Proximal and distal mechanisms through which arbuscular mycorrhizal associations alter terrestrial denitrification

Plant and Soil - The vast majority of terrestrial plants, including most crops, associate with fungi of the phylum Glomeromycota to form symbiotic associations, known as arbuscular mycorrhizas....     

Dogfish egg case structural studies by ATR FT-IR and FT-Raman spectroscopy

The dogfish egg case is a composite structure that combines mechanical tensile strength, toughness and elasticity with high permeability to small molecules and ions. Presumably, it provides both a protective and a filtering role for the egg/embryo contained within it. In this work, we performed structural studies of the Galeus melastomus egg case at two different stages of the hardening process, utilizing ATR FT-IR and FT-Raman spectroscopy. Based on these data we deduce that: (a) The G. melastomus egg case, in close analogy to that of the related species Scyliorhinus cunicula, is a complex, composite structure which consists mainly of an analogue of collagen IV. This network forming protein appears to have common secondary structural characteristics in the entire egg case. (b) The outermost layer of the non-sclerotized egg case is especially rich in tyrosine, while the innermost layer is rich in polysaccharides, presumably glycosaminoglycans, and lipids. These differences are diminished upon hardening. (c) Disulfide bonds do not appear to play a significant role in cross-linking. However, cross-links involving tyrosine residues appear to sclerotize the egg case. It is proposed that the intensity of the Raman band at ca. 1615 cm(-1), which is due to ring stretching vibrations of Tyr, might be a useful indicator of the sclerotization status of a certain proteinaceous tissue, when tyrosines are involved in sclerotization mechanisms.     

Cdt1 associates dynamically with chromatin throughout G1 and recruits Geminin onto chromatin

To maintain genome integrity, eukaryotic cells initiate DNA replication once per cell cycle after assembling prereplicative complexes (preRCs) on chromatin at the end of mitosis and during G1. In S phase, preRCs are disassembled, precluding initiation of another round of replication. Cdt1 is a key member of the preRC and its correct regulation via proteolysis and by its inhibitor Geminin is essential to prevent premature re-replication. Using quantitative fluorescence microscopy, we study the interactions of Cdt1 with chromatin and Geminin in living cells. We find that Cdt1 exhibits dynamic interactions with chromatin throughout G1 phase and that the protein domains responsible for chromatin and Geminin interactions are separable. Contrary to existing in vitro data, we show that Cdt1 simultaneously binds Geminin and chromatin in vivo, thereby recruiting Geminin onto chromatin. We propose that dynamic Cdt1-chromatin associations and the recruitment of Geminin to chromatin provide spatio-temporal control of the licensing process.     

Collagen fiber alignment does not explain mechanical anisotropy in fibroblast populated collagen gels

Many load-bearing soft tissues exhibit mechanical anisotropy. In order to understand the behavior of natural tissues and to create tissue engineered replacements, quantitative relationships must be developed between the tissue structures and their mechanical behavior. We used a novel collagen gel system to test the hypothesis that collagen fiber alignment is the primary mechanism for the mechanical anisotropy we have reported in structurally anisotropic gels. Loading constraints applied during culture were used to control the structural organization of the collagen fibers of fibroblast populated collagen gels. Gels constrained uniaxially during culture developed fiber alignment and a high degree of mechanical anisotropy, while gels constrained biaxially remained isotropic with randomly distributed collagen fibers. We hypothesized that the mechanical anisotropy that developed in these gels was due primarily to collagen fiber orientation. We tested this hypothesis using two mathematical models that incorporated measured collagen fiber orientations: a structural continuum model that assumes affine fiber kinematics and a network model that allows for nonaffine fiber kinematics. Collagen fiber mechanical properties were determined by fitting biaxial mechanical test data from isotropic collagen gels. The fiber properties of each isotropic gel were then used to predict the biaxial mechanical behavior of paired anisotropic gels. Both models accurately described the isotropic collagen gel behavior. However, the structural continuum model dramatically underestimated the level of mechanical anisotropy in aligned collagen gels despite incorporation of measured fiber orientations; when estimated remodeling-induced changes in collagen fiber length were included, the continuum model slightly overestimated mechanical anisotropy. The network model provided the closest match to experimental data from aligned collagen gels, but still did not fully explain the observed mechanics. Two different modeling approaches showed that the level of collagen fiber alignment in our uniaxially constrained gels cannot explain the high degree of mechanical anisotropy observed in these gels. Our modeling results suggest that remodeling-induced redistribution of collagen fiber lengths, nonaffine fiber kinematics, or some combination of these effects must also be considered in order to explain the dramatic mechanical anisotropy observed in this collagen gel model system.     

A novel symbolization scheme for multichannel recordings with emphasis on phase information and its application to differentiate EEG activity from different mental tasks

Symbolic dynamics is a powerful tool for studying complex dynamical systems. So far many techniques of this kind have been proposed as a means to analyze brain dynamics, but most of them are restricted to single-sensor measurements. Analyzing the dynamics in a channel-wise fashion is an invalid approach for multisite encephalographic recordings, since it ignores any pattern of coordinated activity that might emerge from the coherent activation of distinct brain areas. We suggest, here, the use of neural-gas algorithm (Martinez et al. in IEEE Trans Neural Netw 4:558–569, 1993) for encoding brain activity spatiotemporal dynamics in the form of a symbolic timeseries. A codebook of k prototypes, best representing the instantaneous multichannel data, is first designed. Each pattern of activity is then assigned to the most similar code vector. The symbolic timeseries derived in this way is mapped to a network, the topology of which encapsulates the most important phase transitions of the underlying dynamical system. Finally, global efficiency is used to characterize the obtained topology. We demonstrate the approach by applying it to EEG-data recorded from subjects while performing mental calculations. By working in a contrastive-fashion, and focusing in the phase aspects of the signals, we show that the underlying dynamics differ significantly in their symbolic representations.     

Inter-alpha-trypsin inhibitor attenuates complement activation and complement-induced lung injury

Complement activation is a central component of inflammation and sepsis and can lead to significant tissue injury. Complement factors are serum proteins that work through a cascade of proteolytic reactions to amplify proinflammatory signals. Inter-alpha-trypsin inhibitor (IaI) is an abundant serum protease inhibitor that contains potential complement-binding domains, and has been shown to improve survival in animal sepsis models. We hypothesized that IaI can bind complement and inhibit complement activation, thus ameliorating complement-dependent inflammation. We evaluated this hypothesis with in vitro complement activation assays and in vivo in a murine model of complement-dependent lung injury. We found that IaI inhibited complement activation through the classical and alternative pathways, inhibited complement-dependent phagocytosis in vitro, and reduced complement-dependent lung injury in vivo. This novel function of IaI provides a mechanistic explanation for its observed salutary effects in sepsis and opens new possibilities for its use as a treatment agent in inflammatory diseases.