Optimization of the first dimension for separation by two-dimensional gel electrophoresis of basic proteins from human brain tissue

A major cause of poor resolution in the alkaline pH range of two-dimensional electrophoresis (2-DE) gels is unsatisfactory separation of basic proteins in the first dimension. We have compared methods for the separation of basic proteins in the isoelectric focusing dimension of human brain proteins. The combined use of anodic cup-loading and the hydroxyethyldisulphide containing solution (DeStreak) produced better resolution in both analytical and micropreparative protein loaded 2-DE gels than the other methods investigated.     

Gradiflow as a prefractionation tool for two-dimensional electrophoresis

The Gradiflow trade mark, a preparative electrophoresis instrument capable of separating proteins on the basis of their size or charge, was used to separate whole cell lysates, prepared from bakers yeast (Saccharomyces cerevisiae) and Chinese snow pea seeds (Pisum sativum macrocarpon), into protein fractions of different pH regions. Both broad and narrow range (with a difference of approximately 1 pH unit) pH fractions were obtained. Analysis of the protein fractions by isoelectric focusing gels and two-dimensional (2-D) polyacrylamide gel electrophoresis indicated minimal overlap between the pH fractions. Further, when the prefractionated acidic samples were analyzed on pH 4-7 immobilized pH gradient 2-D gels, improved resolution of the proteins within the chosen pH region was achieved compared to the unfractionated samples. This study demonstrates that the Gradiflow could be used as a preparative electrophoresis tool for the isolation of proteins into distinct pH fractions.     

Changes in Activities of Enzymes Involved in General Phenylpropanoid Metabolism during the Induction and Reduction of Anthocyanin Synthesis in a Carrot Suspension Culture as Regulated by 2,4-D

The activities of enzymes involved in general phenylpropanoidmetabolism were followed in a carrot suspension culture duringthe induction and reduction of anthocyanin synthesis regulatedby 2,4-D. When no anthocyanin synthesis occurred in a mediumcontaining 2,4-D (+2,4-D medium), the activities of phenylalanineammonia-lyase (PAL) and 4-coumarate:CoA ligase (4CL) increased1 day after transfer due to the transfer effect, but subsequentlydecreased and remained at a low level. Cinnamate-4-hydroxylase(C4H) activity showed a low level throughout culture. When cellswere transferred to a medium lacking 2,4-D (–2,4-D medium),the activities of PAL, C4H and 4CL increased and maximum activitiesof these enzymes were observed 6–7 days after transfer,when anthocyanin was most rapidly synthesized. When cells were cultured in the –2,4-D medium, the additionof 2,4-D immediately reduced the induced activity of PAL. PALactivity was super-induced by the transfer effect, while anthocyaninsynthesis decreased. The addition of intermediates of generalphenylpropanoid metabolism, with 2,4-D, to the medium 6 daysafter transfer to the –2,4-D medium did not promote anthocyaninsynthesis, whereas dihydroquercetin did promote it. Regulationof anthocyanin synthesis by 2,4-D is discussed in relation tochanges in enzyme activities involved in general phenylpropanoidmetabolism. ¹ Present address: Cell Science and Technology Division, FermentationResearch Institute, Agency of Industrial Science and Technology,Yatabe-machi, Ibaraki 305, Japan. ² Present address: Biological Institute, Faculty of Science,Tohoku University, Sendai 980, Japan.     

Brightness and darkness as perceptual dimensions

A common-sense assumption concerning visual perception states that brightness and darkness cannot coexist at a given spatial location. One corollary of this assumption is that achromatic colors, or perceived grey shades, are contained in a one-dimensional (1-D) space varying from bright to dark. The results of many previous psychophysical studies suggest, by contrast, that achromatic colors are represented as points in a color space composed of two or more perceptual dimensions. The nature of these perceptual dimensions, however, presently remains unclear. Here we provide direct evidence that brightness and darkness form the dimensions of a two-dimensional (2-D) achromatic color space. This color space may play a role in the representation of object surfaces viewed against natural backgrounds, which simultaneously induce both brightness and darkness signals. Our 2-D model generalizes to the chromatic dimensions of color perception, indicating that redness and greenness (blueness and yellowness) also form perceptual dimensions. Collectively, these findings suggest that human color space is composed of six dimensions, rather than the conventional three.     

Monitoring mammalian genome rearrangement with mid-repetitive sequences as probes

By utilization of mid-repetitive sequences, the intracisternal A particle (IAP) gene, as a probe, genome rearrangement involving IAP genes and their neighboring sequences in rodent cells can be monitored. This is based on electrophoretic separation of the twice digested restriction fragments of genomic DNA in a 2-D pattern. The first digestion was done in solution followed by electrophoresis of the restriction fragments in the first dimension. A second restriction enzyme digestion was carried out in situ in the gel followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. After Southern blotting, the DNA on the filter is hybridized with a probe that is a fragment located near the 5' end of the IAP gene, but does not overlap with the 5' long terminal repeat (LTR). The exposed X-ray film revealed about 370 distinct spots in the 2-D maps. In comparing the 2-D maps, genome rearrangement involving IAP was detected.     

Analyzing alkaline proteins in human colon crypt proteome

Normal human colon crypt protein extract was resolved by two-dimensional gel electrophoresis using pH 6-11 immobilized pH gradient strips in the first dimension. The optimized isoelectric focusing protocol includes cup-loading sample application at the anode and 1.2% hydroxyethyl disulfide (DeStreak), 15% 2-propanol and 5% glycerol in the rehydration buffer. Spots were well resolved across the entire pH range up to 11. A total of 311 protein spots were identified by mass spectrometry and peptide mass mapping. After combining isoforms, 231 nonredundant proteins were grouped into 16 categories according to their subcellular locations, and 17 categories according to their physiological functions. Histone proteins, ribosomal proteins and mitochondrial proteins were among the well-resolved highest p/ proteins. Application of this protocol to the analysis of normal and neoplastic colon crypts will contribute to the proteomic study of colorectal tumorigenesis since a significant portion of the human proteins is in basic pH range.     

狗牙根颖果胚性愈伤组织的诱导和胚性细胞的超微结构及植株再生

以普通狗牙根[Cynodon dacylon(L.)Pers.cv.'Suncitv']颖果为外植体,以MS为基本培养基,外加浓度在2.0～6.0mg/L的2,4-D,能高频率地诱导出高质量的胚性愈伤组织,其中以4.0 mg/L为最佳.胚性愈伤组织最佳继代及分化的培养方法为:用MS 2,4-D 4.0mg/L继代1～2次,然后转入1/2 MS 2,4-D 2.0 mg/L中继代1～2次,再在无激素的1/2MS中光照培养10 d,最后在MS 6-BA 3.0 mg/L中诱导分化,分化成苗率达31.7%.经电镜观察发现,胚性愈伤组织结构紧密,细胞较小,内容物丰富,而非胚性愈伤组织结构疏松,细胞巨大,内含一大液泡,几无细胞器.     

Synergistic Effects of Cu(II) and Dimethylammonium 2,4-Dichlorophenoxyacetate (U46 D Fluid) on PM2 DNA and Mechanism of Dna Damage

Dimethylammonium 2,4-dichlorophenoxyacetate (2,4-D · DMA) induced strand breaks in PM2 DNA when incubated with CuCl₂, whereas 2,4-D · DMA alone or CuCl₂ alone did not show any or only a negligible effect. The formation of single strand breaks increased linearly with time and concentration of 2,4-D · DMA. Neocuproine, a specific Cu(I) chelator totally prevented strand break formation. So did catalase (up to 100mM 2,4-D · DMA), but DMSO had only a small protective effect. 2,4-Dichlorophenol, CO₂ and formaldehyde were detected as reaction products of 2,4-D and CuCl₂. From these results a redox reaction of Cu(II) and 2,4-D is proposed, which could explain the DNA damaging properties of CuCl₂/2,4-D · DMA.     

Dimensionality Controls Cytoskeleton Assembly and Metabolism of Fibroblast Cells in Response to Rigidity and Shape

Background

Various physical parameters, including substrate rigidity, size of adhesive islands and micro-and nano-topographies, have been shown to differentially regulate cell fate in two-dimensional (2-D) cell cultures. Cells anchored in a three-dimensional (3-D) microenvironment show significantly altered phenotypes, from altered cell adhesions, to cell migration and differentiation. Yet, no systematic analysis has been performed that studied how the integrated cellular responses to the physical characteristics of the environment are regulated by dimensionality (2-D versus 3-D).

Methodology/Principal Findings

Arrays of 5 or 10 µm deep microwells were fabricated in polydimethylsiloxane (PDMS). The actin cytoskeleton was compared for single primary fibroblasts adhering either to microfabricated adhesive islands (2-D) or trapped in microwells (3-D) of controlled size, shape, and wall rigidity. On rigid substrates (Young''s Modulus = 1 MPa), cytoskeleton assembly within single fibroblast cells occurred in 3-D microwells of circular, rectangular, square, and triangular shapes with 2-D projected surface areas (microwell bottom surface area) and total surface areas of adhesion (microwell bottom plus wall surface area) that inhibited stress fiber assembly in 2-D. In contrast, cells did not assemble a detectable actin cytoskeleton in soft 3-D microwells (20 kPa), regardless of their shapes, but did so on flat, 2-D substrates. The dependency on environmental dimensionality was also reflected by cell viability and metabolism as probed by mitochondrial activities. Both were upregulated in 3-D cultured cells versus cells on 2-D patterns when surface area of adhesion and rigidity were held constant.

Conclusion/Significance

These data indicate that cell shape and rigidity are not orthogonal parameters directing cell fate. The sensory toolbox of cells integrates mechanical (rigidity) and topographical (shape and dimensionality) information differently when cell adhesions are confined to 2-D or occur in a 3-D space.     

Human neuroblastoma (SH-SY5Y) cell culture and differentiation in 3-D collagen hydrogels for cell-based biosensing

Cell-based three-dimensional systems are desirable in the field of high throughput screening assays due to their potential similarity to in vivo environment. We have used SH-SY5Y human neuroblastoma cells cultured in 3-D collagen hydrogel, confocal microscopy and immunofluorescence staining, to assess the merit of the system as a functional, cell-based biosensor. Our results show differences between 2-D and 3-D resting membrane potential development profile upon differentiation. There was no statistically significant difference in SH-SY5Y proliferation rate between 2-D monolayer and 3-D collagen culture formats. A large percentage of cells (2-D, 91.30% and 3-D, 84.93%) did not develop resting membrane potential value equal to or lower than -40 mV; instead cells exhibited a heterogeneous resting membrane potential distribution. In response to high K(+) (50 mM) depolarization, 3-D cells were less responsive in terms of increase in intracellular Ca(2+), in comparison to 2-D cells, supporting the hypothesis that 2-D cell calcium dynamics may be exaggerated. L-Type Ca(2+) expression levels based on staining results was inconsistent with Bay K 8644 channel activation results, strongly suggesting that either the majority of the channels were non-functional or could not be activated by Bay K 8644. In general, the results in this study confirm the depolarization-induced differences in intracellular calcium release when cultured using a 2-D versus a 3-D matrix.     

A functional cell surface type receptor is required for the early action of 1,25-dihydroxyvitamin D3 on the phosphoinositide metabolism in rat enterocytes

1,25-Dihydroxyvitamin D3 (1,25-(OH)2-D3) (0.1 pM to 2 nM) induces a concomitant very rapid (within 5 s) and transient release of inositol trisphosphate and diacylglycerol in enterocytes from 3-month-old rats. This high level is not maintained but declines to a lower level 60 s after stimulation. The stimulating effect is dose-dependent and biphasic with a maximum effect at 10 pM. 1,25-(OH)2-D3 induces a rapid (within 10 s) accumulation of inositol bisphosphate and its effect on inositol monophosphate is delayed (120 s). The primary action of 1,25-(OH)2-D3 is to initiate hydrolysis of phosphatidyl 4,5-bisphosphate to yield inositol trisphosphate and diacylglycerol. In contrast, 1,25-(OH)2-D3, for any of the concentrations and the incubation time periods tested, has no effect on inositol trisphosphate and diacylglycerol formation in enterocytes from 16-day-old rats at a time when specific binding sites for 1,25-(OH)2-D3 cannot be detected. In conclusion, the early (within 5-60 s) effects of 1,25-(OH)2-D3 on small intestinal epithelium may be mediated via the phosphoinositide transduction system and require the presence of functioning cell membrane-type receptors.     

Application of sensitive fluorescent dyes in linkage of laser microdissection and two-dimensional gel electrophoresis as a cancer proteomic study tool

The combination of laser microdissection and two-dimensional gel electrophoresis (2-D PAGE) has been developed to perform proteomic analysis on specific populations of cells in cancer tissues. However, as conventional low sensitivity silver staining was used for spot detection, the microdissection required to obtain an adequate amount of protein for 2-D PAGE is laborious and only a restricted number of protein spots could be visualized. As a consequence, this technology was impractical for direct clinical applications and had a limited impact on cancer studies. To solve these problems, we developed an application in which fluorescent dyes label the proteins extracted from microdissected tissues prior to 2-D PAGE separation. In this application, a small amount of protein, less than 6.6 microg, was enough to generate a 2-D profile with approximately 1500 protein spots. This technique was applied to compare the proteome of normal intestinal epithelium with that of adenoma in Min mice. Thirty-seven protein spots reproducibly showed significant differences in intensities. Mass spectrometric analysis and Western blotting identified eight of them, including prohibitin, 14-3-3zeta, tropomyosin 3 and Hsp84. These results indicate that fluorescence labeling of proteins from microdissected tissues prior to 2-D PAGE is a powerful cancer proteomic study tool.     

Novel monosaccharides as potent inhibitors of cell proliferation

The effects of several novel monosaccharides upon thymidine incorporation into both normal and tumour cells were investigated. The monosaccharide 2-deoxy-3-[1-(R)-(ethoxycarbonyl)ethyl]-α-D -allo-pyranose had the most inhibitory effect on proliferation, with the (S)-enantiomer having less inhibitory effects. The chiral centre at carbon-7 was found to be an important part of the molecule, as 2-deoxy-3-[methoxycarbonyl methyl]-α-D -allo-pyranose had greatly decreased anti-proliferative properties in comparison with the parent compound. In addition, the 2-deoxy structure at carbon-2 was also found to be important, as 3-[1-(S)-(ethoxycarbonyl)ethyl]-α-D -allo-hexopyranose had greatly decreased inhibitory properties in comparison with the parent compound. The results indicate that these novel monosaccharides possess potent anti-proliferative properties, related to their chiral carbon-7 and 2-deoxy carbon-2 structure and suggest that further substitutions of the functional group at carbon-7 may improve these properties and possibly produce inhibitor selectivity for tumour cells in preference to normal cells. © 1997 John Wiley & Sons, Ltd.     

Effect of diclofop-methyl and 2,4-D on transmembrane proton gradient: a mechanism for their antagonistic interaction

The site of action of the postemergence graminicide, diclofop-methyl (DM), in susceptible plants is possibly the plasmalemma. Indole-acetic acid (IAA)- and fusicoccin (FC)-induced net proton excretion in Avena coleoptiles was inhibited by the free acid, diclofop. However, net proton excretion recovered within 2 h when 2,4-dichlorophenoxy acid (2,4-D) was added simultaneously with diclofop. Diclofop depolarized the membrane potential (Em) within 12 min but the Em recovered within 30 min when diclofop was removed and replaced with either IAA or 2,4-D. The inhibition of IAA-induced coleoptile growth by DM and the membrane effects of its acid, diclofop, were partially reversed by 2,4-D if it was added shortly after treatment of the tissue. These results are consistent with the reversal of DM injury in whole plants with 2,4-D.     

Metabolism of 2,4-dichlorophenoxyacetic Acid in soybean root callus and differentiated soybean root cultures as a function of concentration and tissue age

The metabolism of [1-¹⁴C]2,4-dichlorophenoxyacetic acid (2,4-D) in soybean (Glycine max [L.] Merrill var. Amsoy) root callus and in differentiated soybean root cultures was investigated as a function of pesticide concentration and age of tissue. The chronological age of the tissue was found to be correlated with the mitotic index which reached a peak at 2 weeks and then declined. The metabolism of 2,4-D changed with age of the root callus tissue. The amount of free 2,4-D found in 3-week-old root callus tissue rapidly increased as the concentration of 2,4-D in the medium was increased from 10⁻⁶ to 10⁻⁵ molar, whereas the low level of aqueous (glycosides) and ether soluble metabolites (2,4-D amino acid conjugates) increased slowly. With 9-week-old root callus tissue, the amount of free 2,4-D remained at a relatively low, constant level (saturation level) as the concentration of 2,4-D in the medium increased. Under these conditions the aqueous metabolites increased only slightly but the ether fraction (2,4-D amino acid conjugates) rapidly increased. Thus, the older root callus tissue appeared to regulate the level of free 2,4-D at about 4 nanomoles per gram by converting any excess 2,4-D into amino acid conjugates.

In 3-week-old, differentiated root cultures the metabolism of 2,4-D closely paralleled the metabolism found in the older 9-week-old callus tissue. The saturation level of free 2,4-D found in this tissue was only about 1 to 2 nanomoles per gram.

     

Control of Morphogenesis in Sorghum by 2,4-Dichlorophenoxyacetic Acid and Cytokinins

2, 4-Dichlorophenoxyacetic acid caused a shortening of rootsand shoots when mature seeds of Sorghum bicolor (L.) Moenchcv. BT3197 were germinated on Murashige and Skoog (MS) mediumthat contained 2,4-D. Shoot growth was restored with cytokinins.A callus formed at the nodal region, the further differentiationof which was determined by the ratio of 2,4-D and cytokininsin the initial culture medium. A high auxin to cytokinin ratiopromoted primarily root differentiation while a high cytokininto auxin ratio promoted multiple bud development. Isolated shootapical meristem with the subtending node produced embryogeniccallus at low cytokinin levels and green buds on high cytokininlevels when cultured in the presence of 2,4-D. It is concludedthat cells potentially capable of differentiation into roots,somatic embryos or axillary buds are present in the first nodalregion. Sorghum bicolor, organogenesis, embryogenesis, 2, 4-D: cytokinin ratios, tissue culture     

Two-dimensional gel electrophoresis as a taxonomic tool: Evidence from the centrospermae

Two-dimensional polyacrylamide gel (2-D PAGE) electrophoresis was appraised as an experimental technique for assessing systematic relationships among higher plants and to determine at which level in the taxonomic hierarchy this technique is most generally applicable. 2-D PAGE was performed on denatured extracts of mature leaves from 25 species representing five families of the order Centrospermae (Caryophyllales, Chenopodiales) in the Angiospermae as well as Welwitschia mirabilis (Gymnospermae). Cluster analysis of a 256 spot binary-coded data set derived from the computer-encoded spot patterns of the 25 species successfully separated taxa from the individual to the familial levels of the taxonomic hierarchy in accordance with traditional taxonomic delineations of the taxa.     

Efficient solubilization buffers for two-dimensional gel electrophoresis of acidic and basic proteins extracted from wheat seeds

Plant tissues are made up of a broad range of proteins with a variety of properties. After extraction, solubilization of a diverse range of plant proteins for efficient proteomic analysis using two-dimensional electrophoresis is a challenging process. We tested the efficiency of 12 solubilization buffers in dissolving acidic and basic proteins extracted from mature seeds of wheat. The buffer containing two chaotropes (urea and thiourea), two detergents (3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propane-sulfonate and N-decyl-N,N-dimethyl-3-ammonio-1-propane-sulfonate), two reducing agents (dithiothreitol and tris (2-carboxyethyl) phosphine hydrochloride) and two types of carrier ampholytes (BioLyte pH 4-6 and pH 3-10) solubilized the most acidic proteins in the pH range between 4 and 7. The buffer made up of urea, thiourea, 3-[(3-cholamidopropyl) dimethyl-ammonio]-1-propane-sulfonate, DeStreak reagent (Amersham Biosciences, Uppsala, Sweden) and immobilized pH gradient buffer, pH 6-11 (Amersham Biosciences) solubilized the most basic proteins in the pH range between 6 and 11. These two buffers produced two-dimensional gels with high resolution, superior quality and maximum number of detectable protein (1425 acidic protein and 897 basic protein) spots.