The dual aptamer approach: rational design of a high-affinity FAD aptamer.

A design strategy for high-affinity aptamers of complex biomolecules is presented. We developed an RNA with FAD-binding properties by combining known ATP- and FMN-aptamers. Cooperative binding of FAD was shown by SPR spectroscopy and fluorescence assays. The strategy should be transferable to several other biomolecules.

Analysis of subcellular surface structure, function and dynamics.

Analytics of single biological cells allows quantitative investigation from a structural, functional and dynamical point of view and opens novel possibilities to an unamplified subcellular analysis. In this article, we report on three different experimental methods and their applications to single cellular systems with a subcellular sensitivity down to the single molecule level. First, the subcellular surface structure of living bacteria (Corynebacterium glutamicum) was investigated with atomic force microscopy (AFM) at the resolution of individual surface layer (S-layer) proteins; discrimination of bacterial strains that lack the expression of hexagonally packed surface layer proteins was possible. Second, quantitative measurement of individual recognition events of membrane-bound receptors on living B-cells was achieved in single cell manipulation and probing experiments with optical tweezers (OT) force spectroscopy. And third, intracellular dynamics of translocating photoactivatable GFP in plant protoplasts (Nicotiana tabacum BY-2) was quantitatively monitored by two-photon laser scanning microscopy (2PLSM).

A novel model for the investigation of orthotopically growing primary and secondary bone tumours using intravital microscopy.

Here is reported the development of an experimental model using intravital microscopy as a tool to orthotopically investigate malignant bone tumours. Although up to 85% of the most frequently occurring malignant solid tumours, such as lung and prostate carcinomas, metastasize into the bone, and despite the knowledge that a tumour's course may be altered by its surrounding tissue, there is no adequate experimental model available enabling the investigation of orthotopically grown bone tumours in vivo. Intravital microscopy is an internationally accepted experimental method, used in various acute and chronic animal models, that enables qualitative and quantitative analysis of the angiogenesis, microcirculation, growth behaviour, etc. of various benign and malignant tissues. Non-invasive investigations of up to several weeks are possible. Additionally, tissue samples can be taken after termination of the in vivo experiments for further ex vivo investigation (histology, immunohistochemistry, molecular biology, etc.), elucidating the mechanisms that underlie the in vivo observations. Severe combined immunodeficient mice were fitted with a cranial window preparation where the calvaria served as the site for orthotopic implantation of the solid human tumours Saos-2 osteosarcoma (primary) and A 549 lung carcinoma and PC-3 prostate carcinoma (secondary). In all preparations, the take rate was 100%. Histological assessment confirmed the data obtained in vivo, showing typical tumour growth with infiltration of the surrounding osseous and soft tissues. This novel model serves as a valuable tool in understanding the biology of primary and secondary bone tumours in physiological and pathophysiological situations, with implications for the most areas of tumour therapy such as chemotherapy, radiation and antiangiogenesis.

Developmentally regulated expression of a cyclic nucleotide-gated ion channel from Arabidopsis indicates its involvement in programmed cell death.

Cyclic nucleotide-gated ion channels have been identified in animals and plants. However, the physiological role of these ion channels in plant cells and in non-receptor cells of animals is still unknown. Here, we focused on one member of the large gene family of cyclic nucleotide-gated ion channels from Arabidopsis thaliana (L.) Heynh., AtCNGC2. The analysis of the transcriptional regulation revealed that expression of AtCNGC2 is low in etiolated seedlings but increases substantially during de etiolation. The use of promoter::GUS plants revealed that expression of AtCNGC2 in seedlings is highest in cotyledons after release of the developmental arrest by light. Expression of AtCNGC2 was also observed in later stages of plant development. Investigations using the promoter::GUS plants demonstrated that AtCNGC2 is expressed in flowers during organ senescence and in the dehiscence zone of siliques. Furthermore, expression of AtCNGC2 was transiently induced during leaf and cell culture senescence. These results indicate a potential function for AtCNGC2 in the initiation of developmentally regulated cell death programs.

Import of Agrobacterium T-DNA into plant nuclei: two distinct functions of VirD2 and VirE2 proteins.

To study the mechanism of nuclear import of T-DNA, complexes consisting of the virulence proteins VirD2 and VirE2 as well as single-stranded DNA (ssDNA) were tested for import into plant nuclei in vitro. Import of these complexes was fast and efficient and could be inhibited by a competitor, a nuclear localization signal (NLS) coupled to BSA. For import of short ssDNA, VirD2 was sufficient, whereas import of long ssDNA additionally required VirE2. A VirD2 mutant lacking its C-terminal NLS was unable to mediate import of the T-DNA complexes into nuclei. Although free VirE2 molecules were imported into nuclei, once bound to ssDNA they were not imported, implying that when complexed to DNA, the NLSs of VirE2 are not exposed and thus do not function. RecA, another ssDNA binding protein, could substitute for VirE2 in the nuclear import of T-DNA but not in earlier events of T-DNA transfer to plant cells. We propose that VirD2 directs the T-DNA complex to the nuclear pore, whereas both proteins mediate its passage through the pore. Therefore, by binding to ssDNA, VirE2 may shape the T-DNA complex such that it is accepted for translocation into the nucleus.

DNA-interactions and nuclear localisation of the chromosomal HMG domain protein SSRP1 from maize.

The structure-specific recognition protein 1 (SSRP1) is a member of the protein family containing a high mobility group (HMG) domain DNA-binding motif. We have functionally characterised the 71.4 kDa Zm-SSRP1 protein from maize. The chromatin-associated Zm-SSRP1 is detected by immunoblot analysis in maize leaves, kernels and suspension culture cells, but not in roots. Mediated by its HMG domain, recombinant Zm-SSRP1 interacts structure-specifically with supercoiled DNA and DNA minicircles when compared with linear DNA. In linear duplex DNA, the protein does not recognise a specific sequence, but it binds preferentially to sequences containing the deformable dinucleotide TG, as demonstrated by a random oligonucleotide selection experiment. Zm-SSRP1 modulates DNA structure by bending the target sequence, since it promotes the circularisation of short DNA fragments in the presence of DNA ligase. Moreover, Zm-SSRP1 facilitates the formation of nucleoprotein structures, as measured using the bacterial site-specific beta-mediated recombination reaction. Analysis of the subcellular localisation of various SSRP1-GFP fusions revealed that, in contrast to HMG domain transcription factors, the nuclear localisation sequence of Zm-SSRP1 is situated within a 20-amino acid residue region adjacent to the HMG domain rather than within the DNA-binding domain. The results are discussed in the context of the likely function of SSRP1 proteins in transcription and replication.

Plant heterotrimeric G protein beta subunit is associated with membranes via protein interactions involving coiled-coil formation.

Gbeta subunits from animals are anchored to membranes via Ggamma subunits. No Ggamma has been identified in plants to date. Using differential centrifugation of Arabidopsis and broccoli extracts, Gbeta was highly enriched in the microsomal pellet. Treatment of microsomes with detergents and salts indicates that plant Gbeta is located at the membrane surface and attached to membranes by hydrophobic interactions. Analysis of transgenic plants expressing Gbeta-GFP fusion proteins showed that mutations in the heptad repeat domain of Gbeta severely diminished their membrane association. We propose that plant Gbeta is anchored to membranes by an unknown protein similar to animal Gbeta by Ggamma, via coiled-coil formation.

Characterisation of a novel gene family of putative cyclic nucleotide- and calmodulin-regulated ion channels in Arabidopsis thaliana.

In plants, cyclic GMP is involved in signal transduction in response to light and gibberellic acid. For cyclic AMP, a potential role during the plant cell cycle was recently reported. However, cellular targets for cyclic nucleotides in plants are largely unknown. Here we report on the identification and characterisation of a new gene family in Arabidopsis, which share features with cyclic nucleotide-gated channels from animals and inward-rectifying K+ channels from plants. The identified gene family comprises six members (Arabidopsis thaliana cyclic nucleotide-gated channels, AtCNGC1-6) with significant homology among the deduced proteins. Hydrophobicity analysis predicted six membrane-spanning domains flanked by hydrophilic amino and carboxy termini. A putative cyclic nucleotide binding domain (CNBD) which contains several residues that are invariant in other CNBDs was located in the carboxy terminus. This domain overlaps with a predicted calmodulin (CaM) binding site, suggesting interaction between cyclic nucleotide and CaM regulation. We demonstrated interaction of the carboxy termini of AtCNGC1 and AtCNGC2 with CaM in yeast, indicating that the CaM binding sites are functional. Furthermore, it was shown that both AtCNGC1 and AtCNGC2 can partly complement the K(+)-uptake-deficient yeast mutant CY162. Therefore, we propose that the identified genes constitute a family of plant cyclic nucleotide- and CaM-regulated ion channels.

Nuclear export of proteins in plants: AtXPO1 is the export receptor for leucine-rich nuclear export signals in Arabidopsis thaliana.

Transport across the nuclear envelope is mediated by transport receptors from the Importin beta family. We identified Exportin 1 from Arabidopsis (AtXPO1/AtCRM1) as the nuclear export receptor for proteins carrying leucine-rich nuclear export signals (NESs). AtXPO1 shares 42-50% identity with its functional homologues from humans and yeasts. We functionally characterised AtXPO1 by its interaction with NESs of animal and plant proteins, which is inhibited by the cytotoxin leptomycin B (LMB), and also by its interaction with the small GTPase Ran1 in the yeast two-hybrid system. Furthermore, we demonstrated the existence of a nuclear export pathway for proteins in plants. For the characterisation of nuclear export activities, we established an in vivo assay based on the localisation equilibrium of a GFP reporter protein fused to both a nuclear localisation signal (NLS) and an NES motif. Using this in vivo assay we demonstrated that the NES of the heterologous protein Rev is also functional in plants and that its export is inhibited by LMB. In addition, we identified a leucine-rich NES in the Arabidopsis protein AtRanBP1a. The NES, which is located at the carboxy terminus of the protein, is disrupted by mutating three long chain hydrophobic amino acid residues to alanine (L176A, L179A, V181A). In BY-2 protoplasts the NES of AtRanBP1a is functionally indistinguishable from the Rev NES. Our results demonstrate that the machinery for the nuclear export of proteins is functionally conserved in plants.

Characterization of proteins that interact with the GTP-bound form of the regulatory GTPase Ran in Arabidopsis.

Ran, a small soluble GTP-binding protein, has been shown to be essential for the nuclear translocation of proteins and it is also thought to be involved in regulating cell cycle progression in mammalian and yeast cells. Genes encoding Ran-like proteins have been isolated from different higher plant species. Overexpression of plant Ran cDNAs, similarly to their mammalian/yeast homologues, suppresses the phenotype of the pim46-1 cell cycle mutant in yeast cells. The mammalian/yeast Ran proteins have been shown to interact with a battery of Ran-binding proteins, including the guanidine nucleotide exchange factor RCC1, the GTPase-activating Ran-GAP, nucleoporins and other Ran-binding proteins (RanBPs) specific for Ran-GTP. Here, the characterization of the first Ran-binding proteins from higher plants is reported. The yeast two-hybrid system was used to isolate cDNA clones encoding proteins of approximately 28 kDa (At-RanBP1a, At-RanBP1b) that interact with the GTP-bound forms of the Ran1, Ran2 and Ran3 proteins of Arabidopsis thaliana. The deduced amino acid sequences of the At-RanBP1s display high similarity (60%) to mammalian/yeast RanBP1 proteins and contain the characteristic Ran-binding domains. Furthermore, interaction of the plant Ran and RanBP1 proteins, is shown to require the acidic C-terminal domain (-DEDDDL) of Ran proteins in addition to the presence of an intact Ran-binding domain. In whole cell extracts, the GST-RanBP1a fusion protein binds specifically to GTP-Ran and will not interact with Rab/Ypt-type small GTP-binding proteins. Finally, in good agreement with their proposed biological function, the At-Ran and the At-RanBP genes are expressed coordinately and show the highest level of expression in meristematic tissues.

A plant in vitro system for the nuclear import of proteins.

This paper reports the development of an in vitro system that allows the direct assay of protein import into plant nuclei. In this assay the import of fluorescently labelled karyophilic protein substrates into nuclei isolated from evacuolated tobacco BY-2 suspension cells is monitored. It is demonstrated that import of the fluorescently labelled peptide conjugates is rapid, saturable and nuclear localization signal (NLS)-dependent. Exclusion of high molecular weight (70 kDa) dextran and substrates carrying mutated NLS sequences further underline the specificity of this system. Nuclear translocation of karyophilic import substrates in tobacco, similar to mammalian systems, is inhibited by the non-hydrolysable GTP analogue GTP-gamma-S. In contrast, protein uptake is not blocked by wheat germ agglutinin, N-ethyl-maleinimide and iodoacetic acid. Furthermore, it is shown that nuclear import of proteins is only partially inhibited by low temperature (0-4 degrees C). The in vitro nuclear import assay does not depend on exogenously added ATP or cytosolic factors. However, a block of nuclear import with GTP-gamma-S could be overcome by the addition of cytosolic extract, suggesting the dependence on cytosolic factors or proteins. These data indicate that the characteristics of nuclear protein import in plant and mammalian cells are similar, but may be, at least in some respects, also different from each other.

Characterization of membrane-bound small GTP-binding proteins from Nicotiana tabacum.

We have cloned nine cDNAs encoding small GTP-binding proteins from leaf cDNA libraries of tobacco (Nicotiana tabacum). These cDNAs encode distinct proteins (22-25 kD) that display different levels of identity with members of the mammalian Rab family: Nt-Rab6 with Rab6 (83%), Nt-Rab7a-c with Rab7 (63-70%), and Nt-Rab11a-e with Rab11 (53-69%). Functionally important regions of these proteins, including the "effector binding" domain, the C-terminal Cys residues for membrane attachment, and the four regions involved in GTP-binding and hydrolysis, are highly conserved. Northern and western blot analyses show that these genes are expressed, although at slightly different levels, in all plant tissues examined. We demonstrate that the plant Rab5, Rab6, and Rab11 proteins, similar to their mammalian and yeast counterparts, are tightly bound to membranes and that they exhibit different solubilization characteristics. Furthermore, we show that the yeast GTPase-activating protein Gyp6, shown to be specifically required to control the GTP hydrolysis of the yeast Ypt6 protein, could interact with tobacco GTP-binding proteins. It increases in vitro the GTP hydrolysis rate of the wild-type Nt-Rab7 protein. In addition, it also increases, at different levels, the GTP hydrolysis rates of a Nt-Rab7m protein with a Rab6 effector domain and of two other chimaeric Nt-Rab6/Nt-Rab7 proteins. However, it does not interact with the wild-type Nt-Rab6 protein, which is most similar to the yeast Ypt6 protein.

Phenotype of the fission yeast cell cycle regulatory mutant pim1-46 is suppressed by a tobacco cDNA encoding a small, Ran-like GTP-binding protein.

Mutations in which the onset of mitosis is uncoupled from the completion of DNA replication has recently been described. Characterization of these mutants led to the identification of Pim1/Spi1 in fission yeast and RCC1/Ran proteins in mammalian cells. Their Saccharomyces cerevisae homologues, the MTR1/CNR1 proteins, appear to be involved in controlling RNA metabolism and transport. Here the isolation and partial characterization of plant cDNA clones which encode proteins homologous to the mammalian/fission yeast/budding yeast Ran/Spi/CNR proteins are reported. Higher plants appear to contain more than one gene per haploid genome which codes for Ran proteins. These genes are expressed in different plant tissues, including root tips and stems, known to contain mitotically active cells. The tobacco Ran-like proteins, like their mammalian and yeast homologues, are soluble proteins which are found in the cytoplasm and in the nucleus. In addition, it has been shown that overexpression of the tobacco Nt-Ran-A1 cDNA suppressed the phenotype of the temperature-sensitive fission yeast pim1-46 mutant. These results suggest that the plant Ran genes can be functionally equivalent to the mammalian/fission yeast/budding yeast Ran/Spi/CNR genes and that they may play a role: (i) in maintaining a coordinated cell cycle; (ii) in controlling RNA metabolism and transport in higher plants; and/or (iii) in protein import into the nucleus.

The ABCD rule of dermatoscopy. High prospective value in the diagnosis of doubtful melanocytic skin lesions.

BACKGROUND: The difficulties in accurately assessing pigmented skin lesions are ever present in practice. The recently described ABCD rule of dermatoscopy (skin surface microscopy at x10 magnification), based on the criteria asymmetry (A), border (B), color (C), and differential structure (D), improved diagnostic accuracy when applied retrospectively to clinical slides. OBJECTIVE: A study was designed to evaluate the prospective value of the ABCD rule of dermatoscopy in melanocytic lesions. METHODS: In 172 melanocytic pigmented skin lesions, the criteria of the ABCD rule of dermatoscopy were analyzed with a semiquantitative scoring system before excision. RESULTS: According to the retrospectively determined threshold, tumors with a score higher than 5.45 (64/69 melanomas [92.8%]) were classified as malignant, whereas lesions with a lower score were considered as benign (93/103 melanocytic nevi [90.3%]). Negative predictive value for melanoma (True-Negative divided by [True-Negative+False-Negative]) was 95.8%, whereas positive predictive value (True-Positive divided by [True-Positive+False-Positive]) was 85.3%. Diagnostic accuracy for melanoma (True-Positive divided by [True-Positive+False-Positive+False-Negative]) was 80.0%, compared with 64.4% by the naked eye. Melanoma showed a mean final dermatoscopy score of 6.79 (SD, +/- 0.92), significantly differing from melanocytic nevi (mean score, 4.27 +/- 0.99; p < 0.01, U test). CONCLUSION: The ABCD rule can be easily learned and rapidly calculated, and has proven to be reliable. It should be routinely applied to all equivocal pigmented skin lesions to reach a more objective and reproducible diagnosis and to obtain this assessment preoperatively.

Analysis of the parsley chalcone-synthase promoter in response to different light qualities.

We examined the chalcone synthase (chs) promoter from parsley [Petroselinum crispum Miller (A.W. Hill)] for the existence of separate promoter elements responsible for transcriptional activation of the chs gene by UV-B and by blue light. A combination of in-vivo foot-printing in parsley cells and light-induced transient expression assays with different chs promoter constructs in parsley protoplasts was used. Dark controls and blue-light-irradiated cells gave identical in-vivo footprints on the chs promoter. Pre-irradiation with blue light prior to a UV-B-light pulse is known to cause a shift in the timing of UV-B-light-induced increase in chs transcription rates. This shift was also manifested on the DNA template, since UV-B-light-induced in-vivo footprints in cells pretreated with blue light were detected earlier than in cells which had been irradiated with a UV-B-light pulse only. Although there was a clear shift in the timing of footprint appearance, the patterns of footprinting did not change. Light-induced transient-expression assays revealed that the shortest tested chs promoter which retained any light responsiveness, was sufficient for mediating both induction by UV light and the blue-light-mediated kinetic shift. These findings argue against a spatial separation of UV-B- and blue-light-responsive elements on the chs promoter. We interpret these data by postulating that the signal transduction pathways originating from the excitation of UV-B- and blue-light receptors merge at the chs promoter, or somewhere between light perception and protein-DNA interaction.

Reticulate porokeratosis--successful treatment with CO2-laser vaporization.

A 35-year-old male patient affected with extensive, itching skin lesions of reticulate porokeratosis is reported. He was successfully treated by CO2-laser vaporization.

[Pigmented urticarial erythema with flaccid atrophy as expression of an unusual manifestation of Lyme borreliosis]. / Pigmentierte urtikarielle Erytheme mit schlaffer Atrophie als Ausdruck einer ungewöhnlichen Manifestation der Lyme-Borreliose.

Unusual courses of infections with borrelia burgdorferi can make diagnosis problematic, but early and adequate therapy is mandatory to avoid further complications. In this paper a patient is presented who developed urticarial erythemas and hyperpigmentation with slack skin atrophy. Positive serological findings and the regression of the skin eruptions under antibiotic therapy confirmed the diagnosis of an unusual manifestation of Lyme borreliosis.