Let's go bananas: revisiting the endocytic BAR code

Against the odds of membrane resistance, members of the BIN/Amphiphysin/Rvs (BAR) domain superfamily shape membranes and their activity is indispensable for a plethora of life functions. While crystal structures of different BAR dimers advanced our understanding of membrane shaping by scaffolding and hydrophobic insertion mechanisms considerably, especially life-imaging techniques and loss-of-function studies of clathrin-mediated endocytosis with its gradually increasing curvature show that the initial idea that solely BAR domain curvatures determine their functions is oversimplified. Diagonal placing, lateral lipid-binding modes, additional lipid-binding modules, tilde shapes and formation of macromolecular lattices with different modes of organisation and arrangement increase versatility. A picture emerges, in which BAR domain proteins create macromolecular platforms, that recruit and connect different binding partners and ensure the connection and coordination of the different events during the endocytic process, such as membrane invagination, coat formation, actin nucleation, vesicle size control, fission, detachment and uncoating, in time and space, and may thereby offer mechanistic explanations for how coordination, directionality and effectiveness of a complex process with several steps and key players can be achieved.     

Comprehensive proteomics

Extensive proteome discovery projects using a variety of mass spectrometric techniques have identified proteins matching to 50-70% of the predicted gene models of various species. Comprehensive proteome coverage is desirable for the unbiased comparison of protein quantities between different biological states and for the meaningful comparison of data from multiple samples. Here we discuss the feasibility of this goal in the light of recent technological developments.     

The velocity of calcium waves is expected to depend non-monotonously on the density of the calcium release units

In this paper we develop a reaction-diffusion system describing the calcium dynamics in an agarose gel system with resuspended vesicles from the sarcoplasmic reticulum (SR vesicles). We focus on a simple model: compared with living cells (e.g. cardiac myocytes) an important property of the agarose gel system is the absence of the sarcolemma and the spatial separation of the calcium release units (CRUs). Our model includes the kinetics of ryanodine sensitive receptors (RyRs), the activity of the SERCA pumps and the diffusion of free calcium. We describe numerical simulations which show a biphasic relationship between the density of the CRUs and the propagation velocity of spreading waves. The non-monotony can be explained by changes in the amplitude of the local calcium concentration. We formulate implications for the in vitro system which could be verified in future experiments.     

Repair rate in human fibroblasts measured by thymine dimer excorporation

Summary The UV photoproduct, thymine dimer ( ), is excorporated with a remarkably low rate from the DNA of human fibroblasts grown in cell culture. An UV dose of 18 J/m² creates 0.045% (related to thymine). Within the first two days of repair logarithmically growing and quiescent fibroblasts exhibit the same repair rates; thereafter, the proportion of is lower in growing cells due to recovery of DNA replication. Only about 50% of the lesions are excised within 24 h. In quiescent cells, 13% of the thymine dimers originally present can be detected as late as a week after UV-irradiation. Two distinct first-order rate constants indicate that approximately half of the dimers are less accessible to repair. Repair measured by the nucleoid decondensation technique corresponds to the faster repair rate, whereas the slow repair rate cannot be detected by this method. Saturation of repair is found beyond 27 J/m². The remarkably slow rate of excision indicates that thymine dimers are not lethal lesions in human fibroblasts.     

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry

The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD) simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG) membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5)bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.     

The strategy concept and John Maynard Smith’s influence on theoretical biology

Here we argue that the concept of strategies, as it was introduced into biology by John Maynard Smith, is a prime illustration of the four dimensions of theoretical biology in the post-genomic era. These four dimensions are: data analysis and management, mathematical and computational model building and simulation, concept formation and analysis, and theory integration. We argue that all four dimensions of theoretical biology are crucial to future interactions between theoretical and empirical biologists as well as with philosophers of biology.     

Fungal and bacterial biomass in tundra soils along an arctic transect from Taimyr Peninsula, central Siberia

Microscopic analyses of tundra soils from northern central Siberia, Taimyr Peninsula (74.5°N, 98.5°E) were performed in order to investigate spatial variation of fungal and bacterial biomass. Biomass figures of fungi and bacteria (µg C g^-1 dry wt.) were measured from 11 permafrost soil pits. Fungal biovolume of up to 3.5 mm³ g^-1 dry wt. (median 0.19 mm³ g^-1 dry wt.) and a maximum hyphal length of 393 m g^-1 dry wt. (median 21 m g^-1 dry wt.) were determined. Fungal biomass was found up to 455 µg C g^-1 dry wt. (median 24 µg C g^-1 dry wt.). The amounts generally decreased with depth but increased within organic horizons. Little fungal biomass was found in the unvegetated soils or deep horizons above the permafrost table. Bacterial counts ranged from 0.16 to 7.38*10⁹ g^-1 dry wt. and bacterial biomass ranged from 0.68 to 20.38 µg C g^-1 dry wt. (median 6.19 µg C g^-1 dry wt.) because of small cell volume (median 0.04 µm³). Microbial biomass was generally dominated by fungi as shown by the ratio of fungal to bacterial biomass, which was between 0 and 174.1 (median 4.5). Plant cover and soil organic matter content were found to be the important keys in understanding microbial ecology in arctic tundra soils.     

Zur cytotaxonomie vonVeronica chamaedrys L. agg., II.: subsp.micans M.Fischer,subsp. nova,eine weitere diploide Sippe

Zusammenfassung Veronica chamaedrys L. subsp.micans M.Fischer, unterscheidet sich vonV. chamaedrys L. subsp.chamaedrys hauptsächlich durch die meist hellgrün gefärbten und im Leben oberseits stets schwach glänzenden Laubblätter, deren Blattrand durchschnittlich mehr (9–11) Zähne aufweist, durch die stets drüsenlose Infloreszenzbehaarung, die kleineren Blüten mit schmäleren Sepalen und hellblau (nicht leuchtend-sattblau) gefärbten Corollen sowie durch die diploide Chromosomenzahl (2 n=16). Sie tritt in der mittleren Bergstufe zusammen mit subsp.chamaedrys auf, ersetzt sie jedoch in der oberen Bergstufe und in der Krummholzstufe an±gleichen Standorten fast vollständig (mit Ausnahme der stark eutrophierten Standorte, die ausschließlich von subsp.chamaedrys besiedelt sind). Die neue Sippe ist bisher nur aus den nordöstlichen Alpen bekannt geworden (vgl. S. 77).

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Cytotaxonomy ofveronica chamaedrys L. agg., II.: subsp.micans M.Fischer, a new diploid race

Summary Veronica chamaedrys L. subsp.micans M.Fischer differs fromV. chamaedrys L. subsp.chamaedrys mainly by: leaves bright green, in the living state always slightly but distinctly shining on the upper surface; margins on the average with more (9–11) teeth at each side; indumentum of the inflorescence without any glands; flowers relatively small with bright blue corollas and narrow sepals; chromosome number diploid: 2 n=16. In the upper mountain and subalpine region, where it replaces the common tetraploid subsp.chamaedrys L.; it is known up to now only from the Northeastern Alps (see p. 77).