Distinctive synaptic structural motifs link excitatory retinal interneurons to diverse postsynaptic partner types

1. Download : Download high-res image (160KB)
2. Download : Download full-size image

     

Validating and improving elastic network models with molecular dynamics simulations

Elastic network models (ENMs) are a class of simple models intended to represent the collective motions of proteins. In contrast to all‐atom molecular dynamics simulations, the low computational investment required to use an ENM makes them ideal for speculative hypothesis‐testing situations. Historically, ENMs have been validated via comparison to crystallographic B‐factors, but this comparison is relatively low‐resolution and only tests the predictions of relative flexibility. In this work, we systematically validate and optimize a number of ENM‐type models by quantitatively comparing their predictions to microsecond‐scale all‐atom simulations of three different G protein coupled receptors. We show that, despite their apparent simplicity, well‐optimized ENMs perform remarkably well, reproducing the protein fluctuations with an accuracy comparable to what one would expect from all‐atom simulations run for several hundred nanoseconds. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Eukaryotes first: how could that be?

In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through ‘streamlining’. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested.     

The origin of ascophoran bryozoans was historically contingent but likely

The degree to which evolutionary outcomes are historically contingent remains unresolved, with studies at different levels of the biological hierarchy reaching different conclusions. Here we examine historical contingency in the origin of two evolutionary novelties in bryozoans, a phylum of colonial animals whose fossil record is as complete as that of any major group. In cheilostomes, the dominant living bryozoans, key innovations were the costal shield and ascus, which first appeared in the Cretaceous 85–95 Myr ago. We establish the parallel origin of these structures less than 12 Myr ago in an extant bryozoan genus, Cauloramphus, with transitional stages remarkably similar to those inferred for a Cretaceous clade. By one measure, long lag times in the first origins of costal shield and ascus suggest a high degree of historical contingency. This, however, does not equate with dependence on a narrow set of initial conditions or a low probability of evolution. More than one set of initial conditions may lead to an evolutionary outcome, and alternative sets are not entirely independent. We argue that, although historically contingent, the origin of ascus and costal shield was highly likely with sufficient possibilities afforded by time.     

Modern tropical analogs for Carboniferous standing forests: Comparison of extinct Mesocalamites with extant Montrichardia

Assemblages of in situ upright stem casts, or fossil standing forests, provide information on the composition and spatial arrangement of the original plant communities they record, with minimal taphonomic bias. Stands of calamites and lycopsids are found repeatedly as fossil forests in the Late Carboniferous, while other major groups of plants are only rarely preserved in this way. The Carboniferous coal measures of Europe and North America were formed in low‐latitude, tropical environments. The ancient plant communities of these settings can be interpreted by comparison of their taxa with specific, modern tropical analogs. Here, ancient standing forests of the extinct sphenopsid Mesocalamites suckowii are compared with modern stands of the monocot Montrichardia arborescens. These modern analogs occur in the Orinoco Delta of Venezuela and the mouth of the Amazon. Montrichardia and its ancient counterparts occur in comparable clastic facies of fluvio‐deltaic and estuarine depositional systems. Although Mesocalamites and Montrichardia are very different anatomically and taxonomically, they exhibit some intriguing morphological similarities that can be linked to a common ecology. These modern and ancient taxa have evolved convergent forms of vegetative propagation that enable the plants to colonize and survive in environments characterized by very high rates of sedimentation, or episodic sedimentation events. Such environments have an unusually high potential to preserve standing forests.     

Intraspecific trait variation and reversals of trait strategies across key climate gradients in native Hawaiian plants and non-native invaders

Background and AimsDisplacement of native plant species by non-native invaders may result from differences in their carbon economy, yet little is known regarding how variation in leaf traits influences native–invader dynamics across climate gradients. In Hawaii, one of the most heavily invaded biodiversity hotspots in the world, strong spatial variation in climate results from the complex topography, which underlies variation in traits that probably drives shifts in species interactions.MethodsUsing one of the most comprehensive trait data sets for Hawaii to date (91 species and four islands), we determined the extent and sources of variation (climate, species and species origin) in leaf traits, and used mixed models to examine differences between natives and non-native invasives.Key ResultsWe detected significant differences in trait means, such that invasives were more resource acquisitive than natives over most of the climate gradients. However, we also detected trait convergence and a rank reversal (natives more resource acquisitive than invasives) in a sub-set of conditions. There was significant intraspecific trait variation (ITV) in leaf traits of natives and invasives, although invasives expressed significantly greater ITV than natives in water loss and photosynthesis. Species accounted for more trait variation than did climate for invasives, while the reverse was true for natives. Incorporating this climate-driven trait variation significantly improved the fit of models that compared natives and invasives. Lastly, in invasives, ITV was most strongly explained by spatial heterogeneity in moisture, whereas solar energy explains more ITV in natives.ConclusionsOur results indicate that trait expression and ITV vary significantly between natives and invasives, and that this is mediated by climate. These findings suggest that although natives and invasives are functionally similar at the regional scale, invader success at local scales is contingent on climate.     

Climate variability in the Stephanian B based on environmental record of the Mšec Lake deposits (Kladno–Rakovník Basin, Czech Republic)

In the Stephanian B in eastern equatorial Pangaea, a large freshwater lake was formed in the continental basins of the west, central and northeast Bohemia, Czech Republic with a total area estimated at 5000–10,000 km² and a lifetime of 50 to 500 ky. Its size exceeded that of any Permian–Carboniferous lake in the European basins of that period so far described. Continual sedimentation of organic-rich, seasonally laminated clayey–silty lake deposits produced a unique high-resolution record of part of the Stephanian B climate in the studied region. An extraordinarily large trophic web of fish assemblages also proves the temporal stability of this meromictic oligotrophic lake. The lake hydrology was inferred from the chemical and isotopic analyses of the autochthonous carbonates, particularly siderite, and analysis of organic matter. The environmental and weathering conditions in the lake watershed were inferred from analysis of palynospectra and detrital clay minerals. The lake passed through several stages of development including an initial highstand with peak productivity, a stepwise increase in mineralization accompanying gradual lake regression, a lowstand in the middle part of its lifetime, a partial lake recovery, and then a final transition to a shallow lacustrine-deltaic system. Lake regression was triggered by a long-term decrease in the P/E ratio coupled with increasing seasonality and accompanied by a decrease in intensity of chemical weathering in the drainage basin. Considerable vegetation response to fluctuating lake levels suggests complex environmental changes. During the initial lake highstand, abundant and diversified assemblages of xerophilous elements prevailed, spores of ferns prevailed during the regressive episode, and spores of lycopsids abruptly increased at the lowstand and remained dominant in the palynospectra of the second lake highstand. Final transition to a lacustrine-deltaic system was associated with pronounced increase in sphenopsids and ferns. These changes can be attributed to Milankovitch-like climate change from warm–wet to warm–seasonal dry, and may be inferred to have been responsible for Stephanian continental cyclothems. The entire Stephanian B period was more humid than the preceding Barruelian and subsequent Stephanian C in the Czech basins, thus revealing a climate cycle at a timescale of several million years, which is discussed in relation to southern Gondwana ice sheet stability.     

Almost-one Parameter Hypothesis of Individuality in Height Growth

Thus far an individual height growth curve h_ij(t) of the i-th person in the j-th period, t being his (or her) age, has been studied as a function of t associated with its velocity curve. In this note we introduce a natural scale X(t) in place of t, which linearizes this personal curve and facilitates its analysis, in the sense that this equation of growth contains apparently two personal parameters for one period but one of them plays an essential role. The effectiveness of this approach will be seen in four figures.