Differential distribution of DHA-phospholipids in rat brain after feeding: A lipidomic approach

On a per-weight basis, the brain is the organ richest in lipids, including a remarkable proportion of polyunsaturated fatty acids (PUFAs) of the omega 3 series, namely eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids. The cerebral effects of exogenous DHA likely depend on its degree of incorporation into neuronal phospholipids and on its distribution among the various brain structures, after intake. Hence, because PUFAs are not evenly distributed among the brain phospholipid classes and because the existence of class-specific phospholipases that regulate their turnover, we sought to investigate the incorporation of omega 3 PUFAs in selected brain areas regions and specific phospholipid classes. Rats (n=7) were administered, by oral gavage, 100mg/kg/d of a commercially available fish oil (containing ～84% of long-chain omega 3 fatty acids, of which ～38% of DHA and ～46% of EPA). Control rats (n=7) received liquid paraffin. This treatment was continued for 30 days. Thereafter, we dissected three areas, namely the hippocampus, the striatum, and the cortex. Quantization of individual phospholipid classes and their molecular species was performed by ESI-MS/MS. Principal component analysis was used to examine the variation of the molecular lipid profiles (as percentage) induced by omega 3 supplementation. Our results show that provision of omega 3 fatty acids to rats results in their incorporation into brain phospholipids, the extent of which is lower in the striatum as compared with cortex and hippocampus. These data might in part explain the mixed therapeutic results obtained in neurological disorders, many of which are likely region-specific.     

The genetic code and its optimization for kinetic energy conservation in polypeptide chains

Why is the genetic code the way it is? Concepts from fields as diverse as molecular evolution, classical chemistry, biochemistry and metabolism have been used to define selection pressures most likely to be involved in the shaping of the genetic code.     

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

This is a PLOS Computational Biology Software Article

     

The C-terminal domain of Nup93 is essential for assembly of the structural backbone of nuclear pore complexes

Nuclear pore complexes (NPCs) are large macromolecular assemblies that control all transport across the nuclear envelope. They are formed by about 30 nucleoporins (Nups), which can be roughly categorized into those forming the structural skeleton of the pore and those creating the central channel and thus providing the transport and gating properties of the NPC. Here we show that the conserved nucleoporin Nup93 is essential for NPC assembly and connects both portions of the NPC. Although the C-terminal domain of the protein is necessary and sufficient for the assembly of a minimal structural backbone, full-length Nup93 is required for the additional recruitment of the Nup62 complex and the establishment of transport-competent NPCs.     

Nuclear pore complex assembly through the cell cycle: regulation and membrane organization

In eukaryotes, all macromolecules traffic between the nucleus and the cytoplasm through nuclear pore complexes (NPCs), which are among the largest supramolecular assemblies in cells. Although their composition in yeast and metazoa is well characterized, understanding how NPCs are assembled and form the pore through the double membrane of the nuclear envelope and how both processes are controlled still remains a challenge. Here, we summarize what is known about the biogenesis of NPCs throughout the cell cycle with special focus on the membrane reorganization and the regulation that go along with NPC assembly.     

Association of mesenchymal cells and immunoglobulins with differentiating epithelial cells

Background

Mesenchymal-epithelial interactions play an important role in the physiology and pathology of epithelial tissues. Mesenchymal cells either associate with epithelium basement membrane [pericytes and perivascular monocyte-derived cells (MDC)] or reside within epithelium (MDC and T cells). Although intraepithelial mesenchymal cells were suggested to contribute to the epithelium physiology, their association with particular steps in differentiation of epithelial cells, interactions among themselves, and their fate remain unclear. We studied epitopes of mesenchymal cells and their products (immunoglobulins) in stratified epithelium of uterine ectocervix, which is one of the prototypes of complete cellular differentiation from stem into the aged cells.

Results

Perivascular CD14 primitive MDC associated with basal (stem) epithelial cells. Thy-1 pericytes of microvasculature secreted intercellular vesicles, which associated with Ki67 postmitotic epithelial cells expressing MHC class I. Intraepithelial T cells showed an association with veiled type MDC [dendritic cell (DC) precursors] among parabasal cells, and exhibited fragmentation after entering intermediate (mature) epithelial layers. Mature DC secreted CD68 and exhibited fragmentation after reaching mid intermediate layers. Binding of IgM was detected at the top of each layer: in the upper parabasal, upper intermediate, and most surface epithelial cells. IgG was confined to the entire superficial layer.

Conclusions

These data suggest that the phylogenetically and ontogenetically developed hierarchy of mesenchymal cells (MDC, pericytes, T cells) and immunoglobulins (IgM, IgG) accompanies differentiation of epithelial cells from immature into the mature and aged phenotype. Further studies of an involvement of mesenchymal cells in the regulation of tissue homeostasis may bring novel approaches to the prevention and therapy of tissue dysfunctions characterized by permanent tissue immaturity (muscular dystrophy) or accelerated aging (degenerative diseases).