A graphical user interface for quantitative imaging and analysis of electrophoretic gels and autoradiograms.

DNA/GUI (DNA Graphical User Interface) is an interactive software system for rapid and efficient analysis of images of the types used in genome mapping, such as autoradiograms and electrophoretic gels. Images are digitized using a commercially available charge-coupled-device (CCD) camera system and analyzed on a graphics workstation using a menu-driven user interface. DNA/GUI features automatic lane and band detection, simultaneous display of multiple images and a unique spatial-normalization algorithm. Images and their associated data are archived and easily available for later recall. Preliminary results indicate that DNA/GUI is a useful tool in the analysis and comparison of images used in a variety of applications such as genetic-linkage analysis and DNA restriction mapping. The interactive display software is based on the X Window System and is therefore readily portable to a variety of graphics workstations.     

A laser densitometer for selective spot analysis on dot blots and two-dimensional gel autoradiograms

We describe an inexpensive densitometer, employing a small HeNe laser and an IBM-compatible personal computer that performs accurate measurements of selected spots on two-dimensional gel autoradiograms or chromatograms with an accuracy and a sensitivity equal or superior to those of many commercial instruments. Our open-table design allows the operator to visually monitor the scanning process in room lighting, and provides great flexibility in both the size and the nature of items to be scanned. The instrument has two moving parts (a prism and a small motor). A commercially available software package (ASYST) acquires digital data, graphs the data on the TV monitor, converts the data to optical density or to radioactive incorporation (cpm), subtracts background, integrates peak areas, and stores data on disk. The total time for these operations is 20-30 s per spot. The instrument has a dynamic range of 0.25 to 3.0 OD units and can measure a 10,000-fold range of 14C or 35S isotope concentrations on autoradiograms. The complete device can be assembled with a hobbyist's knowledge of electronics, moderate programming abilities (no machine language required), and a cost of less than $3000, not including the IBM PC.     

Spatial normalization of one-dimensional electrophoretic gel images

A strategy for using processed, digitized images of one-dimensional electrophoretic gels to facilitate the analysis of large sets of overlapping clones is described. The images are acquired from fluorescently stained gels or from transilluminated gel photographs using a cooled, solid-state charge-coupled device camera. By employing sets of bands in the size-standard lanes as reference points, all the gel images are spatially normalized to a common reference template. After normalization, lane images from different gels can be compared as though the gels had been electrophoresed under identical, uniform-field conditions. Applications of this procedure to the analysis of a large set of overlapping lambda clones from chromosome VII of Saccharomyces cerevisiae and to the estimation of fragment sizes are illustrated.     

Quantitative evaluation of gel electrophoretic patterns by videodensitometry

Videodensitometry based on television technique has been shown to be suitable for recording gel electrophoretic patterns. Its speed of operation is about 60 times as fast as that of conventional densitometers, whereas the patterns recorded are practically the same.     

Caldesmon: anomalous electrophoretic behaviour in polyacrylamide gel

In SDS gels caldesmon (Mr = 140 kDa) and myosin light chain kinase (Mr = 130 kDa) migrate as a closely separated doublet. When glycerol is added to the gel caldesmon is characterized by an anomalous migration. In fact under this latter condition, the distance between caldesmon and myosin light chain kinase is enhanced by two-three times. The nature of putative caldesmon and myosin light chain kinase was confirmed by physicochemical, enzymatic and immunological methods.     

A pitfall in the computer-aided quantitation of autoradiograms

Computer-aided quantitation of autoradiograms is now available as a result of recent developments in optical scanners and microcomputers. Data expressed as optical density values, however, are based on the unverified assumption that optical density and radioactivity density are linearly correlated. This article demonstrates the need to construct a calibration curve which should be used to calculate radioactivity density values more precisely.     

A computer program for displaying two-dimensional gel electrophoresis data

A computer program is described which facilitates comparison between the pattern of spots seen on different two-dimensional polyacrylamide electrophoresis gels. Essentially, the position of each spot is replotted on a graph by the computer using its molecular weight and isoelectric point as coordinates. An intensity factor is also assigned to each point by the operator which will determine the size and shape of the final plotted spot on the computer drawn figure. The resulting plot makes it more feasible to compare patterns of spots between independently run two-dimensional electrophoresis gels.     

Lymphokines which influence electrophoretic mobility of macrophages.

Supernatants of blood lymphocytes from immunized guinea pigs after incubation with purified protein derivative (PPD) were fractionated on Sephadex G-75. The fractions were tested for activity to change the electrophoretic mobility of macrophages. Dependent on incubation time, three different regions of activity with an average molecular weight of 13 000, 40 000 and more than 100 000 were estimated.     

Two-dimensional gel electrophoretic method for mapping DNA replicons.

We describe in detail a method which allows determination of the directions of replication fork movement through segments of DNA for which cloned probes are available. The method uses two-dimensional neutral-alkaline agarose gel electrophoresis followed by hybridization with short probe sequences. The nascent strands of replicating molecules form an arc separated from parental and nonreplicating strands. The closer a probe is to its replication origin or to the origin-proximal end of its restriction fragment, the shorter the nascent strands that are detected by the probe. The use of multiple probes allows determination of directions of replication fork movement, as well as locations of origins and termini. In this study, we used simian virus 40 as a model to demonstrate the feasibility of the method, and we discuss its applicability to other systems.     

A neutral pH acrylamide gel electrophoretic system for histones and other basic proteins.

A method has been devised whereby measurement of the acid-labile sulfide content of spinach subchloroplast particles is free of interference resulting from the presence of Triton X-100. Quantitative extraction into an organic solvent allows accurate detection of micromolar concentrations of sulfide.     

autoinfer1.0: a computer program to infer biogeographical events automatically

autoinfer is a computer program for biogeographical inference based on nested clade analysis. To reduce the obscurity caused by manual inference, we defined geographically concordant clades and intermediate geographical areas between two clades. The program will perform most of the inferences automatically with a minimum of input from the user. We believe that autoinfer will save much time for the user compared with using the inference key by hand and, furthermore, will reduce the errors of inference resulting from different criteria in deduction.     

Purification of the photoaffinity-labeled glucagon receptor by gel electrophoretic methods

Rat liver plasma membrane glucagon receptor has been purified with a yield of 0.01% to an estimated homogeneity of 32-60%, using a 2-stage electrophoretic procedure. SDS-solubilized membrane proteins labeled by the photoaffinity-agent, Ne-4-azidophenylamidinoglucagon (APA-glucagon), were separated by polyacrylamide gel electrophoresis in SDS-containing buffers. Gel slices corresponding to the molecular weight of the receptor were excised, electrophoretically extracted and concentrated. The concentrate was subjected to isoelectric focusing on Sephadex to yield a purified product in which the photoaffinity-labeled receptor, with a molecular weight of 56K and a pI' of 5.9, is the sole major component.     

Two-dimensional fluorescence difference gel electrophoretic analysis of Streptococcus mutans biofilms

Compared with traditional two-dimensional (2D) proteome analysis of Streptococcus mutans grown as a biofilm from a planktonic culture at steady state (Rathsam et al., Microbiol. 2005, 151, 1823-1837), the use of 2D fluorescence difference gel electrophoresis (DIGE) led to a 3-fold increase in the number of identified protein spots that were significantly altered in their level of expression (P < 0.050). Of the 73 identified proteins, only nine were up-regulated in biofilm grown cells. The results supported the previously surmised hypothesis that general metabolic functions were down-regulated in response to a reduction in growth rate in mature S. mutans biofilms. Up-regulation of competence proteins without any concomitant increase in stress-responsive proteins was confirmed, while the levels of glucosyltransferase C (GtfC), involved in glucan formation, O-acetylserine sulfhyrylase (cysteine synthetase A; CsyK), implicated in the formation of [Fe-S] clusters, and a hypothetical protein encoded by the open reading frame, SMu0188, were also up-regulated.     

Automated band mapping in electrophoretic gel images using background information

Some popular methods for polymorphism and mutation discovery involve ascertainment of novel bands by the examination of electrophoretic gel images. Although existing strategies for mapping bands work well for specific applications, such as DNA sequencing, these strategies are not well suited for novel band detection. Here, we describe a general strategy for band mapping that uses background banding patterns to facilitate lane calling and size calibration. We have implemented this strategy in GelBuddy, a user-friendly Java-based program for PC and Macintosh computers, which includes several utilities to assist discovery of mutations and polymorphisms. We demonstrate the use of GelBuddy in applications based on single-base mismatch cleavage of heteroduplexed PCR products. Use of software designed to facilitate novel band detection can significantly shorten the time needed for image analysis and data entry in a high-throughput setting. Furthermore, the interactive strategy implemented in GelBuddy has been successfully applied to DNA fingerprinting applications, such as AFLP. GelBuddy promises to make electrophoretic gel analysis a viable alternative to DNA resequencing for discovery of mutations and polymorphisms.