[Immune anticancer response: recent advances in the treatment of renal cell carcinoma]. / Réponse immunitaire antitumorale: nouvelles perspectives dans le traitement du carcinome à cellules rénales.

Recent advances in the field of immunobiology have provided many opportunities for anticancer-immunotherapy. Because they express tu-mor antigen, tumor cells can be kill by T cells. Renal Cell Carcinoma (RCC) is an immunogenic tumor and metastatic RCC is presently treated by cytokines. Anticancer immunity may be achieved by different strategies: allogeneic hematopoietic cell transplantation, vaccination with peptides, vaccination with loaded dendritic cells or adoptive cellular therapy in which specific T cells are isolated and expanded in vitro and then infused to patients. In our group, we have chosen the adoptive transfer of in vitro activated T cells with autologous tumor antigen loaded dendritic cells. To determine the best strategy of anticancer-immunotherapy, we need rigorous control of the specificity and the phenotype of the cell therapy product linked with the immunological status of the patient (before and after infusion) and with the clinical response.

A new omega-conotoxin that targets N-type voltage-sensitive calcium channels with unusual specificity.

A new specific voltage-sensitive calcium channel (VSCC) blocker has been isolated from the venom of the fish-hunting cone snail Conus consors. This peptide, named omega-Ctx CNVIIA, consists of 27 amino acid residues folded by 3 disulfide bridges. Interestingly, loop 4, which is supposed to be crucial for selectivity, shows an unusual sequence (SSSKGR). The synthesis of the linear peptide was performed using the Fmoc strategy, and the correct folding was achieved in the presence of guanidinium chloride, potassium buffer, and reduced/oxidized glutathione at 4 degrees C for 3 days. Both synthetic and native toxin caused an intense shaking activity, characteristic of omega-conotoxins targeting N-type VSCC when injected intracerebroventricularly to mice. Binding studies on rat brain synaptosomes revealed that the radioiodinated omega-Ctx CNVIIA specifically and reversibly binds to high-affinity sites with a K(d) of 36.3 pM. Its binding is competitive with omega-Ctx MVIIA at low concentration (K(i) = 2 pM). Moreover, omega-Ctx CNVIIA exhibits a clear selectivity for N-type VSCCs versus P/Q-type VSCCs targeted respectively by radioiodinated omega-Ctx GVIA and omega-Ctx MVIIC. Although omega-Ctx CNVIIA clearly blocked N-type Ca(2+) current in chromaffin cells, this toxin did not inhibit acetylcholine release evoked by nerve stimuli at the frog neuromuscular junction, in marked contrast to omega-Ctx GVIA. omega-Ctx CNVIIA thus represents a new selective tool for blocking N-type VSCC that displays a unique pharmacological profile and highlights the diversity of voltage-sensitive Ca(2+) channels in the animal kingdom.

Structural implications on the interaction of scorpion alpha-like toxins with the sodium channel receptor site inferred from toxin iodination and pH-dependent binding.

The alpha-like toxin from the venom of the scorpion Leiurus quinquestriatus hebraeus (Lqh III) binds with high affinity to receptor site 3 on insect sodium channels but does not bind to rat brain synaptosomes. The binding affinity of Lqh III to cockroach neuronal membranes was fivefold higher at pH 6.5 than at pH 7.5. This correlated with an increase in the electropositive charge on the toxin surface resulting from protonation of its four histidines. Radioiodination of Tyr(14) of Lqh III abolished its binding to locust but not cockroach sodium channels, whereas the noniodinated toxin bound equally well to both neuronal preparations. Radioiodination of Tyr(10) or Tyr(21) of the structurally similar alpha-toxin from L. quinquestriatus hebraeus (LqhalphaIT), as well as their substitution by phenylalanine, had only minor effects on binding to cockroach neuronal membranes. However, substitution of Tyr(21), but not Tyr(14), by leucine decreased the binding affinity of LqhalphaIT approximately 87-fold. Thus, Tyr(14) is involved in the bioactivity of Lqh III to locust receptor site 3 and is not crucial for the binding of LqhalphaIT to this site. In turn, the aromatic ring of Tyr(21) takes part in the bioactivity of LqhalphaIT to insects. These results highlight subtle architectural variations between locust and cockroach receptor site 3, in addition to previous results demonstrating the competence of Lqh III to differentiate between insect and mammalian sodium channel subtypes.

Detection of modifications in the glucose metabolism induced by genetic mutations in Saccharomyces cerevisiae by 13C- and H-NMR spectroscopy.

NMR spectroscopy may offer a suitable technique to characterize the glucose metabolism in response to genetic mutations in cells. The effects of various genetic modifications in Saccharomyces cerevisiae yeast were investigated using 13C- and 1H-NMR spectroscopy associated with biochemical techniques. Cells were incubated with [1-13C]glucose in order to study glucose consumption and the formation of various end-products (ethanol, trehalose, glycerol, glutamate and amino acids) as a function of time. Two types of genetic modifications were studied in S. cerevisiae. A genetic modification deleted the N-terminal part of the TFC7 protein which is the smallest subunit (tau55) of the TFIIIC transcription factor. One secondary effect of this mutation was a large deletion of mitochondrial DNA giving the rho-phenotype. The other genetic modification corresponded to the disruption of the HUF gene; the mutated cells were rho+ like the reference strain. Both mutations increase the glycolysis rate and glycerol synthesis and decrease trehalose production. The most modified cells, which contain both TFC7 deletion and HUF gene disruption, utilize glucose in the most extreme manner as in these cells the largest production of the two glycolytic products (ethanol and glycerol) and the smallest trehalose formation occur. The HUF gene disruption serves as a positive modulator of glycolysis and respiration. However, the TFC7 deletion, associated with the phenotype rho-, induces the most damage in the cellular function, dramatically altering the behaviour of the Krebs cycle. The cycle becomes blocked at the level of 2-oxoglutarate, detected by a characteristic pattern of the 13C-NMR glutamate spectra. These NMR spectra corroborate the phenotypic data, the rho-phenotype corresponding to deletions of mitochondria DNA which block all mitochondria protein synthesis and render the cells unable to derive energy from respiration. Moreover, as a consequence of the Krebs cycle blocking, alanine formation is also observed.

A new conotoxin isolated from Conus consors venom acting selectively on axons and motor nerve terminals through a Na+-dependent mechanism.

A novel conotoxin was isolated and characterized from the venom of the fish-hunting marine snail Conus consors. The peptide was identified by screening chromatography fractions of the crude venom that produced a marked contraction and extension of the caudal and dorsal fins in fish, and noticeable spontaneous contractions of isolated frog neuromuscular preparations. The peptide, named CcTX, had 30 amino acids and the following scaffold: X11CCX7CX2CXCX3C. At the frog neuromuscular junction, CcTx at nanomolar concentrations selectively increased nerve terminal excitability so that a single nerve stimulation triggered trains of repetitive or spontaneous synaptic potentials and action potentials. In contrast, CcTx had no noticeable effect on muscle excitability even at concentrations 100 x higher than those that affected motor nerve terminals, as revealed by direct muscle stimulation. In addition, CcTx increased miniature endplate potential (MEPP) frequency in a Ca2+-free medium supplemented with ethylene glycol-bis-(beta-aminoethyl ether)-N,N,N', N'-tetraacetic acid (EGTA). Blockade of voltage-dependent sodium channels with tetrodotoxin (TTX) either prevented or suppressed the increase of MEPP frequency induced by the toxin. CcTx also produced a TTX-sensitive depolarization of the nodal membrane in single myelinated axons giving rise, in some cases, to repetitive and/or spontaneous action potential discharges. In addition, CcTx increased the nodal volume of myelinated axons, as determined using confocal laser scanning microscopy. This increase was reversed by external hyperosmolar solutions and was prevented by pretreatment of axons with TTX. It is suggested that CcTx, by specifically activating neuronal voltage-gated sodium channels at the resting membrane potential, produced Na+ entry into nerve terminals and axons without directly affecting skeletal muscle fibres. CcTx belongs to a novel family of conotoxins that targets neuronal voltage-gated sodium channels.

Biochemical characterization and nuclear magnetic resonance structure of novel alpha-conotoxins isolated from the venom of Conus consors.

Two novel alpha-conotoxins were purified and characterized from the venom of the fish-hunting cone snail Conus consors. These peptides were identified by screening HPLC fractions of the crude venom and by binding experiments with Torpedo nicotinic acetylcholine receptor. The toxins named alpha-CnIA and alpha-CnIB exhibited sequences of 14 and 12 amino acids, respectively. The alpha-CnIA represents the main alpha-conotoxin contained in the venom, whereas alpha-CnIB is present in a relatively small amount. Chemical synthesis of alpha-CnIA was carried out using the Fmoc methodology by selective disulfide bond formation. The biological activity of the toxin was assessed in fish and mice. The alpha-CnIA inhibited the fixation of iodinated alpha-bungarotoxin to Torpedo nicotinic acetylcholine receptors with an IC50 of 0.19 microM which can be compared to the IC50 of 0.31 microM found for the previously characterized alpha-MI isolated from the piscivorous Conus magus. The synthetic alpha-CnIA blocked spontaneous and evoked synaptic potentials in frog and mouse isolated neuromuscular preparations at sub-micromolar concentrations. Solution NMR of this toxin indicated a conformational heterogeneity with the existence of different conformers in solution, at slow and intermediate exchange rates relative to the NMR chemical shift time scale, similar to that reported for alpha-GI and alpha-MI. NMR structures were calculated for the major NMR signals representing more than 80% of the population at 5 degrees C.

Divergent and common groups of proteins in glands of venomous snakes.

Protein contents of venom-producing glands from the sea-snake Laticauda colubrina (LC) and terrestrial Vipera Russelli (VR) were studied using high-resolution two-dimensional gels: isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (IEF/SDS-PAGE) and nonequilibrium pH gradient electrophoresis (NEPHGE) followed by SDS-PAGE. Tentative identities of numerous proteins were established using their amino acid compositions and in certain cases the identities were verified by microsequencing of their N-terminals and internal fragments. As expected, we found several proteins known to be present in the venom of the respective snakes. These include numerous isoforms of phospholipase A2 (PLA2) in both snake glands, various neurotoxins in LC glands and factor IX/factor X-binding protein, hemorrhagic factor and coagulation factor X activating enzyme in Russell's viper glands (VR). Not unexpectedly, we also found a number of cell housekeeping proteins, cytoskeletal proteins, proteins that are necessary for folding, such as heat-shock proteins, protein disulfide-isomerase and peptidyl-prolyl cis/trans isomerases. Unexpectedly, however, the glands of Laticauda colubrina and Russell's viper include a large quantity of antihemorrhagic factor and inhibitor of PLA2, respectively, that have been previously described in snake plasma. The possible reason associated with the presence of these components in venom glands is discussed.

Purification of guinea pig YKL40 and modulation of its secretion by cultured articular chondrocytes.

The aim of this study was to purify, characterize, and study the regulation at the chondrocyte level of the guinea pig (gp) homologue of human (R) YKL40, a putative marker of arthritic disorders. Studying YKL40 in guinea pigs is of particular interest, as age-related osteoarthritis develops in this species spontaneously. Both N-terminal sequencing and total amino acid composition of gpYKL40 purified from the secretion medium of cultured articular chondrocytes indicate a high degree of identity with hYKL40. gpYKL40 was found to contain complex N-linked carbohydrate, as demonstrated by N-glycosidase F and endoglycosidase F digestion. Isoelectric focusing demonstrated the presence of a major band at pI 6.7. The secretion of gpYKL40 by confluent articular chondrocytes in the extracellular medium was studied by immunoblotting. gpYKL40 was released by chondrocytes continuously over a 7 day period and did not appear to be degraded by proteinases, as its signal intensity in cell-free medium at 37 degrees C did not decrease with time. Thus, gpYKL40 displays high stability and accumulates in extracellular medium without reaching a steady-state level. Among the main factors known to regulate cartilage metabolism, IL-1beta, TNF-alpha, bFGF, or 1,25(OH)2D3 did not alter the basal level of gpYKL40, and retinoic acid had a slight inhibitory effect; TGF-beta and IGF-I and -II dose-dependently and inversely modulated this basal level. TGF-beta at 5 ng/ml decreased extracellular gpYKL40 2.9-fold, whereas IGF-I and IGF-II at 50 ng/ml increased extracellular gpYKL40 3.6- and 3.4-fold, respectively. The present biochemical and biological findings give new insights for studying the function of YKL40 in cartilage.

Consequence of the removal of evolutionary conserved disulfide bridges on the structure and function of charybdotoxin and evidence that particular cysteine spacings govern specific disulfide bond formation.

Scorpion toxins are miniglobular proteins containing a common structural motif formed by an alpha-helix on one face, an antiparallel beta-sheet on the opposite face, and three disulfide bonds making up most of its internal volume. We have investigated the role of these evolutionary conserved bonds by replacing each couple of bridged cysteine residues of the scorpion charybdotoxin by a pair of nonbridging L-alpha-aminobutyric acid (Aba) residues. Three analogues were obtained by solid-phase synthesis, Chab I, Chab II, and Chab III, containing the Aba residues in positions 7 and 28, 13 and 33, 17 and 35, respectively. Circular dichroism analysis showed that the purified Chab II acquired a conformation similar to that of charybdotoxin, while the Chab I and Chab III possess decreased nativelike characteristics. All analogues block single high-conductance Ca(2+)-activated K+ channels from rat skeletal muscle inserted into planar lipid bilayers, but with different potencies. Chab II is the most active analogue (KD = 8.0 x 10(-8) M), with a 9-fold lower affinity as compared to native charybdotoxin. Chab I and Chab III have, respectively, 180- and 580-fold lower affinity. Therefore, the removal of evolutionary conserved disulfide bridges does not prevent the toxin to adopt a functional and presumably nativelike structure. However, removal of one disulfide bond affects the yields of formation of correct pairing between the remaining cysteine residues, and only Chab I preserves the ability to form the native disulfide pairings with high efficiency. This is the only analogue to preserve particular spacings of three and one residue between the cysteines, which have been described to thermodynamically disfavor disulfide bond formation between the cysteines [Zhang R., and Snyder, G. H. (1989) J. Biol. Chem. 264, 18472-18479]. Therefore, we conclude that the position of the cysteine residues in the sequence of charybdotoxin, by disfavoring specific pairings and favoring others, may govern selective formation of specific disulfide bonds, thus, explaining the efficient folding properties of Chab I and of native charybdotoxin. The structural properties of the Chab analogues and the discovered role of the cysteine spacings have interesting implications in protein design and engineering.

Subunit of glycosylation-inhibiting factor is an abundant protein that binds to certain glycoproteins and sugars.

12 kDa subunit of glycosylation-inhibiting factor (GIF) is an abundant protein that can be isolated to homogeneity from different mammalian organs by successive application of the carboxymethylcellulose cation exchanger CM52, preparative flat-bed isoelectrofocusing and repeated application of CM52-cellulose. Several isoforms of the 12 kDa GIF subunit exist in mammalian tissues. Conformational stability of two isoforms of a 12 kDa porcine GIF subunit have been studied by CD. Conformation of the protein remains stable within the range 20 degrees to 60 degrees C. Over 60 degrees C the protein undergoes irreversible denaturation. The 12 kDa GIF subunit is not stable within the pH range 2 to 3, adopts quasi-native structure within the pH range 3.5 to 5 while it remains stable between the pHs 6 to 10. The 12 kDa GIF subunit strongly binds to CM52-cellulose from which it can be eluted at concentrations of NaCl higher than 0.6 M. The GIF subunit may also be eluted from the modified cellulose using certain glycoproteins and sugars. High abundance of the 12 kDa GIF subunit in different mammalian tissues and its capacity to bind certain glycoproteins and sugars may suggest that the protein might be involved in regulatory mechanisms of glycoprotein transport (chaperone for glycoproteins) and modulation of interactions between secreted glycoproteins and the cell surface receptors.

Cytotoxicity of copper complexes of 2-furaldehyde oxime derivatives in murine and human tissue cultured cell lines.

The copper complexes of furan oxime derivatives were found to be potent cytotoxic agents in both murine and human tissue cultured cell lines which were either suspended or solid tumors. The ED50 values were frequently improved over the clinically useful antineoplastic agents. These copper complexes of 2-furaldehyde oximes were effective inhibitors of L1210 lymphoid leukemia DNA synthesis followed by RNA synthesis. Purine synthesis regulatory enzyme activities were markedly reduced by the compounds with marginal inhibition of t-RNA polymerase, and nucleoside kinases activities. L1210 DNA topoisomerase II activity was markedly reduced with IC50 values better than the standard VP-16, etoposide. Yet, the copper complexes caused no further protein linked breaks than VP-16 did, but did block phosphorylation activation of the topoisomerase II enzyme.

A simple mathematical model and practical approach for evaluating citric acid cycle fluxes in perfused rat hearts by 13C-NMR and 1H-NMR spectroscopy.

We propose a simple mathematical model and a practical approach for evaluating the flux constant and the absolute value of flux in the citric acid cycle in perfused organs by 13C-NMR and 1H-NMR spectroscopy. We demonstrate that 13C-NMR glutamate spectra are independent of the relative sizes of the mitochondrial and cytosolic compartments and the exchange rates of glutamates, unless there is a difference in 13C chemical shifts of glutamate carbons between the two compartments. Wistar rat hearts (five beating and four KCl-arrested hearts) were aerobically perfused with 100% enriched [2-(13)C]acetate and the kinetics of glutamate carbon labeling from perchloric acid extracts were studied at various perfusion times. Under our experimental conditions, the citric acid cycle flux constant, which represents the fraction of glutamate in exchange with the citric acid cycle per unit time, is about 0.350 +/- 0.003 min(-1) for beating hearts and 0.0741 +/- 0.004 min(-1) for KCl-arrested hearts. The absolute values of the citric acid flux for beating hearts and for KCl-arrested hearts are 1.06 +/- 0.06 micromol x min(-1) x mg(-1) and 0.21 +/- 0.02 micromol x min(-1) x g(-1), respectively. The fraction of unlabeled acetate determined from the proton signal of the methyl group is small and essentially the same in beating and arrested hearts (7.4 +/- 1.7% and 8.8 +/- 2.1%, respectively). Thus, the large difference in the Glu C2/C4 between beating and arrested hearts is not due to the important contribution from anaplerotic sources in arrested hearts but simply to a substantial difference in citric acid cycle fluxes. Our model fits the experimental data well, indicating a fast exchange between 2-oxoglutarate and glutamate in the mitochondria of rat hearts. Analysis of the flux constant, calculated from the half-time of glutamate C4 labeling given in the literature, allows for a comparison of the citric acid flux for various working conditions in different animal species.

A potassium-channel toxin from the sea anemone Bunodosoma granulifera, an inhibitor for Kv1 channels. Revision of the amino acid sequence, disulfide-bridge assignment, chemical synthesis, and biological activity.

The potassium channel toxin secreted by the sea anemone Bunodosoma granulifera (BgK) is a 37-amino-acid peptide containing three disulfide bridges. Because a synthetic peptide corresponding to the reported sequence of BgK was found not to fold properly, the sequence was determined again. The new sequence differed from the previous one in the C-terminal tetrapeptide, which contains two cysteines involved in disulfide bridging. The revised sequence is: V C R D W F K E T A C R H A K S L G N C R T S Q K Y R A N C A K T C E L C. The toxin BgK was synthesized according to the new sequence and folded successfully. Disulfide bridges were assigned by peptide mapping on both natural and synthetic forms to be between Cys2-Cys37, Cys11-Cys30 and Cys20-Cys34. The toxin contains a C-terminal free carboxylate as shown by comparing the native toxin with two synthetic peptides containing the C-terminus in either the carboxylate or carboxamido form. Synthetic BgK inhibits binding of 125I-alpha-dendrotoxin to rat brain synaptosomal membranes, similarly to natural BgK (nanomolar range). No activity was observed on maxi-K+ channels incorporated into planar lipid bilayers. The ability of BgK to block voltage-dependent K+ channels was determined from recordings of whole cell currents in Xenopus oocytes injected with cRNA encoding three cloned Kv1 channels (Kv1.1, Kv1.2, Kv1.3) and one Kv3 (Kv3.1) channel. The Shaker-related Kv1 channels are equally affected by BgK, while the Shaw-related channel Kv3.1 is insensitive up to 0.125 microM toxin. Indeed, half blockage of the current through the three Kv1 channels tested occurred in the same concentration range (Kd = 6 nM for Kv1.1, 15 nM for Kv1.2, 10 nM for Kv1.3). The specificity of BgK for the Shaker-related K+ channels indicates that BgK is able to discriminate a large group of neuronal Kv1 channels in situ. The sequence, the disulfide bridge pattern, the secondary structure and the biological activity of BgK demonstrated that the sea anemone toxins, i.e. BgK, ShK and Kaliseptine, constitute novel molecular probes useful for investigating K+ channel properties.

Erythrocyte spermine levels: a prognostic parameter in childhood common acute lymphoblastic leukemia.

Polyamines have been implicated to play a role in cell proliferation and in cancer development. Ninety percent of the circulating spermidine (Spd) and spermine (Spm) are transported by red blood cells (RBC). RBC Spd and Spm levels were prospectively determined in 63 unselected children with common acute lymphoblastic leukemia. The Spm and Spd levels were not correlated with white blood cell (WBC) count. On the basis of the polyamine levels it was possible to discriminate four groups with P< 10(-3). In C1, C2, C3 and C4 group the Spm level was respectively 90 (39-597), 3.75 (1-7.45), 9.95 (2.9-12.6) and 17(6.3-33.8). The probability of relapse-free survival (RFS) of the 58 children who entered complete remission was 55% +/- 9. For the groups C1 (n = 6), C2 (n = 16), C3 (n = 21) and C4 (n= 15) groups, the RFS was 25% +/- 20, 73% +/- 12, 73% +/- 13 and 32% +/- 13 respectively. For children with Spm levels <13/> or = 13nmol/8 x 10(9) RBC, event-free survival (EFS) was 54% +/- 11/33% +/- 10 and RFS was 64% +/- 12/38% +/- 11 respectively (P < 0.03, P < 0.005). Our clinical study shows clearly that an RBC spermine level could be used as parameter of prognosis at the time of diagnosis, particularly for patients with intermediary WBC count.

Mathematical model for evaluating the Krebs cycle flux with non-constant glutamate-pool size by 13C-NMR spectroscopy. Evidence for the existence of two types of Krebs cycles in cells.

A practical method using matrix operations is proposed for studying the isotopic transformation of glutamate, or any other metabolite isotopomers, in the Krebs cycle. Two mathematical models were constructed for evaluating the Krebs cycle flux where the enrichment of [2-13C]acetyl-CoA is not 100% and the total glutamate concentration remains constant or varies during incubation. A comparative study of [1-13C]glucose metabolism was subsequently carried out using Saccharomyces cerevisiae cells from two different strains (ATCC-9763 and NCYC-239) by 13C-NMR spectroscopy and biochemical techniques. The results show that there are two types of Krebs cycles in cells. The first is represented by the ATCC cells which contain a small amount of 2-oxoglutarate dehydrogenase and hence the flux in the Krebs cycle is negligible. With [1-13C]glucose as a carbon source, the 13C-NMR spectra of glutamate exhibit the C2 and C4 resonances that are almost equivalent and much greater than that of the C3. Labeled metabolites derived from [1-13C]glucose enter the Krebs cycle at two points: oxaloacetate and citrate. The second cell type is represented by NCYC-239. The C2 and C3 areas are equivalent and smaller than the C4 resonance. The results suggest that labeled metabolites enter the Krebs cycle only at the citrate level via acetyl-CoA, 2-oxoglutarate dehydrogenase is present but pyruvate carboxylase is virtually absent or inactivated. When both are incubated with glucose, the total concentration of glutamate was found to decrease with the incubation time. The fraction of glutamate in isotopic exchange with the Krebs cycle in NCYC-239 cells is about 2.6% and the reduction in glutamate concentration is about 0.5%/min. Using our model, with a variable glutamate pool size, good agreement between the theoretical and experimental data is obtained.

Mathematical models for determining metabolic fluxes through the citric acid and the glyoxylate cycles in Saccharomyces cerevisiae by 13C-NMR spectroscopy.

We propose, first, a practical method for studying the isotopic transformation of glutamate or any other metabolite isotopomers in the citric acid and the glyoxylate cycles; second, two mathematical models, one for evaluating the flux through the citric acid cycle and the other for evaluating the flux through the latter coupled to the glyoxylate cycle in yeast. These models are based on the analysis of 13C-NMR spectra of glutamate obtained from Saccharomyces cerevisiae, NCYC strain, fed with 100% enriched [2-13C]acetate. The population of each glutamate isotopomer, the change in intensity of each multiplet component or the enrichment of any glutamate carbon is expressed by a specific analytical equation from which the flux in the citric acid and the glyoxylate cycles can be deduced. The aerobic metabolism of 100% [2-13C]acetate in acetate-grown S. cerevisiae cells was studied as a function of time using 13C-NMR. 1H-NMR and biochemical techniques. The C1 and C6 doublet and singlet of labeled trehalose increase continuously with time indicating that there is no isotopic transformation between trehalose isotopomers even though the corresponding formation rates are different. By contrast, the glutamate C4 singlet increases then decreases with time. The C4 doublet, which is lower than the singlet for t < 60 min, increases continuously and becomes higher than the singlet for t > 90 min. A similar observation was made for the C2 resonance singlet and doublet. In addition, the glutamate C2 multiplet consists of only seven instead of nine peaks as in random labeling. These results agree well with our models and demonstrate that, in the presence of acetate, anaplerotic carbon sources involved in the synthesis of acetyl-CoA are negligible in yeast. The flux in the citric acid cycle was deduced from a plot of the C4 area versus incubation time, while the flux within the glyoxylate cycle was determined from the relative intensity of the glutamate C4 doublet and singlet. The fluxes in the citric acid and the glyoxylate cycles were found to be comparable. The proportion of glutamate in isotopic exchange with the citric acid cycle is about 2.5% min1 in yeast.

Amino acid analysis of proteins separated by two-dimensional electrophoresis in maize: isoform detection and function identification.

The possibility of using experimentally determined amino acid composition to assess relatedness between 75 proteins separated by two-dimensional electrophoresis (2-DE) and to identify them was tested on maize. Two independent parameters, the relative Euclidean distance and the correlation coefficient between the amino acid compositions, were evaluated and used. Previous sequence information for 31 out of the 75 proteins made it possible to evaluate the method for the detection of isoforms and for identification. However, the extension of the interrogation beyond maize to all plant sequences raised the problem of false positives that could nevertheless be limited by replications and by using additional information. The efficiency of the method to assess relatedness between proteins should make amino acid composition analysis a valuable tool in large protein characterization programs based on 2-DE, by facilitating the transfer of information from one well-documented organ/tissue or genotype to another.

Proteins and their amino acid compositions: uniqueness, variability, and applications.

Amino acid compositions (AAC) of proteins were analyzed in terms of their uniqueness and variability. Using several measures of convergence between the AACs of randomly chosen proteins versus those stored in protein data banks, it was established that certain families of proteins have unique AACs despite the mutations of their sequences which were imposed in the process of evolution. AACs may be used to establish the identities of many proteins which were sorted through various chromatographic media prior to their fractionation on two-dimensional (2D) gels. Subfractionations of proteins markedly enhance the chances for proper identification of low-abundant proteins which rest inaccessible if the total protein extract of an organ is analyzed on 2D gels. Although the amino acid composition versus protein identity (AAC-PI) method allows identification with high confidence of unique proteins resolved on monodimensional SDS-PAGE (1D) gels and arrays of protein isoforms resolved on two-dimensional (2D) gels, selective immunoblotting is still a more robust method. Thus, in principle, the AAC-PI method may allow limiting the number of "unknown" spots on 2D gels which could be further investigated by microsequencing and/or mass spectroscopy. However, to resolve certain ambiguities inherently linked with protein identities derived only from their AACs, the AAC-PI method must be sometimes aided by microsequencing and immunoblotting, especially in the construction of high-resolution 2D maps of proteins. A suite of algorithms which form the AAC-PI method are described in detail.

Determination of erythrocyte polyamines as a predictive method in tumour diagnosis. An animal study with chemically induced tumours.

There have been numerous attempts in the past to use polyamine determinations in body fluids for tumour diagnosis. Since spermidine (Spd) and spermine (Spm) are mainly transported in blood by erythrocytes, this study was concerned with the diagnostic possibilities of red blood cell (RBC) polyamine determinations. In tumour-grafted animals we observed that RBC polyamine levels correlated with the tumour mass progression and increased before the tumour was palpable. Discrepancies between the evolution of RBC polyamine levels in tumour-grafted animals and in cancer patients were probably due to the non-continuous growth of the tumours in patients. Therefore, an animal model was sought which mimicked the clinical situation. In the present experiments, ethylnitrosourea induced tumours were used which, in analogy to the clinical situation, had an undetermined time of the appearance in a non-predetermined proportion of the animals. RBC polyamines were determined over a period of 7 months in 154 rats. A total of 2,290 RBC polyamine determinations were performed during this study. The data clearly demonstrate the appearance of elevated Spd concentrations in advance of tumour diagnosis by conventional clinical methods. In 71% of the rats which later developed a tumour, abnormal Spd levels (> 40 nmol/8.109 RBC) preceded, by 35 +/- 31 days, the first clinical symptoms for the presence of a tumour. In 29% of the animals, abnormal RBC Spd concentrations were observed at the time of tumour diagnosis. Elevation of Spm concentrations (> 6 nmol/8.10(9) RBC) was less frequent. RBC polyamine levels did not allow discrimination between malignant and non malignant tumours. This confirms earlier findings that RBC polyamines are markers of the cell proliferation rate, but not for the presence of a malignant tumour. Elevated RBC polyamine concentrations are an index of the intensity of hyperplastic processes, which can be clinically used for the early detection of proliferative phases of tumours, thus allowing timely therapeutic measures.

Amino acid compositions of proteins and their identities.

A critical overview is given on the application of amino acid composition data for the establishment of the protein's identity (amino acids composition vs. protein identity, the AAC-PI method). Several criteria are used to measure the differences between the amino acid compositions of various proteins. The AAC-PI method unambiguously identifies proteins which belong to the families with a high phylogenetic conservancy of their sequences. The identification of pure proteins can be accomplished with a relatively high level of confidence. The AAC-PI method, however, sometimes needs the support of N-terminal or internal sequencing of proteins since, alone, it cannot distinguish whether the lack of finding a candidate protein in protein data bases is because the investigated amino acid composition corresponds to an unknown protein or its processed form or because it is a sum of at least two protein components, or whether it is due to other experimental errors. The identification of a few new proteins such as "arginine-rich protein", macrophage migration inhibitory factor (MIF) and the preformed neurotrophic factor present in the calf brain cytosol is also reported.