Rate of iron transfer through the horse spleen ferritin shell determined by the rate of formation of Prussian Blue and Fe-desferrioxamine within the ferritin cavity

Iron (2+ and 3+) is believed to transfer through the three-fold channels in the ferritin shell during iron deposition and release in animal ferritins. However, the rate of iron transit in and out through these channels has not been reported. The recent synthesis of [Fe(CN)6]3-, Prussian Blue (PB) and desferrioxamine (DES) all trapped within the horse spleen ferritin (HoSF) interior makes these measurements feasible. We report the rate of Fe2+ penetrating into the ferritin interior by adding external Fe2+ to [Fe(CN)6]3- encapsulated in the HoSF interior and measuring the rate of formation of the resulting encapsulated PB. The rate at which Fe2+ reacts with [Fe(CN)6]3- in the HoSF interior is much slower than the formation of free PB in solution and is proceeded by a lag period. We assume this lag period and the difference in rate represent the transfer of Fe2+ through the HoSF protein shell. The calculated diffusion coefficient, D approximately 5.8x10(-20) m2/s corresponds to the measured lag time of 10-20 s before PB forms within the HoSF interior. The activation energy for Fe2+ transfer from the outside solution through the protein shell was determined to be 52.9 kJ/mol by conducting the reactions at 10 approximately 40 degrees C. The reaction of Fe3+ with encapsulated [Fe(CN)6]4- also readily forms PB in the HoSF interior, but the rate is faster than the corresponding Fe2+ reaction. The rate for Fe3+ transfer through the ferritin shell was confirmed by measuring the rate of the formation of Fe-DES inside HoSF and an activation energy of 58.4 kJ/mol was determined. An attempt was made to determine the rate of iron (2+ and 3+) transit out from the ferritin interior by adding excess bipyridine or DES to PB trapped within the HoSF interior. However, the reactions are slow and occur at almost identical rates for free and HoSF-encapsulated PB, indicating that the transfer of iron from the interior through the protein shell is faster than the rate-limiting step of PB dissociation. The method described in this work presents a novel way of determining the rate of transfer of iron and possibly other small molecules through the ferritin shell.     

Ontogeny of the proliferous spikelet in Eleocharis viridans (Cyperaceae)

Cyperaceae, the third largest family of monocotyledons, show unusual asexual reproductive strategies, such as pseudovivipary involving the formation of new individuals from somatic tissues of floral structures. In Eleocharis pseudovivipary is an important reproductive process in series Tenuissimae, which results in a structure called a proliferous spikelet. With the aim of describing the ontogenetic process of the pseudovivipary in E. viridans, proliferous spikelets at different developmental stages were analysed by light microscopy and scanning electron microscopy. The proliferous spikelet develops from a meristem located in the axil of the basal glume, homologous to bracts of other groups of Cyperaceae, in the culm of the parental plant. Each proliferous spikelet is formed by sympodial units, which consist of an addorsed prophyll, an outer and inner sheath and a culm, which develops a primordium of floriferous spikelet at the terminal region, which can be aborted, and may develop a proliferous spikelet lateral in the axil of the basal glume. The second internode of each sympodial unit contains a root primordium and an intercalary meristem at the culm base. Our results indicate that pseudovivipary can coexist with sexual reproduction as an alternative reproductive strategy, allowing the rapid spread of populations. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 524–539.     

No Differences in Soil Carbon Stocks Across the Tree Line in the Peruvian Andes

Reliable soil organic carbon (SOC) stock measurements of all major ecosystems are essential for predicting the influence of global warming on global soil carbon pools, but hardly any detailed soil survey data are available for tropical montane cloud forests (TMCF) and adjacent high elevation grasslands above (puna). TMCF are among the most threatened of ecosystems under current predicted global warming scenarios. We conducted an intensive soil sampling campaign extending 40 km along the tree line in the Peruvian Andes between 2994 and 3860 m asl to quantify SOC stocks of TMCF, puna grassland, and shrubland sites in the transition zone between the two habitats. SOC stocks from the soil surface down to the bedrock averaged (±standard error SE) 11.8 (±1.5, N = 24) kg C/m² in TMCF, 14.7 (±1.4, N = 9) kg C/m² in the shrublands and 11.9 (±0.8, N = 35) kg C/m² in the grasslands and were not significantly different (P > 0.05 for all comparisons). However, soil profile analysis revealed distinct differences, with TMCF profiles showing a uniform SOC distribution with depth, shrublands a linear decrease, and puna sites an exponential decrease in SOC densities with soil depth. Organic soil layer thickness reached a maximum (~70 cm) at the upper limit of the TMCF and declined with increasing altitude toward puna sites. Within TMCF, no significant increase in SOC stocks with increasing altitude was observed, probably because of the large variations among SOC stocks at different sites, which in turn were correlated with spatial variation in soil depth.     

Regulated expression of the pathogen receptor dendritic cell-specific intercellular adhesion molecule 3 (ICAM-3)-grabbing nonintegrin in THP-1 human leukemic cells, monocytes, and macrophages

Dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN) is a type II C-type lectin that functions as an adhesion receptor and mediates binding and internalization of pathogens such as virus (human immunodeficiency virus, hepatitis C), bacteria (Mycobacterium), fungi, and parasites. DC-SIGN expression in vivo is primarily restricted to interstitial dendritic cells (DC) and certain tissue macrophages. We now report that leukemic THP-1 cells, widely used as a model for monocyte-macrophage differentiation, express very low basal levels of DC-SIGN and that DC-SIGN expression in THP-1 cells is regulated during differentiation. Differentiation-inducing agents (phorbol ester, bryostatin) conveyed THP-1 cells with the ability to up-regulate DC-SIGN mRNA levels and cell surface expression in response to interleukin-4 (IL-4) or IL-13. DC-SIGN up-regulation required a functional JAK-STAT signaling pathway, was inhibited in the presence of lipopolysaccharide (LPS) or tumor necrosis factor-alpha (TNF-alpha), and conferred THP-1 cells with increased pathogen recognition and T cell stimulatory capabilities. The up-regulation of DC-SIGN on THP-1 cells resembles its inducible expression on monocytes and macrophages, where DC-SIGN expression is also induced by IL-4/IL-13 and negatively regulated by TNF-alpha, LPS, and vitamin D(3). These results point to THP-1 cells as a useful cellular system to characterize the pathogen-binding capabilities of DC-SIGN and to dissect the molecular mechanisms that control its regulated and tissue-specific expression in myeloid dendritic cells, and the results suggest that DC-SIGN constitutes a marker for both DC and alternatively activated macrophages.     

DC-SIGN (CD209) expression is IL-4 dependent and is negatively regulated by IFN, TGF-beta, and anti-inflammatory agents

Dendritic cell-specific ICAM-3 grabbing nonintegrin (DC-SIGN) is a monocyte-derived dendritic cell (MDDC)-specific lectin which participates in dendritic cell (DC) migration and DC-T lymphocyte interactions at the initiation of immune responses and enhances trans-infection of T cells through its HIV gp120-binding ability. The generation of a DC-SIGN-specific mAb has allowed us to determine that the acquisition of DC-SIGN expression during the monocyte-DC differentiation pathway is primarily induced by IL-4, and that GM-CSF cooperates with IL-4 to generate a high level of DC-SIGN mRNA and cell surface expression on immature MDDC. IL-4 was capable of inducing DC-SIGN expression on monocytes without affecting the expression of other MDDC differentiation markers. By contrast, IFN-alpha, IFN-gamma, and TGF-beta were identified as negative regulators of DC-SIGN expression, as they prevented the IL-4-dependent induction of DC-SIGN mRNA on monocytes, and a similar inhibitory effect was exerted by dexamethasone, an inhibitor of the monocyte-MDDC differentiation pathway. The relevance of the inhibitory action of dexamethasone, IFN, and TGF-beta on DC-SIGN expression was emphasized by their ability to inhibit the DC-SIGN-dependent HIV-1 binding to differentiating MDDC. These results demonstrate that DC-SIGN, considered as a MDDC differentiation marker, is a molecule specifically expressed on IL-4-treated monocytes, and whose expression is subjected to a tight regulation by numerous cytokines and growth factors. This feature might help in the development of strategies to modulate the DC-SIGN-dependent cell surface attachment of HIV for therapeutic purposes.     

Structure-Function Analysis of MurJ Reveals a Solvent-Exposed Cavity Containing Residues Essential for Peptidoglycan Biogenesis in Escherichia coli

Gram-negative bacteria such as Escherichia coli build a peptidoglycan (PG) cell wall in their periplasm using the precursor known as lipid II. Lipid II is a large amphipathic molecule composed of undecaprenyl diphosphate and a disaccharide-pentapeptide that PG-synthesizing enzymes use to build the PG sacculus. During PG biosynthesis, lipid II is synthesized at the cytoplasmic face of the inner membrane and then flipped across the membrane. This translocation of lipid II must be assisted by flippases thought to shield the disaccharide-pentapeptide as it crosses the hydrophobic core of the membrane. The inner membrane protein MurJ is essential for PG biogenesis and homologous to known and putative flippases of the MOP (multidrug/oligo-saccharidyl-lipid/polysaccharide) exporter superfamily, which includes flippases that translocate undecaprenyl diphosphate-linked oligosaccharides across the cytoplasmic membranes of bacteria. Consequently, MurJ has been proposed to function as the lipid II flippase in E. coli. Here, we present a three-dimensional structural model of MurJ generated by the I-TASSER server that suggests that MurJ contains a solvent-exposed cavity within the plane of the membrane. Using in vivo topological studies, we demonstrate that MurJ has 14 transmembrane domains and validate features of the MurJ structural model, including the presence of a solvent-exposed cavity within its transmembrane region. Furthermore, we present functional studies demonstrating that specific charged residues localized in the central cavity are essential for function. Together, our studies support the structural homology of MurJ to MOP exporter proteins, suggesting that MurJ might function as an essential transporter in PG biosynthesis.     

Conversion from electrocardiosignals to equivalent electrical sources on heart surface

In biomarker discovery, applying domain knowledge is an effective approach to eliminating false positive features, prioritizing functionally impactful markers and facilitating the interpretation of predictive signatures. Several computational methods have been developed that formulate the knowledge-based biomarker discovery as a feature selection problem guided by prior information. These methods often require that prior information is encoded as a single score and the algorithms are optimized for biological knowledge of a specific type. However, in practice, domain knowledge from diverse resources can provide complementary information. But no current methods can integrate heterogeneous prior information for biomarker discovery. To address this problem, we developed the Know-GRRF (know-guided regularized random forest) method that enables dynamic incorporation of domain knowledge from multiple disciplines to guide feature selection. Know-GRRF embeds domain knowledge in a regularized random forest framework. It combines prior information from multiple domains in a linear model to derive a composite score, which, together with other tuning parameters, controls the regularization of the random forests model. Know-GRRF concurrently optimizes the weight given to each type of domain knowledge and other tuning parameters to minimize the AIC of out-of-bag predictions. The objective is to select a compact feature subset that has a high discriminative power and strong functional relevance to the biological phenotype. Via rigorous simulations, we show that Know-GRRF guided by multiple-domain prior information outperforms feature selection methods guided by single-domain prior information or no prior information. We then applied Known-GRRF to a real-world study to identify prognostic biomarkers of prostate cancers. We evaluated the combination of cancer-related gene annotations, evolutionary conservation and pre-computed statistical scores as the prior knowledge to assemble a panel of biomarkers. We discovered a compact set of biomarkers with significant improvements on prediction accuracies. Know-GRRF is a powerful novel method to incorporate knowledge from multiple domains for feature selection. It has a broad range of applications in biomarker discoveries. We implemented this method and released a KnowGRRF package in the R/CRAN archive.     

Identification of free-living amoebas and amoeba-resistant bacteria accumulated in Dreissena polymorpha

To identify the free-living amoeba (FLA) and amoeba-resistant bacteria (ARB) accumulated in zebra mussels and in the water in which they are found, mussels were collected at two locations in the Ebro river basin (North East Spain). FLAs and bacteria were isolated from mussel extracts and from natural water. PCR techniques were used to identify the FLAs and endosymbiont bacteria (Legionella, Mycobacterium, Pseudomonas and cyanobacteria), and to detect Giardia and Cryptosporidium. The most frequently found FLAs were Naegleria spp. The presence of Legionella, Mycobacterium and Pseudomonas inside the FLA was demonstrated, and in some cases both Legionella and Pseudomonas were found together. Differences between FLAs and ARB identified inside the mussels and in the water were detected. In addition, Escherichia coli, Clostridium perfringens, Salmonella spp. and Enterococcus spp. were accumulated in mussels in concentrations unconnected with those found in water. The results show the ability of the zebra mussel to act as a reservoir of potentially pathogenic FLAs, which are associated with potentially pathogenic ARB, although the lack of association between microorganisms inside the mussels and in the water suggests that they are not useful for monitoring microbiological contamination at a specific time.