycle

The proliferative activity in the endometrium of 58 bitches in different stages of the estrous cycle was assessed by immunohistochemical detection of the Ki-67 proliferation associated nuclear antigen and by counting mitotic figures. The Ki-67 labelling index and the mitotic index were determined in the surface epithelium, the stroma, the crypts and the basal glands by calculating the percentage of Ki-67 positive cells and mitotic figures, respectively, on a total of 500 cells of each category. Endometrial vascular proliferation was also verified by counting the number of Ki-67 positive cells on a total of 100 endothelial cells. The present study showed two proliferation peaks involving different cell groups. In the surface epithelium, the stroma, the blood vessels and the crypts, the highest labelling and mitotic indexes were noticed during proestrus, whereas for the basal glands these indexes significantly increased (P < 0.05) during estrus compared to late metestrus and anestrus. Furthermore, a slightly positive correlation (P < 0.05) was found between the labelling index in the basal glands and the serum progesterone levels, whereas the labelling indexes in the other cell groups were positively correlated with the estradiol-17 beta levels, although not always significantly. These findings suggest that regulation of the proliferation in the surface epithelium, the stroma, the blood vessels and the crypts is different from the proliferation in the basal glands.     

Automated topographical cell proliferation analysis

BACKGROUND: Cell proliferation is often studied using the incorporation of bromodeoxyuridine (BrdU). Immunohistochemical staining is then used to detect BrdU in the nucleus. To circumvent the observer bias and labor-intensive nature of manually counting BrdU-labeled nuclei, an automated topographical cell proliferation analysis method is developed. METHODS: Sections stained with fluorescein-labeled anti-BrdU and counterstained with To-Pro-3 are scanned using confocal laser scanning microscopy (CLSM). For every point in the image, the nucleus density of BrdU-labeled nuclei and the total nucleus density of the neighborhood of that point are calculated from the BrdU and the To-Pro-3 signal, respectively. The ratio of these densities gives an indication of the amount of cell proliferation at that point. The automated measure is validated by comparing it with the ratio of BrdU-stained nuclei to the total number of nuclei obtained from a manual count. RESULTS: A positive correlation is found between the automated measure and the ratios calculated from the manual counting (r = 0.86, P < 0.001). Calculating the topographical cell proliferation using the automated method is faster and does not suffer from interobserver variability. CONCLUSIONS: Automated topographical cell proliferation analysis is a fast method to objectively find differences in cell proliferation within a tissue. This can be visualized by a topographical map that corresponds to the tissue under study.     

Constructing biological pathways by a two-step counting approach

Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network.     

Reliability of DNA cytometric S-phase analysis in surgical biopsies: assessment of systematic and sampling errors and comparison between results obtained by image and flow cytometry

Three major parameters in DNA histograms that contribute to the reliability of S-phase analysis were evaluated. These parameters are (1) the extent of background in relation to the amount of S-phase cells (and the validity of its subtraction), (2) the size of the "free" S-phase range (S(free)), and (3) the sampling error of cell counting. Tests in histograms obtained from surgical biopsies by flow cytometry (FCM) showed that the background subtraction is reliable if the found S-phase fraction is higher than the fraction of background events in the histogram range of the cell population. The size of S(free) was determined in computer-generated test histograms as a function of variables such as the coefficient of variation (CV) and the DNA index (DI). To calculate the sampling error of cell counting above background and in S(free), a model was developed that was validated by experimental data. This error can serve as an indicator of the uncertainty in S-phase analysis. The poor correlation found between %S values measured by image cytometry (ICM) and FCM in surgical biopsies was assigned to high uncertainty by low cell numbers in ICM histograms. A method is proposed to estimate quantitatively the reliability of S-phase analysis that can facilitate the interpretation of results.     

Quantitative analysis of disseminated tumor cells in the bone marrow by automated fluorescence image analysis

Accurate quantification of disseminated tumor cells in hematological samples is of fundamental importance in clinical oncology. However, even highly standardized protocols allow only a rough estimation of the total analyzed cell number, as sample processing may have adverse effects on the number of cells available for analysis. The fluorescence-based microscopic scanning system (MetaCyte) detects, counts, captures, and relocates immunolabeled tumor cells in hematopoietic samples. We report on a cell-counting approach that has been implemented into the scanning system to precisely quantify the number of cells per slide. The cell-counting function, which was designed to determine the number of all nucleated (DAPI-stained) cells on the slide, allows an accurate counting of the tumor cells and the total number of cells analyzed in the given microscopic sample. The reliability of the cell-counting approach was demonstrated by the analysis of DAPI-stained images with 18-1,363 nucleated cells. A good correlation (r(2) = 0.965) between the manually and automatically gained results was observed. The counting accuracy could even be optimized after implementing a correction factor. To prove or disprove an interslide variation, routine bone marrow cytospin preparations from neuroblastoma patients were immunostained for GD2/FITC and counterstained with DAPI. Automatic cell counting of cytospin preparations from the same patients showed significant differences in the total cell number (up to 67% cell loss during preparation, with a maximum interslide difference of 4.7 x 10(5) mononuclear cells). We conclude that determination of the tumor cell content in hematopoietic samples is only reliable when it is performed together with accurate cell counting.     

Characterization of the motility of maturing rat spermatozoa by computer-aided objective measurement.

A computer-aided sperm analysis system was optimized for objective assessment of the movement characteristics of mature and immature rat spermatozoa by testing different settings. Measurements of straight line velocity of individual motile cells were validated by manual tracking with a digitizer. Better agreement between the two methods and better performance in distinguishing between mature and immature spermatozoa was obtained by reducing the tracking rate to increase the time of analysis. However, numbers of motile and immotile cells could not be determined accurately. Manual counting of videotaped images revealed no significant differences in percentage motility of spermatozoa from five epididymal regions. Caput spermatozoa were characterized by low straight-line (VSL) and averaged-path (VAP) velocities and low path straightness (STR), whereas mature cells displayed high VSL, VAP and STR. An increase in curvilinear velocity on maturation was less obvious. Spermatozoa in the proximal corpus epididymidis were heterogeneous in their acquisition of motility maturation and the uniformity of movement pattern achieved in the distal corpus and proximal cauda regions tended to decrease again in the distal cauda epididymidis. Such objective measurements of motility patterns will facilitate studies on the regulation of motility development upon sperm maturation.     

不同龄级划分方法对种群存活分析的影响——以水灾迹地油松和华山松种群生存分析为例

 生命表、存活曲线和生存分析是研究种群动态的重要工具,其关键就是科学正确地划分龄级。该文研究了水灾迹地不同龄级划分方法对油松（Pinus abulaeformis）和华山松（P. armandii）种群存活曲线和生存分析函数曲线的影响。华山松以实际年龄作为龄级划分指标时,存活曲线为Ⅱ型;地径和树高作为划分指标时,存活曲线为Ⅲ型。生存函数和累计死亡率函数也发生类似的类型变化。油松实际年龄、地径和树高作为龄级的划分指标时,存活曲线(Ⅱ型)、生存率函数和累计死亡率函数类型一致,均为直线型。死亡率函数和危险率函数在不同树种和不同龄级划分方法间不存在明显差异。因此,华山松地径和树高作为龄级划分的代用指标不可行,而油松可行。其主要原因是华山松树高和地径与年龄的关系为指数函数关系,而油松则为直线函数关系。在此基础上把华山松地径和树高取自然对数后重新划分龄级,则存活曲线关系在地径、树高和实际年龄之间不存在差异,均为Ⅱ型。从而得出结论,地径、树高和年龄之间线性关系与否是地径和树高作为实际年龄代用指标可行性和准确性的关键。因此,在植物种群统计研究中,大小作为龄级划分代用指标要慎用。在未来研究中,种群个体年龄和大小关系及其影响因素的研究对植物种群数量动态分析和种群统计学的发展具有重要意义。     

A simplified method for the determination of nitric oxide in biological solutions.

A new simplified procedure for determination of nitric oxide (NO) in biological solutions is described utilizing a new reducing system of nitric oxide prior to chemiluminescence. Advantages of the new method makes heating of the reducing solution unnecessary and avoids cooling and condensation of generated vapors. Only traces of acid with a high boiling point are used. The method permits analysis of small sample volumes (200 microL). The basal production of nitric oxide by freshly harvested endothelial cells ranged from 100 to 880 picomoles.     

Personal computer software for the stereologic evaluation of sympathetic ganglia

Software was developed on a personal computer for a quantitative study of some ultrastructural aspects of sympathetic ganglia (the neuronal cell body, the surrounding satellite cell layer and the nearby capillaries). A low-cost digitizer, originally designed for teaching, semiprofessional graphics applications and games, was utilized to sample areas and distances on electron micrographs. The processing program derives stereologic parameters from the crude data stored in the memory. Further algorithms then assess the mean thickness and the volume densities of the satellite cell layer, endothelial basal lamina and endothelial layer.     

In vitro comparative analysis of cryopreservation of undifferentiated mesenchymal cells derived from human periodontal ligament

Cryopreservation aims to cease all biological functions of living tissues in a reversible and controlled manner, i.e., to permit the recovery of cells by maintaining a high degree of their viability and functional integrity. The objective of this study was to evaluate in vitro the influence of cryopreservation on undifferentiated mesenchymal cells derived from the periodontal ligament of human third molars. Mesenchymal cells were isolated from six healthy teeth and cultured in α-MEM medium supplemented with antibiotics and 15% FBS in a humid atmosphere with 5% CO(2) at 37°C. The cells isolated from each tooth were divided into two groups: group I (fresh, non-cryopreserved cells) was immediately cultured, and group II was submitted to cryopreservation for 30 days. The rates of cell adhesion and proliferation were analyzed in the two groups by counting the cells adhered to the wells at 24, 48 and 72 h after plating. The number of cells per well was obtained by counting viable cells in a hemocytometer using the Trypan blue exclusion method. Differences between groups at each time point were evaluated by the Wilcoxon test. The Friedman test was used to determine differences between time points and, if detected, the Wilcoxon test with Bonferroni correction was applied. The results showed no significant difference in the in vitro growth capacity of undifferentiated mesenchymal cells between the two groups. In conclusion, cryopreservation for 30 days had no influence on periodontal ligament mesenchymal cells.     

Quantitative analysis of SILAC data sets using spectral counting

We report a new quantitative proteomics approach that combines the best aspects of stable isotope labeling of amino acids in cell culture (SILAC) labeling and spectral counting. The SILAC peptide count ratio analysis (SPeCtRA, http://proteomics.mcw.edu/visualize ) method relies on MS² spectra rather than ion chromatograms for quantitation and therefore does not require the use of high mass accuracy mass spectrometers. The inclusion of a stable isotope label allows the samples to be combined before sample preparation and analysis, thus avoiding many of the sources of variability that can plague spectral counting. To validate the SPeCtRA method, we have analyzed samples constructed with known ratios of protein abundance. Finally, we used SPeCtRA to compare endothelial cell protein abundances between high (20 mM) and low (11 mM) glucose culture conditions. Our results demonstrate that SPeCtRA is a protein quantification technique that is accurate and sensitive as well as easy to automate and apply to high‐throughput analysis of complex biological samples.     

A carbon dioxide collection accessory for the rapid combustion apparatus for preparation of biological samples for liquid scintillation analysis

A carbon dioxide collection accessory is described for the previously reported combustion system for preparation of biological samples for liquid scintillation counting. A sample can be burned and collected every 3 min. Sample size is limited by the capacity of the solvent to absorb carbon dioxide without precipitation. The system can be used for collecting water as well as carbon dioxide, for double isotope counting. The method has a collection recovery of 97%, is calibrated by internal standards, and shows a coefficient of variation of 1.1%.     

A simplified Boyden chamber assay for neutrophil chemotaxis based on quantitation of myeloperoxidase

Cell locomotion and chemotaxis are usually assayed by the Boyden chamber technique, in which the response is measured by microscopical counting of the cells migrated into a micropore filter. We report a simplified Boyden chamber method which utilizes myeloperoxidase (MPO) specific to neutrophilic and monocytic leukocytes. The chamber is incubated for a period long enough for the neutrophils to migrate through the first of two superimposed filters. The cells entering the second filter are then lysed and the released MPO activity is quantitated. Random migration, chemokinesis, and chemotaxis measurements of neutrophils were compared by the enzymatic and the conventional cell count methods. There was good agreement between the two methods (0.84 less than r less than 0.98). The intraassay precision of the enzymatic and the cell count methods was equal; the coefficients of variation were 14 and 15%, respectively. The enzymatic method provides a more objective, reliable, and rapid modification of the Boyden chamber assay for analysis of neutrophil chemotaxis.     

Lipidomics: an analysis of cellular lipids by ESI-MS

Recognition of the importance of lipid signaling in cellular function has led to rapid progress in the technology of lipid analysis. Measurements of lipid species changes are central to defining the networks of cell signaling (e.g., receptor activation by hormones or drugs) and lipids are involved in many biochemical and pathological processes. During the last several years our laboratory has focused on developing efficient methods for extraction of glycerophospholipids from biological systems and their detection and identification by mass spectrometry. We analyze phospholipid changes in mammalian cells as a result of a defined ligand stimulation strategy that supports the research questions of the consortium. The improvement of mass spectrometry techniques for phospholipid analysis combined with sophisticated computational methods developed in our group has facilitated simultaneous analysis of hundreds of phospholipid species in mammalian cells. This information is presented as Lipid Arrays (or more precisely as virtual arrays) and allows identification of temporal changes in membrane phospholipid species between two contrasting biological conditions (e.g., unstimulated basal vs. stimulated or as a contrast between normal and disease stages). Using the lipidomics approach, we are able to identify approximately 450 phospholipid species from total membrane extracts and qualitatively measure pattern response changes initiated by cell surface receptors. As such, this approach facilitates the elucidation of the metabolic changes induced by a perturbation in the cell and recognition of patterns of signaling.     

Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ)

We assess the reliability of isobaric-tags for relative and absolute quantitation (iTRAQ), based on different types of replicate analyses taking into account technical, experimental, and biological variations. In total, 10 iTRAQ experiments were analyzed across three domains of life involving Saccharomyces cerevisiae KAY446, Sulfolobus solfataricus P2, and Synechocystis sp. PCC 6803. The coverage of protein expression of iTRAQ analysis increases as the variation tolerance increases. In brief, a cutoff point at +/-50% variation (+/-0.50) would yield 88% coverage in quantification based on an analysis of biological replicates. Technical replicate analysis produces a higher coverage level of 95% at a lower cutoff point of +/-30% variation. Experimental or iTRAQ variations exhibit similar behavior as biological variations, which suggest that most of the measurable deviations come from biological variations. These findings underline the importance of replicate analysis as a validation tool and benchmarking technique in protein expression analysis.