Susan R. Dowd

Difference gel electrophoresis.

Difference gel electrophoresis (DIGE) was invented to circumvent the inherent variability of 2‐DE. This variability is a natural consequence of separating thousands of proteins over a large space, such as a 15×20 cm slab of polyacrylamide gel. The originators of 2‐DE envisioned being able to compare cancerous cells and normal cells to understand what makes these cells different. Gel‐to‐gel variability made this an extremely difficult task. We reasoned that if both samples could be run on the same gel, then the inherent variability would be obviated. Thus, we created matched sets of fluorescent dyes that allows one to compare two or three protein samples on a single gel. In the 12 years since the description of DIGE first appeared in Electrophoresis, this founding paper has been cited over 660 times. This review highlights some of the improvements and applications of DIGE. We hope these examples are illustrative of what has been done and where the field is headed.

Drosophila ventral furrow morphogenesis: a proteomic analysis.

Ventral furrow formation is a key morphogenetic event during Drosophila gastrulation that leads to the internalization of mesodermal precursors. While genetic analysis has revealed the genes involved in the specification of ventral furrow cells, few of the structural proteins that act as mediators of ventral cell behavior have been identified. A comparative proteomics approach employing difference gel electrophoresis was used to identify more than fifty proteins with altered abundance levels or isoform changes in ventralized versus lateralized embryos. Curiously, the majority of protein differences between these embryos appeared well before gastrulation, only a few protein changes coincided with gastrulation, suggesting that the ventral cells are primed for cell shape change. Three proteasome subunits were found to differ between ventralized and lateralized embryos. RNAi knockdown of these proteasome subunits and time-dependent difference-proteins caused ventral furrow defects, validating the role of these proteins in ventral furrow morphogenesis.

31P-NMR spectroscopy of perifused rat hepatocytes immobilized in agarose threads: application to chemical-induced hepatotoxicity

A system consisting of isolated rat hepatocytes immobilized in agarose threads continuously perifused with oxygenated Krebs-Henseleit (KH) solution has been found to maintain cell viability with excellent metabolic activity for more than 6 h. The hepatocytes were monitored by phosphorus-31 nuclear magnetic resonance (31P-NMR) spectroscopy at 4.7 Tesla, by measurement of oxygen consumption and by the leakage of lactate dehydrogenase (LD) and alanine aminotransferase (ALT). The data obtained were comparable to those found for an isolated perfused whole liver in vitro. The effects of allyl alcohol (AA), ethanol, and 4-acetaminophenol (AP) were examined. A solution of 225 microM AA perifused for 90 min caused the disappearance of the beta-phosphate resonance of adenosine triphosphate (ATP) in the 31P-NMR spectra, a 7-fold increase in LD leakage and a 70% reduction in oxygen consumption. Ethanol (1.0 M) perifused for 90 min reduced the beta-ATP signal intensity ratio by 20%, the phosphomonoester (PME) signal by 50% and inorganic phosphate (Pi) by 33% (P less than 0.05). AP (10 mM) caused only mild liver-cell damage. The results demonstrate that perifused immobilized hepatocytes can be used as a liver model to assess the effects of a wide range of chemicals and other xenobiotics by NMR spectroscopy.

19F NMR investigations of membranes

Publisher Summary The molecular biology of membranes is an important and active area of science. The principal components of membranes and of the cell surfaces of many organisms are proteins and lipid-like molecules. This chapter presents a number of physical techniques that have been used to investigate the structural and dynamic properties of lipids, proteins, and membranes. Some of these techniques are X-ray diffraction, neutron diffraction, electron microscopy, differential scanning calorimetry, Raman spectroscopy, optical rotary dispersion, fluorescence spectroscopy, nuclear magnetic resonance (NMR), and electron paramagnetic resonance employing nitroxide spin labels. NMR spectroscopy has been applied mainly to the polar membrane phospholipids. Such polar lipids usually exist in bilayers whether dispersed individually in water or present in biological membranes. Lipid bilayers undergo phase transitions with changing temperature. At higher temperatures, they exist in a fluid-like liquid crystalline state while at lower temperatures, they are characterized by a gel-like state. The first NMR studies of lipids used the most abundant nucleus of lipids, hydrogen-1. The broad lines in the 1 H NMR spectra of lipids consist of many overlapping proton pair contributions, with each resonance broadened by interpair interactions. One way to resolve the intrapair and interpair interactions is to orient the lipids between glass slides and record the spectrum as a function of the orientation with respect to the magnetic field. It was found that the lipid chains can be divided roughly into two parts: (1) a less ordered part in the interior of the bilayer and (2) a more ordered part in the upper half of the chain

A biochemical study of the reconstitution of d-lactate dehydrogenase-deficient membrane vesicles using fluorine-labeled components

Fluorine-19 labeled compounds have been incorporated into lipids and proteins of Escherichia coli. 19F-Labeled membrane vesicles, prepared by growing a fatty acid auxotroph of a D-lactate dehydrogenase-deficient strain on 8,8-difluoromyristic acid, can be reconstituted for oxidase and transport activities by binding exogenous D-lactate dehydrogenase. 19F-Labeled D-lactate dehydrogenases prepared by addition of fluorotryptophans to a tryptophan-requiring strain are able to reconstitute D-lactate dehydrogenase-deficient membrane vesicles. Thus, lipid and protein can be labeled independently and used to investigate protein-lipid interactions in membranes.

Proteomic analysis reveals CCT is a target of Fragile X mental retardation protein regulation in Drosophila

Fragile X mental retardation protein (FMRP) is an RNA-binding protein that is required for the translational regulation of specific target mRNAs. Loss of FMRP causes Fragile X syndrome (FXS), the most common form of inherited mental retardation in humans. Understanding the basis for FXS has been limited because few in vivo targets of FMRP have been identified and mechanisms for how FMRP regulates physiological targets are unclear. We have previously demonstrated that Drosophila FMRP (dFMRP) is required in early embryos for cleavage furrow formation. In an effort to identify new targets of dFMRP-dependent regulation and new effectors of cleavage furrow formation, we used two-dimensional difference gel electrophoresis and mass spectrometry to identify proteins that are misexpressed in dfmr1 mutant embryos. Of the 28 proteins identified, we have identified three subunits of the Chaperonin containing TCP-1 (CCT) complex as new direct targets of dFMRP-dependent regulation. Furthermore, we found that the septin Peanut, a known effector of cleavage, is a likely conserved substrate of fly CCT and is mislocalized in both cct and in dfmr1 mutant embryos. Based on these results we propose that dFMRP-dependent regulation of CCT subunits is required for cleavage furrow formation and that at least one of its substrates is affected in dfmr1- embryos suggesting that dFMRP-dependent regulation of CCT contributes to the cleavage furrow formation phenotype.

Stopped-flow kinetic and biophysical studies of membrane-associated d-lactate dehydrogenase of Escherichia coli

The enzyme kinetics of the FAD-containing membrane-associated D-lactate dehydrogenase (D-LDH) of Escherichia coli have been investigated by stopped-flow spectroscopy. The reduction of D-LDH by the substrate, D-lactate, exhibits a two-stage behavior as observed by the absorbance change for the enzyme-bound FAD. The fast stage with a maximum rate of 400 s-1 represents the rapid formation of the enzyme-substrate complex and the formation of the equilibrium between the oxidized and the reduced enzyme-substrate complexes. The slow stage, which occurs on the order of 0.36 s-1, represents the slow release of the product, pyruvate, from the reduced enzyme. The formation of a D-LDH semiquinone radical was not observed during the oxidation of D-lactate by D-LDH at 25 degrees C. However, during the subsequent electron transfer from the reduced enzyme to a nitroxide spin-label, a one-electron acceptor, an enzyme intermediate has been observed and identified by both optical and EPR spectroscopies as an anionic semiquinone. Results from 1H-NMR spectroscopic studies suggest the possible formation of a substrate carbanion when D-lactate is bound at the active site of D-LDH.

Effect of FK 506 and Cyclosporins on Model Membranes Studied by Nuclear Magnetic Resonance Spectroscopy

Cyclosporin A (CsA) is a drug that has allowed the field of human organ transplantation to develop from an experimental stage to a practical and effective form of therapy (1). FK 506, a novel compound, is now becoming of interest as an alternative immunosuppressive agent (2, 3), and preliminary reports have appeared to demonstrate its usefulness in organ transplantation (4).