Hydrophobic organization of α-helix membrane bundle in bacteriorhodopsin

The hydrophobic organization of the intramembraneα-helical bundle in bacteriorhodopsin (BRh) was assessed based on a new approach to characterization of spatial hydrophobic properties of transmembrane (TM)α-helical peptides. The method employs two independent techniques: Monte Carlo simulations of nonpolar solvent around TM peptides and analysis of molecular hydrophobicity potential on their surfaces. The results obtained by the two methods agree with each other and permit precise hydrophobicity mapping of TM peptides. Superimposition of such data on the experimentally derived spatial model of the membrane moiety together with 2D maps of hydrophobic hydrophilic contacts provide considerable insight into the hydrophobic organization of BRh. The helix bundle is stabilized to a large extent by hydrophobic interactions between helices—neighbors in the sequence of BRh, by long-range interactions in helix pairs C-E, C-F, and C-G, and by nonpolar contracts between retinal and helices C, D, E, F. Unlike globular proteins, no polar contacts between residues distantly separated in the sequence of BRh were found in the bundle. One of the most striking results of this study is the finding that the hydrophobic organization of BRh is significantly different from those in bacterial photoreaction centers. Thus, TMα-helices in BRh expose their most nonpolar sides to the bilayer as well as to the neighboring helices and to the interior of the bundle. Some of them contact lipids with their relatively hydrophilic surfaces. No correlation was found between disposition of the most hydrophobic and the most variable sides of the TM helices.     

Modeling analysis of the lipid bilayer–cytoskeleton coupling in erythrocyte membrane

Studies of thermal fluctuations in discocytes, echinocytes, and spherocytes suggest that the coupling between lipid bilayer and cytoskeleton can affect viscoelastic behavior of single erythrocyte membranes. To test this hypothesis, we developed a 3D constitutive model describing viscoelastic behavior of erythrocyte membranes, at long relaxation times \(t \in [0.20\,\mathrm {s}, 1.05\,\mathrm {s}]\) and short relaxation times \(t \in [0.03\,\mathrm {s}, 0.20\,\mathrm {s}]\) . The model was constructed using combination of spring and spring pot rheological elements arranged in parallel. The rearrangement of cytoskeleton induced by changing the bending state of lipid bilayer was described by a modified Eyring model. The model predictions point to an anomalous nature of energy dissipation and an ordered harmonic nature of the coupling mechanism described by a series of fractional derivatives of the order n \(\alpha \) (where \( n \in [- 1, 2]\) ). As a result, the stress generated within the lipid bilayer is related to the rate of change of the irreversible stress within the cytoskeleton.     

Is the nuclear envelope a ‘generator’ of membrane?

Summary Early diplotene oocytes from Necturus maculosus ranging from 0.2 to 0.5 mm in diameter were examined by electron microscopy. In the smallest oocytes of this range, the cytoplasm is largely devoid of membranes, but contains primarily ribosomes and mitochondria. In slightly larger oocytes, smooth-surfaced cytomembranes first appear in the perinuclear cytoplasm. At this time, the outer layer of the germinal vesicle nuclear envelope (GVNE) shows frequent connections with long membranous lamellae that extend for considerable, but variable distances into the juxtanuclear ooplasm. The number of smooth membranous lamellae increases tremendously as the oocytes increase in diameter. In such oocytes as well, frequent continuities are observed between the outer membrane of the GVNE and many of the cytoplasmic membranes. Eventually, as the ooplasm becomes populated with extensive numbers of membranous lamellae, instances of continuity between the membranous lamellae and nuclear envelope now become sparse and eventually non-existent. The frequent connections observed between membranous lamellae and the outer membrane of the GVNE during a circumscribed interval of diplotene strongly implicate the GVNE in the generation of extensive amounts of cytoplasmic membrane. The ooplasm of larger oocytes in the size range indicated contain numerous Golgi complexes and large quantities of annulate lamellae most of which are positioned in the peripheral or subcortical ooplasm, as well as extensive quantities of smooth membranes of the endoplasmic reticulum and lipid droplets.     

Dynamics of the ‘echo’ effect in a phytoplankton system with nitrogen fixation

Consideration of nitrogen fixation adds a positive nonlinear feedback to plankton ecosystem models. We investigate the consequences of this feedback for secondary phytoplankton blooms and the response of phytoplankton dynamics to physical forcing. The dynamics of phytoplankton, Trichodesmium (the nitrogen fixer), and nutrients is modeled with a system of three differential equations. The model includes two types of nonlinear interactions: the competition of phytoplankton and Trichodesmium for light, and the positive feedback resulting from Trichodesmium recycling. A typical simulation of the model in time, with forcing by a varying mixed-layer depth, reveals a clear successional sequence including a secondary or ‘echo’ bloom of the phytoplankton. We explain this sequence of events through the stability analysis of three different steady states of the model. Our analysis shows the existence of a critical biological parameter, the ratio of normalized growth rates, determining the occurrence of ‘echo’ blooms and the specific sequence of events following a physical perturbation. The interplay of positive and negative feedbacks appears essential to the timing and the type of events following such a perturbation.     

Rethinking the ‘everyday’ in ‘ethnicity and everyday life’

While ‘ethnicity and everyday life’ is a familiar collocation, sociologists concerned with racism and ethnicity have not engaged very much with the extensive body of social theory that takes the ‘everyday’ as its central problematic. In this essay, I consider some of the ways in which the sociology of the everyday might be of use to those concerned with investigating ethnicity and racism. For its part, however, the sociology of the everyday has tended to be remarkably blind to the role played by racism and racialization in the modern world. It is thus no less crucial to consider how the experiences of racialized groups might help us rethink influential accounts of the everyday. To this end, I provide a discussion of pioneering texts by C. L. R. James and W. E. B. du Bois, both of whom were driven by their reflections on racism and resistance to recognize the everyday not as an unremarked context, but as, precisely, a problematic one.     

Evidence for ‘dawn’ and ‘dusk’ oscillators in the Nasonia photoperiodic clock

Females of Nasonia vitripennis were maintained in light cycles from 12 to 72 hr in length, with 4 to 28 hr photoperiods, and their offspring examined for larval diapause. This ‘resonance’ technique revealed periodic maxima of diapause induction, about 24 hr apart. The ‘ascending slopes’ of these maxima appeared to obtain their principal time cue from dusk and the ‘descending slopes’ from dawn. This suggests that two independent—dawn and dusk—oscillators are involved in the Nasonia photoperiodic clock. The results are interpreted in terms of ‘internal coincidence’.N. vitripennis was shown to be able to distinguish between 12 and 18 hr of red light (>600 nm) in the photoperiodic sense. A ‘positive’ resonance experiment using such a red light was also performed. This shows that the spectral sensitivity of the pigment coupling the circadian system to the environmental light cycle extends into the red end of the spectrum.     

Introduction to ‘Origin and evolution of the nervous system’

In 1665, Robert Hooke demonstrated in Micrographia the power of the microscope and comparative observations, one of which revealed similarities between the arthropod and vertebrate eyes. Utilizing comparative observations, Saint-Hilaire in 1822 was the first to propose that the ventral nervous system of arthropods corresponds to the dorsal nervous system of vertebrates. Since then, studies on the origin and evolution of the nervous system have become inseparable from studies about Metazoan origins and the origins of organ systems. The advent of genome sequence data and, in turn, phylogenomics and phylogenetics have refined cladistics and expanded our understanding of Metazoan phylogeny. However, the origin and evolution of the nervous system is still obscure and many questions and problems remain. A recurrent problem is whether and to what extent sequence data provide reliable guidance for comparisons across phyla. Are genetic data congruent with the geological fossil records? How can we reconcile evolved character loss with phylogenomic records? And how informative are genetic data in relation to the specification of nervous system morphologies? These provide some of the background and context for a Royal Society meeting to discuss new data and concepts that might achieve insights into the origin and evolution of brains and nervous systems.     

Introduction to ‘Homology and convergence in nervous system evolution’

The origin of brains and central nervous systems (CNSs) is thought to have occurred before the Palaeozoic era 540 Ma. Yet in the absence of tangible evidence, there has been continued debate whether today''s brains and nervous systems derive from one ancestral origin or whether similarities among them are due to convergent evolution. With the advent of molecular developmental genetics and genomics, it has become clear that homology is a concept that applies not only to morphologies, but also to genes, developmental processes, as well as to behaviours. Comparative studies in phyla ranging from annelids and arthropods to mammals are providing evidence that corresponding developmental genetic mechanisms act not only in dorso–ventral and anterior–posterior axis specification but also in segmentation, neurogenesis, axogenesis and eye/photoreceptor cell formation that appear to be conserved throughout the animal kingdom. These data are supported by recent studies which identified Mid-Cambrian fossils with preserved soft body parts that present segmental arrangements in brains typical of modern arthropods, and similarly organized brain centres and circuits across phyla that may reflect genealogical correspondence and control similar behavioural manifestations. Moreover, congruence between genetic and geological fossil records support the notion that by the ‘Cambrian explosion’ arthropods and chordates shared similarities in brain and nervous system organization. However, these similarities are strikingly absent in several sister- and outgroups of arthropods and chordates which raises several questions, foremost among them: what kind of natural laws and mechanisms underlie the convergent evolution of such similarities? And, vice versa: what are the selection pressures and genetic mechanisms underlying the possible loss or reduction of brains and CNSs in multiple lineages during the course of evolution? These questions were addressed at a Royal Society meeting to discuss homology and convergence in nervous system evolution. By integrating knowledge ranging from evolutionary theory and palaeontology to comparative developmental genetics and phylogenomics, the meeting covered disparities in nervous system origins as well as correspondences of neural circuit organization and behaviours, all of which allow evidence-based debates for and against the proposition that the nervous systems and brains of animals might derive from a common ancestor.     

Microbial contributions to the evolution of the ‘steady state’ carbon dioxide system

Various processes for the production of carbon dioxide by microorganisms are presented. It is postulated that a microniche developed in a reducing environment; a symbiotic relationship between alga-like organisms and bacterium-like organisms in the microniche governed the production of carbon dioxide resulting in the establishment of the steady state carbon dioxide system in the sea.     

Oddity and the ‘confusion effect’ in predation

We report on two sets of experiments designed to clarify the roles of sensory ‘confusion’ and prey ‘oddity’ as they interact to influence the hunting success of a pursuit predator, the largemouth bass (Micropterus salmoides), on silvery minnows (Hybognathus nuchalis). Bass quickly captured solitary minnows, but performed many unsuccessful attacks and took much longer to make a capture as prey school size was increased. At school sizes of eight and above, bass were effectively stymied, demonstrating the ‘confusion effect’. The inclusion of one or two ‘odd’ (blue-dyed) minnows in a school of eight greatly increased the ability of bass to capture both normal and odd prey, but this effect of oddity disappeared at a school size of 15. The implications of these results for understanding the adaptive basis of mixed species flocks, herds and schools is discussed.     

Morphology and accessibility of the ‘transverse’ tubular system in frog sartorius muscle after glycerol treatment

Summary Sartorius muscles were exposed to a hypertonic Ringer's fluid containing 400mm glycerol and subsequently returned to normal Ringer's fluid. Employing lanthanum as an extracellular marker and after suitable preparation, sections of muscle fibers were examined with an electron-microscope. Extensive alteration in transverse tubular morphology occurs after glycerol treatment. The number of sites at the Z line level usually containing complete triads decreases by about two-thirds. In about half of the sites with altered morphology no transverse tubules were present, while in the other half the sites were completely empty. Fibers at all depths in glycerol-treated muscles were equally affected. The remnants of the transverse tubules which remain were not very accessible to extracellular lanthanum. Estimates based on measurements of the presence or absence of lanthanum indicate that glycerol treatment disconnects 90% of the transverse tubules from the external solution. The remaining tubules connected to the external solution are largely but not entirely located in a surface layer of about one-tenth the fiber radius in depth.     

The ‘fluid mosaic model’ and the ‘lattice model’ as two nonequilibrium states of the same membrane and the significance for biochemical control

Summary Biochemical control involves steep and hysteretic response. But the law of mass action does not allow for cooperativity. Therefore resort is classically made to concerted conformational change of protomers. This explanation of steepness and hysteresis by cooperativity is supported by regular surface patterns often observed by electron microscopy. But at other times the lattice appearance which gave rise to the lattice model is not observed. By contrast, a random appearance is observed and the fluid mosaic model of the membrane is assumed. So we are faced with the choice between the fluid mosaic model and the lattice model. Recently the fluid mosaic model is favoured but unlike the lattice model it does not explain the steep hyteretic response.It is suggested that the lattice model and the fluid mosaic model are in fact expression of two states of the very same membrane. The random state corresponds to a resting state. The lattice state corresponds to an active or inhibited state. Thus the transition from random distribution to hexagonal distribution provides simultaneously for triggering and hysteretic cycle with respect to both chemical production and transport across the membrane. This is a universal mechanism for rapid responsiveness and cyclic activity which is largely independent of the chemical mechanism assumed. It is based on the law of mass action supplemented by lateral diffusion. Conformational change and cooperativity are not invoked at all.