i‐Patch: Interprotein contact prediction using local network information

Biological processes are commonly controlled by precise protein‐protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i‐Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i‐Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i‐Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i‐Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i‐Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Litter elemental stoichiometry and biomass densities of forest soil invertebrates

To maintain constant chemical composition, i.e. elemental homeostasis, organisms have to consume resources of sufficient quality to meet their own specific stoichiometric demand. Therefore, concentrations of elements indicate resource quality, and rare elements in the environment may act as limiting factors for individual organisms scaling up to constrain population densities. We investigated how the biomass densities of invertebrate populations of temperate forest soil communities depend on 1) the stoichiometry of the basal litter according to ecological stoichiometry concepts and 2) the population average body mass as predicted by metabolic theory. We used a large data set on biomass densities of 4959 populations across 48 forests in three regions of Germany. Following various ecological stoichiometry hypotheses, we tested for effects of the carbon‐to‐element ratios of 10 elements. Additionally, we included the abiotic litter characteristics habitat size (represented by litter depth), litter diversity and pH, as well as forest type as an indicator for human management. Across 12 species groups, we found that the biomass densities scaled significantly with population‐averaged body masses thus supporting metabolic theory. Additionally, 10 of these allometric scaling relationships exhibited interactions with stoichiometric and abiotic co‐variables. The four most frequent co‐variables were 1) forest type, 2) the carbon‐to‐phosphorus ratio (C:P), 3) the carbon‐to‐sodium ratio (C:Na), and the carbon‐to‐nitrogen ratio (C:N). Hence, our analyses support the sodium shortage hypothesis for microbi‐detritivores, the structural elements hypothesis for some predator groups (concerning N), and the secondary productivity hypothesis (concerning P) across all trophic groups in our data. In contrast, the ecosystem size hypothesis was only supported for some meso‐ and macrofauna detritivores. Our study is thus providing a comprehensive analysis how the elemental stoichiometry of the litter as the basal resource constrain population densities across multiple trophic levels of soil communities.     

Endogenous Brain Pericytes Are Widely Activated and Contribute to Mouse Glioma Microvasculature

Glioblastoma multiforme (GBM) is the most common brain tumor in adults. It presents an extremely challenging clinical problem, and treatment very frequently fails due to the infiltrative growth, facilitated by extensive angiogenesis and neovascularization. Pericytes constitute an important part of the GBM microvasculature. The contribution of endogenous brain pericytes to the tumor vasculature in GBM is, however, unclear. In this study, we determine the site of activation and the extent of contribution of endogenous brain pericytes to the GBM vasculature. GL261 mouse glioma was orthotopically implanted in mice expressing green fluorescent protein (GFP) under the pericyte marker regulator of G protein signaling 5 (RGS5). Host pericytes were not only activated within the glioma, but also in cortical areas overlying the tumor, the ipsilateral subventricular zone and within the hemisphere contralateral to the tumor. The host-derived activated pericytes that infiltrated the glioma were mainly localized to the tumor vessel wall. Infiltrating GFP positive pericytes co-expressed the pericyte markers platelet-derived growth factor receptor-β (PDGFR-β) and neuron-glial antigen 2. Interestingly, more than half of all PDGFR-β positive pericytes within the tumor were contributed by the host brain. We did not find any evidence that RGS5 positive pericytes adopt another phenotype within glioma in this paradigm. We conclude that endogenous pericytes become activated in widespread areas of the brain in response to an orthotopic mouse glioma. Host pericytes are recruited into the tumor and constitute a major part of the tumor pericyte population.     

The secretome of mesenchymal stem cells: Potential implications for neuroregeneration

Mesenchymal stem cells have shown regenerative properties in many tissues. This feature had originally been ascribed to their multipotency and thus their ability to differentiate into tissue-specific cells. However, many researchers consider the secretome of mesenchymal stem cells the most important player in the observed reparative effects of these cells. In this review, we specifically focus on the potential neuroregenerative effect of mesenchymal stem cells, summarize several possible mechanisms of neuroregeneration and list key factors mediating this effect. We illustrate examples of mesenchymal stem cell treatment in central nervous system disorders including stroke, neurodegenerative disorders (such as Parkinson's disease, Huntington's disease, multiple system atrophy and cerebellar ataxia) and inflammatory disease (such as multiple sclerosis). We specifically highlight studies where mesenchymal stem cells have entered clinical trials.     

Spillover of trap-nesting bees and wasps in an urban–rural interface

A mismatch of resource availability in certain periods can lead to spillover of insects between habitats, resulting in temporal differences in insect diversity. Urban gardens are important anthropogenic habitats but it is unknown whether, when and why spillover of beneficial insects occurs between gardens and agricultural habitats. We used trap nests for Hymenoptera to monthly monitor bee and wasp abundance and species richness in 12 gardens and 12 rapeseed fields. Half of the gardens and rapeseed fields were located in the urban–rural interface and bordered each other (a garden paired with a rapeseed field) and the other half were isolated in the rural landscape (isolated rapeseed fields) and in the urban city centre (isolated gardens). In general, gardens in the urban–rural interface comprised the highest richness of bees and wasps. The abundance of bees but not of wasps was highest in paired habitats and peaked at full rapeseed blooming, indicating that mass-flowering rapeseed offers foraging resources for bees nesting in adjacent gardens. Thus, bees nest and increase their populations in both areas, benefiting from the mass-flowering resource in the agricultural habitat as well as the nesting resources from gardens, suggesting spillover of bees but not of wasps between paired gardens and rapeseed fields. Our study highlights the value of gardens in the urban–rural interface for the biodiversity of functionally important insects. Implementing urban gardening and small-scale agriculture in cities and suburban habitats can promote local pollinator populations and benefit adjacent croplands.     

Secondary phenolic products in isolated guard cell,epidermal cell and mesophyll cell protoplasts from pea (Pisum sativum L.) leaves: Distribution and determination

Summary Guard cells and epidermal cells of the abaxial (lower) and adaxial (upper) epidermis ofPisum sativum L., mutant Argenteum, are the predominant sites of flavonoid accumulation within the leaf. This was demonstrated by the use of a new method of simultaneous isolation and separation of intact, highly-purified guard cell and epidermal cell protoplasts from both epidermal layers and of protoplasts from the mesophyll. Isolated guard and epidermal protoplasts retained flavonoid patterns of the parent epidermal tissue; quercetin 3-triglucoside and its p-coumaric acid ester as major constituents, kaempferol 3-triglucoside and its p-coumaric acid ester as minor compounds. Total flavonoid content in the lower epidermis was estimated to be ca. 80 fmol per guard cell protoplast and 500 fmol per epidermal cell protoplast. Protoplasts isolated from the upper epidermis had about 20–30% as much of these flavonoids. Mesophyll protoplasts retained only about 25 fmol total flavonoid per protoplast.By fluorescence microscopy, using the alkaline-induced yellow-green fluorescence characteristics of flavonols, we suggest that these flavonol glycosides are present in cell vacuoles. There was no indication for the presence of flavine-like compounds.Abbreviations uE adaxial (upper) epidermis - IE abaxial (lower) epidermis - GCP guard cell protoplasts - ECP epidermal cell protoplasts - MCP mesophyll cell protoplasts - PP protoplasts - HPLC high performance liquid chromatography - TLC thin layer chromatography - CC column chromatography - HOAc acetic acid     

Novel rodent models for macular research

Background

Many disabling human retinal disorders involve the central retina, particularly the macula. However, the commonly used rodent models in research, mouse and rat, do not possess a macula. The purpose of this study was to identify small laboratory rodents with a significant central region as potential new models for macular research.

Methodology/Principal Findings

Gerbillus perpallidus, Meriones unguiculatus and Phodopus campbelli, laboratory rodents less commonly used in retinal research, were subjected to confocal scanning laser ophthalmoscopy (cSLO), fluorescein and indocyanine green angiography, and spectral-domain optical coherence tomography (SD-OCT) using standard equipment (Heidelberg Engineering HRA1 and Spectralis™) adapted to small rodent eyes. The existence of a visual streak-like pattern was assessed on the basis of vascular topography, retinal thickness, and the topography of retinal ganglion cells and cone photoreceptors. All three species examined showed evidence of a significant horizontal streak-like specialization. cSLO angiography and retinal wholemounts revealed that superficial retinal blood vessels typically ramify and narrow into a sparse capillary net at the border of the respective area located dorsal to the optic nerve. Similar to the macular region, there was an absence of larger blood vessels in the streak region. Furthermore, the thickness of the photoreceptor layer and the population density of neurons in the ganglion cell layer were markedly increased in the visual streak region.

Conclusions/Significance

The retinal specializations of Gerbillus perpallidus, Meriones unguiculatus and Phodopus campbelli resemble features of the primate macula. Hence, the rodents reported here may serve to study aspects of macular development and diseases like age-related macular degeneration and diabetic macular edema, and the preclinical assessment of therapeutic strategies.     

Three-dimensional co-culture of primary human liver cells in bioreactors for in vitro drug studies: effects of the initial cell quality on the long-term maintenance of hepatocyte-specific functions

In vitro culture models that employ human liver cells could be potent tools for predictive studies on drug toxicity and metabolism in the pharmaceutical industry. A bioreactor culture model was developed that permits the three-dimensional co-culture of liver cells under continuous medium perfusion with decentralised mass exchange and integral oxygenation. We tested the ability of the system to support the long-term maintenance and differentiation of primary human liver cells. The effects of the initial cell quality were investigated by comparing cultures from resected, non-preserved liver with cultures from liver graft tissue damaged by long-term preservation. In cultures originating from non-preserved liver, protein and urea synthesis, glucose metabolism, and cytochrome (CYP450) activities were stable over the 2-week culture period, with maximal activities at the end of the first week in culture. Enzyme induction led to increased 7-ethoxyresorufin O-deethylase activities of up to 20 times the basal value. In cultures from preservation-damaged liver, recovery of metabolic activities was detected during bioreactor culture. After two weeks, most biochemical parameters approached those of cultures from non-preserved human liver. Light microscopy demonstrated the three-dimensional reorganisation of hepatocytes and non-parenchymal cells in co-culture. Long-term maintenance, and even the regeneration of specific functional activities of human liver cells, can be achieved in the bioreactor. This could facilitate the introduction into the pharmaceutical industry of in vitro drug testing with primary human liver cells.