Molecular Dynamics Simulations of PIP2 and PIP3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Roughness on a Poisson-Boltzmann Description

Molecular dynamics (MD) simulations of phosphatidylinositol (4,5)-bisphosphate (PIP₂) and phosphatidylinositol (3,4,5)-trisphosphate (PIP₃) in 1-palmitoyl 2-oleoyl phosphatidylcholine (POPC) bilayers indicate that the inositol rings are tilted ∼40° with respect to the bilayer surface, as compared with 17° for the P-N vector of POPC. Multiple minima were obtained for the ring twist (analogous to roll for an airplane). The phosphates at position 1 of PIP₂ and PIP₃ are within an Ångström of the plane formed by the phosphates of POPC; lipids in the surrounding shell are depressed by 0.5-0.8 Å, but otherwise the phosphoinositides do not substantially perturb the bilayer. Finite size artifacts for ion distributions are apparent for systems of ∼26 waters/lipid, but, based on simulations with a fourfold increase of the aqueous phase, the phosphoinositide positions and orientations do not show significant size effects. Electrostatic potentials evaluated from Poisson-Boltzmann (PB) calculations show a strong dependence of potential height and ring orientation, with the maxima on the −25 mV surfaces (17.1 ± 0.1 Å for PIP₂ and 19.4 ± 0.3 Å for PIP₃) occurring near the most populated orientations from MD. These surfaces are well above the background height of 10 Å estimated for negatively charged cell membranes, as would be expected for lipids involved in cellular signaling. PB calculations on microscopically flat bilayers yield similar maxima as the MD-based (microscopically rough) systems, but show less fine structure and do not clearly indicate the most probable regions. Electrostatic free energies of interaction with pentalysine are also similar for the rough and flat systems. These results support the utility of a rigid/flat bilayer model for PB-based studies of PIP₂ and PIP₃ as long as the orientations are judiciously chosen.     

Does maternal condition or predation risk influence small mammal population dynamics?

There is strong debate over whether the intrinsic traits of individuals or the extrinsic environment exert the greater influence on small mammal population dynamics. We test the roles of maternal effects (an intrinsic factor) and predation risk (an extrinsic factor) in the population dynamics of wild strain house mice using a 2-factor enclosure experiment. Pre-release supplemental feeding with a high-fat diet created female treatment founders that were 6–10% heavier than controls, a condition that we predicted would be passed on as a maternal effect. Predation risk was enhanced using regular application of predator (red fox Vulpes vulpes ) scats. Founder populations of six females and six males released into eight, 15×15 m enclosures showed near exponential population growth over 17 weeks (maximum 3 generations). But there were no responses to either treatment in terms of survival, inherited body weights, fecundity or population size. We suggest that elevated maternal condition may have only minor and transient intergenerational effects with little long-term consequence. We also suggest that the general significance of predator scats as a cue to predation risk to alter prey behaviour may have been overestimated. Hence our results question the role of either factor in causing long-term responses that influence condition to affect population processes.     

Ecosystem function and species loss – a microcosm study

There are too many kinds of organisms to be able to study and manage each, yet the loss of a single species can sometimes unravel an ecosystem. Such `fusewire species'– critical in the same sense that an electrical fuse can cut out a whole circuit – would be a rewarding focus for research and management effort. However, this approach can only be effective if these `fusewires' represent but a small proportion of the number of species in the system.  

Aim

To demonstrate methods for measuring what proportion of the species in a system are critical to ecosystem function.  

Methods

The prevalence of fusewire species was measured in manipulative experiments on an aquatic microcosm.  

Results

No single genus deletion caused changes in key characteristics of the system.  

Main conclusions

Comparison of these results with other published studies shows that the proportion of critical fusewire species varies amongst different ecosystems. The oxidation pond microcosms were shown to contain no single species indispensable to system function. They appear to be ill-suited to a management strategy which focuses on priority eukaryote species. However, a single study provides no evidence that this result is general or even typical of other kinds of ecosystems; it is presented here as an empirical model. Other methods of investigation are available; they are less experimentally rigorous but more practical. These could provide important guidance in planning an approach to management in a particular ecosystem.     

Patterns of junctional communication in skin: Studies on cultured keratinocytes

Junctional communication has long been suggested to play a role in coordinating the development of multicellular tissues. A better understanding of the patterns of communication between cells in such tissues is important for the identification of areas where this process may have a role. We have investigated the patterns of communication in cultures of human epidermal keratinocytes by iontophoretic injection of Lucifer Yellow CH, using involucrin expression as a marker of cells undergoing terminal differentiation. Cells that lack involucrin (i.e., the basal, proliferating cells) transfer dye preferentially to other involucrin-negative cells, whereas involucrin-positive cells either are not coupled or transfer dye with similar frequency to involucrin-positive and involucrin-negative neighbors. This decrease in communication associated with terminal differentiation was observed in both the presence and the absence of assembled desmosomes. Our observations lead us to speculate that loss of junctional communication may influence the commitment of basal keratinocytes to terminal differentiation.     

Cytoplasmic enzyme activities involved in energy and amino acid metabolism in pathological human renal cortex

Enzyme levels of lactate dehydrogenase (LDH), alpha-hydroxybutyrate dehydrogenase (HBDH), aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were measured in the cytosol of renal cortex samples from either normal and pathologic kidney tissue. The mean enzyme activity values, expressed in Units per gram of cytosolic protein decreased in the following order: normal cortex (LDH = 4,299 +/- 654; AST = 522 +/- 101; ALT = 197 +/- 44). chronic pyelonephritis (LDH = 2,360 +/- 876; AST = 297 +/- 117; ALT = 90 +/- 48), hydronephrosis (LDH = 2,208 +/- 1,264; AST = 279 +/- 165; ALT = 82 +/- 61), pyonephrosis (LDH = 1,410 +/- 596; AST = 158 +/- 69; ALT = 23.4 +/- 16.4) and renal tuberculosis (LDH = 1,149 +/- 481; AST = 93 +/- 34; ALT = 5.6 +/- 2.8). The decrease in the enzyme activities paralleled tissue damage and it was shown to affect cellular functionality in relation with energy and amino acid metabolism.     

Evidence of abortive recombination in ruv mutants of Escherichia coli K12

Summary Genetic recombination in Escherichia coli was investigated by measuring the effect of mutations in ruv and rec genes on F-prime transfer and mobilization of nonconjugative plasmids. Mutation of ruv was found to reduce the recovery of F-prime transconjugants in crosses with recB recC sbcA strains by about 30-fold and with recB recC sbcB sbcC strains by more than 300-fold. Conjugative plasmids lacking any significant homology with the chromosome were transferred normally to these ruv mutants. Mobilization of the plasmid cloning vectors pHSG415, pBR322, pACYC184 and pUC18 were reduced by 20- to 100-fold in crosses with ruv rec ⁺ sbc ⁺ strains, depending on the plasmid used. Recombinant plasmids carrying ruv ⁺ were transferred efficiently. With both F-prime transfer and F-prime cointegrate mobilization, the effect of ruv was suppressed by inactivating recA. It is proposed that the failure to recover transconjugants in ruv recA ⁺strains is due to abortive recombination and that the ruv genes define activities which function late in recombination to help convert recombination intermediates into viable products.     

Quantification of choline and ethanolamine phospholipids in rabbit myocardium

To facilitate evaluation of the influence of myocardial phospholipid metabolites on the development of electrophysiologic abnormalities induced by ischemia, a method for the quantification of choline and ethanolamine phospholipids suitable for accurate and reproducible analysis of small amounts of myocardium was developed. The procedure combines chloroform and methanol extraction of phospholipids after tissue homogenization with subsequent separation by sequential thin-layer and high-performance liquid chromatography. Phosphorus in purified lipid classes was determined with the correction for recovery based on 14C-labeled internal standards.