Topological Small-World Organization of the Fibroblastic Reticular Cell Network Determines Lymph Node Functionality

Fibroblastic reticular cells (FRCs) form the cellular scaffold of lymph nodes (LNs) and establish distinct microenvironmental niches to provide key molecules that drive innate and adaptive immune responses and control immune regulatory processes. Here, we have used a graph theory-based systems biology approach to determine topological properties and robustness of the LN FRC network in mice. We found that the FRC network exhibits an imprinted small-world topology that is fully regenerated within 4 wk after complete FRC ablation. Moreover, in silico perturbation analysis and in vivo validation revealed that LNs can tolerate a loss of approximately 50% of their FRCs without substantial impairment of immune cell recruitment, intranodal T cell migration, and dendritic cell-mediated activation of antiviral CD8⁺ T cells. Overall, our study reveals the high topological robustness of the FRC network and the critical role of the network integrity for the activation of adaptive immune responses.     

Impaired Chloroplast Biogenesis in Immutans,an Arabidopsis Variegation Mutant,Modifies Developmental Programming,Cell Wall Composition and Resistance to Pseudomonas syringae

The immutans (im) variegation mutation of Arabidopsis has green- and white- sectored leaves due to action of a nuclear recessive gene. IM codes for PTOX, a plastoquinol oxidase in plastid membranes. Previous studies have revealed that the green and white sectors develop into sources (green tissues) and sinks (white tissues) early in leaf development. In this report we focus on white sectors, and show that their transformation into effective sinks involves a sharp reduction in plastid number and size. Despite these reductions, cells in the white sectors have near-normal amounts of plastid RNA and protein, and surprisingly, a marked amplification of chloroplast DNA. The maintenance of protein synthesis capacity in the white sectors might poise plastids for their development into other plastid types. The green and white im sectors have different cell wall compositions: whereas cell walls in the green sectors resemble those in wild type, cell walls in the white sectors have reduced lignin and cellulose microfibrils, as well as alterations in galactomannans and the decoration of xyloglucan. These changes promote susceptibility to the pathogen Pseudomonas syringae. Enhanced susceptibility can also be explained by repressed expression of some, but not all, defense genes. We suggest that differences in morphology, physiology and biochemistry between the green and white sectors is caused by a reprogramming of leaf development that is coordinated, in part, by mechanisms of retrograde (plastid-to-nucleus) signaling, perhaps mediated by ROS. We conclude that variegation mutants offer a novel system to study leaf developmental programming, cell wall metabolism and host-pathogen interactions.     

Identification of tumor promoters by their inhibitory effect on intercellular transfer of lucifer yellow

The effect of the tumor promoters 12-O-tetradecanoylphorbol-13-acetate (TPA), mezerein, teleocidin, anthralin, the Ca²⁺-ionophore A23187, butylated hydroxytoluene (BHT), dichlordiphenyltrichloroethane (DDT) and phenobarbital (PB) on lucifer yellow transfer in cultures of SV-40-transformed Djungarian hamster fibroblasts was studied. TPA, mezerein, teleocidin, A23187, DDT and BHT exerted a strong inhibitory effect on cell-to-cell dye transfer. Anthralin uncoupled cells in 3 experiments out of 6. PB appeared to enhance lucifer yellow transfer. Sodium nitrite, a substance with unknown promoting activity, effectively uncoupled cells. All the promoters investigated had a reversible effect on the dye transfer. The value of the dye transfer method for promoter screening is discussed.Abbreviations BHT butylated hydroxytoluene - DDT dichlordiphenyltrichloroethane - LY Lucifer Yellow - PB phenobarbital - TPA 12-O-tetradecanoylphorbol-13-acetate     

Inhibition of GGTase‐I and FTase disrupts cytoskeletal organization of human PC‐3 prostate cancer cells

The mevalonate synthesis pathway produces intermediates for isoprenylation of small GTPases, which are involved in the regulation of actin cytoskeleton and cell motility. Here, we investigated the role of the prenylation transferases in the regulation of the cytoskeletal organization and motility of PC‐3 prostate cancer cells. This was done by using FTI‐277, GGTI‐298 or NE‐10790, the specific inhibitors of FTase (farnesyltransferase), GGTase (geranylgeranyltransferase)‐I and ‐II, respectively. Treatment of PC‐3 cells with GGTI‐298 and FTI‐277 inhibited migration and invasion in a time‐ and dose‐dependent manner. This was associated with disruption of F‐actin organization and decreased recovery of GFP–actin. Immunoblot analysis of various cytoskeleton‐associated proteins showed that the most striking change in GGTI‐298‐ and FTI‐277‐treated cells was a markedly decreased level of total and phosphorylated cofilin, whereas the level of cofilin mRNA was not decreased. The treatment of PC‐3 cells with GGTI‐298 also affected the dynamics of GFP–paxillin and decreased the levels of total and phosphorylated paxillin. The levels of phosphorylated FAK (focal adhesion kinase) and PAK (p‐21‐associated kinase)‐2 were also lowered by GGTI‐298, but levels of paxillin or FAK mRNAs were not affected. In addition, GGTI‐298 had a minor effect on the activity of MMP‐9. RNAi knockdown of GGTase‐Iβ inhibited invasion, disrupted F‐actin organization and decreased the level of cofilin in PC‐3 cells. NE‐10790 did not have any effect on PC‐3 prostate cancer cell motility or on the organization of the cytoskeleton. In conclusion, our results demonstrate the involvement of GGTase‐I‐ and FTase‐catalysed prenylation reactions in the regulation of cytoskeletal integrity and motility of prostate cancer cells and suggest them as interesting drug targets for development of inhibitors of prostate cancer metastasis.     

Fundamental measure theory of hydrated hydrocarbons

To calculate the solvation of hydrophobic solutes, we have developed a method based on the fundamental measure treatment of density functional theory. This method allows us to carry out calculations of density profiles and the solvation energy for various hydrophobic molecules with high accuracy. We have applied the method to the hydration of various hydrocarbons (linear, branched and cyclic). The calculations of the entropic and enthalpic parts are also carried out. We have examined the question of the temperature dependence of the entropy convergence. Finally, we have calculated the mean force potential between two large hydrophobic nanoparticles immersed in water. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

The abp gene in Geobacillus stearothermophilus T-6 encodes a GH27 β-L-arabinopyranosidase

In this study we demonstrate that the abp gene in Geobacillus stearothermophilus T-6 encodes a family 27 glycoside hydrolase β-L-arabinopyranosidase. The catalytic constants towards the chromogenic substrate pNP-β-L-arabinopyranoside were 0.8±0.1 mM, 6.6±0.3 s(-1), and 8.2±0.3 s(-1) mM(-1) for K(m), k(cat) and k(cat)/K(m), respectively. (13)C NMR spectroscopy unequivocally showed that Abp is capable of removing β-L-arabinopyranose residues from the natural arabino-polysaccharide, larch arabinogalactan. Most family 27 enzymes are active on galactose and contain a conserved Asp residue, whereas in Abp this residue is Ile67, which shifts the specificity of the enzyme towards arabinopyranoside.     

Climate and cyclic hydrobiological changes of the Barents Sea from the twentieth to twenty-first centuries

The Barents Sea is a transition zone between North Atlantic and Arctic waters, so its marine ecosystem is highly sensitive to climate dynamics. Understanding of marine biota response to climate changes is necessary to assess the environmental stability and the state of marketable biological resources. These processes are analyzed using a database from the Murmansk Marine Biological Institute which holds oceanographic and hydrobiological data sets collected for more than 100?years along the meridional Kola Transect in the Barents Sea. The data demonstrate high variability in thermal state of the upper layer of the Barents Sea, which is regulated by varying the inflow of Atlantic water and by regional climate. At irregular intervals, cold periods with extended seasonal ice cover are followed by warm periods. The most recent warm period started in the late 1980s and reached its maximum from 2001 to 2006. These cyclic changes in hydrologic regime across the twentieth century and first decade of the twenty-first century are reflected (with a specific lag of 1–5?years) by changes in species composition, as well as abundance and distribution of boreal and arctic groups of macrozoobenthos and fish fauna. For instance, cod and cod fisheries in the Barents Sea are closely linked to the marine climate. Furthermore, Kamchatka crab stock recruitment benefited from the warm climate of 1989 and 1990. In general, studies in this region have shown that climatic dynamics may be assessed using biological indices of abundance, biomass, and migration of marine organisms, including commercial species.     

Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era

More than 150 Ma, the avian lineage separated from that of other dinosaurs and later diversified into the more than 10,000 species extant today. The early neoavian bird radiations most likely occurred in the late Cretaceous (more than 65 Ma) but left behind few if any molecular signals of their archaic evolutionary past. Retroposed elements, once established in an ancestral population, are highly valuable, virtually homoplasy-free markers of species evolution; after applying stringent orthology criteria, their phylogenetically informative presence/absence patterns are free of random noise and independent of evolutionary rate or nucleotide composition effects. We screened for early neoavian orthologous retroposon insertions and identified six markers with conflicting presence/absence patterns, whereas six additional retroposons established before or after the presumed major neoavian radiation show consistent phylogenetic patterns. The exceptionally frequent conflicting retroposon presence/absence patterns of neoavian orders are strong indicators of an extensive incomplete lineage sorting era, potentially induced by an early rapid successive speciation of ancestral Neoaves.     

ATP-consuming and ATP-generating enzymes secreted by pancreas

Pancreatic acini release ATP in response to various stimuli, including cholecystokinin octapeptide (CCK-8), as we show in the present study. There were indications that pancreatic juice also contains enzymes that could hydrolyze ATP during its passage through the ductal system. The aim of this study was to determine which ATP-degrading and possibly ATP-generating enzymes were present in pancreatic secretion. For this purpose, pancreatic juice was collected from anesthetized rats stimulated with infusion of CCK-8. Purine-converting activities in juice samples were assayed by TLC using either [gamma-(32)P]ATP or (14)C/(3)H-labeled and unlabeled nucleotides as appropriate substrates. Data show that the juice contains the enzyme ecto-nucleoside triphosphate diphosphohydrolase that can hydrolyze both [(14)C]ATP and [(3)H]ADP about equally well, i.e. CD39. Reverse-phase high-performance liquid chromatography analysis additionally shows that this enzyme has broad substrate specificity toward other nucleotides, UTP, UDP, ITP, and IDP. In addition, secretion contains ecto-5'-nucleotidase, CD73, further converting [(3)H]AMP to adenosine. Along with highly active hydrolytic enzymes, there were also ATP-generating enzymes in pancreatic juice, adenylate kinase, and NDP kinase, capable of sequentially phosphorylating AMP via ADP to ATP. Activities of nonspecific phosphatases, nucleotide pyrophosphatase/phosphodiesterases, and adenosine deaminase were negligible. Taken together, CCK-8 stimulation of pancreas causes release of both ATP-consuming and ATP-generating enzymes into pancreatic juice. This newly discovered richness of secreted enzymes underscores the importance of purine signaling between acini and pancreatic ducts lumen and implies regulation of the purine-converting enzymes release.