Serial-section atlas of the Tritonia pedal ganglion.

The pedal ganglion of the nudibranch gastropod Tritonia diomedea has been the focus of neurophysiological studies for more than 50 yr. These investigations have examined the neural basis of behaviors as diverse as swimming, crawling, reflex withdrawals, orientation to water flow, orientation to the earth's magnetic field, and learning. Despite this sustained research focus, most studies have confined themselves to the layer of neurons that are visible on the ganglion surface, leaving many neurons, which reside in deeper layers, largely unknown and thus unstudied. To facilitate work on such neurons, the present study used serial-section light microscopy to generate a detailed pictorial atlas of the pedal ganglion. One pedal ganglion was sectioned horizontally at 2-µm intervals and another vertically at 5-µm intervals. The resulting images were examined separately or combined into stacks to generate movie tours through the ganglion. These were also used to generate 3D reconstructions of individual neurons and rotating movies of digitally desheathed whole ganglia to reveal all surface neurons. A complete neuron count of the horizontally sectioned ganglion yielded 1,885 neurons. Real and virtual sections from the image stacks were used to reveal the morphology of individual neurons, as well as the major axon bundles traveling within the ganglion to and between its several nerves and connectives. Extensive supplemental data are provided, as well as a link to the Dryad Data Repository site, where the complete sets of high-resolution serial-section images can be downloaded. NEW & NOTEWORTHY Because of the large size and relatively low numbers of their neurons, gastropod mollusks are widely used for investigations of the neural basis of behavior. Most studies, however, focus on the neurons visible on the ganglion surface, leaving the majority, located out of sight below the surface, unexamined. The present light microscopy study generates the first detailed visual atlas of all neurons of the highly studied Tritonia pedal ganglion.

Effects of topoclimatic complexity on the composition of woody plant communities.

Topography can create substantial environmental variation at fine spatial scales. Shaped by slope, aspect, hill-position and elevation, topoclimate heterogeneity may increase ecological diversity, and act as a spatial buffer for vegetation responding to climate change. Strong links have been observed between climate heterogeneity and species diversity at broader scales, but the importance of topoclimate for woody vegetation across small spatial extents merits closer examination. We established woody vegetation monitoring plots in mixed evergreen-deciduous woodlands that spanned topoclimate gradients of a topographically heterogeneous landscape in northern California. We investigated the association between the structure of adult and regenerating size classes of woody vegetation and multidimensional topoclimate at a fine scale. We found a significant effect of topoclimate on both single-species distributions and community composition. Effects of topoclimate were evident in the regenerating size class for all dominant species (four Quercus spp., Umbellularia californica and Pseudotsuga menziesii) but only in two dominant species (Quercus agrifolia and Quercus garryana) for the adult size class. Adult abundance was correlated with water balance parameters (e.g. climatic water deficit) and recruit abundance was correlated with an interaction between the topoclimate parameters and conspecific adult abundance (likely reflecting local seed dispersal). However, in all cases, the topoclimate signal was weak. The magnitude of environmental variation across our study site may be small relative to the tolerance of long-lived woody species. Dispersal limitations, management practices and patchy disturbance regimes also may interact with topoclimate, weakening its influence on woody vegetation distributions. Our study supports the biological relevance of multidimensional topoclimate for mixed woodland communities, but highlights that this relationship might be mediated by interacting factors at local scales.

A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans.

Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral effects of neuronal ablations and genetic perturbations, as well as unexpected aspects of wild type behavior. The predictive success of the model indicates that random search in C. elegans can be understood in terms of a neuronal flip-flop circuit involving reciprocal inhibition between two populations of stochastic neurons. Our findings establish a unified theoretical framework for understanding C. elegans locomotion and a testable neuronal model of random search that can be applied to other organisms.

Topography as a driver of diversification in the Cape Floristic Region of South Africa.

The rugged topography of the Cape Floristic Region (CFR), South Africa, is frequently invoked to explain the spectacular radiation of the Cape flora, but the mechanisms involved remain unclear. Where recent authors emphasize the importance of elevation gradients as stimuli for ecological speciation, earlier workers stressed the role of topography as an isolating mechanism, particularly in montane lineages. Using six Cape plant lineages, we tested whether elevation niches are phylogenetically conserved. We then assessed whether high-elevation species are more consistently range-restricted than low-elevation species, and whether high-elevation sisters show stronger range exclusivity (allopatry) and weaker ecological and phenotypic differentiation, suggestive of nonecological speciation. Elevation niches tend to be phylogenetically conserved. Also, high-elevation species are more consistently range-restricted than low-elevation species, potentially explaining the generally stronger range exclusivity of high-elevation sisters. While the high-elevation zone is less homogeneous ecologically, more data are required to demonstrate that high-elevation sister species show generally weaker ecological and phenotypic differentiation. Topographic complexity promotes geographical isolation at high elevations, thereby providing opportunities for nonecological, vicariant speciation. While recognizing the need for additional data, we suggest that the upland and lowland floras of the CFR may differ with regard to predominant speciation mode.

Topography as a driver of cryptic speciation in the high-elevation cape sedge Tetraria triangularis (Boeck.) C. B. Clarke (Cyperaceae: Schoeneae).

Since some speciation mechanisms are more likely to generate morphological disparity than others, the general failure of vascular plant taxonomists to recognize cryptic diversity may bias perceptions about speciation process in plants. While the exceptional floristic richness of the South African Cape has largely been attributed to adaptive divergence ('ecological' speciation), a combination of climatic dynamism and complex topography has likely provided ample opportunities for 'non-ecological' vicariant speciation, a mechanism which is perhaps more likely to produce cryptic species. We explore the role of topography as a driver of 'non-ecological' speciation in the high-elevation sedge Tetraria triangularis. Within this species, molecular and morphological data reveal five cryptic or semi-cryptic lineages of Miocene-Pliocene age which qualify as evolutionary species. At least three of these maintain their distinctness in sites of sympatry, identifying them as biological species. Negligible range overlap, and the identification of topography as a significant predictor of range turnover, identifies speciation as allopatric and a result of impeded gene flow across low-elevation topographic features. Weak morphological and ecological divergence implies a limited role for adaptive divergence in powering speciation, with character displacement in sympatry possibly arising as a consequence of interspecific competition. Although we cannot exclude a role for disruptive selection in species differentiation, we identify isolation of populations on topographically separated mountains as the principal motor of speciation. We suggest that the importance of topography in the genesis of Cape floristic diversity has been inadequately acknowledged.

Ecology limits the diversity of the Cape flora: phylogenetics and diversification of the genus Tetraria.

Understanding the ecology and evolution of the hyper-diverse Cape flora is dependent on developing an understanding of its component parts, best epitomized by the Cape floral clades that have diversified and are largely endemic to the region. Here we employ a new dated phylogenetic hypothesis for the sedge genus Tetraria, one of the smaller Cape floral clades, to develop an understanding of timing and rates of diversification in the group. Specifically, we test whether diversification in Tetraria slowed as the number of extant lineages increased, suggesting that available ecological niche space has become increasingly saturated through time. The radiation of Tetraria began approximately 18million years ago, concordant with that of many other Cape clades. Diversification rates in the genus showed no drastic shifts in response to major environmental changes, but declined as lineage diversity accumulated, indicative of ecological limitation on speciation rates. This allows the development of heuristic predictions about the composition of Tetraria assemblages at various spatial scales, and suggests that closely related species should either be ecologically differentiated or have non-overlapping geographic distributions. The question of whether ecological limitation of diversity is a common phenomenon in other Cape lineages has important implications for our understanding of the evolution and ecology of the contemporary Cape flora as a whole.

Specific cell-permeable inhibitor of proteasome trypsin-like sites selectively sensitizes myeloma cells to bortezomib and carfilzomib.

Proteasomes degrade the majority of proteins in mammalian cells, are involved in the regulation of multiple physiological functions, and are established targets of anticancer drugs. The proteasome has three types of active sites. Chymotrypsin-like sites are the most important for protein breakdown and have long been considered the only suitable targets for antineoplastic drugs; however, our recent work demonstrated that inhibitors of caspase-like sites sensitize malignant cells to inhibitors of the chymotrypsin-like sites. Here, we describe the development of specific cell-permeable inhibitors and an activity-based probe of the trypsin-like sites. These compounds selectively sensitize multiple myeloma cells to inhibitors of the chymotrypsin-like sites, including antimyeloma agents bortezomib and carfilzomib. Thus, trypsin-like sites are cotargets for anticancers drugs. Together with inhibitors of chymotrypsin- and caspase-like sites developed earlier, we provide the scientific community with a complete set of tools to separately modulate proteasome active sites in living cells.

Nature of pharmacophore influences active site specificity of proteasome inhibitors.

Proteasomes degrade most proteins in mammalian cells and are established targets of anti-cancer drugs. The majority of proteasome inhibitors are composed of short peptides with an electrophilic functionality (pharmacophore) at the C terminus. All eukaryotic proteasomes have three types of active sites as follows: chymotrypsin-like, trypsin-like, and caspase-like. It is widely believed that active site specificity of inhibitors is determined primarily by the peptide sequence and not the pharmacophore. Here, we report that active site specificity of inhibitors can also be tuned by the chemical nature of the pharmacophore. Specifically, replacement of the epoxyketone by vinyl sulfone moieties further improves the selectivity of ß5-specific inhibitors NC-005, YU-101, and PR-171 (carfilzomib). This increase in specificity is likely the basis of the decreased cytotoxicity of vinyl sulfone-based inhibitors to HeLa cells as compared with that of epoxyketone-based inhibitors.

Selective inhibitor of proteasome's caspase-like sites sensitizes cells to specific inhibition of chymotrypsin-like sites.

Proteasomes degrade most proteins in mammalian cells and are established targets of anticancer drugs. All eukaryotic proteasomes have three types of active sites: chymotrypsin-like, trypsin-like, and caspase-like. Chymotrypsin-like sites are the most important in protein degradation and are the primary target of most proteasome inhibitors. The biological roles of trypsin-like and caspase-like sites and their potential as cotargets of antineoplastic agents are not well defined. Here we describe the development of site-specific inhibitors and active-site probes of chymotrypsin-like and caspase-like sites. Using these compounds, we show that cytotoxicity of proteasome inhibitors does not correlate with inhibition of chymotrypsin-like sites and that coinhibition of either trypsin-like and/or caspase-like sites is needed to achieve maximal cytotoxicity. Thus, caspase-like and trypsin-like sites must be considered as cotargets of anticancer drugs.

Large-scale wave-front reconstruction for adaptive optics systems by use of a recursive filtering algorithm.

We propose a new recursive filtering algorithm for wave-front reconstruction in a large-scale adaptive optics system. An embedding step is used in this recursive filtering algorithm to permit fast methods to be used for wave-front reconstruction on an annular aperture. This embedding step can be used alone with a direct residual error updating procedure or used with the preconditioned conjugate-gradient method as a preconditioning step. We derive the Hudgin and Fried filters for spectral-domain filtering, using the eigenvalue decomposition method. Using Monte Carlo simulations, we compare the performance of discrete Fourier transform domain filtering, discrete cosine transform domain filtering, multigrid, and alternative-direction-implicit methods in the embedding step of the recursive filtering algorithm. We also simulate the performance of this recursive filtering in a closed-loop adaptive optics system.