Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle

Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B₁₂ was produced by 70% of the isolates. Since growth of F. spiralis depends on B₁₂ supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.     

Development of ligase-assisted spacer addition for the measurement of microsatellites

Conventional methods for detecting differences in microsatellite repeat lengths rely on electrophoretic fractionation on long denaturing polyacrylamide gels, a time-consuming and labor-intensive method. Therefore, there is a need for the development of new and rapid approaches to routinely detect such length polymorphisms. The advent of techniques allowing the coupling of DNA molecules to solid surfaces has provided new prospects in the area of mutation detection. We describe here the development and optimization of the ligase-assisted spacer addition (LASA) method, a novel and rapid procedure based on an ELISA format to measure microsatellite repeat lengths. The LASA assay was successfully applied to a set of 11 bird samples to assess its capabilities as a genotyping method.     

Isothermal amplification and multimerization of DNA by Bst DNA polymerase

We have demonstrated the isothermal in vitro amplification and multimerization of several different linear DNA targets using only two primers and the strongly strand-displacing exonuclease-negative Bst DNA polymerase. This reaction has been termed linear target isothermal multimerization and amplification (LIMA). LIMA has been compared with cascade rolling-circle amplification and has been found to be less sensitive but to yield similar variable-length multimeric dsDNA molecules. Products from several different LIMA reactions were characterized by restriction analysis and partial sequence determination. They were found to be multimers of subsets of the target sequence and were not purely primer derived. The sensitivities with respect to target concentration of several different LIMA reactions were determined, and they varied from 0.01 amol to 1 fmol. The sensitivity and specificity of LIMA were further tested using E. coli genomic DNA, and the selective amplification of a transposon fragment was demonstrated. A successful strategy for reducing LIMA-dependent background DNA synthesis in rolling-circle amplification embodiments was devised. This entailed the affinity purification of circular DNA templates before amplification.     

When no catches matter: Coping with zeros in environmental assessments

The environmental legislation of many countries increasingly requires the continuous monitoring of fish assemblages to evaluate the success of river and stream restorations. Predicting species–environment relationships on the basis of monitoring data is central in the evaluation of ecological integrity and planning of rehabilitation strategies. Monitoring data are, however, often plagued by a substantial proportion of zeros (no catch at single sampling points) which are caused by relevant ecological processes, but complicate the use of commonly used statistical methods. This study compares mere count regression models, mixture and hurdle models based on Poisson and negative binomial distribution and logistic regressions with respect to their ability to cope with large zero-inflated data sets obtained by point abundance sampling of young-of-the-year fish from three large German rivers. Only mixture and hurdle models based on negative binomial distribution could satisfactorily be fitted to the zero-inflated and overdispersed count data. The logistic regression models applied to transliterated catch data simplified the computational procedure and yielded qualitative similar results to the count regression models indicating that the use of more complex count data did not generally provide better predictions. Therefore, presence/absence sampling may be a suitable and less costly alternative to abundance surveys for identifying environmental factors which affect the spatial distribution of fish populations at least if information on subtly abundance fluctuations is not needed. Mixture or hurdle models are particularly worth the additional effort if it is reasonable to distinguish between those environmental factors influencing the occurrence probability and others affecting the abundance. All models showed low sensitivity to rare guilds pointing to the need for a further development of statistical models for rare species whose management is a matter of growing environmental concern.     

Vergleichende Mikromorphologie der Narbenoberflächen bei den Angiospermen; Zusammenhänge mit Pollenoberflächen bei heterostylen Sippen

Stigmatic surfaces of about 250 species from more than 100 families were examined by scanning electron microscopy. There are five main groups which differ by the amount of secretion, the morphology of the surface and the distribution of receptive cells. The types of stigmatic surfaces are often remarkably constant on the family level.Ericaceae andLiliaceae are examples for very heterogenous families. Particular interest was paid to heteromorphic (heterostylous and cleistogamous) species. In most heterostylous species there is a close morphological correlation between the stigmatic surface and the sculpture of compatible pollen. Heterostyly was established for the genusGoniolimon. The dimorphism of plants with chasmogamous and cleistogamous flowers is a phenomenon which is not comparable to the polymorphism of heterostylous forms.

     

Incidence and causes of heparin-induced skin lesions

Background

Little is known about the incidence and causes of heparin-induced skin lesions. The 2 most commonly reported causes of heparin-induced skin lesions are immune-mediated heparin-induced thrombocytopenia and delayed-type hypersensitivity reactions.

Methods

We prospectively examined consecutive patients who received subcutaneous heparin (most often enoxaparin or nadroparin) for the presence of heparin-induced skin lesions. If such lesions were identified, we performed a skin biopsy, platelet count measurements, and antiplatelet-factor 4 antibody and allergy testing.

Results

We enrolled 320 patients. In total, 24 patients (7.5%, 95% confidence interval [CI] 4.7%–10.6%) had heparin-induced skin lesions. Delayed-type hypersensitivity reactions were identified as the cause in all 24 patients. One patient with histopathologic evidence of delayed-type hypersensitivity tested positive for antiplatelet-factor 4 antibodies. We identified the following risk factors for heparin-induced skin lesions: a body mass index greater than 25 (odds ratio [OR] 4.6, 95% CI 1.7–15.3), duration of heparin therapy longer than 9 days (OR 5.9, 95% CI 1.9–26.3) and female sex (OR 3.0, 95% CI 1.1–8.8).

Interpretation

Heparin-induced skin lesions are relatively common, have identifiable risk factors and are commonly caused by a delayed-type hypersensitivity reaction (type IV allergic response). (ClinicalTrials.gov trial register no. {"type":"clinical-trial","attrs":{"text":"NCT00510432","term_id":"NCT00510432"}}NCT00510432.)Hpeparin has been used as an anticoagulant for over 60 years.¹ Well-known adverse effects of heparin therapy are bleeding, osteoporosis, hair loss, and immune and nonimmune heparin-induced thrombocytopenia. The incidence of heparin-induced skin lesions is unknown, despite being increasingly reported.^2–4 Heparin-induced skin lesions may be caused by at least 5 mechanisms: delayed-type (type IV) hypersensitivity responses,^2,4–6 immune-mediated thrombocytopenia,³ type I allergic reactions,^7,8 skin necrosis⁹ and pustulosis.¹⁰Heparin-induced skin lesions may indicate the presence of life-threatening heparin-induced thrombocytopenia¹¹ — even in the absence of thrombocytopenia.³ There are no data available on the incidence of heparin-induced skin lesions or their causes. Given the rising number of reports of heparin-induced skin lesions and the importance of correctly diagnosing this condition, we sought to determine the incidence of heparin-induced skin lesions.     

Cluster analysis of comparative genomic hybridization (CGH) data using self-organizing maps: application to prostate carcinomas.

Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome-wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that region. Usually it is not possible to evaluate all 46 chromosomes of a metaphase, therefore several (up to 20 or more) metaphases are analyzed per individual, and expressed as average. Mostly one does not study one individual alone but groups of 20-30 individuals. Therefore, large amounts of data quickly accumulate which must be put into a logical order. In this paper we present the application of a self-organizing map (Genecluster) as a tool for cluster analysis of data from pT2N0 prostate cancer cases studied by CGH. Self-organizing maps are artificial neural networks with the capability to form clusters on the basis of an unsupervised learning rule, i.e., in our examples it gets the CGH data as only information (no clinical data). We studied a group of 40 recent cases without follow-up, an older group of 20 cases with follow-up, and the data set obtained by pooling both groups. In all groups good clusterings were found in the sense that clinically similar cases were placed into the same clusters on the basis of the genetic information only. The data indicate that losses on chromosome arms 6q, 8p and 13q are all frequent in pT2N0 prostatic cancer, but the loss on 8p has probably the largest prognostic importance.     

Limited contribution of predation by zooplanktivorous cyprinids to 0+ fish mortality

Predation by zooplanktivorous cyprinids was hypothesized as substantially contributing to larval fish mortality. To test this assumption, potential predators were sampled by electric fishing at sites and times of high fish larvae densities in the lower Oder River, Germany, in 2002 and 2003. At ten sites with high prey fish densities, all fishes ≥1+ and 0+ pike – all considered potentially predating on fish larvae – were captured, anaesthetised, and fixed. In the laboratory, 982 guts, respectively, stomachs were dissected and checked for fish larvae and larvae remains. Predation on 0+ fish was detected in the primary piscivorous fishes Esox lucius L. and Aspius aspius (L.), and facultative piscivorous Perca fluviatilis L., whilst none of the other nine species examined consumed fish. These findings implicate that predation by planktivorous cyprinids did not explain the typically strong decline in larval fish densities in the first weeks after hatching.