An automated device for the preparation of complex reagent mixtures

A microcomputer-controlled device was built that automatically prepares small volumes of mixtures of up to eight reagents. The operation of the system is fast, flexible, and reliable, thus making possible the routine use of experimental protocols that require large numbers of small volume reagent samples, each having a different composition. In particular, the software we developed for this device handles the preparation of three-antibody staining solutions to be used in triple labeling immunofluorescent flow cytometry experiments that involve only two fluorochromes. In this role, the device is known as an “Immunofluorescence Tomograph.”     

An automated method for DNA preparation from thousands of YAC clones.

We describe an automated method for the preparation of yeast genomic DNA capable of preparing thousands of DNAs in parallel from a YAC library. Briefly, the protocol involves four steps: (1) Yeast clones are grown in the wells of 96-well microtiter plates with filter (rather than plastic) well-bottoms, which are embedded in solid growth media; (2) These yeast cultures are resuspended and their concentrations determined by optical density measurement; (3) Equal numbers of cells from each well are embedded in low-melting temperature agarose blocks in fresh 96-well plates, again with filter bottoms; and (4) DNA is prepared in the agarose blocks by a protocol similar to that used for preparing DNA for pulsed-field gels, with the reagents being dialyzed through the (filter) bottoms of the microtiter plate. The DNA produced by this method is suitable for pulsed-field gel electrophoresis, for restriction enzyme digestion, and for the polymerase chain reaction (PCR). Using this protocol, we produced 3000 YAC strain DNAs in three weeks. This automated procedure should be extremely useful in many genomic mapping projects.     

Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures

Characterization of the chemical components of complex mixtures in solution is important in many areas of biochemistry and chemical biology, including metabolomics. The use of 2D NMR total correlation spectroscopy (TOCSY) experiments has proven very useful for the identification of known metabolites as well as for the characterization of metabolites that are unknown by taking advantage of the good resolution and high sensitivity of this homonuclear experiment. Due to the complexity of the resulting spectra, automation is critical to facilitate and speed-up their analysis and enable high-throughput applications. To better meet these emerging needs, an automated spin-system identification algorithm of TOCSY spectra is introduced that represents the cross-peaks and their connectivities as a mathematical graph, for which all subgraphs are determined that are maximal cliques. Each maximal clique can be assigned to an individual spin system thereby providing a robust deconvolution of the original spectrum for the easy extraction of critical spin system information. The approach is demonstrated for a complex metabolite mixture consisting of 20 compounds and for E. coli cell lysate.     

An alcohol-soluble Schiff's reagent: a histochemical application of the complex between Schiff's reagent and phosphotungstic acid.

A schedule for staining partially hydrated PAS-positive structures using non-aqueous solutions has been devised. Tissues are dewaxed, taken down to 70% alcohol, oxidised for 10 min in a 1% w/v alcoholic solution of periodic acid, treated with an alcoholic solution of phosphotungstic acid-Schiff reagent complex (PTA-Schiff reagent) for 25 min, washed in alcohol, cleared in xylene and mounted in a synthetic medium. The PTA-Schiff reagent complex prepared from de Tomasi Schiff reagent by precipitation with PTA may be stored in the deep freeze for many months and dissolved freshly in alcohol for use. The PTA-Schiff reagent used as above allows staining of highly water soluble materials such as dextran. From blocking and digestion studies the mode of action seems similar to de Tomasi Schiff reagent. The partial hydration of the tissues prior to reaction was found to be essential for effective staining.     

Techniques in the preparation of a monolayer of gynecologic cells for automated cytology. An overview

The computer-assisted microscope demands rigid specifications for specimen preparation. This paper addresses the variety of techniques developed by researchers attempting to automatically screen uterine cervical specimens. These same techniques could also be utilized for specimens from other body sites. In contrast to the easily prepared routine Papanicolaou smear, these techniques can be broken down into various steps as follows: transport media, cellular disaggregation, cell number estimation, cell separation and specimen enrichment, cellular adhesion to glass slide and cell transfer onto the slide. Variations on the theme are contrasted among specimen preparation methods utilized by prominent research groups. The plea for a simpler preparation method or, hopefully, utilization of the routine Papanicolaou smear for computer-assisted microscopy is made.     

A new reagent for the preparation of glycoconjugates

The thioglycoside derivative 2-carbazoylethyl 1-thio-beta-D-galactopyranoside hydrochloride was synthesized. Conversion of the carbazoyl group into the reactive azidocarbonyl function leads to a well suited reagent for the preparation of glycoconjugates via amidation of proteins or synthetic carriers in aqueous media.     

The use of enzyme mixtures for complex biosyntheses

Biocatalysis is currently employed to produce known substances more economically and for the synthesis of new compounds. Increased production or novel product synthesis can be achieved through the use of mutant organisms, tailored enzymes or novel combinations of enzymes in reactors. These complex biosyntheses, once only in the realm of the biopharmaceutical industry, have now been embraced by the food and textile industries and are finding geochemical and environmental applications. New uses are dictating novel methods of manufacture that utilize knowledge of systems level biology. Increased understanding of the functional interaction of proteins and protein-protein networks is also altering the practice of in vitro biosynthesis.     

Plug flow cytometry: An automated coupling device for rapid sequential flow cytometric sample analysis.

BACKGROUND: The tools for high throughput flow cytometry have been limited in part because of the requirement that the samples must flow under pressure. We describe a simple system for sampling repetitively from an open vessel. METHODS: Under computer control, the sample is loaded into a sample loop in a reciprocating eight-way valve by the action of a syringe. When the valve position is switched, the plug of sample in the sample loop is transported to the flow cytometer by a pressure-driven fluid line. By coupling the plug-forming capability to a second multi-port valve, samples can be delivered sequentially from separate vessels. RESULTS: The valve is able to deliver samples at rates ranging up to about 9 samples per minute. Each plug of sample has uniform delivery characteristics with a reproducible coefficient of variation (CV). Even at the highest sampling rate, carryover between samples is limited. CONCLUSIONS: Plug-flow flow cytometry has the potential to automate the delivery of small samples from unpressurized sources at rates compatible with many screening and assay applications.     

An alcohol-soluble Schiff's reagent: A histochemical application of the complex between Schiff's reagent and phosphotungstic acid

Summary A schedule for staining partially hydrated PAS-positive structures using non-aqueous solutions has been devised. Tissues are dewaxed, taken down to 70% alcohol, oxidised for 10 min in a 1% w/v alcoholic solution of periodic acid, treated with an alcoholic solution of phosphotungstic acid-Schiff reagent complex (PTA-Schiff reagent) for 25 min, washed in alcohol, cleared in xylene and mounted in a synthetic medium. The PTA-Schiff reagent complex prepared from de Tomasi Schiff reagent by precipitation with PTA may be stored in the deep freeze for many months and dissolved freshly in alcohol for use. The PTA-Schiff reagent sued as above allows staining of highly water soluble materials such as dextran. From blocking and digestion studies the mode of action seems similar to de Tomasi Schiff reagent. The partial hydration of the tissues prior to reaction was found to be essential for effective staining.     

Microinjection of Xenopus oocytes: An automated device for volume control in the nanoliter range

Injection of Xenopus oocytes is a technique widely used in studies of gene expression for both qualitative and quantitative analysis of DNA and mRNA. Published methods for controlling and assessing volumes transferred into oocytes are tedious, time consuming, and require considerable expertise. We describe the construction of an apparatus which automatically controls nanoliter injection volumes. For injection volumes from 50 to 10 nl, the mean volume injected into 10 oocytes was within 10% of the expected value and often better, and even for 1-nl injections was within 20% of the expected value. The precision of volume dispensing into individual oocytes decreased with decreasing volume; the standard deviation was about 10–15% of the mean for volumes in the 30- to 50-nl range and about 30–40% of the mean for volumes in the 1- to 2-nl range.     

The preparation of cervical scrape material for automated cytology using gallocyanin chrome-alum stain.

A method is described for preparing cervical scrape specimens for automated analysis on the Cerviscan prescreening system. In order to reduce the cellular clumping found in cervical scrape material, cells are collected in suspension, syringed to disaggregate the cell clumps, and then pipetted onto a glass to give a monolayer of cells. The cells are then stained with gallocyanin chrome-alum to give the required quantitation of nucleic acid content, using a rapid staining procedure. Experimental results are given which show that specimens prepared by this method are more suitable for automated analysis than the conventional Papanicolaou stained preparation.     

Developments in mass spectrometry for the analysis of complex protein mixtures.

State-of-the-art proteomics workflows involve multiple interdependent steps: sample preparation, protein-peptide separation, mass spectrometry and data analysis. While improvements in any of these steps can increase the depth and breadth of analysis, advances in mass spectrometry have catalysed many of the most important developments. We discuss common classes of mass analysers and how these analysers are put together to produce some of the most popular mass spectrometry platforms. The capabilities of these platforms determine how they can be used in a variety of common proteomic strategies and, in turn, what types of biological questions can be addressed. Moving forward, powerful new hybrid mass spectrometers and application of emerging types of tandem mass spectrometry promise that our ability to analyse complex mixtures of proteins will continue to advance.     

Folin试剂制备中的一个改进

本文介绍了Folin试剂制备中的一个改进,使制备过程得到简化.     

An automated analysis of highly complex flow cytometry-based proteomic data

The combination of color-coded microspheres as carriers and flow cytometry as a detection platform provides new opportunities for multiplexed measurement of biomolecules. Here, we developed a software tool capable of automated gating of color-coded microspheres, automatic extraction of statistics from all subsets and validation, normalization, and cross-sample analysis. The approach presented in this article enabled us to harness the power of high-content cellular proteomics. In size exclusion chromatography-resolved microsphere-based affinity proteomics (Size-MAP), antibody-coupled microspheres are used to measure biotinylated proteins that have been separated by size exclusion chromatography. The captured proteins are labeled with streptavidin phycoerythrin and detected by multicolor flow cytometry. When the results from multiple size exclusion chromatography fractions are combined, binding is detected as discrete reactivity peaks (entities). The information obtained might be approximated to a multiplexed western blot. We used a microsphere set with >1,000 subsets, presenting an approach to extract biologically relevant information. The R-project environment was used to sequentially recognize subsets in two-dimensional space and gate them. The aim was to extract the median streptavidin phycoerythrin fluorescence intensity for all 1,000+ microsphere subsets from a series of 96 measured samples. The resulting text files were subjected to algorithms that identified entities across the 24 fractions. Thus, the original 24 data points for each antibody were compressed to 1-4 integrated values representing the areas of individual antibody reactivity peaks. Finally, we provide experimental data on cellular protein changes induced by treatment of leukemia cells with imatinib mesylate. The approach presented here exemplifies how large-scale flow cytometry data analysis can be efficiently processed to employ flow cytometry as a high-content proteomics method.     

An automated, pressure-driven sampling device for harvesting from liquid cultures for genomic and biochemical analyses

Here we describe an automated, pressure-driven, sampling device for harvesting 10 to 30 ml samples, in replicate, with intervals as short as 10 s. Correlation between biological replicate time courses measured by microarrays was extremely high. The sampler enables sampling at intervals within the range of many important biological processes.