Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem

Bacteria of the phyla Proteobacteria and Bacteroidetes are known to be the most prominent heterotrophic organisms in marine surface waters. In order to investigate the occurrence of these phyla in a coastal environment, the tidal flat ecosystem German Wadden Sea, we analyzed a clone library of PCR-amplified and sequenced 16S rRNA gene fragments and isolated 46 new strains affiliated with these phyla from the water column with various polymers and complex media as substrates. The phylogenetic affiliation of these strains was analyzed on the basis of sequenced 16S rRNA gene fragments. Subsequently, a comprehensive phylogenetic analysis of Proteobacteria and Bacteroidetes including available sequences from oxic habitats of earlier studies of this ecosystem was performed. Sequences of the earlier studies were derived from isolation approaches and from denaturing gradient gel electrophoresis (DGGE) analyses of environmental samples and high dilution steps of MPN (most probable number) cultures. The majority of the 265 sequences included in this analysis affiliated with alpha-Proteobacteria (45.3%), gamma-Proteobacteria (31.7%), and Bacteroidetes (16.2%). Almost 7% belong to the delta-Proteobacteria and several of these clones affiliated with the Myxococcales, a group comprising obligate aerobic organisms. Within the alpha- and gamma-Proteobacteria specific clusters were identified including isolates from high dilution steps of dilution cultures and/or clones from the clone library or DGGE gels, implying a high abundance of some of these organisms. Within the gamma-Proteobacteria a new cluster is proposed, which consists of marine surface-attached organisms. This SAMMIC (Surface Attached Marine MICrobes) cluster comprises only uncultured phylotypes and exhibits a global distribution. Overall, the analysis indicates that Proteobacteria and Bacteroidetes of the Wadden Sea have a surprisingly high diversity, presumably a result of the signature of this ecosystem as a melting pot at the land-sea interface and comprising a great habitat variety.     

Production of macroaggregates from dissolved exopolymeric substances (EPS) of bacterial and diatom origin

Exopolymeric substances (EPS) isolated from a pure culture of the marine bacterium Marinobacter sp. and the marine diatom Skeletonema costatum (axenic) were partially purified, chemically characterized and used as dissolved organic matter (DOM) for the production of macroaggregates. The role of organic particles such as transparent exopolymeric particles (TEP) and Coomassie stained particles (CSP) in the production of macroaggregates was experimentally assessed. Three experimental rolling tanks containing sterile medium with: (1) EPS, (2) EPS + live diatom cells and (3) EPS + killed bacteria, and three control tanks without any added EPS were used for macroaggregate production. Changes in abundance and average size of macroaggregates were monitored using image analysis, whereas TEP and CSP were enumerated microscopically. In the presence of microbial EPS, macroaggregates of a size of 23-35 mm(2) were produced. Aggregate size and abundance considerably varied with both time and source of EPS. No correlation was observed for macroaggregate size and abundance with either TEP or CSP. One-way ANOVA demonstrated significant differences in the variance of particle abundance and size in tanks having only EPS or EPS in combination with live diatom cells. Our data suggest that production of macroaggregates was influenced by polymer chemistry and surface properties of colliding particles, whereas TEP and CSP concentrations were influenced by molecular weight of EPS and the presence of growing cells. Interestingly, macroaggregates were formed in the near absence of TEP and CSP, highlighting the role of other unknown processes in the transformation of DOM to particulate organic matter (POM) in aquatic environments.     

Growth characteristics of small and large free-living and attached bacteria in Lake Constance

The growth characteristics of small (0.2–1.0m) and large (1.0–3.0 (m) free-living and attached bacteria were studied in Lake Constance by comparing the spatial and seasonal dynamics of their biomass turnover time (ratio of biomass/production). The biomass of small free-living bacteria usually turned over significantly faster than that of large free-living bacteria throughout the water column. The turnover of attached bacterial biomass was characterized by large fluctuations. Occasionally, in aphotic water layers, it was as long as that of large free-living bacteria, but when large amounts of decaying organic particles were present, it was shorter than that of small free-living cells. Biomass turnover times of free-living bacteria were in the same range as their generation times, which were estimated from the increase in bacterial abundance in 3m prefiltered samples. The biomass turnover time of actively metabolizing bacteria was comparable to the generation time of actively metabolizing cells. These results indicate that the biomass turnover time is a useful indicator of the growth of different bacterial fractions, as it reflects their different amounts of participation in microbial processes of aquatic ecosystems.     

Polymorphism of the pentanucleotide repeat d(AAAAT) within intron 1 of the human tumor suppressor gene p53 (17p13.1)

DyeDeoxy terminator cycle sequencing of allele-specific polymerase chain reaction products has shown that there is a highly polymorphic d(AAAAT) pentanucleotide repeat within the first intron of the human p53 gene. This provides a genetic marker for tumor suppressor p53 gene alterations.     

Migration of leukocytes across an endothelium-epithelium bilayer as a model of renal interstitial inflammation

Interstitial inflammation has emerged as a key event in the development of acute renal failure. To gain better insight into the nature of these inflammatory processes, the interplay between tubular epithelial cells, endothelial cells, and neutrophils (PMN) was investigated. A coculture transmigration model was developed, composed of human dermal microvascular endothelial (HDMEC) and human renal proximal tubular cells (HK-2) cultured on opposite sides of Transwell growth supports. Correct formation of an endoepithelial bilayer was verified by light and electron microscopy. The model was used to study the effects of endotoxin (LPS), tumor necrosis factor (TNF)-, and -melanocyte-stimulating hormone (-MSH) by measuring PMN migration and cytokine release. To distinguish between individual roles of microvascular endothelial and epithelial cells in transmigration processes, migration of PMN was investigated separately in HK-2 and HDMEC monolayers. Sequential migration of PMN through endothelium and epithelium could be observed and was significantly increased after proinflammatory stimulation with either TNF- or LPS (3.5 ± 0.58 and 2.76 ± 0.64-fold vs. control, respectively). Coincubation with -MSH inhibited the transmigration of PMN through the bilayer after proinflammatory stimulation with LPS but not after TNF-. The bilayers produced significant amounts of IL-8 and IL-6 mostly released from the epithelial cells. Furthermore, -MSH decreased LPS-induced IL-6 secretion by 30% but had no significant effect on IL-8 secretion. We established a transmigration model showing sequential migration of PMN across microvascular endothelial and renal tubular epithelial cells stimulated by TNF- and LPS. Anti-inflammatory effects of -MSH in this bilayer model are demonstrated by inhibition on PMN transmigration and IL-6 secretion. coculture; polymorphonuclear neutrophil migration; HK-2; interleukin-8; interleukin-6; -melanocyte-stimulating hormone     

Proof of Safety in Toxicology Based on the Ratio of Two Means for Normally Distributed Data

The aim of toxicology testing is the safety assessment of a substance such as a new pharmaceutical compound or a pesticide relative to a vehicle or negative control. This paper is concerned with the direct safety approach when safety is expressed in terms of the ratio of population means and when the toxicological endpoint is normally distributed. The methodology for power and sample size calculation is derived for the parallel group design and results are presented for various situations.     

A newly adapted pulsed-field gel electrophoresis technique allows to detect distinct types of DNA damage at low frequencies in human dermal fibroblasts upon exposure to non-toxic H2O2 concentrations

Reactive oxygen species (ROS) comprise several oxygen containing compounds, among them hydrogen peroxide (H₂O₂), which are generated by internal and external sources and play pleiotropic roles in physiological and pathological states. Skin cells as well as cells from other tissues have developed antioxidant defense mechanisms to protect themselves from high concentrations of ROS. Although biological and pathological roles of ROS have previously been elucidated, so far only limited knowledge exists regarding ROS-mediated generation of DNA breaks and base lesions occurring at low frequency in intact skin cells. This study was therefore designed to probe a newly adapted pulsed-field gel electrophoresis technique for the adequate measurement of high molecular weight DNA fragments as well as to investigate the protective role of the antioxidant enzyme catalase against H₂O₂-mediated damage in human dermal fibroblasts. We stably transfected and overexpressed the full-length catalase cDNA in the human dermal fibroblast cell line 1306 in culture and found that these cells are significantly more protected from cytotoxicity, overall DNA strand breaks, and 8-oxodeoxyguanine base lesions resulting from H₂O₂-triggered oxidative stress compared to vector-transfected 1306 cells or secondary dermal fibroblasts. This work has outlined the importance of catalase in the protection from H₂O₂-mediated cytotoxicity and DNA damage which — if unbalanced — even when occurring at low frequency are known to lead to genomic instability, a hallmark in carcinogenesis and premature aging.     

The first seriatim study of human growth and middle aging

The serial record of growth and recumbent length and stature for one individual during nearly 50 years is presented, together with increments derived from these data.     

Optimal adaptive two‐stage designs for phase II cancer clinical trials

In oncology, single‐arm two‐stage designs with binary endpoint are widely applied in phase II for the development of cytotoxic cancer therapies. Simon's optimal design with prefixed sample sizes in both stages minimizes the expected sample size under the null hypothesis and is one of the most popular designs. The search algorithms that are currently used to identify phase II designs showing prespecified characteristics are computationally intensive. For this reason, most authors impose restrictions on their search procedure. However, it remains unclear to what extent this approach influences the optimality of the resulting designs. This article describes an extension to fixed sample size phase II designs by allowing the sample size of stage two to depend on the number of responses observed in the first stage. Furthermore, we present a more efficient numerical algorithm that allows for an exhaustive search of designs. Comparisons between designs presented in the literature and the proposed optimal adaptive designs show that while the improvements are generally moderate, notable reductions in the average sample size can be achieved for specific parameter constellations when applying the new method and search strategy.     

2‐D DIGE analysis of the proteome of extracts from peanut variants reveals striking differences in major allergen contents

Over the last decade, an increasing prevalence of peanut allergies was observed worldwide. Peanuts are meanwhile categorized among the most dangerous food allergens. This is particularly relevant since peanut‐derived ingredients are widely used in industrial food production. To minimize the problem of hidden food allergens causing severe anaphylactic reactions, pre‐packaged food containing peanut components needs to be classified according to European ruling since 2005. Food companies search for strategies to reduce the allergenicity of peanut‐derived food additives either by genetically altering the allergen content or by identifying peanut varieties with low levels of major allergens. In our study, we focused on peanut extracts from Indonesia that apparently contain lower levels of the major Arachis hypogaea allergen 1 (Ara h 1). Basic extracts of Virginia‐type and Indonesian peanuts were compared by 1‐ and 2‐DE. We identified more than hundred individual components in these extracts by MS and provide a high‐resolution allergen map that also includes so far unknown fragments of major peanut allergens. The reduced level of Ara h 1 associated with a significantly lower abundance of the most potent peanut allergen Ara h 2 in various Indonesian peanuts was also confirmed by Western blotting with monoclonal antibodies and sera of allergic patients.