Analysis and interpretation of quadratic models of receptive fields

In this protocol, we present a procedure to analyze and visualize models of neuronal input-output functions that have a quadratic, a linear and a constant term, to determine their overall behavior. The suggested interpretations are close to those given by physiological studies of neurons, making the proposed methods particularly suitable for the analysis of receptive fields resulting from physiological measurements or model simulations.     

Dual effect of acid pH on purinergic P2X3 receptors depends on the histidine 206 residue

Whole cell patch clamp investigations were carried out to clarify the pH sensitivity of native and recombinant P2X(3) receptors. In HEK293 cells permanently transfected with human (h) P2X(3) receptors (HEK293-hP2X(3) cells), an acidic pH shifted the concentration-response curve for alpha,beta-methylene ATP (alpha,beta-meATP) to the right and increased its maximum. An alkalic pH did not alter the effect of alpha,beta-meATP. Further, a low pH value increased the activation time constant (tau(on)) of the alpha,beta-meATP current; the fast and slow time constants of desensitization (tau(des1), tau(des2)) were at the same time also increased. Finally, acidification accelerated the recovery of P2X(3) receptors from the desensitized state. Replacement of histidine 206, but not histidine 45, by alanine abolished the pH-induced effects on hP2X(3) receptors transiently expressed in HEK293 cells. Changes in the intracellular pH had no effect on the amplitude or time course of the alpha,beta-meATP currents. The voltage sensitivity and reversal potential of the currents activated by alpha,beta-meATP were unaffected by extracellular acidification. Similar effects were observed in a subpopulation of rat dorsal root ganglion neurons expressing homomeric P2X(3) receptor channels. It is suggested that acidification may have a dual effect on P2X(3) channels, by decreasing the current amplitude at low agonist concentrations (because of a decrease in the rate of activation) and increasing it at high concentrations (because of a decrease in the rate of desensitization). Thereby, a differential regulation of pain sensation during e.g. inflammation may occur at the C fiber terminals of small DRG neurons in peripheral tissues.     

Vertical and areal distribution of foraminiferal abundance and biomass in microhabitats around inhabited tubes of marine echiurids

Three examples of microhabitats of foraminifera around inhabited macrofaunal tubes (Echiurus echiurus) from the German Bight are given. Compared to ambient sediments, abundances and biomass of foraminifera were up to 3 times higher within the tube. Bacterial abundances were about 2 times higher and bacterial biomass was up to 5 times higher within the tube. Data suggest that tubes and burrows provide microhabitats with increased food concentrations and foraminiferal abundances.     

Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells

The developing visual system of many mammalian species is partially structured and organized even before the onset of vision. Spontaneous neural activity, which spreads in waves across the retina, has been suggested to play a major role in these prenatal structuring processes. Recently, it has been shown that when employing an efficient coding strategy, such as sparse coding, these retinal activity patterns lead to basis functions that resemble optimal stimuli of simple cells in primary visual cortex (V1). Here we present the results of applying a coding strategy that optimizes for temporal slowness, namely Slow Feature Analysis (SFA), to a biologically plausible model of retinal waves. Previously, SFA has been successfully applied to model parts of the visual system, most notably in reproducing a rich set of complex-cell features by training SFA with quasi-natural image sequences. In the present work, we obtain SFA units that share a number of properties with cortical complex-cells by training on simulated retinal waves. The emergence of two distinct properties of the SFA units (phase invariance and orientation tuning) is thoroughly investigated via control experiments and mathematical analysis of the input-output functions found by SFA. The results support the idea that retinal waves share relevant temporal and spatial properties with natural visual input. Hence, retinal waves seem suitable training stimuli to learn invariances and thereby shape the developing early visual system such that it is best prepared for coding input from the natural world.     

Slowness and sparseness lead to place, head-direction, and spatial-view cells

We present a model for the self-organized formation of place cells, head-direction cells, and spatial-view cells in the hippocampal formation based on unsupervised learning on quasi-natural visual stimuli. The model comprises a hierarchy of Slow Feature Analysis (SFA) nodes, which were recently shown to reproduce many properties of complex cells in the early visual system []. The system extracts a distributed grid-like representation of position and orientation, which is transcoded into a localized place-field, head-direction, or view representation, by sparse coding. The type of cells that develops depends solely on the relevant input statistics, i.e., the movement pattern of the simulated animal. The numerical simulations are complemented by a mathematical analysis that allows us to accurately predict the output of the top SFA layer.     

Analysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools

A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.     

Classification and ordination of plant formations in the Pantanal of Brazil

Classification and ordination of plant formations are presented for a seasonally flooded plain of the Brazilian Pantanal. Phytosociological data were collected on 10 physiognomically distinct formations during the rainy, flood, and dry seasons. The degree of association among plant species was measured with Jaccard similarity index, and both Jaccard similarity index and Bray Curtis distance index were employed to classify sample units into similar groups. The ordination of plant species and sample units were performed with Correspondence Analysis. Four groups of plant formations were significantly distinct on a quantitative basis: marsh ponds/waterlogged basins, short grasslands, tall grassland/scrub, and forest-edges. These formations were ordered along a gradient of topographic relief from depressions with permanent standing water (marshes) through flats subject to seasonal flooding (grasslands and scrub) and mounds of sandy soil above the flood level (forests). Although hydroperiod appears to be one of the most important variables, the distribution of plant species within wetlands is most probably explained by the interaction of many additional factors. A few plant species could be used as indicators of the local hydrological and edaphic conditions, e.g., Eleocharis elegans, Aeschynomene fluminensis, Hydrolea spinosa, and Hymenachne amplexicaulis for marsh ponds, and Caperonia castaneifolia, Diodia kuntzei, and Eleocharis acutangula for waterlogged basins. The procedure presented in this study could be developed as a tool for the inventory and management of the Pantanal and other palustrine wetland habitats.     

Novel ketolide antibiotics with a fused five-membered lactone ring--synthesis, physicochemical and antimicrobial properties

In an effort to find novel semisynthetic macrolides with extended antibacterial spectrum and improved activity we prepared a series of compounds based on commercially available clarithromycin, a potent and safe antimicrobial agent of outstanding clinical and commercial interest. According to the literature, improvement of antibacterial activity of erythromycin type antibiotics can be achieved by introduction of fused heterocycles such as cyclic carbonates or carbamates at positions 11 and 12 (such as in telithromycin). In the course of the work presented here, a similar, hitherto unprecedented set of compounds bearing a five-membered lactone ring fused to positions 11 and 12 was prepared based on carbon-carbon bond formation via intramolecular Michael addition of a [(hetero)arylalkylthio]acetic acid ester enolate to an alpha,beta-unsaturated ketone as the key step. Some of the ketolide compounds described in this paper were highly active against a representative set of erythromycin sensitive and erythromycin resistant test strains. The best compound showed a similar antimicrobial spectrum and comparable activity in vitro as well as in vivo as telithromycin. Furthermore, some physicochemical properties of these compounds were determined and are presented here. On the basis of these results, the novel ketolide lactones presented in this paper emerged as valuable lead compounds with comparable properties as the commercial ketolide antibacterial telithromycin (Ketek).     

Effects of Ocean Acidification on the Ballast of Surface Aggregates Sinking through the Twilight Zone

The dissolution of CaCO₃ is one of the ways ocean acidification can, potentially, greatly affect the ballast of aggregates. A diminution of the ballast could reduce the settling speed of aggregates, resulting in a change in the carbon flux to the deep sea. This would mean lower amounts of more refractory organic matter reaching the ocean floor. This work aimed to determine the effect of ocean acidification on the ballast of sinking surface aggregates. Our hypothesis was that the decrease of pH will increase the dissolution of particulate inorganic carbon ballasting the aggregates, consequently reducing their settling velocity and increasing their residence time in the upper twilight zone. Using a new methodology for simulation of aggregate settling, our results suggest that future pCO₂ conditions can significantly change the ballast composition of sinking aggregates. The change in aggregate composition had an effect on the size distribution of the aggregates, with a shift to smaller aggregates. A change also occurred in the settling velocity of the particles, which would lead to a higher residence time in the water column, where they could be continuously degraded. In the environment, such an effect would result in a reduction of the carbon flux to the deep-sea. This reduction would impact those benthic communities, which rely on the vertical flow of carbon as primary source of energy.     

Mosses modify effects of warmer and wetter conditions on tree seedlings at the alpine treeline

Climate warming enables tree seedling establishment beyond the current alpine treeline, but to achieve this, seedlings have to establish within existing tundra vegetation. In tundra, mosses are a prominent feature, known to regulate soil temperature and moisture through their physical structure and associated water retention capacity. Moss presence and species identity might therefore modify the impact of increases in temperature and precipitation on tree seedling establishment at the arctic‐alpine treeline. We followed Betula pubescens and Pinus sylvestris seedling survival and growth during three growing seasons in the field. Tree seedlings were transplanted along a natural precipitation gradient at the subarctic‐alpine treeline in northern Sweden, into plots dominated by each of three common moss species and exposed to combinations of moss removal and experimental warming by open‐top chambers (OTCs). Independent of climate, the presence of feather moss, but not Sphagnum, strongly supressed survival of both tree species. Positive effects of warming and precipitation on survival and growth of B. pubescens seedlings occurred in the absence of mosses and as expected, this was partly dependent on moss species. P. sylvestris survival was greatest at high precipitation, and this effect was more pronounced in Sphagnum than in feather moss plots irrespective of whether the mosses had been removed or not. Moss presence did not reduce the effects of OTCs on soil temperature. Mosses therefore modified seedling response to climate through other mechanisms, such as altered competition or nutrient availability. We conclude that both moss presence and species identity pose a strong control on seedling establishment at the alpine treeline, and that in some cases mosses weaken climate‐change effects on seedling establishment. Changes in moss abundance and species composition therefore have the potential to hamper treeline expansion induced by climate warming.