Palmitate-induced changes in protein expression of insulin secreting INS-1E cells

Elevated blood levels of glucose and lipids in individuals with type 2 diabetes mellitus have been observed to cause impairment of insulin secretion from pancreatic β-cells. Chronic exposure to either of the circulating fatty acid oleate or palmitate has different effects on the β-cell. Whereas palmitate causes functional impairment of the β-cell and apoptosis, oleate has only minor negative effects on β-cell function and mass. The aim of the present study was to delineate mechanisms by which the fatty acids affect the β-cell differently. In particular, the aim was to identify β-cell proteins exclusively regulated by palmitate. INS-1E cells were cultured for 24 h in medium supplemented with palmitate or oleate. After culture, cells were lysed and subjected to two-dimensional gel electrophoresis. Proteins specifically regulated by palmitate were excised from the gel and identified by peptide mass fingerprinting using MALDI-TOF MS. Proteins exclusively regulated by palmitate were classified into proteins of carbohydrate or protein metabolism and Ca²⁺ or mRNA binding proteins. The specific palmitate-induced down-regulation of enzymes of glycolysis, proteins of protein turnover and anti-apoptotic protein may contribute to explain the different effects exerted by palmitate and oleate on β-cell function and mass.     

Demonstration of a highly exposed region in Escherichia coli 5 s RNA by partial hydrolysis with ribonuclease IV and sheep kidney nuclease

Partial digests of ³²P-labelled 5 s RNA with Escherichia coli RNase IV and with sheep kidney nuclease were fractionated by two-dimensional polyacrylamide gel electrophoresis. The nucleotide sequences of the various fractions were determined by fingerprinting analysis. The results show the existence of a single-stranded loop around position G₄₁ of the 5 s RNA molecule.     

RNA sequence determination in the nanogram range by a combination of in vitro labeling procedures.

Recently developed methods which allow one to read RNA sequences directly from polyacrylamide gels do not always provide unequivocal results. A combination of primary and secondary in vitro 5′-labeling, as presented here, is methodically and in its results equivalent to fingerprinting and sequencing techniques developed for in vivo labeled RNA. 5 S RNA was used to demonstrate the applicability and reliability of this combination of postlabeling procedures: 5 μg RNA was partially digested, and the resulting overlapping fragments were 5′-³²P-labeled with T4 phage-induced polynucleotide kinase in vitro. After two-dimensional polyacrylamide gel electrophoresis and carrier-free electrophoretic elution, the labeled long fragments, obtained in the 10-ng range, were completely degraded with RNase T₁ and RNase A, respectively. These digests were again ³²P-phosphorylated with T4 kinase and lead to fingerprints which allowed the deduction of the nucleotide sequences of the corresponding long fragments.     

An evaluation of new gel matrices for the separation of PCR-amplified DNA fragments

It has been shown that the novel gel matrix, PCR Purity Plus which consists of a vinyl-polymer of polyacrylamide, provides a superior and rapid means of separating DNA fragments. As this product has been discontinued, the two new commercial versions of this matrix (MDE^® and GeneAmp^®) with PCR Purity Plus were compared. Optimal conditions for resolving DNA fingerprint profiles for both matrices were defined. Both MDE and GeneAmp gels provided a clear separation of DNA fragments. However, the profiles obtained on GeneAmp gel were closest to that of PCR Purity Plus. These results should be useful to DNA fingerprinting studies where it is critical to obtain a clear resolution of complex DNA profiles.     

Taxonomic discrimination of cyanobacteria by metabolic fingerprinting using proton nuclear magnetic resonance spectra and multivariate statistical analysis

When whole-cell extracts are analyzed, proton nuclear magnetic resonance (¹H NMR) spectroscopy provides biochemical profiles that contain overlapping signals of the majority of the compounds. To determine whether cyanobacteria could be taxonomically discriminated on the basis of metabolic fingerprinting, we subjected whole-cell extracts of the cyanobacteria to¹H NMR. The¹H NMR spectra revealed a predominance of signals in the aliphatic region. Principal component analysis (PCA) of the data then enabled discrimination of the cyanobacteria. The hierarchical dendrogram, based on PCA of the aliphatic region data, showed that six cyanobacterial taxa were discriminated from two eukaryotic microalgal species, and that the six taxa could be subsequently divided into three groups. This agrees with the current taxonomy of cyanobacteria. Therefore, our overall results indicate that metabolic fingerprinting using¹H NMR spectra and multivariate statistical analysis provide a simple, rapid method for the taxonomical discrimination of cyanobacteria.     

Novel Techniques for Identification and Characterization of Proteins Loaded on Gels in Femtomole Amounts

A combination of techniques is presented allowing gel-purified protein identification in the femtomole range using matrix-assisted-laser-desorption-ionization mass spectrometry. The proteins are detected in the primary gel by a sensitive negative staining procedure, transferred, and concentrated in a secondary gel matrix. There, they are digested in the presence of H₂ ¹⁸O and their sequences are predicted (1) by peptide mass fingerprinting, (2) by comparing the post-source-decay (PSD) spectra with theoretical spectra of candidate isobaric peptides using a computer algorithm called MassFrag, and (3) by a manual readout of the ¹⁸O/¹⁶O-labeled fragmentation ions in the PSD spectra.     

Selection and identification of proteins bound to DNA triple-helical structures by combination of 2D-electrophoresis and MALDI-TOF mass spectrometry

Identification of proteins binding specifically to peculiar nucleic acid structures can lead to comprehension of their role in vivo and contribute to the discovery of structure-related gene regulation. This work was devoted to establishing a reliable procedure to select proteins on the basis of their interaction with a nucleic acid probe chosen to fold into a given structure. 2D-electrophoresis and mass spectrometry were combined for protein identification. We applied this procedure to select and identify triplex-binding activities in HeLa nuclear extracts. To achieve this, we used a panel of deoxyribonucleic probes adopting intramolecular triple-helices, varying in their primary sequence, structure or triple-helix motif. A limited number of spots was reproducibly revealed by South-western blotting. Spots of interest were localised among a complex population of ³⁵S-labelled proteins according to their ³²P-specific emission. Position of the same spots was extrapolated on a preparative gel coloured with Coomassie blue, allowing excision and purification of the corresponding proteins. The material was subjected to mass spectrometry upon trypsin digestion and MALDI-TOF peptide fingerprinting was used for research in databases: five of them were identified and found to belong to the hnRNP family (K, L, A2/B1, E1 and I). The identities of several of them were confirmed by comparing western and South-western blots on the same membrane using specific antibodies. The recognition specificity of most of these proteins is large, according to previous reports and our own experiments. It includes pyrimidine-rich DNA sequences in different contexts: single strand to a small extent, triplex and possibly other higher-order structures.     

A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars

 Commercial scale fingerprinting of potato cultivars is made difficult by the need for speed, reliability and the ability to distinguish between large numbers of genotypes. There are also problems in extrapolating the results of small experimental studies to predict the performance of techniques or primers for larger applications. The potential of ISSR-PCR for fingerprinting purposes was evaluated using four primers on 34 potato cultivars. The complex band profiles generated were reproducible between repeat PCRs, DNA extractions, electrophoreses and gel scorings. Two primers were each able to distinguish all cultivars. The combined use of any two of the four primers also allowed complete diagnosis. It is concluded that ISSR-PCR provides a quick, reliable and highly informative system for DNA fingerprinting that is amenable for routine applications. Two possible correlates of the ability of primers to distinguish between genotypes were then examined. Marker Index failed to correlate significantly with genotype diagnosis, but a strong and seemingly linear relationship was observed between Resolving Power of a primer and its ability to distinguish genotypes (r²=0.98). Resolving Power of one or a pair of primers was found to provide a moderately accurate estimate of the number of genotypes identified. Possible implications for future studies on DNA fingerprinting are discussed. Received: 7 May 1998 / Accepted: 15 July 1998     

Physical and chemical characteristics of Aloe ferox leaf gel

Aloe ferox leaf gel differs substantially from that of Aloe vera but almost no commercially relevant data is available this species. Leaf dimensions, gel yields and gel compositions were studied, based on samples from several natural populations. Glucose is the only free sugar in aloe gel (0.1 to 0.4 mg ml^− 1 in A. ferox). Monosaccharides released after hydrolysis show potential for gel fingerprinting and allow for a distinction between A. ferox and A. vera. The former yields various combinations of glucose and galactose as main monosaccharides, while the latter yields only mannose. Further variation studies are recommended because A. ferox appears to have three different gel chemotypes. Conductivity shows species-specific ranges — in A. ferox below 3000 μS cm^− 1 in fresh gel and above 3100 μS cm^− 1 in aged gel (corresponding values for A. vera were 1670 and 1990 μS cm^− 1). The level of phenolic (bitter) compounds in A. ferox gel can be reduced by treatment with activated charcoal, resulting in a small loss of total dissolved solids. Alcohol precipitable solids and insolubility are useful variables for quality control of gel powder. The methods and data presented are the first steps towards developing quality criteria for A. ferox leaf gel.     

Stoichiometry of phosphorylation of hepatic ATP-citrate lyase by protein kinase

Hepatic ATP-citrate lyase prepared with a fluoride-free step to allow endogenous phosphatases to dephosphorylate the enzyme was phosphorylated in vitro by the catalytic subunit of cyclic AMP-dependent protein kinase and [γ-³²P]ATP. After electrophoresis the radioactive phosphate was located predominantly in the gel slice containing the Coomassie blue stained protein corresponding to ATP-citrate lyase. The Stoichiometry of phosphorylation of hepatic ATP-citrate lyase in vitro by the catalytic subunit was such that 0.53 ± 0.02 molecules of phosphate were incorporated per subunit. The degree of phosphorylation was independent of the amount of ATP-citrate lyase present as substrate in the concentration range 1.2–6.4 μm. In the absence of catalytic subunit there was very little labeled phosphate incorporated into ATP-citrate lyase. Phosphorylation of ATP-citrate lyase by catalytic subunit was abolished by the specific protein inhibitor of cyclic AMP-dependent protein kinase. When ATP-citrate lyase was subjected to electrophoresis under nondenaturing conditions, lyase activity was recovered from the gel slice corresponding to the Coomassie blue staining phosphoprotein of a stained gel run in parallel.     

Development and assessment of microarray-based DNA fingerprinting in <Emphasis Type="Italic">Eucalyptus grandis</Emphasis>

Development of improved Eucalyptus genotypes involves the routine identification of breeding stock and superior clones. Currently, microsatellites and random amplified polymorphic DNA markers are the most widely used DNA-based techniques for fingerprinting of these trees. While these techniques have provided rapid and powerful fingerprinting assays, they are constrained by their reliance on gel or capillary electrophoresis, and therefore, relatively low throughput of fragment analysis. In contrast, recently developed microarray technology holds the promise of parallel analysis of thousands of markers in plant genomes. The aim of this study was to develop a DNA fingerprinting chip for Eucalyptus grandis and to investigate its usefulness for fingerprinting of eucalypt trees. A prototype chip was prepared using a partial genomic library from total genomic DNA of 23 E. grandis trees, of which 22 were full siblings. A total of 384 cloned genomic fragments were individually amplified and arrayed onto glass slides. DNA fingerprints were obtained for 17 individuals by hybridizing labeled genome representations of the individual trees to the 384-element chip. Polymorphic DNA fragments were identified by evaluating the binary distribution of their background-corrected signal intensities across full-sib individuals. Among 384 DNA fragments on the chip, 104 (27%) were found to be polymorphic. Hybridization of these polymorphic fragments was highly repeatable (R²>0.91) within the E. grandis individuals, and they allowed us to identify all 17 full-sib individuals. Our results suggest that DNA microarrays can be used to effectively fingerprint large numbers of closely related Eucalyptus trees.     

Gel Electrophoretic Procedures Potentially Applicable to the Isolation of Human Growth Hormone from A Transformed Bacterial Source at the Gram-Preparative Scale

A crude bacterial extract containing approximately 4 mg/ml protein, 25% of which was human growth hormone (hGH), was subjected to two alternative gel electrophoret ic isolation procedures, designated I and II. Procedure I exploits the high electrophoretic net mobility (RM² larger than 0.127) at pH 7.6, 0°C, of the bacterial contaminants relative to hGH. This allows one to stack ³ the contaminants at a protein load of 31.5 mg/cm² of gel, using a “non-restrictive” gel concentration. Unstacked hGH is collected from the gel section between 0.3 and 0.6 of relative gel length and extracted electrophoretically as described previously⁴ Alternatively, the unstacked hGH was concentrated on the gel by dispatching a second moving boundary behind the original stack (“re-stacking”) and a gel section (relative gel length 0.45 to 0.6) between the two moving boundaries was excised and subjected to electrophoretic extraction. The yield of hGH ranged from 70 to 82%, and its purity (weight/Lowry) ranged from 86 to 115%. Procedure II exploits the high electrophoretic net mobility (RM larger than 0.064) at pH 10.5, 0°C, of hGH relative to its bacterial contaminants at a gel concentration of 9 %T, 2 %C_. ², at a protein load of 2.5 mg/cm² of gel. The selectively stacked hGH is collected by preparative elution-PAGE, using an apparatus with 17.6 cm² gel surface area. The yield of hGH was 90% and its purity ranged from 84–92%.     

Whole Surface Image of Mycoplasma mobile,Suggested by Protein Identification and Immunofluorescence Microscopy

Mycoplasma mobile, a freshwater fish pathogen featured with robust gliding motility, binds to the surface of the gill, where it then colonizes. Here, to obtain a whole image of its cell surface, we identified the proteins exposed on the surface using the following methods. (i) The cell surface was labeled with sulfosuccinimidyl-6-(biotinamido) hexanoate and recovered by an avidin column. (ii) The cells were subjected to phase partitioning using Triton X-114, and the hydrophobic proteins were recovered. (iii) The membrane fraction was analyzed by two-dimensional gel electrophoresis. These recovered proteins were subjected to peptide mass fingerprinting, and a final list of 36 expressed surface proteins was established. The ratio of identified proteins to whole surface proteins was estimated through two-dimensional gel electrophoresis of the membrane fraction. The localization of three newly found proteins, Mvsps C, E, and F, has been clarified by immunofluorescence microscopy. Integrating all information, a whole image of the cell surface showed that the proteins for gliding that were localized at the base of the protrusion of flask-shaped M. mobile account for more than 12% of all surface proteins and that Mvsps, surface variants that were localized at both parts other than the neck, account for 49% of all surface proteins.     

Isolation of Two Radiation Resistant and Desiccation Tolerant Bacteria, <Emphasis Type="Italic">Modestobacter</Emphasis> sp. A2 and <Emphasis Type="Italic">Maritalea</Emphasis> sp. B9, from Gandom Beryan Hill in the Lut Desert of Iran

Although dryland ecosystems are the most abundant terrestrial biomes on the Earth, relatively little is known about their microbial diversity and potential metabolic activities. Therefore, the bacterial diversity of the Lut Desert in Iran has been remained largely obscure. In this study, ionizing radiation resistant bacteria from arid Gandom Beryan region was investigated by a culture-dependent method. After exposing the soil and surface sand samples to different periods of dehydration in a desiccator containing silica gel, two nonendospore- forming bacterial isolates were recovered by plating on R2A and TSA agar media and then subjected to a desiccation and ionizing radiation resistance assay. The isolates A2 and B9 were still recovered after 8 weeks in a desiccator containing silica gel and were moderately resistant to gamma radiation with a D10 value between 2 and 4 kGy. Strains A2 and B9 were affiliated with Modestobacter muralis MDVD1^T (99.7% similarity) and Maritalea mobilis E6^T (97.3% similarity) respectively, using 16S rRNA gene sequence analysis. This is the first report of radiation resistant bacteria which belongs to the genus Maritalea.     

Preparative two-dimensional polyacrylamide gel electrophoresis of 32 P-labeled RNA

Complex mixtures of RNA molecules may be separated by two-dimensional electrophoresis on polyacrylamide gel slabs. The first dimension of the separation is carried out on acid gels in the presence of a high urea concentration, the second on more concentrated gels buffered at pH 8. The method has been applied to the complete separation of RNA fractions obtained after a preliminary gel electrophoresis of partial enzymic digests of ³²P-labeled bacteriophage RNA. Another application is the fractionation of partial digests as obtained in sequence determination of RNA molecules. Spots are detected by autoradiography and extracted by a simple micro procedure which yields the material in a concentrated form suitable for sequence analysis by fingerprinting.     

Chemical Evidence for the Separation of Gy and AY Globin Chains by Polyacrylamide Gel Electrophoresis in Urea and Triton X-100

Polyacrylamide gel electrophoresis in urea and Triton X-100 of a hemolysate from human fetal red blood cells produces four major protein bands: α, β, and 2 γ globin chains. We have verified that the latter two are the ^Gγ and ^Aγ globin chains which have respectively glycine or alanine at position 136. After incorporation of either [³H] alanine or [³H] glycine into newly synthesized globin each y chain was isolated by preparative electrophoresis. The chains were cleaved with cyanogen bromide at methionines 55 and 133, then subjected to automated sequencing, and the residues from each sequencer turn counted. Glycine incor-poration was detected for the third turn (position 136) of the ^Gγ chain and alanine for the ^Aγ. Substantial metabolic conversion of [³H] glycine to serine and proline was also noted.     

Chemical Evidence for the Separation of Gγ and Aγ Globin Chains by Polyacrylamide Gel Electrophoresis in Urea and Triton X-100

Polyacrylamide gel electrophoresis in urea and Triton X-100 of a hemolysate from human fetal red blood cells produces four major protein bands: α, β, and 2 γ globin chains. We have verified that the latter two are the ^Gγ and ^Aγ globin chains which have respectively glycine or alanine at position 136. After incorporation of either [³H] alanine or [³H] glycine into newly synthesized globin each y chain was isolated by preparative electrophoresis. The chains were cleaved with cyanogen bromide at methionines 55 and 133, then subjected to automated sequencing, and the residues from each sequencer turn counted. Glycine incorporation was detected for the third turn (position 136) of the ^Gγ chain and alanine for the ^Aγ Substantial metabolic conversion of [³H] glycine to serine and proline was also noted.     

In vitro binding of labeled 20-methylcholanthrene to a specific cytosol-protein

In vitro binding kinetics and specificity of [20-³H]methylcholanthrene ([³H]MC) interaction with mouse epidermal cytosol in the presence or absence of microsomal metabolizing systems were investigated. After an incubation period of 30 roin at 22°, the samples were dialyzed, subjected to gel filtration, ultrafiltration, and analyzed by 7 % basic polyacrylamide gel electrophoresis. A major portion of the binding appeared in a single peak on the gel which had the same mobility as bovine or mouse serum albumin. In vitro competition by other hydrocarbons or by promoters for binding of MC to this cytosol receptor protein showed an impressive correlation to carcinogenic and promoting activities. Essentially 100% of the MC bound to cytosol without a microsomal metabolizing system was non-covalent. However, binding Of MC to cytosol in the presence of microsomes plus reduced NADPH was party covalent which has previously been reported by Grover and Sims and Meunier and Chaveau. When bovine (BSA) or mouse serum albumin (MSA) was incubated with radioactive MC in the presence of competing non-radioactive carcinogens or promoters, little or no inhibition of binding was found. The finding that both a powerful tumor promoter and a strong carcinogen are competitors for the specific MC binding to the cytosol receptor protein indicates that it may represent a critical interaction for the promoting stage of chemical carcinogenesis in mouse skin.     

Characterization of the molecular form of cardiac phospholamban

The native form of phospholamban is not known and it is presently under debate whether this protein exists as a monomer or an oligomer in cardiac sarcoplasmic reticulum. The currently accepted model for phospholamban is pentameric, based primarily on its behavior in SDS-polyacrylamide gel electrophoresis. In this study, sucrose density gradient centrifugation and gel filtration chromatography were used to determine the form of phospholamban under nondenaturing conditions. Purified phospholamban or phospholamban present in solubilized cardiac sarcoplasmic reticulum was centrifuged through 5–20% sucrose density gradients in the absence or presence ofn-octylgucoside. The sucrose density gradient fractions were assayed for acid precipitable³²P-incorporation in the presence of [-³²P]ATP and cAMP-dependent protein kinase catalytic subunit.³²P-containing peak fractions were subjected to SDS-polyacrylamide gel electrophoresis and immunoblot analysis, using a phospholamban-polyclonal antibody, to confirm the presence of phospholamban. Purified phosphoblamban migrated with an apparent molecular weight of 25,000 daltons in the sucrose gradients in either the absence or presence of detergent. Phospholamban present in solubilized cardiac sarcoplasmic reticulum migrated with a similar apparent molecular weight when detergent was included in the sucrose gradients. In addition, solubilized cardiac sarcoplasmic reticulum was subjected to gel filtration chromatography in the presence of deoxycholate. Under these conditions phospholamban migrated with an apparent molecular weight of 24,500 daltons. These data suggest that phospholamban prefers an oligomeric assembly and this may be the form present in cardiac sarcoplasmic reticulum membranes.     

Involvement of a low molecular weight component(s) in the mechanism of action of the glucocorticoid receptor.

[³H]Dexamethasone-receptor complexes from rat liver cytosol preincubated at 0° bind poorly to DNA-cellulose. However, if the steroid-receptor complex is subjected to gel filtration at 0–4° separating it from the low molecular weight components of cytosol, the steroid-receptor complex becomes “activated” enabling its binding to DNA-cellulose. This activation can be prevented if the gel filtration column is first equilibrated with the low molecular weight components of cytosol. In addition, if adrenalectomized rat liver cytosol, in the absence of exogeneous steroid, is subjected to gel filtration the macromolecular fractions separated from the “small molecules” of that cytosol have much reduced binding activity towards [³H]dexamethasone. These results suggest that rat liver cytosol contains a low molecular weight component(s) which maintains the glucocorticoid receptor in a conformational state that allows the binding of dexamethasone. Furthermore, this component must be removed from the steroid-receptor complex before binding to DNA can occur.