Kinetics of Oxygen Release from ORC

Oxygen release compounds (ORC) are one possibility to enhance aerobic degradation in contaminated aquifers. However, some applications have been reported where oxygen concentrations did not meet expectations, this was attributed to ground water composition, e.g., high pH. Column experiments have been performed and the measurements were interpreted using a numerical model to investigate oxygen release kinetics from ORC in more detail. Because the zero-order rate law recommended by the manufacturer did not reflect the measurements, a more complex kinetic scheme was developed. The simulations show a minor influence of inorganic ground water constituents on oxygen release from ORC in the columns due to buffering by mineral precipitation, but an enhanced oxygen release if aerobic degradation takes place. If ORC is applied as socks, the impact of inorganic ground water composition increases compared to the application in column experiments. A simple quadratic equation is provided to estimate oxygen release rate from the buffer capacity of the ground water versus increasing pH—a parameter easily determinable in the laboratory. For slightly mineralized waters with high pH, this equation forecasts decreased oxygen release, but no total inhibition of oxygen release.     

Energy-dependent receptor activities of Escherichia coli K-12: mutated TonB proteins alter FhuA receptor activities to phages T5, T1, ⊘80 and to colicin M

Abstract The activity of the FhuA receptor in the outer membrane of Escherichia coli is dependent on the TonB, ExbB and ExbD proteins which are anchored to the cytoplasmic membrane. Only infection by phage T5 occurs independently of TonB, ExbB and ExbD. In this paper we describe mutated FhuA proteins which displayed either an increased or decreased FhuA activity to phage T5 when combined with mutated TonB proteins. These results suggest conformational changes in FhuA by TonB which are recognized by phage T5. Similar results were obtained with colicin M and the phages T1 and ⊘80. It is proposed that the FhuA mutant proteins assume conformations which are either improved or impaired by the TonB derivatives. For the direct interaction of FhuA with TonB regions which are located outside the TonB box of FhuA and the region around residue 160 of TonB are important.     

New Gromov-Inspired Metrics on Phylogenetic Tree Space

We present a new class of metrics for unrooted phylogenetic X-trees inspired by the Gromov–Hausdorff distance for (compact) metric spaces. These metrics can be efficiently computed by linear or quadratic programming. They are robust under NNI operations, too. The local behaviour of the metrics shows that they are different from any previously introduced metrics. The performance of the metrics is briefly analysed on random weighted and unweighted trees as well as random caterpillars.     

European Multi-Centre Validation Study of NucliSens Extractor in Combination with HCV Amplicor 2·0 Assay for HCV-NAT Screening of Plasma Pools

The NucliSens Extractor in combination with the 2.0 version of the Roche Cobas HCV Amplicor test has been validated by five European blood screening laboratories in a multi-centre study. For testing the performance characteristics of this HCV-NAT method, the European Pharmacopoeia validation guidelines were followed. The CLB VQC reference reagents were used for testing robustness and sensitivity. After a technical improvement in the extraction stations, the NucliSens Extractor appeared to be contamination-free as was proved by testing negative controls alternating with samples containing a high HCV-RNA concentration. The Pelicheck HCV-RNA genotype 1 dilution panel was tested 74 times in the five laboratories and an overall 95% detection limit of 80 genome equivalents (geq)/ml was found. In one laboratory the Pelicheck panel was tested in 25 runs and here a 95% detection limit of 32 geq/ml was achieved. In this laboratory the Pelispy HCV-RNA run control samples of 140 geq/ml were consistently picked up in all extractor stations. In addition the laboratories have tested a WHO HCV-RNA genotype 1 standard dilution series 39 times and a Pelicheck HCV-RNA genotype 3 reference panel in 32 test runs. The limiting dilution analysis enabled us to compare the detection efficiency of the NucliSens-Amplicor method for the genoype 1 and genotype 3 isolates and to calibrate the reference reagents against each other. The combined Nuclisens-Amplicor method was found to detect the genotype 3 isolate in the Pelicheck HCV-RNA panels with 2-3 fold lower efficiency than the genotype 1 standard (assuming that the historical calibration of the genotype 3 against the genotype 1 standard is correct). In this study of a single method 1 IU of the WHO HCV-RNA standard was found to be equivalent to 5.1 geq of the VQC HCV-RNA standard (95% confidence intervals 3.1-9.1 geq). To avoid confusion with the use of the CLB VQC reagents we accept the NIBSC collaborative study in which calibration by a variety of methods showed that the Pelispy 380 geq/ml run control is equivalent to 100 IU/ml of the WHO standard. This multi-centre validation study demonstrates that the 95% detection limit of the NucliSens HCV Amplicor method lies far below the detection limits required by the international regulatory bodies.     

Characterization of Colicin S4 and Its Receptor, OmpW, a Minor Protein of the Escherichia coli Outer Membrane

Analysis of the nucleotide sequence of an Escherichia coli colicin S4 determinant revealed 76% identity to the pore-forming domain of the colicin A protein, 77% identity to the colicin A immunity protein, and 82% identity to the colicin A lysis protein. The N-terminal region, which is responsible for the Tol-dependent uptake of colicin S4, has 94% identity to the N-terminal region of colicin K. By contrast, the predicted receptor binding domain shows no sequence similarities to other colicins. Mutants that lacked the OmpW protein were resistant to colicin S4.     

A population of serum deprivation-induced bone marrow stem cells (SD-BMSC) expresses marker typical for embryonic and neural stem cells

The bone marrow represents an easy accessible source of adult stem cells suitable for various cell based therapies. Several studies in recent years suggested the existence of pluripotent stem cells within bone marrow stem cells (BMSC) expressing marker proteins of both embryonic and tissue committed stem cells. These subpopulations were referred to as MAPC, MIAMI and VSEL-cells. Here we describe SD-BMSC (serumdeprivation-induced BMSC) which are induced as a distinct subpopulation after complete serumdeprivation. SD-BMSC are generated from small-sized nestin-positive BMSC (S-BMSC) organized as round-shaped cells in the top layer of BMSC-cultures. The generation of SD-BMSC is caused by a selective proliferation of S-BMSC and accompanied by changes in both morphology and gene expression. SD-BMSC up-regulate not only markers typical for neural stem cells like nestin and GFAP, but also proteins characteristic for embryonic cells like Oct4 and SOX2. We hypothesize, that SD-BMSC like MAPC, MIAMI and VSEL-cells represent derivatives from a single pluripotent stem cell fraction within BMSC exhibiting characteristics of embryonic and tissue committed stem cells. The complete removal of serum might offer a simple way to specifically enrich this fraction of pluripotent embryonic like stem cells in BMSC cultures.     

Spatial proximity of proteins surrounding zyxin under force-bearing conditions

Sensing physical forces is a critical first step in mechano-transduction of cells. Zyxin, a LIM domain-containing protein, is recruited to force-bearing actin filaments and is thought to repair and strengthen them. Yet, the precise force-induced protein interactions surrounding zyxin remain unclear. Using BioID analysis, we identified proximal proteins surrounding zyxin under normal and force-bearing conditions by label-free mass spectrometry analysis. Under force-bearing conditions, increased biotinylation of α-actinin 1, α-actinin 4, and AFAP1 were detected, and these proteins accumulated along force-bearing actin fibers independently from zyxin, albeit at a lower intensity than zyxin. VASP also accumulated along force-bearing actin fibers in a zyxin-dependent manner, but the biotinylation of VASP remained constant regardless of force, supporting the model of a free zyxin–VASP complex in the cytoplasm being corecruited to tensed actin fibers. In addition, ARHGAP42, a RhoA GAP, was also identified as a proximal protein of zyxin and colocalized with zyxin along contractile actin bundles. The overexpression of ARHGAP42 reduced the rate of small wound closure, a zyxin-dependent process. These results demonstrate that the application of proximal biotinylation can resolve the proximity and composition of protein complexes as a function of force, which had not been possible with traditional biochemical analysis.     

Nazca Booby (Sula granti) inputs maintain the terrestrial food web of Malpelo Island

Most of the known food webs are based on organic compounds provided by photoautotrophic organisms. The terrestrial ecosystem of Malpelo Island (Colombia) seems to be an exception, however, since it supports several trophic guilds without hosting an adequate amount of primary producers. It has been suggested that this apparent paradox might be explained by external inputs provided by seabirds, namely Nazca Boobies (Sula granti), forming a huge colony on Malpelo. This hypothesis has never been tested. Here, we present a first approach to quantify the significance of Nazca Booby inputs into the Malpelo ecosystem via excrement, second eggs/chicks (which are prone to die), and carcasses, respectively, during the major breeding season. The total input was calculated to amount to 171.6 t per breeding season, with excrements accounting for almost 99% (170 t) of this input. Second eggs/chicks contributed approximately 1.1 t (0.64%) and carcasses around 0.1 t (0.06%). These finding support the idea of the Nazca Booby facilitating a food chain that pairs the pelagic primary producers of the open ocean with the terrestrial consumers of an island. Species most strongly profiting from this process include three endemic lizard species (Anolis agassizi, Diploglossus millepunctatus, Phyllodactylus transversalis) and the land crab (Johngarthia malpilensis).