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.     

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).     

Changes in land use and habitat availability affect the population genetic structure of Metrioptera roeselii (Orthoptera: Tettigoniidae)

The impact of temporal changes in habitat availability and land use on the present genetic diversity of the grassland katydid species Metrioptera roeselii was investigated in an extensively used agricultural landscape (Lahn-Dill-Bergland, Germany) based on six microsatellite loci. By integrating spatial and temporal dimensions, this study contrasts to conventional approaches that usually record landscape changes at discrete points in time. Molecular data suggest little geographical substructuring of the species. Nevertheless, time-dependent effects on genetic diversity in terms of observed heterozygosity and allelic richness within subpopulations were detected by general linear models (GLM), explaining up to 82 and 13%, respectively. The results indicated that allelic richness was significantly reduced with higher rates of land-use change. Contrastingly, the level of heterozygosity even increased with increasing land-use change, if this rate increase was accompanied by a reduction in grassland amount, while with an increase of grassland amount the level of heterozygosity remained similar. Furthermore, depending on the study site, heterozygosity was differently affected by grassland age of sampled patches and of the surrounding. This is presumably induced by contrasting levels of heterozygosity in combination with differing modes of dispersal due to habitat availability and site-specific matrix effects. The loss of genetic diversity due to frequent land-use change might result in a reduced ability to adapt to landscape change, which is even more relevant in intensively used agricultural landscapes and in the course of climate change.     

How do soil fauna and soil microbiota respond to beech forest growth?

The dynamics and performance of soil biota during forest rotation were studied in monoculture beech stands forming a chronosequence of four different age-classes(30,62,111,153 yr).Biomass was monitored in major groups of microflora,microfauna,mesofauna,and macrofauna.Resource availability(litter layer,soil organic mater),biomass of the two dominant decomposer groups(microflora,earthworms)as well as the biomass of mesofauna and microfauna were found to remain quite stable during forest succession.Nevertheles...     

Oligomeric structure of ExbB and ExbB-ExbD isolated from Escherichia coli as revealed by LILBID mass spectrometry

Energy-coupled transporters in the outer membrane of Escherichia coli and other Gram-negative bacteria allow the entry of scarce substrates, toxic proteins, and bacterial viruses (phages) into the cells. The required energy is derived from the proton-motive force of the cytoplasmic membrane, which is coupled to the outer membrane via the ExbB-ExbD-TonB protein complex. Knowledge of the structure of this complex is required to elucidate the mechanisms of energy harvesting in the cytoplasmic membrane and energy transfer to the outer membrane transporters. Here we solubilized an ExbB oligomer and an ExbB-ExbD subcomplex from the cytoplasmic membrane with the detergent undecyl maltoside. Using laser-induced liquid bead ion desorption mass spectrometry (LILBID-MS), we determined at moderate desorption laser energies the oligomeric structure of ExbB to be mainly hexameric (ExbB(6)), with minor amounts of trimeric (ExbB(3)), dimeric (ExbB(2)), and monomeric (ExbB(1)) oligomers. Under the same conditions ExbB-ExbD formed a subcomplex consisting of ExbB(6)ExbD(1), with a minor amount of ExbB(5)ExbD(1). At higher desorption laser intensities, ExbB(1) and ExbD(1) and traces of ExbB(3)ExbD(1), ExbB(2)ExbD(1), ExbB(1)ExbD(1), ExbB(3), and ExbB(2) were observed. Since the ExbB(6) complex and the ExbB(6)ExbD(1) complex remained stable during solubilization and subsequent chromatographic purification on nickel-nitrilotriacetate agarose, Strep-Tactin, and Superdex 200, and during native blue gel electrophoresis, we concluded that ExbB(6) and ExbB(6)ExbD(1) are subcomplexes on which the final complex including TonB is assembled.