Neural cross-correlation and signal decorrelation: insights into coding of auditory space

The auditory systems of humans and many other species use the difference in the time of arrival of acoustic signals at the two ears to compute the lateral position of sound sources. This computation is assumed to initially occur in an assembly of neurons organized along a frequency-by-delay surface. Mathematically, the computations are equivalent to a two-dimensional cross-correlation of the input signals at the two ears, with the position of the peak activity along this surface designating the position of the source in space. In this study, partially correlated signals to the two ears are used to probe the mechanisms for encoding spatial cues in stationary or dynamic (moving) signals. It is demonstrated that a cross-correlation model of the auditory periphery coupled with statistical decision theory can predict the patterns of performance by human subjects for both stationary and motion stimuli as a function of stimulus decorrelation. Implications of these findings for the existence of a unique cortical motion system are discussed.     

Chimpanzees’ constructional praxis (Pan paniscus, P. troglodytes)

This study investigated chimpanzees spontaneous spatial constructions with objects and especially their ability to repeat inter-object spatial relations, which is basic to understanding spatial relations at a higher level than perception or recognition. Subjects were six chimpanzees—four chimpanzees and two bonobos—aged 6–21 years, all raised in a human environment from an early age. Only minor species differences, but considerable individual differences were found. The effect of different object samples was assessed through a comparison with a previous study. A common overall chimpanzee pattern was also found. Chimpanzees repeated different types of inter-object spatial relations such as insertion (I), or vertical (V), or next-to (H) relations. However chimpanzees repeated I or V relations with more advanced procedures than when repeating H relations. Moreover, chimpanzees never repeated combined HV relations. Compared with children, chimpanzees showed a specific difficulty in repeating H relations. Repeating H relations is crucial for representing and understanding multiple reciprocal spatial relations between detached elements and for coordinating independent positions in space. Therefore, the chimpanzees difficulty indicates a fundamental difference in constructive space in comparison to humans. The findings are discussed in relation to issues of spatial cognition and tool use.     

An assessment of dead space in pulmonary ventilation of the toad Bufo schneideri

The respiratory cycles of Rana and Bufo has been disputed in relation to flow patterns and to the respiratory dead-space of the buccal volume. A small tidal volume combined with a much larger buccal space motivated the "jet steam" model that predicts a coherent expired flow within the dorsal part of the buccal space. Some other studies indicate an extensive mixing of lung gas within the buccal volume. In Bufo schneideri, we measured arterial, end-tidal and intrapulmonary PCO(2) to evaluate dead-space by the Bohr equation. Dead-space was also estimated as: V(D)=(total ventilation-effective ventilation)/f(R), where total ventilation and f(R) were measured by pneumotachography, while effective ventilation was derived from the alveolar ventilation equation. These approaches were consistent with a dead space of 30-40% of tidal volume, which indicates a specific pathway for the expired lung gas.     

Urban Domestic Gardens (IV): The Extent of the Resource and its Associated Features

Domestic (‘private’) gardens constitute a substantial proportion of ‘green space’ in urban areas and hence are of potential significance for the maintenance of biodiversity in such areas. However, the size and nature of this resource and its associated features are poorly known. In this study, we provide the first detailed audit, using domestic gardens in the city of Sheffield as a model study system. Domestic gardens, the mean area of which was 151 m², cover approximately 33 km² or 23% of the predominantly urban area of the city. The smaller gardens contribute disproportionately to this total because, although individually they add little, they are large in number. Conversely, the regions of the city with proportionately more garden area contribute most to the total garden area of the city, although such regions are limited in number. Based on the findings of a telephone based survey, 14.4% of dwellings with gardens were estimated to have ponds, 26% to have nest-boxes, 29% to have compost heaps, 48% to hold trees more than 3 m tall, and 14% of dwellings were estimated to be home to one or more cats. Whilst the absolute frequency of these features is low to moderate, by extrapolation they nonetheless yield estimates for domestic gardens in Sheffield of a total of 25,200 ponds, 45,500 nest boxes, 50,750 compost heaps, 360,000 trees, and a population of 52,000 domestic cats. These results are considered in the context of the role of gardens in urban areas as habitats for wildlife and the implications for housing policy.     

Comparative molecular dynamics—Similar folds and similar motions?

Proteins possessing the same fold may undergo similar motions, particularly if these motions involve large conformational transitions. The increasing amounts of structural data provide a useful starting point with which to test this hypothesis. We have performed a total of 0.29 micros of molecular dynamics across a series of proteins within the same fold family (periplasmic binding proteinlike) in order to address to what extent similarity of motion exists. Analysis of the local conformational space on these timescales (10-20 ns) revealed that the behavior of the proteins could be readily distinguished between an apo-state and a ligand-bound state. Moreover, analysis of the root-mean-square fluctuations reveals that the presence of the ligand exerts a stabilizing effect on the protein, with similar motions occurring, but with reduced magnitude. Furthermore, the conformational space in the presence of the ligand appears to be dictated by sequence but not by the type of ligand present. In contrast, apo-simulations showed considerable overlap of conformational space across the fold as a result of their ability to undergo larger fluctuations. Indeed, we observed several transitions from different simulations between states corresponding to the closed-cleft and open-cleft forms of the fold, with the predominant motions being conserved across the different proteins. Thus, large-scale conformational changes do indeed appear to be conserved across this fold architecture, but smaller conformational motions appear to reflect the differences in sequence and local fold.     

Changes of enzyme activity in lipid signaling pathways related to substrate reordering

The static fluid mosaic model of biological membranes has been progressively complemented by a dynamic membrane model that includes phospholipid reordering in domains that are proposed to extend from nanometers to microns. Kinetic models for lipolytic enzymes have only been developed for homogeneous lipid phases. In this work, we develop a generalization of the well-known surface dilution kinetic theory to cases where, in a same lipid phase, both domain and nondomain phases coexist. Our model also allows understanding the changes in enzymatic activity due to a decrease of free substrate concentration when domains are induced by peptides. This lipid reordering and domain dynamics can affect the activity of lipolytic enzymes, and can provide a simple explanation for how basic peptides, with a strong direct interaction with acidic phospholipids (such as beta-amyloid peptide), may cause a complex modulation of the activities of many important enzymes in lipid signaling pathways.     

The maize gene space is compositionally compartimentalized

Previous investigations by Southern hybridization of cDNA with compositional DNA fractions showed that the majority of maize genes are located in a narrow GC range of DNA fragments and that the corresponding gene space was GC-richer than the region of the genome where zein genes are found. Here, we revisited the maize gene space using new data from the maize genome sequencing initiative. We found that the maize gene space itself is formed of two compositional compartments, i.e., a GC-poor and a GC-rich, characterized by a different distribution of Opie and Huck retrotransposons. The GC-rich compartment tends to be richer in GC-rich genes than the GC-poor compartment. However, the gene space compartimentalization of maize is much simpler than that of human.     

Extracellular calcium acts as a "third messenger" to regulate enzyme and alkaline secretion

It is generally assumed that the functional consequences of stimulation with Ca2+ -mobilizing agonists are derived exclusively from the second messenger action of intracellular Ca2+, acting on targets inside the cells. However, during Ca2+ signaling events, Ca2+ moves in and out of the cell, causing changes not only in intracellular Ca2+, but also in local extracellular Ca2+. The fact that numerous cell types possess an extracellular Ca2+ "sensor" raises the question of whether these dynamic changes in external [Ca2+] may serve some sort of messenger function. We found that in intact gastric mucosa, the changes in extracellular [Ca2+] secondary to carbachol-induced increases in intracellular [Ca2+] were sufficient and necessary to elicit alkaline secretion and pepsinogen secretion, independent of intracellular [Ca2+] changes. These findings suggest that extracellular Ca2+ can act as a "third messenger" via Ca2+ sensor(s) to regulate specific subsets of tissue function previously assumed to be under the direct control of intracellular Ca2+.     

Determination of mesophyll diffusion resistance in Chamaerion angustifolium by the method of three-dimensional reconstruction of the leaf cell packing

A detailed quantitative analysis of the three-dimensional organization of the mesophyll was performed, and mesophyll diffusion resistance to CO₂ in the leaves of Chamaerion angustifolium formed under different irradiance was calculated using an original method of stereometric cellular packing. For each type of leaves (sun and shade), we determined structural components of gas exchange: the volume of mesophyll per unit leaf area (V _mes), the volume of the intercellular space in the mesophyll (V _is), the area of the total mesophyll surface (S), the area of the free mesophyll surface facing the intercellular spaces (S _mes), and the ratios of the total and the free mesophyll surfaces to its volume (S/V and S _mes/V). As compared with sun leaves, in the shade leaves of Ch. angustifolium, S and V _mes decreased twofold, tissue density was reduced twofold, and the share of the intercellular space in the mesophyll rose from 49 to 72%. In shade, the diffusion resistance of the mesophyll increased by 1.8 times because of changes in the leaf structure. At the same time, the ratio S _mes/V was found to increase by 1.4 times, which facilitated the diffusion of CO₂. In the shade leaves of Ch. angustifolium, the diffusion resistance of the intercellular air spaces was reduced twofold as a result of an increase in their share in the leaf mesophyll and simplification of their geometry. Thus, the method of three-dimensional reconstruction of sun and shade leaves of Ch. angustifolium showed a comprehensive rearrangement of the mesophyll spatial organization in shade and revealed the structural mechanisms of changes in the resistance to CO₂ diffusion within the leaf.