Measurement of the helicity asymmetry E for the reaction γ p → π 0 p : The CBELSA/TAPS Collaboration.

A measurement of the double-polarization observable E for the reaction γ p → π 0 p is reported. The data were taken with the CBELSA/TAPS experiment at the ELSA facility in Bonn using the Bonn frozen-spin butanol (C 4 H 9 OH) target, which provided longitudinally-polarized protons. Circularly-polarized photons were produced via bremsstrahlung of longitudinally-polarized electrons. The data cover the photon energy range from E γ = 600 to 2310 MeV and nearly the complete angular range. The results are compared to and have been included in recent partial wave analyses.

Genetic variation, phylogenetic relationship and spatial distribution of 'Candidatus Phytoplasma ulmi' strains in Germany.

A recent survey in Germany revealed the wide presence of 'Candidatus Phytoplasma ulmi' in native elm stands. Accessions were studied for their genetic variability and phylogenetic relationship based on the conserved groEL and the variable imp gene. While the groEL sequences revealed a high intraspecific homology of more than 99%, the homology of the imp gene dropped to 71% between distantly related sequences. Twenty-nine groEL and 74 imp genotypes were distinguished based on polymorphic sites. Phylogenetic analysis of the groEL gene clustered all 'Ca. P. ulmi' strains and separated them from related phytoplasmas of the 16SrV group. The inferred phylogeny of the imp gene resulted in a different tree topology and separated the 'Ca. P. ulmi' genotypes into two clusters, one closely related to the flavescence dorée phytoplasma strain FD-D (16SrV-D), the other affiliated with the flavescence dorée phytoplasma strains FD-C and FD70 and the alder yellows phytoplasma (16SrV-C). In both phylograms, 'Ca. P. ulmi' genotypes from Scots elm trees formed a coherent cluster, while genotypes from European white elms and field elms grouped less strictly. The regional distribution pattern was congruent for some of the groEL and imp genotypes, but a strict linkage for all genotypes was not apparent.

THE IMPACT OF SILICON ON TRANSCRIPTS RELATED TO CUCUMBER MOSAIC VIRUS INFECTION IN CUCUMBER.

The role of soluble silicon (Si) in alleviating viral plant infections is largely unknown. In order to analyse this gap in knowledge, this study provides insights into the relative gene expression data obtained from 1) control, 2) Cucumber mosaic virus (CMV)-infected and 3) sodium silica-treated, CMV-infected Cucumis sativus line B10 tissue cultures regenerated plants. The absence or presence of CMV was determined through RT-PCR, six days' post-inoculation. qRT-PCR was performed on five selected host genes related to CMV-defence (argonaute protein, WRKY transcription factor) and replication (chaperone, heat shock cognate protein, aquaporin). Relative gene expressions from Si-treated, CMV-infected clones were not significantly different from CMV-infected clones, but they were significantly different from the control plants. The upregulation of the chaperone, and heat shock cognate genes in Si-treated clones, is associated with enhanced virus replication, while the gene expression of the transcription factor increases and is related to defence, in contrast to decreased expression in CMV-infected clones. Aquaporin gene expression was downregulated and the argonaute expression was unaffected in both Si-treated, CMV-infected as well as CMV-infected clones. Since both alleviating and supportive gene shifts are observed in Si-treated plantlets for key genes related to the virus infection examined herein, sodium silica is suggested to have a neutral and limited impact on CMV infection in cucumber cultures.

FIRST REPORT OF 'CANDIDATUS PHYTOPLASMA ULMI' IN ULMUS LAEVIS IN GERMANY.

The wall-less bacteria of the provisory taxon 'Candidatus Phytoplasma' are obligate parasites and associated to diseases in many important crops and trees worldwide. 'Ca. Phytoplasma ulmi', assigned to 16SrV-A subgroup, is a quarantine pest and described to be associated to elm phloem necrosis, leaf yellowing, stunting, witches broom and decline in various elm species. Elm yellows phytoplasmas (EY) have been reported in several European countries but not in Ulmus laevis in Germany so far. Leaf samples from European white elms (Ulmus leavis PALL.) with and without chlorotic symptoms were investigated for EYs infection in Berlin and Brandenburg, Germany, through performing diagnostic nested PCR targeting partial rRNA operon of phytoplasmas. Specific PCR-products were obtained from 30 out of 59 samples. Partial 16S-rDNA sequences were assigned to 'Ca. P. ulmi' through sequence analysis, while sequence variation was observed. This is the first report of U. laevis infected with 'Ca. P. ulmi' in Germany.

N(1520) 3/2(-) helicity amplitudes from an energy-independent multipole analysis based on new polarization data on photoproduction of neutral pions.

New data on the polarization observables T, P, and H for the reaction γp→pπ(0) are reported. The results are extracted from azimuthal asymmetries when a transversely polarized butanol target and a linearly polarized photon beam are used. The data were taken at the Bonn electron stretcher accelerator ELSA using the CBELSA/TAPS detector. These and earlier data are used to perform a truncated energy-independent partial wave analysis in sliced-energy bins. This energy-independent analysis is compared to the results from energy-dependent partial wave analyses.

First measurement of the helicity asymmetry for γp → pπ0 in the resonance region.

The first measurement of the helicity dependence of the photoproduction cross section of single neutral pions off protons is reported for photon energies from 600 to 2300 MeV, covering nearly the full solid angle. The data are compared to predictions from the SAID, MAID, and BnGa partial wave analyses. Strikingly large differences between data and predictions are observed, which are traced to differences in the helicity amplitudes of well-known and established resonances. Precise values for the helicity amplitudes of several resonances are reported.

Complete genome sequences of three Erwinia amylovora phages isolated in north america and a bacteriophage induced from an Erwinia tasmaniensis strain.

Fire blight, a plant disease of economic importance caused by Erwinia amylovora, may be controlled by the application of bacteriophages. Here, we provide the complete genome sequences and the annotation of three E. amylovora-specific phages isolated in North America and genomic information about a bacteriophage induced by mitomycin C treatment of an Erwinia tasmaniensis strain that is antagonistic for E. amylovora. The American phages resemble two already-described viral genomes, whereas the E. tasmaniensis phage displays a singular genomic sequence in BLAST searches.

Cultivation-independent characterization of 'Candidatus Magnetobacterium bavaricum' via ultrastructural, geochemical, ecological and metagenomic methods.

'Candidatus Magnetobacterium bavaricum' is unusual among magnetotactic bacteria (MTB) in terms of cell size (8-10 µm long, 1.5-2 µm in diameter), cell architecture, magnetotactic behaviour and its distinct phylogenetic position in the deep-branching Nitrospira phylum. In the present study, improved magnetic enrichment techniques permitted high-resolution scanning electron microscopy and energy dispersive X-ray analysis, which revealed the intracellular organization of the magnetosome chains. Sulfur globule accumulation in the cytoplasm point towards a sulfur-oxidizing metabolism of 'Candidatus M. bavaricum'. Detailed analysis of 'Candidatus M. bavaricum' microhabitats revealed more complex distribution patterns than previously reported, with cells predominantly found in low oxygen concentration. No correlation to other geochemical parameters could be observed. In addition, the analysis of a metagenomic fosmid library revealed a 34 kb genomic fragment, which contains 33 genes, among them the complete rRNA gene operon of 'Candidatus M. bavaricum' as well as a gene encoding a putative type IV RubisCO large subunit.

Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB.

The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris" strains OY-M and AY-WB showed that the gene order was more conserved between the closely related "Ca. Phytoplasma asteris" strains than to "Ca. Phytoplasma australiense." Differences observed between "Ca. Phytoplasma australiense" and "Ca. Phytoplasma asteris" strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.

DNA sequence and comparative analysis of chimpanzee chromosome 22.

Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.

Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.

Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L- and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses.

Immunocytochemistry and DNA-image cytometry in diagnostic effusion cytology I. Prevalence of markers in tumour cell positive and negative smears.

To determine the prevalence of immunocytochemical positivities for a panel of antibodies in benign and malignant cells in effusions with known follow-up in order to use these as diagnostic markers. Besides their ability to identify malignant epithelial cells their contribution to the differential diagnosis between carcinomatoses and mesotheliomas was investigated. 101 tumour cell positive and 53 negative effusions were stained with 12 different antibodies. Results were scored semiquantitatively per cell type. Furthermore, DNA-image cytometry was performed. While prevalence of Ber-EP4 positivity was 95.4% in metastatic carcinoma cells, it was 0% in those from mesotheliomas. No cell type reacted with this marker in benign effusions (0%). Ber-EP4 correctly differentiated between metastatic carcinoma and mesothelioma in 98.0%. Prevalence of DNA-aneuploidy was 95.4% in metastatic carcinomas, 57.1% in mesotheliomas and 0% in reactive effusions. Combining immunocytochemistry (Ber-EP4 positivity) and DNA-image cytometry (aneuploidy) results in a 100% detection of metastatic carcinomatoses and 57.1% of mesotheliomas. Both markers furthermore allowed a correct differentiation of these entities in 98%.

Immunocytochemistry and DNA-image cytometry in diagnostic effusion cytology. II. Diagnostic accuracy in equivocal smears.

To determine sensitivity and specificity of different antibodies for the immunocytochemical detection of malignant cells in diagnostically equivocal effusions in comparison with those achieved by DNA-image cytometry. 65 cytologically doubtful effusions of the serous cavities were stained with twelve antibodies. Furthermore, DNA-image cytometry was performed. Data were correlated with patient follow-up. Sensitivity of cellular staining of Ber-EP4 for the identification of malignant cells was 77.8%, specificity of absent staining for benign cells was 100%. Positive predictive value for the identification of malignant cells was 100%, negative value 65.5%. Sensitivity of DNA-aneuploidy for the identification of malignancy was 82.9%, specificity of DNA-non-aneuploidy for benignity 94.7%. The positive predictive value of DNA-aneuploidy for the occurrence of malignant cells was 96.7%. Negative predictive value of DNA-non-aneuploidy was 72.0%. Combining immunocytochemistry applying Ber-EP4 only and DNA-cytometry in equivocal effusions resulted in a sensitivity of 88.9% for the identification of malignant cells associated with a 95.0% specificity. Positive predictive value was 97.7%, the negative one 79.2%.

Pleural carcinosis confirmed by adjuvant cytological methods: a case report.

We describe a case of a 43-yr-old woman presenting a progressive pleural effusion. The patient was known to have an acute myeloid leukemia in complete remission after allogenic bone marrow transplantation. Suspicion of pleural carcinosis was raised cytologically and confirmed by immunocytochemistry, DNA-cytometry, and atomic force microscopy. We emphasize the use of these additional methods for the distinction of adenocarcinoma cells in effusions from reactive mesothelial cells.

Atomic force microscopy in effusion cytology.

OBJECTIVE: To investigate whether atomic force microscopy (AFM) in combination with classical light microscopy allows simple identification of surface structures of cells from pleural and ascitic fluids for diagnostic purposes in place of scanning electron microscopy (SEM). STUDY DESIGN: We examined a total of 180 cells obtained from 9 reactive pleural or peritoneal effusions, 14 associated with carcinomatosis from histologically confirmed tumors and 5 from mesotheliomas. Cells of interest were selected in air-dried, uncovered, May-Grünwald-Giemsa (MGG)-stained smears and subsequently investigated by AFM. Incorporation of a very compact AFM scanner into the nose piece of a conventional Axioscope light microscope allowed alternating application of both techniques. RESULTS: AFM was able to detect cell surface structures, such as microvilli, phagocytic pits, secretory blebs and lytic holes. The image resolution was sufficient but not as good as that with SEM. We found differences in number, length and diameter of microvilli between cells from mesotheliomas and from metastatic adenocarcinomas. CONCLUSION: As AFM can be carried out in combination with light microscopy quickly and easily on uncovered, MGG-stained smears, we propose this method as a suitable tool for obtaining additional useful information in routine cytologic diagnosis of effusions.

Use of archival and fresh cytologic material for the polymerase chain reaction. Detection of the bcl-2 oncogene in lymphoid tissue obtained by fine needle biopsy.

A technique for extracting DNA from archival and fresh tissue from fine needle biopsy (FNB) samples for the polymerase chain reaction (PCR) is described. The method was used to detect the bcl-2 oncogene in various cytologic lymphoid preparations. The DNA was amplified with primers specific for the major break point region of the t(14;18) translocation, and the presence of the bcl-2 oncogene was correlated with clinical, cytomorphologic, histologic and immunologic findings. Thirty patients who had FNB of lymphoid tissue were randomly selected, 18 retrospectively and 12 prospectively. Bcl-2 was present in 3 of 8 cases of reactive lymphadenopathy and 9 of 22 cases of non-Hodgkin's lymphoma. Of these, seven had follicular small cleaved cell lymphoma, and two had large cell lymphoma. Smears, both archival and fresh, and cell suspensions provided sufficient DNA for PCR amplification. The technique has potential applications in several areas of cytologic and hematologic practice.

"Learned helplessness" and the patient with progressive supranuclear palsy.

Progressive supra-nuclear palsy is a neurologically debilitating disease of unknown cause and with no effective treatment. Learned helplessness, a major cause of depression in the institutionalized elderly, is a feeling of worthlessness and powerlessness resulting in a decreased incentive to try. This article provides insight into these two problems and specific nursing interventions to enhance self care.