Comparison of digital focus criteria for a TV microscope system

Existing focusing methods, such as standard deviation of gray values, gradients, information content of the image and the lateral inhibition function, were compared, and a new combination criterion was developed. This combined method consists of using the standard deviation of the image for coarse focusing followed by a modified form of the lateral inhibition for the fine focus. The lateral inhibitor model of the eye is a recursive filter that can be simplified to a nonrecursive filtering algorithm, as postulated by Rechenberg. The reported focus method operates over a focusing range (z-axis) of +/- 300 micron and is accurate within +/- 0.1 micron in the transmission, dark-field, and phase contrast microscope.     

Rapid DNA fingerprinting of pathogens by flow cytometry

BACKGROUND: A new method for rapid discrimination among bacterial strains based on DNA fragment sizing by flow cytometry is presented. This revolutionary approach combines the reproducibility and reliability of restriction fragment length polymorphism (RFLP) analysis with the speed and sensitivity of flow cytometry. METHODS: Bacterial genomic DNA was isolated and digested with a rare-cutting restriction endonuclease. The resulting fragments were stained stoichiometrically with PicoGreen dye and introduced into an ultrasensitive flow cytometer. A histogram of burst sizes from the restriction fragments (linearly related to fragment length in base pairs) resulted in a DNA fingerprint that was used to distinguish among different bacterial strains. RESULTS: Five different strains of gram-negative Escherichia coli and six different strains of gram-positive Staphylococcus aureus were distinguished by analyzing their restriction fragments with DNA fragment sizing by flow cytometry. Fragment distribution analyses of extracted DNA were approximately 100 times faster and approximately 200,000 times more sensitive than pulsed-field gel electrophoresis (PFGE). When sample preparation time is included, the total DNA fragment analysis time was approximately 8 h by flow cytometry and approximately 24 h by PFGE. CONCLUSIONS: DNA fragment sizing by flow cytometry is a fast and reliable technique that can be applied to the discrimination among species and strains of human pathogens. Unlike some polymerase chain reaction (PCR)-based methods, sequence information about the bacterial strains is not required, allowing the detection of unknown, newly emerged, or unanticipated strains.     

Estimation of sampling errors in a high-resolution TV microscope image-processing system

The basic postulate of this paper is that the commonly accepted sampling density of 2-4 pixels/micron in a high-resolution TV microscope system is too low to digitize exactly and analyze the complex cellular detail found in stained cell images. Depending on the specific microscope system, the required sampling density is much higher, lying between 15 and 30 pixels/micron. This sampling density is derived from the aliasing error, the resolution loss, and computational limitations. The mathematical and optical methods and equipment used to obtain these results are described in detail.     

Measurement of DNA with an automatic spectrophotometer

A method that uses an automated spectrophotometer to read microtiter plates in a modification of the diphenylamine method of DNA determination in tissue extracts, is presented. The micromethod saves technician time, and reduces exposure to acetic acid fumes. The reproducibility of the method is superior to the manual method. Fewer pipetting steps are required, and the method is suited to large batches of samples.     

Analysis of DNA distributions from flow cytometry. Validation of an automatic procedure against simulated data

A recently proposed automatic procedure for analyzing DNA distribution from flow cytometric data is extensively tested against simulated data. After a discussion of the procedure itself and of the simulation program, the results obtained are reported. They are evidence of the reliability of the procedure in extracting the proper underlying DNA distribution from sets of data obtained under various simulated instances. The different sources of error are then analyzed, along with their quantitative effects on the fit of the fluorescence histogram.     

DNA analysis of stimulated lymphocytes by automatic sampling for flow cytometry

A microsample delivery system (MSDS) was tested for automatic flow cytometry (FCM) analysis of DNA synthesis in stimulated human peripheral blood lymphocytes (PBL) cultivated in wells of microtiter plates. After incubation, either for 1-3 days with phytohemagglutinin, concanavalin A, and pokeweed mitogen, or for 7 days with allogenic PBL, the cells, while in the wells, were washed in hypotonic Tris buffer and stained with ethidium bromide-RNAse solution. The results obtained from quintuplicate replicated wells, each of the five containing the same control or stimulated cultures, were reproducible in terms of the number of nuclei counted in each histogram of control, mitogen-stimulated PBL, and mixed lymphocyte cultures (MLC). Using a computer program that superimposes histograms and calculates their differences on the scale of fluorescence intensity, it was possible to quantify the intensity of the response to the mitogenic stimuli. This approach to the study of lymphocyte proliferation offers not only a simpler and faster analysis of DNA synthesis than the method of 3H-thymidine incorporation, but it also allows for the analysis of other FCM parameters, such as forward and 90 degrees light scatter and double fluorescence labelling of PBL nuclei.     

Exfoliative-cytologic diagnosis of basal-cell carcinoma, with the use of DNA image cytometry as a diagnostic aid

Eighty-four skin lesions clinically suspected of being basal-cell carcinomas were investigated by exfoliative cytology. Specific criteria were found for the cytologic diagnosis of basal-cell carcinoma. All 37 cases of basal-cell carcinoma were correctly classified cytologically and could be differentiated from the 8 cases of squamous-cell carcinoma. There were no false-positive or false-negative diagnoses. Insufficient cellular material was obtained in 17% of the cases. The technique for collecting exfoliated epidermal cells with a new swab is described. DNA image cytometry was used as a diagnostic aid in doubtful cases. DNA image cytometry showed that 83% of the basal-cell carcinomas had an aneuploid nuclear DNA content.     

Cell motility measurements with an automated microscope system

The motility of 3T3 cells has been studied using a newly developed automated microscope system which is capable of recognizing live unstained cells growing in tissue culture. A large number of individual cells can be rapidly identified and characterized and their precise positions recorded. All cells can be revisited automatically every few minutes, and the new cell positions can be determined. Quantitative data from up to 1 000 cells can then be obtained, and cell movement parameters like cell speed, distance travelled, direction of movement, etc., can be measured for individual cells and for the whole cell population. In addition, for any number of chosen cells, high-resolution digitized images can be taken for further morphological studies, including acquisition of images of individual cells.     

Visualization of hemiknot DNA structure with an atomic force microscope

The hemiknot, a novel type of DNA structure in which a loop is stabilized by threading one end of the duplex through another, has been studied in this paper. The hemiknot was obtained by reassociation of a DNA fragment with (CA/TG)_n inserts of different lengths. Slow and fast migrating products were purified by gel electrophoresis and imaged by atomic force microscopy (AFM) using the aminopropylsilatrane–mica technique for sample preparation. Slow migrating product was characterized by the formation of small blobs for the short insert (60 bp) and clear loops and other morphologies for the long insert (188 bp). These structural features were found in almost 100% of the molecules of the slow migrating sample and were not present in the control sample. Measurements showed that the location of the blobs coincided with the positions of the inserts. The sample with the 188 bp insert in the 573 bp fragment had large structural irregularities. The majority of the molecules (77%) had asymmetrically located loops. The location of the loop in the molecules correlated well with the position of the insert in the fragment. The measured sizes of the loops were in agreement with the insert size. Altogether, these data support the hypothesis for hemiknot formation suggested earlier. In addition to looped structures, other morphologies of the hemiknot were identified in AFM images. Possible models for hemiknot formation and structure are discussed.     

Rapid sizing of individual fluorescently stained DNA fragments by flow cytometry.

Large, fluorescently stained restriction fragments of lambda phage DNA are sized by passing individual fragments through a focused continuous wave laser beam in an ultrasensitive flow cytometer at a rate of 60 fragments per second. The size of the fluorescence burst emitted by each stained DNA fragment, as it passes through the laser beam, is measured in one millisecond. One hundred sixty four seconds of fluorescence burst data allow linear sizing of DNA with an accuracy of better than two percent over a range of 10 to 50 kbp. This corresponds to analyzing less than 1 pg of DNA. Sizing of DNA fragments by this approach is much faster, requires much less DNA, and can potentially analyze large fragments with better resolution and accuracy than with gel-based electrophoresis.     

Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

Background

To overcome the problem of increasing drug resistance, traditional medicines are an important source for potential new anti-malarials. Caesalpinia pluviosa, commonly named "sibipiruna", originates from Brazil and possess multiple therapeutic properties, including anti-malarial activity.

Methods

Crude extract (CE) was obtained from stem bark by purification using different solvents, resulting in seven fractions. An MTT assay was performed to evaluate cytotoxicity in MCF-7 cells. The CE and its fractions were tested in vitro against chloroquine-sensitive (3D7) and -resistant (S20) strains of Plasmodium falciparum and in vivo in Plasmodium chabaudi-infected mice. In vitro interaction with artesunate and the active C. pluviosa fractions was assessed, and mass spectrometry analyses were conducted.

Results

At non-toxic concentrations, the 100% ethanolic (F4) and 50% methanolic (F5) fractions possessed significant anti-malarial activity against both 3D7 and S20 strains. Drug interaction assays with artesunate showed a synergistic interaction with the F4. Four days of treatment with this fraction significantly inhibited parasitaemia in mice in a dose-dependent manner. Mass spectrometry analyses revealed the presence of an ion corresponding to m/z 303.0450, suggesting the presence of quercetin. However, a second set of analyses, with a quercetin standard, showed distinct ions of m/z 137 and 153.

Conclusions

The findings show that the F4 fraction of C. pluviosa exhibits anti-malarial activity in vitro at non-toxic concentrations, which was potentiated in the presence of artesunate. Moreover, this anti-malarial activity was also sustained in vivo after treatment of infected mice. Finally, mass spectrometry analyses suggest that a new compound, most likely an isomer of quercetin, is responsible for the anti-malarial activity of the F4.     

Visualization of interaction between ribosome-inactivating proteins and supercoiled DNA with an atomic force microscope

The interaction between ribosome-inactivating proteins (RIPs) and supercoiled DNA was observed with an atomic force microscope (AFM). It was found that RIPs can bind to both supercoiled DNA and the unwound double stranded loop region in supercoiled DNA. The RIPs hound to the supercoils can induce the conformational change of supercoiled DNA. Furthermore, the supercoiled DNA was relaxed and cleaved into nick or linear form by RIPs. It indicated that RIP seemed to be a supercoil-dependent DNA binding protein and exhibited the activity of su-percoil-dependent DNA endonuclease.     

DNA methylation with a sting: an active DNA methylation system in the honeybee

The existence of DNA methylation in insects has been a controversial subject over a long period of time. The recently completed genome sequence of the honeybee Apis mellifera has revealed the first insect with a full complement of DNA methyltransferases. A parallel study demonstrated that these enzymes are catalytically active and that Apis genes can be methylated in specific patterns. These findings establish bees as a model to analyze the function of DNA methylation systems in invertebrate organisms and might also be important to understand evolutionary aspects of DNA methylation in higher eukaryotes.     

DNA flow cytometry on breast carcinomas: comparison of a detergent and an enzyme-detergent preparation method

In this study we have compared two different preparation methods for DNA flow cytometry on breast cancer. Tumour cell suspensions from 49 breast cancers were analysed on a Facscan flow cytometer. In seven of 49 cases, additional aneuploid peaks were found after enzyme/detergent treatment (E/D), not seen after the detergent (D) preparation. S-Phase fractions were significantly higher after D than after E/D preparation (mean values, 15 and 8%, respectively), although the correlation was high between the two methods. S-Phase fraction estimated after background correction diminished the differences between the two methods (mean values, 8 and 6%). Furthermore, the fraction of G2/M cells were generally greater with the D method. These differences can be explained by increased number of cell doublets and nuclear fragments after D compared to E/D preparation. This clearly shows that the preparation method influences the result of DNA flow cytometry on human breast cancers.