A combined perceptual, physico-chemical, and imaging approach to 'odour-distances' suggests a categorizing function of the Drosophila antennal lobe

How do physico-chemical stimulus features, perception, and physiology relate? Given the multi-layered and parallel architecture of brains, the question specifically is where physiological activity patterns correspond to stimulus features and/or perception. Perceived distances between six odour pairs are defined behaviourally from four independent odour recognition tasks. We find that, in register with the physico-chemical distances of these odours, perceived distances for 3-octanol and n-amylacetate are consistently smallest in all four tasks, while the other five odour pairs are about equally distinct. Optical imaging in the antennal lobe, using a calcium sensor transgenically expressed in only first-order sensory or only second-order olfactory projection neurons, reveals that 3-octanol and n-amylacetate are distinctly represented in sensory neurons, but appear merged in projection neurons. These results may suggest that within-antennal lobe processing funnels sensory signals into behaviourally meaningful categories, in register with the physico-chemical relatedness of the odours.     

The rules of formation of the olfactory representations found in the orbitofrontal cortex olfactory areas in primates.

Approximately 35% of neurons in the orbitofrontal cortex taste and olfactory areas with olfactory responses provide a representation of odour that depends on the taste with which the odour has been associated previously. This representation is produced by a slowly acting learning mechanism that learns associations between odour and taste. Other neurons in the orbitofrontal cortex respond to both the odour and to the mouth feel of fat. The representation of odour thus moves for at least some neurons in the orbitofrontal cortex beyond the domain of physico-chemical properties of the odours to a domain where the ingestion-related significance of the odour determines the representation provided. Olfactory neurons in the primate orbitofrontal cortex decrease their responses to a food eaten to satiety, but remain responsive to other foods, thus contributing to a mechanism for olfactory sensory-specific satiety. It has been shown in neuroimaging studies that the human orbitofrontal cortex provides a representation of the pleasantness of odour, in that the activation produced by the odour of a food eaten to satiety decreases relative to another food-related odour not eaten in the meal. In the same general area there is a representation of the pleasantness of the smell, taste and texture of a whole food, in that activation in this area decreases to a food eaten to satiety, but not to a food that has not been eaten in the meal.     

Perceptual and neural olfactory similarity in honeybees

The question of whether or not neural activity patterns recorded in the olfactory centres of the brain correspond to olfactory perceptual measures remains unanswered. To address this question, we studied olfaction in honeybees Apis mellifera using the olfactory conditioning of the proboscis extension response. We conditioned bees to odours and tested generalisation responses to different odours. Sixteen odours were used, which varied both in their functional group (primary and secondary alcohols, aldehydes and ketones) and in their carbon-chain length (from six to nine carbons).The results obtained by presentation of a total of 16 × 16 odour pairs show that (i) all odorants presented could be learned, although acquisition was lower for short-chain ketones; (ii) generalisation varied depending both on the functional group and the carbon-chain length of odours trained; higher generalisation was found between long-chain than between short-chain molecules and between groups such as primary and secondary alcohols; (iii) for some odour pairs, cross-generalisation between odorants was asymmetric; (iv) a putative olfactory space could be defined for the honeybee with functional group and carbon-chain length as inner dimensions; (v) perceptual distances in such a space correlate well with physiological distances determined from optophysiological recordings of antennal lobe activity. We conclude that functional group and carbon-chain length are inner dimensions of the honeybee olfactory space and that neural activity in the antennal lobe reflects the perceptual quality of odours.     

Ab initio Molecular Electrostatic Potential Grid Maps for Quantitative Similarity Calculations of Organic Compounds

The program MolSim designed to calculate the similarity of different molecules quantitatively in a fast and easy way is described. The molecular similarity is estimated for the molecular shape as well as for the electrostatic potentials of the molecules derived from ab initio calculations. A grid-based method is used to determine the steric and electrostatic similarities between a lead compound and the corresponding test set by calculating the Spearman correlation coefficient. The superpositioning of the molecules was accomplished with the SEAL algorithm incorporating a Monte Carlo simulated annealing approach while preserving the conformational flexibility of the calculated structures.The ability of the program was tested on a set of Sandalwood odour compounds, a class of substances that is difficult to analyse with respect to its structure-activity relationship because of the structural diversity of Sandalwood odour compounds, in contrast to their high selectivity and pronounced structural specificity. The application of the program on a small test set of these compounds showed that the program is able to explain the Sandalwood odour activity correctly.Electronic Supplementary Material available.     

Comparison of Amino Acids Physico-Chemical Properties and Usage of Late Embryogenesis Abundant Proteins,Hydrophilins and WHy Domain

Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance.     

Predicting Odor Perceptual Similarity from Odor Structure

To understand the brain mechanisms of olfaction we must understand the rules that govern the link between odorant structure and odorant perception. Natural odors are in fact mixtures made of many molecules, and there is currently no method to look at the molecular structure of such odorant-mixtures and predict their smell. In three separate experiments, we asked 139 subjects to rate the pairwise perceptual similarity of 64 odorant-mixtures ranging in size from 4 to 43 mono-molecular components. We then tested alternative models to link odorant-mixture structure to odorant-mixture perceptual similarity. Whereas a model that considered each mono-molecular component of a mixture separately provided a poor prediction of mixture similarity, a model that represented the mixture as a single structural vector provided consistent correlations between predicted and actual perceptual similarity (r≥0.49, p<0.001). An optimized version of this model yielded a correlation of r = 0.85 (p<0.001) between predicted and actual mixture similarity. In other words, we developed an algorithm that can look at the molecular structure of two novel odorant-mixtures, and predict their ensuing perceptual similarity. That this goal was attained using a model that considers the mixtures as a single vector is consistent with a synthetic rather than analytical brain processing mechanism in olfaction.     

Definition of supertypes for HLA molecules using clustering of specificity matrices

Major histocompatibility complex (MHC) proteins are encoded by extremely polymorphic genes and play a crucial role in immunity. However, not all genetically different MHC molecules are functionally different. Sette and Sidney (1999) have defined nine HLA class I supertypes and showed that with only nine main functional binding specificities it is possible to cover the binding properties of almost all known HLA class I molecules. Here we present a comprehensive study of the functional relationship between all HLA molecules with known specificities in a uniform and automated way. We have developed a novel method for clustering sequence motifs. We construct hidden Markov models for HLA class I molecules using a Gibbs sampling procedure and use the similarities among these to define clusters of specificities. These clusters are extensions of the previously suggested ones. We suggest splitting some of the alleles in the A1 supertype into a new A26 supertype, and some of the alleles in the B27 supertype into a new B39 supertype. Furthermore the B8 alleles may define their own supertype. We also use the published specificities for a number of HLA-DR types to define clusters with similar specificities. We report that the previously observed specificities of these class II molecules can be clustered into nine classes, which only partly correspond to the serological classification. We show that classification of HLA molecules may be done in a uniform and automated way. The definition of clusters allows for selection of representative HLA molecules that can cover the HLA specificity space better. This makes it possible to target most of the known HLA alleles with known specificities using only a few peptides, and may be used in construction of vaccines. Supplementary material is available at .     

Demystifying wine expertise: olfactory threshold,perceptual skill and semantic memory in expert and novice wine judges

We investigated recognition and identification of wine-relevant odours as a function of domain-specific expertise. Eleven wine experts and 11 wine novices participated in tasks measuring olfactory threshold, odour recognition, odour identification, and consistency of odour naming. Twenty-four wine-relevant odorants were sampled orthonasally by each participant in the semantic (identification; consistency of naming) and episodic (recognition) memory tasks. Results showed superior olfactory recognition by expert wine judges, despite their olfactory sensitivity and bias measures being similar to those of novices. Contrary to predictions based on reports of an association between odour memory and semantic processing, wine experts did not perform better than novices on the verbal memory tasks. Further, ability to recognize odours and ability to name odours were not positively correlated, although the novices' data showed a trend in this direction. The results imply that the source of superior odour recognition in wine experts was not enhanced semantic memory and linguistic capabilities for wine-relevant odours. One interpretation of the data is that wine experts were less susceptible than wine novices to verbal overshadowing. When forced to identify the odorants, experts' superior perceptual skills protected them from verbal interference, whereas novices' generated verbal representations of the odours were emphasized at the expense of the odorant itself. This has implications for training in wine-evaluation skills.     

An analysis of anemotactic flight in female moths stimulated by host odour and comparison with the males' response to sex pheromone

ABSTRACT. The flight pattern of mated female navel orangeworm moths, Amyelois transitella (Walker), responding to odour from potential larval hosts is zigzagging upwind flight. However, at times these moths are capable of flying nearly directly upwind towards the odour source (track angles near 0). This response indicates that these females are capable of very accurate anemotactic control of their heading or course angle, since small angular errors in this measure would translate into larger deviations from direct upwind flight. Males of this species exhibit flight patterns similar to those of females, including track angles clustered about 0 when flying upwind to a source of the female-produced pheromone, but under these experimental conditions they flew with a higher average airspeed than the females. When females lose contact with an odour plume they initiate a well-defined programme of cross-wind counterturning or casting, which may normally increase their chances of retrieving contact with that plume when the wind direction shifts. The resultant track angles of females increase significantly by 0.8 s after plume loss, indicating that the female has initiated changes in both her course angle and airspeed. By 1 s after plume loss the females' track angles are no longer unimodally distributed about 0, but are bimodally distributed about -90 and +90. Males responded more rapidly to the loss of a pheromone plume, demonstrating a significant change in track angle 0.4 s after plume loss. Overall, female and male A.transitella exhibited remarkably similar anemotactic flight manoeuvres during upwind flight to odour sources as well as after plume loss.     

Immobilization and clustering of structurally defined oligosaccharides for sugar chips: an improved method for surface plasmon resonance analysis of protein-carbohydrate interactions

Oligosaccharides are increasingly being recognized as important partners in receptor-ligand binding and cellular signaling. Surface plasmon resonance (SPR) is a very powerful tool for the real-time study of the specific interactions between biological molecules. We report here an advanced method for the immobilization of oligosaccharides in clustered structures for SPR and their application to the analysis of heparin-protein interactions. Reductive amination reactions and linker molecules were designed and optimized. Using mono-, tri-, or tetravalent linker compounds, we incorporated synthetic structurally defined disaccharide units of heparin and immobilized them as ligands for SPR. Their binding to an important hemostatic protein, von Willebrand factor (vWf), and its known heparin-binding domain was quantitatively analyzed. These multivalent ligand conjugates exhibited reproducible binding behavior, with consistency of the surface conditions of the SPR chip. This novel technique for oligosaccharide immobilization in SPR studies is accurate, specific, and easily applicable to both synthetic and naturally derived oligosaccharides.     

Heterocyclic nitrogenous pollutants in the environment and their treatment options--an overview

Heterocyclic nitrogenous bases are one of the most important class of compounds containing N as a heteroatom, like pyridine and its derivatives. These compounds are of immense concern from point view of environment since they are known for their toxic and carcinogenic properties, lethal effect on natural biogenic environment and severe odour potential. There is a need to control these compounds from getting discharged into the environment. This paper addresses the different natural/anthropogenic sources which generate these pollutants, their toxicity profile, different physico-chemical treatment methods and especially focuses on biological methods of treatment and combination of these for the efficient removal to achieve a treated effluent quality fit for disposal without causing any damage to the environment.     

Improving odour assessment in LCA—the odour footprint

Purpose

Odour is an important aspect of systems for human and agricultural waste management and many technologies are developed with the sole purpose of reducing odour. Compared with greenhouse gas assessment and the assessment of toxicity, odour assessment has received little attention in the life cycle assessment (LCA) community. This article aims to redress this.

Methods

Firstly, a framework for the assessment of odour impacts in LCA was developed considering the classical LCA framework of emissions, midpoint and endpoint indicators. This suggested that an odour footprint midpoint indicator was worth striving for. An approach to calculating an areal indicator we call “odour footprint”, which considers the odour detection threshold, the diffusion rate and the kinetics of degradation of odourants, was implemented in MATLAB. We demonstrated the use of the characterisation factors we calculated in a case study based on odour removal technology applied to a pig barn.

Results and discussion

We produced a list of 33 linear characterisation factors based on hydrogen sulphide equivalents, analogous to the linear carbon dioxide equivalency factors in use in carbon footprinting, or the dichlorobenzene equivalency factors developed for assessment of toxic impacts in LCA. Like the latter, this odour footprint method does not take local populations and exposure pathway analysis into account—its intent is not to assess regulatory compliance or detailed design. The case study showed that despite the need for materials and energy, large factor reductions in odour footprint and eutrophication potential were achieved at the cost of a smaller factor increase in greenhouse emissions.

Conclusions

The odour footprint method is proposed as an improvement on the established midpoint method for odour assessment in LCA. Unlike it, the method presented here considers the persistence of odourants. Over time, we hope to increase the number of characterised odourants, enabling analysts to perform simple site-generic LCA on systems with odourant emissions.