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In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commer- cially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30%) and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA. Key words: phylogenetic relationships, Chametrachea, cytochrome c oxidase I

We investigated the phylogenetic relationships among different size groups of the pelagic microcopepod Oncaea venusta Philippi, 1843, by comparing the patterns of genetic variation of specimens collected at five locations of the Indo-West Pacific Ocean. Phylogenetic analyses were based on sequence data obtained from two DNA markers: A 310 bp fragment of the mitochondrial cytochrome b (cyt b) gene and a 480 bp fragment of the nuclear internal transcribed spacer 1 (ITS1). The cyt b sequences showed a much higher level of variation than those from ITS1, but the conclusion from both genes was concordant. Four genetic clades could be differentiated. A small- and a large-size group were unambiguously assigned to two distinct clades or lineages. Unexpectedly, the medium-sized individuals could be divided into another two different genetic clades. All four lineages were supported by high bootstrap values. The high levels of sequence divergence under sympatric conditions indicated that at least the two main groups, the large and the small one, may be assigned to different species. For the medium-size group additional morphological studies and more sensitive nuclear markers are required to clarify their taxonomic status.

The aim of this study is to reveal gene flow between populations of the coral reef dwelling lionfish Pterois miles in the Gulf of Aqaba and northern Red Sea. Due to the fjord-like hydrography and topology of the Gulf of Aqaba, isolation of populations might be possible. Analysis of 5' mitochondrial control region sequences from 94 P. miles specimens detected 32 polymorphic sites, yielding 38 haplotypes. Sequence divergence among different haplotypes ranged from 0.6% to 9.9% and genetic diversity was high (h=0.85, pi=1.9%). AMOVA indicates panmixia between the Gulf of Aqaba and northern Red Sea, but analysis of migration pattern shows an almost unidirectional migration originating from the Red Sea.

The distribution of Octopus vulgaris has not yet been completely clarified. For a long time, a cosmopolitan distribution with unknown distribution limits had been assumed. This assumption has recently been questioned and it has been postulated that the distribution is restricted to the Mediterranean and the northeastern Atlantic. However, as our previous studies show, the existence of O. vulgaris can be confirmed for the Mediterranean and the whole eastern Atlantic, and evidence is provided for its occurrence in the western Atlantic. The aim of the present work is to extend our previous data matrix and to clarify whether O. vulgaris exists in the northwestern Pacific. Therefore, the sequence variation in ostensible O. vulgaris from 13 localities in the Mediterranean (France), the Atlantic Ocean [Lanzarote, Senegal, South Africa (Atlantic, Indian Ocean), Tristan da Cunha, north, middle and south Brazil], the Caribbean Sea (Venezuela) and the Pacific Ocean (Taiwan, Japan and Costa Rica) was examined using the mitochondrial genes coding for the 16S rRNA and cytochrome oxidase subunit III (COIII). Sequence divergence was relatively low between populations of O. vulgaris from the Mediterranean, the eastern and western Atlantic (except north Brazil), Venezuela, Taiwan and Japan compared with other species of the genus Octopus. Trees constructed by using maximum likelihood, neighbour joining and maximum parsimony algorithms (PAUP) show the above-mentioned populations from the Mediterranean, the western and eastern Atlantic, Venezuela and the northwestern Pacific (Japan and Taiwan) as a monophyletic cluster. Thus, even if the Octopus vulgaris-like octopus from north Brazil should turn out a cryptic species, the data of this work not only support our hypothesis of the distribution of O. vulgaris in the Mediterranean, the eastern and western Atlantic but also show that O. vulgaris is present in the northwestern Pacific, namely in the waters of Taiwan and Japan. Zusammenfassung Die Verbreitung von Octopus vulgaris ist immer noch nicht vollstandig geklart. Ursprunglich ging man von einer kosmopolitischen Verbreitung mit unbekannten Verbreitungsgrenzen aus. Diese kosmopolitische Verbreitung wurde allerdings kurzlich in Frage gestellt und die Verbreitung auf das Mittelmeer zuzuglich des angrenzenden Nordost-Atlantiks beschrankt. Unsere vorausgegangenen Untersuchungen bestatigten das Vorkommen von O. vulgaris im Mittelmeer und im ostlichen Atlantik. Wir haben jedoch auch Hinweise fur die Verbreitung im westlichen Atlantik gefunden. Das Ziel dieser Arbeit ist, unsere bereits vorhandene Datenmatrix zu erweitern und auserdem zu prufen, ob O. vulgaris ebenfalls im nordwestlichen Pazifik auftritt. Daher wurden Sequenzen von 12 voneinander weit entfernt lebenden Populationen von vulgaris-ahnlichen Oktopoden gewonnen. Die Gewebeproben stammen aus Kustengewassern des Mittelmeeres (Frankreich), des Atlantiks (Lanzarote, Senegal, Sudafrika [Atlantik, Indischer Ozean], Tristan da Cunha, Nord-, Mittel- und Sudbrasilien), des Karibischen Meeres (Venezuela) und des Pazifiks (Taiwan, Japan und Costa Rica). Als Zielsequenz dienten die mitochondrialen Gene 16S rRNA und Cytochromoxidase III (COIII). Verglichen mit den Divergenzen zu anderen Arten der Gattung Octopus wurden zwischen den Sequenzen von O. vulgaris aus dem Mittelmeer, dem Ost- und West-Atlantik (ohne Nordbrasilien), Venezuela, Taiwan und Japan nur relativ geringe Divergenzen festgestellt. Fur die Auswertung wurden MP-, Neighbour-Joining- und ML-Algorithmen verwendet. Diese phylogenetischen Analysen ergaben eine Monophylie fur die Populationen aus dem Mittelmeer, dem Ost- und West-Atlantik (ohne Nordbrasilien), Venezuela, Taiwan und Japan. Die Daten dieser Arbeit stutzen daher die Hypothese, dass O. vulgaris auch im West-Atlantik sowie im Nordwestpazifik vor Taiwan und Japan auftritt.

This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois . MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) “ Pterois ” clade ( Pterois miles and Pterois volitans ), and (2) “ Pteropterus–Dendrochirus ” clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the “ Pteropterus–Dendrochirus ” clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus . The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4–8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean.

Seventeen specimens of Octopus vulgaris and Octopus mimus were investigated using randomly amplified polymorphic DNA (RAPD). Clearly differentiable RAPD fingerprints allowed a fast and reliable genotypic discrimination of these species. Thus, molecular genetic evidence from total DNA complements recent results of a comparative analysis of mitochondrial sequence data supporting the taxonomic separation of Octopus mimus and Octopus vulgaris.

DNA sequence diversity of octopods was investigated using the mitochondrial cytochrome oxi- dase III gene (mtCOIII). DNA was obtained from eth- anol- or formalin-fixed tissue of 15 specimens belonging to Octopus mimus Gould, 1852, Octopus vulgaris Cuvier, 1797 and Scaeurgus unicirrhus d'Orbigny, 1840, from coastal waters of the Mediterranean (France), the southwestern Atlantic (Brazil), the Caribbean (Costa Rica) and the southeastern/tropical Pacific (north Chile/ Costa Rica). A 612 bp fragment of the mtCOIII gene was sequenced and aligned to the orthologous sequences available from northeastern Pacific Octopus species. Possible phylogenetic relationships were reconstructed. The mtCOIII gene tree revealed two main clusters, one comprised O. rubescens, O. dofleini and O. californicus, while the other included all O. vulgaris specimens, O. bimaculatus, O. bimaculoides and O. mimus. With one exception all South American haplotypes including O. bimaculatus and O. bimaculoides appeared as the sister group of the Mediterranean haplotype of O. vul- garis, indicating that most of the South American O. vulgaris specimens investigated would not belong to the recently redescribed species O. vulgaris restricted to the Mediterranean and eastern Atlantic. The treatment of O. mimus as a species distinct from Mediterranean O. vulgaris is supported by a high nucleotide divergence of 12.7%. Based on the mtCOIII gene tree the existence of cryptic species among O. vulgaris-like octopods is suggested.

Covalent DNA-streptavidin conjugates are versatile biomolecular coupling reagents, since they have binding capacity for both a complementary nucleic acid and four molecules of biotin. The DNA-streptavidin hybrid molecules have been investigated for their capabilities to bind two different types of biotinylated components. Thus, (i) a functional biomolecule, e.g., a single-stranded DNA fragment or an enzyme and (ii) low-molecular weight biotin derivatives ("modulators") were coupled stepwise with the hybrid molecules. Modulators were D-biotin, aminobiotin, and biotin-fluorescein conjugate as well as a lysine-rich 10mer peptide, containing a biotin and a fluorescein substituent. These modulators were chosen to affected the hybridization properties of the DNA-streptavidin conjugates. As investigated by surface-plasmon resonance and microplate solid-phase hybridization measurements, D-biotin, biotin-fluorescein, and aminobiotin decreased the efficiency of hybridization with complementary, surface-bound oligonucleotides to a varying extent. The basic peptide increased the conjugate's hybridization efficiency. Moreover, it was demonstrated in two examples how modulators can be utilized as additional functional domains of streptavidin-based conjugates. First, fluorescein-containing modulators were used as hapten groups, allowing a sensitive detection by means of specific antibodies directed against the modulator. Second, the biotinylated peptide was used as a carrier molecule to attach multiple fluorogenic lanthanide-chelate groups to the streptavidin conjugate, enabling its sensitive detection by time-resolved fluorometry. The applicability of this kind of bioconjugation strategy to generate sensor-probes for gene detection assays was demonstrated.

Oligodendrocytes in culture are characterized by large membranous sheets containing an elaborate network of microtubules. Microtubule-associated proteins (MAPs) participate in microtubule stability and the regulation of the cellular architecture. We have investigated the expression of two major groups of MAPs, MAP2 and tau, in cultured rat brain oligodendrocytes. Alternatively spliced isoforms of mRNAs encoding MAP2 and tau were assessed by means of reverse transcription and polymerase chain reaction using a newly designed set of MAP2- and tau-specific primers. The data were compared with data obtained with cultures of rat brain astrocytes and rat cerebral neurons, and adult rat brain. The results show that oligodendrocytes, similarly to neurons, express mainly MAP2c transcripts containing three microtubule-binding repeats. They also contain small amounts of MAP2b mRNA. Six low molecular weight tau isoforms, namely tau 1-6, have been described in the brain (Goedert et al. 1991). The major isoform of tau mRNA in oligodendrocytes was found to be tau 1, which represents a marker typical for immature neurons. Tau 2 and tau 4 isoforms were also detected, albeit at a very low level. Immunoblot analysis of oligodendroglia cell extracts confirmed the presence of tau protein. It migrates as a single polypeptide with an apparent molecular weight of approximately 55 kDa. In addition, oligodendrocytes express MAP2c protein, which migrates as a close double band with an apparent molecular weight around 70 kDa. Indirect immunofluorescence staining indicated that tau and MAP2 immunoreactivity was expressed in oligodendrocytes of immature and mature morphologies in the cell somata and cellular processes. Tau was particularly found in the end of the cellular extensions, and both proteins exhibited a distribution similar to myelin basic protein. Thus, oligodendroglia, like neuronal cells, contain microtubule-associated proteins, mainly MAP2c and the tau 1 isoform, although at a much lower level. The presence of these MAPs in myelin-forming cells further points to the functional significance of the cytoskeleton during oligodendrocyte differentiation, process outgrowth, and myelin formation.

Corrigendum: Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

Die 3D-Strukturen von Cytochrom c-Oxidase und Proteasom wurden atomar aufgelost, das Wissen uber Tubulin, Ribosom und Spleisosom erweitert. Peptidmodelle und die Charakterisierung teilgefalteter Strukturen helfen, die Proteinfaltung aufzuklaren. Gen- “Targeting” beschleunigt die Neurorezeptorforschung. An Beispielen warden Fortschritte der Molekularen Medizin beschrieben. Biologische Systeme warden nicht mehr nur “genutzt”, sondern durch Biotechnologie “nutzbar gemacht”.

HuD belongs to a family of neurospecific RNA binding proteins found in man, frog and fly [49]. To investigate whether this protein is involved in regulation of neuronal differentiation of rodent cells in vivo and in vitro, the cDNA of the rat homolog gene (r-HuD) was cloned, its expression was studied in rat brain and in neurogenic cell lines, and the splicing of its RNA was analyzed. Coding sequences of HuD from man and rat were found to be 99.5 and 95% identical at protein and DNA level, respectively. In rat brain r-HuD transcripts 3.7 and 4.2 kb in length were detected by Northern blot analysis. RT-PCR and in situ hybridization revealed that rodent homologues of HuD transcripts are present in P19 mouse embryo carcinoma and in PC12 rat pheochromocytoma cell lines both able to differentiate into neurons. In contrast, r-HuD transcripts were not detectable in the rat glioma cell line C6. In P19 cells a strong induction of HuD mRNA was observed after triggering neuronal differentiation by retinoic acid, whereas in PC12 cells the mRNA was present before and after nerve growth factor (NGF) induced neuronal differentiation. In both neuronal cell lines and in brain of adult rat and mouse HuD mRNA is alternatively spliced in a region which encodes a proline rich linker domain between the second and third RNA recognition motif. This RNA processing event seems to be differently regulated in PC12 cells on the one hand, and in P19 cells and brain of rat and mouse on the other.

The factors that affect the formation and stability of DNA/DNA duplexes are complicated and still mostly unknown. In this study attempts were made to look for the crucial factor affecting hybridization failure in DNA microarray assays. A comprehensive range of factors were investigated simultaneously using a 25-mer oligonucleotide Potyvirus microarray. These included steric hindrance, direct/indirect labelling types, distance of a probe to the fluorescent labelling end, target (the DNA fragment used to hybridize with microarray probes) strand types either single strand or double strand, probes without mismatch and with different numbers of mismatch nucleotides (up to 36%) and different mismatch locations (5' end, centre and 3' end), probe GC content and T(m), secondary structures of probes and targets, different target lengths (0.277 kb to ~1.3 kb) and concentrations (0.1-30 nM). The results showed that whilst most of these known factors were unlikely to be the main causes of failed hybridization, there was strong evidence suggesting that the viral amplicon target structure is the most crucial factor. However, computing predicted target secondary structures by Mfold showed no correlation with the hybridization results. One explanation is that the predicted target secondary structures are different from the real structures. Here we postulate that the real target structure might be a combination of secondary structures resulting in a three-dimensional structure from exposure to three types of sub-structures: (1) a completely exposed linear structure to allow probes access for the successful hybridization and showing strong fluorescent signals; (2) a partially exposed structure to allow unstable binding and showing weak fluorescent signals; (3) a closed structure resulting in failed hybridization. These results are very important for microarray based studies as they not only provide an explanation for some current controversial results, but also provide potential resolution for the future studies. Due to the lack of available software for predicting the true target structure, development of microarrays should conduct an initial oligonucleotide probe selection procedure and those probes with capacity to hybridize with the target should be considered for the microarray development.

Die Biotechnica-weltweit wohl die bedeutendste Biotechnologie-Messe-befindet sich in einer Phase der Konsolidierung. Dies ist nicht nur auf die derzeitige Wirtschaftslage zuruckzufuhren, sondern auch Ausdruck des momentanen Entwicklungsstandes der Biotechnologie. Das hat vor allem in Deutschland mit Akzeptanzproblemen, der Verburokratisierung und mit Diskussionen um ihren Einflus auf den Industriestandort zu tun-aber auch mit einem Klarungsprozes, der ihre Identitat als eigenstandige wissenschaftliche Disziplin betrifft.

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridization experiments (, SCOPUS: ar.j, info:eu-repo/semantics/published

The genus Potyvirus is the largest and one of the most economically important virus genera infecting plants. However, current diagnostic techniques are limited in their ability to identify multiple potyvirus infections. An assay that can identify multiple potyviruses simultaneously, with good specificity and sensitivity, is therefore highly desirable. To determine the feasibility of simultaneous detection of multiple potyviruses a 25-mer oligonucleotide microarray was developed targeting four distinct potyviruses: Dasheen mosaic virus (DsMV), Leek yellow stripe virus (LYSV), Potato virus Y (PVY) and Zucchini yellow mosaic virus (ZYMV). A total of 85 probes including 33 perfect-match and 52 mismatch probes were designed from conserved and variable sequence regions of the nuclear inclusion b (NIb) gene, RNA-dependent RNA polymerase (RdRp) gene, coat protein (CP) gene and the 3' untranslated region (UTR), representing the four targeted potyviruses at both species and strain levels. Each probe was synthesized with spacers of either 6 or 12 poly-cytosine or poly-thymine at the 5' terminus. The array showed high specificity when tested with nineteen different geographically diverse potyvirus isolates of the four target species, four distinct but closely related potyviruses, and four healthy plant species. The approaches and protocols developed in this study form a useful basis for developing other potyviruses arrays and the results also provide useful insights into generic issues for the development of arrays for detecting other pathogens.

Phylogenetic assessment of the giant clams need to be improved using various genetic markers since their relaionships are plagued by inconsistency result of several studies. This is especially true for the species under sub-genus Chametrachea . Here we studied the phylogeny of the giant clams using amino acid sequence of the mitochondrial COI gene. This study is aimed to assess and better understand the relationships of the giant clams, especially for three species under subgenus Chametrachea . The result showed close proximity between T. crocea and T. squamosa and between T. maxima and T. gigas . However, amino acids sequences of cytochrome c oxidase I gene was not strong enough to discriminate between T. crocea and T. squamosa . The majority of mutations were hydrophobic to hydrophilic amino acids.

DNA microarrays are currently in use almost exclusively as research tools for gene expression analysis and their application for the identification of organisms is still in its infancy, only documented by a few studies on mammals, bacteria, and viruses. The "Fish & Chips" project aims to demonstrate that DNA chips can be a new innovative tool for the identification of marine animals and phytoplankton. To achieve this goal, fishes, invertebrates, and phytoplankton were sampled in European seas and taxonomically classified. Fragments of their mitochondrial 16S, cyt b, and COI genes and from the nuclear 18S genes were sequenced and served as molecular markers to enable probe design for the microarrays. An on-line data base containing the sequences and all relevant information of the samples has been implemented. A first prototype of a "Fish Chip",is based on more than 400 sequences from the 16S rRNA gene belonging to 46 species. A second microarray prototype serves to identify flatfishes from the North Sea based on COI-and 16S sequences from 70 individuals of 17 fish species. A "Phytoplankton Chip" is now available with probes for all microalgal classes and many toxic species, as well as a "Invertebrate Chip". The results show that this approach is feasible.

To allow for pharmacokinetic studies in adjunction with the current clinical developments of the potent cytostatic anti-cancer drug rViscumin, a sandwich immuno-PCR (IPCR) assay was developed for the detection of rViscumin in blood plasma. The IPCR was carried out with a commercially available reagent kit, consisting of pre-assembled rViscumin-specific antibody-DNA conjugates as well as a specific competitor DNA fragment to be amplified by PCR. Various combinations of capture- and detection-antibodies were compared for performance in IPCR. Using the optimized assay, as few as 50 zeptomol (approx. 100 fg/ml) rViscumin (MW 57 kDa) was detectable in standardized human serum samples. The IPCR assay was very selective for rViscumin and in spiking experiments in proband plasma samples, signal recovery rates between 70% and 120% were obtained. The linear sensitivity range of the assay covered more than five orders of magnitude. Repeated measurements of rViscumin resulted in a mean standard deviation value of 14.2%.

Antiidiotypic antibodies (Ab2) are needed as tools for a better understanding of molecular mimicry and the immunological network, and for many potential applications in the biomedical and pharmaceutical field. Antiidiotypic antibodies mimicking carbohydrate or conformational epitopes (Ab2beta) are of considerable interest as surrogate immunogens for cancer vaccination. However, it has so far been difficult and tedious to produce Ab2s to a given antigen. Here we describe a fast and reliable technique for generating large diversities of antiidiotypic single chain antibody fragments from non-immunized phagemid libraries using phage display. Key elements are a specific elution with the original antigen followed by trypsin treatment of the eluted phages in combination with the protease sensitive helperphage KM13. This novel method was compared with various conventional selection and elution methods, including, specific elution with or without trypsin treatment, elution with glycine at pH 2.2 with or without trypsin treatment, and elution by trypsin treatment only. The results clearly show that specific elution in combination with trypsin treatment of the eluted phages is by far superior to the other conventional methods, enabling for the first time the generation of a large variety of Ab2s after only two to three rounds of selection, thereby maintaining maximum diversity. We obtained 28 to 88 antiidiotypes out of 96 tested clones after two to three rounds of selection with a diversity of 55-90 %. This was achieved for two carbohydrate (di-, and tetrasaccharides) and one conformational protein epitope using two large naive libraries and their corresponding monoclonal Ab1. The antiidiotypic nature of the selected scFv-phages was verified by ELISA and immunocytochemistry inhibition experiments.

The DNA microarray-based analysis of single nucleotide polymorphisms (SNPs) is important for the correlation of genetic variations and individual phenotypes, and for locating disease-causing genes. To facilitate the development of surfaces suitable for immobilization of oligonucleotides, we report here a novel method for the surface immobilization of DNA using pre-fabricated polyamidoamine (PAMAM) starburst dendrimers as mediator moieties. Dendrimers containing 64 primary amino groups in their outer sphere are covalently attached to silylated glass supports and, subsequently, the dendritic macromolecules are modified with glutaric anhydride and activated with N-hydroxysuccinimide. As a result of the dendritic PAMAM linker system the surfaces reveal both a very high immobilization efficiency for amino-modified DNA-oligomers, and also a remarkable high stability during repeated regeneration and re-using cycles. The performance of dendrimer-based DNA microarrays in the discrimination of SNPs is demonstrated.

Partial DNA and amino acid sequences translated from the mitochondrial cytochrome subunit I gene (408 bp) of 17 mite species have been used for analyzing the phylogenetic relationships within the terrestrial Parasitengona (Trombidia). Due to mutational saturation of the third codon position, only first and second codon positions and amino acid sequences were analyzed, applying neighbor-joining, maximum-parsimony, and maximum-likelihood tree-building methods. The reconstructed trees revealed similar topologies of taxa; however, the phylogenetic relationships could be convincingly resolved only within several trombidioid taxa. The proposed basic relationships within the Parasitengona, in particular those of Calyptostomatoidea, Smarididae, and Erythraeidae, were poorly supported in bootstrap tests. A comparison of the presented gene tree with a phylogenetic tree based upon traditional characters revealed only few contradictions in nodes only weakly supported by morphological data. The most astonishing result is the proposed early derivative position of Microtrombidiidae within the terrestrial Parasitengona.

Microarrays have emerged as indispensable research tools for gene expression profiling and mutation analysis. New classification of cancer subtypes, dissecting the yeast metabolism and large-scale genotyping of human single nucleotide polymorphisms are important results being obtained with this technique. Realizing the microsphere-based massively parallel signature sequencing technique as fluid microarrays, building new types of protein arrays and constructing miniaturized flow-through systems, which can potentially take this technology from the research bench into industrial, clinical and other routine applications, exemplify the intense developments that are now ongoing in this field.

Covalent DNA-streptavidin conjugates have been utilized for the reversible and site-selective immobilization of various biotinylated enzymes and antibodies by DNA-directed immobilization (DDI). Biotinylated alkaline phosphatase, beta-galactosidase, and horseradish peroxidase as well as biotinylated anti-mouse and anti-rabbit immunoglobulins have been coupled to the DNA-streptavidin adapters by simple, two-component incubation and the resulting preconjugates were allowed to hybridize to complementary, surface-bound capture oligonucleotides. Quantitative measurements on microplates indicate that DDI proceeds with a higher immobilization efficiency than conventional immobilization techniques, such as the binding of the biotinylated proteins to streptavidin-coated surfaces or direct physisorption. These findings can be attributed to the reversible formation of the rigid, double-stranded DNA spacer between the surface and the proteins. Moreover, BIAcore measurements demonstrate that DDI allows a reversible functionalization of sensor surfaces with reproducible amounts of proteins. Ultimately, the simultaneous immobilization of different compounds using microstructured oligonucleotide arrays as immobilization matrices demonstrate that DDI proceeds with site selectivity due to the unique specificity of Watson-Crick base pairing.

In a comprehensive study, we examined the expression of the membrane and secretory mucins MUC1 and MUC3, respectively, in normal and neoplastic gastrointestinal and breast epithelia before and after specific alterations of their glycan structures by neuraminidase, α-fucosidase, or carbohydrate-specific periodate oxidation. MUC1 mRNA was also identified in normal colorectal tissues by in situ hybridization. The data revealed that normal colorectal epithelia express both MUC1 mRNA and protein, which were detectable after periodate oxidation with all tested MUC1-specific antibodies. During tumorigenesis in the colon, MUC1 became recognizable without periodate treatment concomitantly with highly dysplastic lesions and the malignant state. In the breast, in which MUC1 is detectable with most antibodies in normal epithelium as well as in carcinomas, staining could be enhanced by pretreatment with periodate and casually by enzyme treatments. MUC3 was detectable in normal and neoplastic colorectal tissues and was more intensely stained after periodate oxidation. It was absent in normal breast even after pretreatment but was expressed in seven of 20 breast carcinomas. Therefore, incomplete glycosylation, abnormal distribution, and ectopic expression of mucins are characteristics of malignancy. Periodate oxidation may be widely applicable to immunohistochemistry for examining changes in glycosylation and for detecting antigens masked by glycans. (J Histochem Cytochem 45:1547–1557, 1997)

Metabotropic glutamate receptors modulate neuronal activity but expression and alternative splicing of their subtypes (mGluR1-mGluR8) during early neuronal differentiation are essentially unknown. In the mouse embryocarcinoma cell line P19, one of the best established systems to study neurogenesis in vitro, it was shown by RT-PCR and in situ hybridization that the neuronal differentiation process, induced by retinoic acid, is characterized by an early increase in the expression of mGluR3, mGluR7 and mGluR8 and a late rise in the mRNA levels of mGluR1 and mGluR5, whereas mGluR2 and mGluR4 seem to be constitutively expressed. In comparison, in primary embryonic neurons all mGluR subtypes were detected at day 3 after plating while primary astrocytes and oligodendrocytes have diverging mGluR pattern. In addition, the splicing pattern of mGluR1 and mGluR5 transcripts differ remarkably between neural cells in vitro and brain tissue. These data, although not comparable to the situation in vivo, might be a hint on so far unknown functions of metabotropic glutamate receptors during neuronal differentiation.

Immuno-polymerase chain reaction (immuno-PCR) allows the detection of protein amounts as low as a few hundred molecules. This enhanced sensitivity is useful for a variety of applications in analytical and biomedical sciences. Application of this technique as a routine method requires the rapid quantification of the PCR products, preferably as an automated readout by microplate-based assays. Here, three methods are compared for detecting such amplified products, i. e., direct staining with a fluorescent intercalating dye, an enzymatic assay utilizing doubly hapten-labeled products, and gel electrophoresis. The enzymatic assay, carried out with either chromogenic or fluorogenic substrate for enzymatic signal amplification, was found to be the most sensitive method. The optimized assay was tested in direct immuno-PCR assays for detecting immunoglobulins (IgG) from mouse and rabbit as well as in a sandwich immuno-PCR assay for detecting recombinant hepatitis B surface antigen (rec. HBsAg). Sensitivity limits were found to be as low as 15 fg (10(-19) mol) IgG, representing a 1000-fold enhancement compared to enzyme-linked immunosorbent assay detection, and about 70 fg (2 x 10(-18) mol) rec. HBsAg, improving the detection limit of currently available methods by a factor of about 700. The well-reproducible enzymatic amplification signal further enhances the sensitivity of immuno-PCR and should render the method suitable for routine laboratories.

The mouse EC cell line P19, differentiating in vitro into neural cell types under the influence of retinoic acid, represents a well established model system for neurogenesis. In this system the expression of the alpha (alpha 1-alpha 3) and beta subunits of the inhibitory glycine receptor (GlyR) and of gephyrin as well as their mRNA splice variants was analyzed by RT-PCR and by immunocytochemistry. In the course of neuronal differentiation of P19 cells mRNA of GlyR beta is constitutively expressed, GlyR alpha 1 and alpha 2 are induced and GlyR alpha 3 was not detected. From the three gephyrin transcripts known to be differently spliced in the C3/C4 cassette region, the C3 transcript was found at all stages while the C4 transcript was not detectable. The insert-free form was measurable in P19 cells only 3-4 days post induction by retinoic acid. In addition a GlyR beta splice variant and a fourth gephyrin transcript were detected. Primary glial cells do not contain significant amounts of GlyR alpha subunits while in primary neuronal cells transcripts of GlyR alpha 2 were found as well as the mRNA of the GlyR beta subunit and of gephyrin. PC12 cells do not express glycine receptor genes but do express gephyrin. Immunocytochemistry confirmed the constitutive expression of gephyrin at the protein level, whereas GlyR antigens could only be detected in islets of the 'P19 neurons'. In conclusion, P19 and primary neuronal cells but not PC12 cells express the transcripts of glycine receptor components, necessary to generate functional receptors.

Three stable murine hybridoma cell lines, which secrete monoclonal antibodies (mAb) to human tumor necrosis factor alpha (TNF alpha), were established. None of the monoclonal antibodies cross-reacted with lymphotoxin, interleukin 2 (IL 2) or Interferon gamma (IFN gamma). The highly species-specific monoclonal antibody, designated as mAb 195, neutralizes the cytotoxic activity of human and chimpanzee TNF alpha. This antibody was further used during in vivo studies to neutralize human TNF alpha in a murine animal model. The mAb 114 is a weakly neutralizing antibody that binds to a different epitope of TNF alpha than mAb 195. mAb 114 shows a wide range of cross-reactivity with TNF alpha of the following species: dog, pig, cynomolgus, rhesus, baboon and chimpanzee. The mAb 199 binds to human TNF alpha, but does not neutralize the cytotoxic activity. The epitope recognized by this mAb is in close proximity to mAb 114. A reproducible, sensitive immunoassay for human TNF7 alpha has been developed using the antibodies mAb 199 and mAb 195. The test is performed within 6 hr and detects TNF7 alpha in serum samples, with a limit of detection of 5 to 10 pg/mL.

Die Immuno-PCR erganzt etablierte Verfahren der PCR-Nucleinsaureanalytik. Mit der neuen Methode konnen Proteine ahnlich empfindlich nachgewiesen werden, wie dies fur Nucleinsauren moglich ist.

Mit DNA-Microarrays und einer Oligonukleotid-Bibliothek lassen sich Hepatitis-C-Viren nachweisen und genotypisieren. Dies ist entscheidend fur Diagnose und Therapie einer unterschatzten chronischen Virenerkrankung.

Besides their cytotoxic effects, Tumor necrosis factor (TNF) and Lymphotoxin (LT) were shown to modulate distinct PMN functions. Therefore, in the present study we evaluated the effect of recombinant human TNF and LT on the oxidative metabolism of isolated human PMN. In addition ultrastructural changes upon stimulation were evaluated. For detection of granulocyte activation different assay systems were used: 1) lucigenin-dependent chemiluminescence (CL), 2) superoxide-dismutase (SOD) inhibitable cytochrome C-reduction (superoxide), 3) horseradish peroxidase-mediated oxidation of phenol red (hydrogen peroxide), 4) release of myeloperoxidase, 5) ultrastructural detection of hydrogen peroxide-production, 6) scanning and transmission electron microscopy (SEM and TEM). TNF at concentrations as low as 10 -3 U/ml induced a distinct CL response, whereas LT appeared to be less active. PMN preincubated with TNF or LT for 150min were completely deactivated to renewed stimulation with TNF, LT, and with GM-CSF, but responded to other triggers of the oxidative burst. Moreover, stimulation with f-met-leu-phe resulted in an enhanced response after preincubation with TNF or LT. The CL response was significantly inhibited by SOD, but not by catalase, D-mannitol, and DMTU, suggesting that mainly ˙ O 2 - is responsible for the CL signal. The effect on PMN could be completely blocked by antibodies to TNF. Significant release of reactive oxygen species upon stimulation with TNF was also demonstrated by cytochrome C reduction and by detection of H 2 2 using functional and ultrastructural assays. Only minimal amounts of peroxidase were released. Activation of PMN could be visualized by SEM and TEM. After addition of TNF at concentration as low as 10 -1 U/ml PMN adhered to the substratum and were typically polarized within 15min. Stimulation with LT resulted in comparable results, but based on its biologic activity in the cytotoxicity assay LT, in comparison to TNF, was significantly less active. Based on the data presented LT and, particularly, TNF appear to be potent activators of PMN aoxidative metabolism.

The attachment of human immunodeficiency virus type 1 (HIV-1) to target cells is mediated by a specific interaction between the viral envelope glycoprotein (gp120) and the CD4 receptor. Here we report that approximately 10% of HIV-1-infected individuals produce antibodies that recognize the extracellular portion of the CD4 molecule. Carboxyl-terminal deletions of CD4 that do not affect HIV-1 gp120 binding eliminate recognition of CD4 by patient antisera. In contrast, mutations in the amino-terminal domain of CD4 that attenuate HIV-1 gp120 binding do not diminish CD4 recognition by patient antisera. These results suggest that HIV-1 infection can generate antibodies directed against a region of the viral receptor distinct from the virus-binding domain.

Fragments of two Ti plasmids from Agrobacterium tumefaciens were cloned and studied for cross-hybridization. Homologous fragments were further investigated for areas of strong homology and mapped with various restriction enzymes. The fragments were inserted in two directions and the recombinant plasmid was brought into E. coli strains producing minicells. About five proteins were found to be coded by those fragments of the Ti plasmids.

Current developments in nanosciences indicate that the self-assembly of macromolecules, such as proteins or metallic nanoclusters, can be conveniently achieved by means of nucleic acid hybridization. Within this context, we here report on the evaluation of single-stranded nucleic acids to be utilized as carrier backbones in DNA-directed self-assembly. A microplate solid-phase hybridization assay is described which allows rapid experimental determination of the hybridization efficiencies of various sequence stretches within a given nucleic acid carrier strand. As demonstrated for two DNA fragments of different sequence, the binding efficiencies of several oligonucleotides depend on the formation of specific secondary structure elements within the carrier molecule. A correlation of sequence-specific hybridization capability with modeled secondary structure is also obvious from experiments using the fluorescence gel-shift analysis. Electrophoretic studies on the employment of helper oligonucleotides in the formation of supramolecular conjugates of several oligonucleotide-tagged proteins indicate, that structural constraints can be minimized by disruption of intramolecular secondary structures of the carrier molecule. To estimate the influences of the chemical nature of the carrier, gel-shift experiments are carried out to compare a 170mer RNA molecule with its DNA analogue. Ternary aggregates, containing two protein components bound to the carrier, are formed with a greater efficiency on the DNA instead of the RNA carrier backbone.