Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms.

Different chemical methods used to attach oligonucleotides by their 5'-end on a glass surface were tested in the framework of solid phase PCR where surface-bound instead of freely-diffusing primers are used to amplify DNA. Each method was first evaluated for its capacity to provide a high surface coverage of oligonucleotides essentially attached via a 5'-specific linkage that satisfyingly withstands PCR conditions and leaves the 3'-ends available for DNA polymerase activity. The best results were obtained with 5'-thiol-modified oligonucleotides attached to amino-silanised glass slides using a heterobifunctional cross-linker reagent. It was then demonstrated that the primers bound to the glass surface using the optimal chemistry can be involved in attaching and amplifying DNA molecules present in the reaction mix in the absence of freely-diffusing primers. Two distinct amplification processes called interfacial and surface amplification have been observed and characterised. The newly synthesised DNA can be detected and quantified by radioactive and fluorescent hybridisation assays. These new surface amplification processes are seen as an interesting approach for attachment of DNA molecules by their 5'-end on a solid support and can be used as an alternative route for producing DNA chips for genomic studies.

New mechanism for electron emission from planar cold cathodes: the solid-state field-controlled electron emitter

A new mechanism for electron emission from planar cathodes is described. The theoretical analysis shows that, with an ultrathin wide band-gap semiconductor layer (UTSC) on a metal, the surface barrier is lowered to approximately 0.1 eV due to the creation of a space charge induced by the electrons injected from the metal. The barrier height depends mostly on the UTSC thickness and not on the state of the surface, as in thermionic and field emissions. This mechanism explains the measured stable emission at 300 K and 10(-7) Torr, with a threshold field of only approximately 50 V/&mgr;m, from these solid-state field-controlled emitters.

Are beta-sheet breaker peptides dissolving the therapeutic problem of Alzheimer's disease?

Alzheimer's disease (AD) is a neurodegenerative disorder for which there is no cure or effective treatment. One of the major neuropathological signatures of AD is the deposition of amyloid plaques in the brain of affected people. Although the role of these structures in the pathogenesis of the disease is not fully understood, recent findings have provided evidence that amyloid may be a key player in the disease. Therefore, preventing and reversing cerebral amyloid deposition have become an attractive therapeutic strategy for AD. We have engineered synthetic beta-sheet breaker peptides to bind soluble amyloid peptide and prevent and reverse its conversion to the beta-sheet rich aggregated structure, precursor of the amyloid plaques. Results in vitro, in cell culture and in vivo suggest that beta-sheet breaker peptides might be candidates for an AD-therapy focused to reduce amyloid deposition.

Theoretical study of field emission by a four atoms nanotip: implications for carbon nanotubes observation.

A fully three-dimensional quantum model is developed to simulate the emission of electrons by a nanotip in applied fields ranging from 0.4 to 0.8 V/A and their diffusion by an extended molecule. It is shown that the widening of the beam, when the applied field is increased, can be attributed to an increase in the number of emitting atoms. Simulated images of a (9,0) carbon nanotube, in a Fresnel projection microscope-type setup, for various applied fields, reproduce the experimental, so-called, "sucking-in" effect. The relationship between this effect and the transmission probability of the nanotube is studied.

Discernibility criterion in Fresnel projection microscopy.

The applicability of the Rayleigh separation criterion in Fresnel electron projection microscopy is studied theoretically. Quantum mechanical simulations of electron scattering by two C60 molecules, at energies of the order of 150 eV, are analysed on the basis of the discernibility criterion of two diffracting apertures. The simple separation criterion derived from Fresnel theory is found to remain pertinent, except for small source to object distances. At these distances, the critical separation distance between the two C60 molecules is such that the 'sucking-in' of the beam between the two nearby C60 molecules cannot be neglected. This leads to a discrepancy with the Rayleigh criterion.

Two-dimensional electrophoresis of membrane proteins: a current challenge for immobilized pH gradients.

Membrane proteins were separated by high resolution two-dimensional (2-D) electrophoresis. On isoelectric focusing (IEF) with immobilized pH gradients severe protein losses in the resulting 2-D map were observed when compared with carrier ampholyte-based IEF. This has been noticed for two different biological systems, namely the chloroplast envelope of spinach and the endocytic vesicles from Dictyostelium discoideum. The possible mechanisms of these losses on immobilized pH gradients are discussed.

Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients.

Membrane and nuclear proteins of poor solubility have been separated by high resolution two-dimensional (2-D) gel electrophoresis. Isoelectric focusing with immobilized pH gradients leads to severe quantitative losses of proteins in the resulting 2-D map, although the resolution is usually high. Protein solubility could be improved by using denaturing solutions containing various detergents and chaotropes. Best results were obtained with a denaturing solution containing urea, thiourea, and detergents (both nonionic and zwitterionic). The usefulness of thiourea-containing denaturing mixtures is shown for microsomal and nuclear proteins as well as for tubulin, a protein highly prone to aggregation.

In vitro reconstituted Dictyostelium discoideum early endosome fusion is regulated by Rab7 but proceeds in the absence of ATP-Mg2+ from the bulk solution.

We characterized the in vitro fusion of endosomal compartments from Dictyostelium discoideum. Fusion activity was restricted to early compartments, was dependent on cytosolic proteins, and was activated by GTP and guanosine 5'-O(3-thio)triphosphate (GTPgammaS). This stimulation suggests the involvement of a small G protein, which we propose to be Rab7 on the basis of the strong inhibitory effect of anti-Rab7 antibodies. It is noteworthy that in the presence of GTPgammaS, the concentration of ATP-Mg2+ could be reduced to less than 1 nM without loss of fusion activity. Under these conditions, competing residual ATP with adenosine 5'-O-(3-thio)triphosphate-Mg2+ also failed to inhibit endosome fusion. The presence of an ATP-depleting system alone blocked fusion probably because endogenous GTP was removed by coupling through NDP kinase. Moreover, whether ATP was present or not, GTPgammaS-activated fusion was equally sensitive to anti-Rab7 antibodies or N-ethylmaleimide and was restricted to early compartments. These results show that soluble ATP-Mg2+ is not needed for endosome fusion. Since homotypic fusion of endosomes in D. discoideum has been shown to depend on the ATPase N-ethylmaleimide-sensitive factor (Lenhard, J. M., Mayorga, L. , and Stahl, P. D. (1992) J. Biol. Chem. 267, 1896-1903), the nucleotide exchange on the N-ethylmaleimide sensitive factor must take place before GTPgammaS activation in this system.

The cysteine proteinase gene cprG in Dictyostelium discoideum has a serine-rich domain that contains GlcNAc-1-P.

A lysosomal cysteine proteinase called proteinase-1 is the major proteolytic enzyme in vegetative cells of Dictyostelium discoideum. This phosphoglycosylated protein contains multiple residues of GlcNAc-1-P linked to peptidyl serines. Here we report the cloning, structure, and expression of its cDNA (cprG). Another cDNA (cprF) closely related to cprG was also cloned and characterized. mRNAs of both genes are present during the vegetative phase and decrease in developing cells. However, the level of cprG mRNA is about 100-fold higher than that of cprF. The predicted protein products of both genes contain a unique serine-rich domain that was previously found only in two Dictyostelium proteinases (CP4 and CP5) that also carry a GlcNAc-1-P-Ser modification. The cprG product, renamed CP7, was tagged with the FLAG-epitope (FLAG-CP7) and shown to bind to cystatin, a highly specific inhibitor of cysteine proteinases. The FLAG-CP7 product also contained both N-linked oligosaccharides and GlcNAc-1-P. Deletion of the serine-rich domain from FLAG-CP7 yields a product that still binds to cystatin, but no longer carries GlcNAc-1-P. This finding supports the idea that the GlcNAc-1-P residues are normally added to the serine-rich domain, found only in vegetative Dictyostelium cysteine proteinases.

Identification of major proteins associated with Dictyostelium discoideum endocytic vesicles.

Magnetic isolation of endocytic vesicles from Dictyostelium discoideum was accomplished after feeding the amoebae with iron oxide particles. Proteins associated with the endocytic vesicles were resolved by SDS-PAGE and digested 'in-gel' with endoproteinase Lys-C or Asp-N to generate peptides for amino acid sequencing. This strategy allowed the identification of the major protein constituents of the vesicles: namely, the A, B, D, E and 110 kDa subunits of a vacuolar type H(+)-ATPase, actin, a Rab 7-like GTPase, a p34 protein corresponding to a new cysteine proteinase and the 25 kDa product of a recently sequenced D. discoideum open reading frame.

Characterization of Dictyostelium discoideum cathepsin D.

Previous studies using magnetic purification of Dictyostelium discoideum endocytic vesicles led us to the identification of some major vesicle proteins. Using the same purification procedure, we have now focused our interest on a 44 kDa soluble vesicle protein. Microsequencing of internal peptides and subsequent cloning of the corresponding cDNA identified this protein as the Dictyostelium homolog of mammalian cathepsins D. The only glycosylation detected on Dictyostelium cathepsin D (CatD) is common antigen 1, a cluster of mannose 6-sulfate residues on N-linked oligosaccharide chains. CatD intracellular trafficking has been studied, showing the presence of the protein throughout the entire endocytic pathway. During the differentiation process, the catD gene presents a developmental regulation, which is also observed at the protein level. catD gene disruption does not alter significantly the cell behaviour, either in the vegetative form or the differentiation stage. However, modifications in the SDS-PAGE profiles of proteins bearing common antigen 1 were detected, when comparing parental and catD(-) cells. These modifications point to a possible role of CatD in the maturation of a few Dictyostelium lysosomal proteins.