Though with constraints imposed by endosymbiosis,preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network

Chloroplasts evolved as a result of endosymbiosis, during which sophisticated mechanisms evolved to translocate nucleus‐encoded plastid‐targeted enzymes into the chloroplast to form the chloroplast metabolic network. Given the constraints and complexity of endosymbiosis, will preferential attachment still be a plausible mechanism for chloroplast metabolic network evolution? We answer this question by analysing the metabolic network properties of the chloroplast and a cyanobacterium, Synechococcus sp. WH8102 (syw). First, we found that enzymes related to more ancient pathways are more connected, and synthetases have the highest connectivity. Most of the enzymes shared by the two densest cores between the chloroplast and syw are synthetases. Second, the highly conserved functional modules mainly consist of highly connected enzymes. Finally, isozymes and enzymes from endosymbiotic gene transfer (EGT) were distributed mainly in conserved modules and showed higher connectivity than nonisozymes or non‐EGT enzymes. These results suggest that even with severe evolutionary constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network. However, the current analysis may not completely differentiate whether the chloroplast network properties reflect the evolution of the chloroplast network through preferential attachment or has been inherited from its cyanobacterial ancestor. To fully differentiate these two possibilities, further analyses of the metabolic network structure properties of organisms at various intermediate evolutionary stages between cyanobacteria and the chloroplast are needed.     

Likelihood-based inference for stochastic models of sexual network formation

Sexually-transmitted diseases (STDs) constitute a major public health concern. Mathematical models for the transmission dynamics of STDs indicate that heterogeneity in sexual activity level allow them to persist even when the typical behavior of the population would not support endemicity. This insight focuses attention on the distribution of sexual activity level in a population. In this paper, we develop several stochastic process models for the formation of sexual partnership networks. Using likelihood-based model selection procedures, we assess the fit of the different models to three large distributions of sexual partner counts: (1) Rakai, Uganda, (2) Sweden, and (3) the USA. Five of the six single-sex networks were fit best by the negative binomial model. The American women's network was best fit by a power-law model, the Yule. For most networks, several competing models fit approximately equally well. These results suggest three conclusions: (1) no single unitary process clearly underlies the formation of these sexual networks, (2) behavioral heterogeneity plays an essential role in network structure, (3) substantial model uncertainty exists for sexual network degree distributions. Behavioral research focused on the mechanisms of partnership formation will play an essential role in specifying the best model for empirical degree distributions. We discuss the limitations of inferences from such data, and the utility of degree-based epidemiological models more generally.     

Secondary flow as a mechanism for the formation of biofilm streamers

In most environments, such as natural aquatic systems, bacteria are found predominantly in self-organized sessile communities known as biofilms. In the presence of a significant flow, mature multispecies biofilms often develop into long filamentous structures called streamers, which can greatly influence ecosystem processes by increasing transient storage and cycling of nutrients. However, the interplay between hydrodynamic stresses and streamer formation is still unclear. Here, we show that suspended thread-like biofilms steadily develop in zigzag microchannels with different radii of curvature. Numerical simulations of a low-Reynolds-number flow around these corners indicate the presence of a secondary vortical motion whose intensity is related to the bending angle of the turn. We demonstrate that the formation of streamers is directly proportional to the intensity of the secondary flow around the corners. In addition, we show that a model of an elastic filament in a two-dimensional corner flow is able to explain how the streamers can cross fluid streamlines and connect corners located at the opposite sides of the channel.     

Spontaneous aggregation as a mechanism for human monocyte purification

A previously unreported property of human mononuclear phagocytes is the ability of these cells to spontaneously aggregate. Fresh mononuclear cells obtained after plateletpheresis were noted to spontaneously form large cellular aggregates. Dual parameter immunofluorescence analysis demonstrated that the aggregating cells were positive for the monocyte marker CD11 (complement receptor, type 3) but were negative for the lymphocyte marker CD3 (T3 antigen). In addition, less than 5% of the nonaggregating cells were CD11+, suggesting that almost all CD11+ cells aggregated. Cellular aggregates were independent of cell concentration and formed more efficiently at 4 degrees C than at either 22 or 37 degrees C. Based on these observations, a purification procedure utilizing Ficoll-Hypaque separation, spontaneous aggregation at 4 degrees C, and transient plastic adherence resulted in a sevenfold enrichment of the CD11+ peripheral blood monocytes. Purified monocytes were contaminated with less than 2% CD3 cells. The size, growth, and adherence characteristics as well as cytologic stains indicated that the monocytes were not significantly altered by the purification procedure. Thus, spontaneous aggregation is an efficient and convenient method for the isolation of large numbers of purified monocytes.     

Engineered antifouling microtopographies: mapping preferential and inhibitory microenvironments for zoospore attachment

An algorithm was developed and implemented to map the locations of attached spores of Ulva linza on patterned surfaces. Using this mapping algorithm, spore preference among regions within a pattern can be detected and quantified. Settlement maps of spores on patterned topographies from several assays showed clear preferences in spore settlement. Over 94% of the spores attached within the depressed regions on the surfaces, including a surface containing pits instead of protruding features. The spores attached primarily at the intersections of several features, with over half and up to 96% of spores settling in these regions. The highest spore densities occurred at intersections where the features were most dissimilar. In contrast, the location of attached beads on the surfaces was nearly uniform across the surface. Identification of preferential attachment locations allows for the study of localized properties that influence cell behavior and aids in the development of new surfaces to control cell–surface interactions.     

Engineered antifouling microtopographies: mapping preferential and inhibitory microenvironments for zoospore attachment

An algorithm was developed and implemented to map the locations of attached spores of Ulva linza on patterned surfaces. Using this mapping algorithm, spore preference among regions within a pattern can be detected and quantified. Settlement maps of spores on patterned topographies from several assays showed clear preferences in spore settlement. Over 94% of the spores attached within the depressed regions on the surfaces, including a surface containing pits instead of protruding features. The spores attached primarily at the intersections of several features, with over half and up to 96% of spores settling in these regions. The highest spore densities occurred at intersections where the features were most dissimilar. In contrast, the location of attached beads on the surfaces was nearly uniform across the surface. Identification of preferential attachment locations allows for the study of localized properties that influence cell behavior and aids in the development of new surfaces to control cell-surface interactions.     

Uniparental disomy as a mechanism for human genetic disease.

A female with cystic fibrosis and short stature was investigated for molecular or cytogenetic abnormalities that might explain the combined phenotype. Analysis with polymorphic DNA markers indicated that the father did not contribute alleles to the propositus for markers near the CF locus or for centromeric markers on chromosome 7. High-resolution cytogenetic analysis was normal, and the result could not be explained on the basis of nonpaternity or a submicroscopic deletion. All of the data indicate that the propositus inherited two identical copies of maternal sequences for much or all of chromosome 7. The occurrence of uniparental disomy could be explained by models postulating postfertilization error, gamete complementation, monosomic conception with subsequent chromosome gain, or trisomic conception followed by chromosome loss. Uniparental disomy in an individual with a normal chromosome analysis is a novel mechanism for the occurrence of human genetic disease.     

Vortex shedding as a mechanism for free emboli formation in mechanical heart valves

The high incidence of thromboembolic complications of mechanical heart valves (MHV) limits their success as permanent implants. The thrombogenicity of all MHV is primarily due to platelet activation by contact with foreign surfaces and by nonphysiological flow patterns. The latter include elevated flow stresses and regions of recirculation of blood that are induced by valve design characteristics. A numerical simulation of unsteady turbulent flow through a bileaflet MHV was conducted, using the Wilcox k-omega turbulence model for internal low-Reynolds-number flows, and compared to quantitative flow visualization performed in a pulse duplicator system using Digital Particle Image Velocimetry (DPIV). The wake of the valve leaflet during the deceleration phase revealed an intricate pattern of interacting shed vortices. Particle paths showed that platelets that were exposed to the highest flow stresses around the leaflets were entrapped within the shed vortices. Potentially activated, such platelets may tend to aggregate and form free emboli. Once formed, such free emboli would be convected downstream by the shed vortices, increasing the risk of systemic emboli.     

Equilibrium-driven mechanism for preferential adhesion between chick embryo cells

The experiments presented here confirm the hypothesis according to which, in our experimental system of differential cell adhesion (where we studied the kinetics of the earliest period of adhesion of a suspension of chick embryo neuroblasts to layers of astroblasts or fibroblasts), the mechanism of adhesion appears to consist of two steps, the first of which is a short-term reversible phase corresponding to a binding equilibrium. In fact, adhesion of neuroblasts to each of the two cell layers occurs according to kinetic constants and attains levels which are characteristic for each of the two adhesion systems. In both systems, neuroblasts that have not adhered at equilibrium are able to adhere if inoculated over a fresh cell layer of the same type, as they do during the first inoculation; conversely, neuroblasts that have adhered to a cell layer can be made to de-adhere by substituting cell-free fresh medium to the inoculation medium containing non-adhering neuroblasts. This shows that, as predicted for a reversible equilibrium system, removal of adhering neuroblasts from the system at equilibrium provokes adhesion, and removal of non-adhered neuroblasts provokes de-adhesion. Furthermore the level of adhesion at equilibrium is, in all cases, the same. The reversibility of adhesion, which is almost quantitative during the onset of the equilibrium, gradually decreases with time, indicating the presence of a process of irreversible attachment between cells after the first reversible step. The developmental implications of the complete sequential mechanisms are briefly discussed.     

Rho family GTPases as key regulators for neuronal network formation

Rho family GTPases act as transducers of signals from extracellular stimuli to the cytoskeleton and gene expression. Their actions are temporal and spatial determinants for cellular functions. The cellular functions of Rho family GTPases have been studied in fibroblasts and endothelial cells, and recent advances have revealed their roles in the regulation of neuronal network formation, including migration, neurite outgrowth, polarity, axon guidance, dendrite maturation and synapse formation. In addition, a significant number of X-linked mental retardation genes have been shown to encode components directly involved in signal transduction pathways of Rho family GTPases, underscoring the view that Rho family GTPases essentially participate in the neuronal network formation. In this review, we will overview current understanding of the functions of Rho family GTPases in neuronal network formation.     

Bacterial vesicle formation as a mechanism of protein transfer to animals

Gram-negative bacterial vesicle formation is a mechanism for specific secretion and transfer of a protein toxin to animals. This discovery should stimulate work on the mechanism of protein sorting into vesicles and the role of vesicles in bacterial pathogenesis.     

A novel function of lipoprotein [a] as a preferential carrier of oxidized phospholipids in human plasma

Oxidized phospholipids (OxPLs) on apolipoprotein B-100 (apoB-100) particles are strongly associated with lipoprotein [a] (Lp[a]). In this study, we evaluated whether Lp[a] is preferentially the carrier of OxPL in human plasma. The content of OxPL on apoB-100 particles was measured with monoclonal antibody E06, which recognizes the phosphocholine (PC) headgroup of oxidized but not native phospholipids. To assess whether OxPLs were preferentially bound by Lp[a] as opposed to other lipoproteins, immunoprecipitation and ultracentrifugation experiments, in vitro transfer studies, and chemiluminescent ELISAs were performed. Immunoprecipitation of Lp[a] from human plasma with an apolipoprotein [a] (apo[a])-specific antibody demonstrated that more than 85% of E06 reactivity (i.e., OxPL) coimmunoprecipitated with Lp[a]. Ultracentrifugation experiments showed that nearly all OxPLs were found in fractions containing apo[a], as opposed to other apolipoproteins. In vitro transfer studies showed that oxidized LDL preferentially donates OxPLs to Lp[a], as opposed to LDL, in a time- and temperature-dependent manner, even in aqueous buffer. Approximately 50% of E06 immunoreactivity could be extracted from isolated Lp[a] following exposure of plasma to various lipid solvents. These data demonstrate that Lp[a] is the preferential carrier of PC-containing OxPL in human plasma. This unique property of Lp[a] suggests novel insights into its physiological function and mechanisms of atherogenicity.     

An assessment of Bacteroides fragilis group organisms as indicators of human faecal pollution

Membrane filtration techniques were used to enumerate Bacteroides fragilis group (BFG) organisms and Escherichia coli in a variety of natural waters, the influents and effluents from three types of sewage treatment plants and faeces of various animals. The results suggest that BFG organisms die off more rapidly than E. coli in water and that animal faeces are not a significant source of BFG. It is suggested that the ratio of BFG to E. coli in water may be used to indicate the proximity of a source of human faecal contamination.     

An assessment of Bacteroides fragilis group organisms as indicators of human faecal pollution

Membrane filtration techniques were used to enumerate Bacteroides fragilis group (BFG) organisms and Escherichia coli in a variety of natural waters, the influents and effluents from three types of sewage treatment plants and faeces of various animals. The results suggest that BFG organisms die off more rapidly than E. coli in water and that animal faeces are not a significant source of BFG. It is suggested that the ratio of BFG to E. coli in water may be used to indicate the proximity of a source of human faecal contamination.     

Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation

Antimicrobial peptides have two binding states in a lipid bilayer, a surface state S and a pore-forming state I. The transition from the S state to the I state has a sigmoidal peptide-concentration dependence indicating cooperativity in the peptide-membrane interactions. In a previous paper, we reported the transition of alamethicin measured in three bilayer conditions. The data were explained by a free energy that took into account the membrane thinning effect induced by the peptides. In this paper, the full implications of the free energy were tested by including another type of peptide, melittin, that forms toroidal pores, instead of barrel-stave pores as in the case of alamethicin. The S-to-I transitions were measured by oriented circular dichroism. The membrane thinning effect was measured by x-ray diffraction. All data were in good agreement with the theory, indicating that the membrane thinning effect is a plausible mechanism for the peptide-induced pore formations.