DETECTION AND INTERPRETATION OF VARIATION WITHIN AND BETWEEN ASSESSORS IN SENSORY PROFILING

In this paper we discuss methods that can be used to evaluate the performance of sensory panels. In particular we concentrate on detection of variation within and among panelists. A systematic presentation of some simple, graphically oriented tools will be given. Interpretation aspects of the tools will be emphasized. The methods will be illustrated by computations from a sensory experiment based on 4 sausage products. The example demonstrates how the tools can be used to evaluate the reproducibility of the assessors and also how they can be used to detect different types of individual differences among the assessors.     

Individual differences in behavioural plasticities

Interest in individual differences in animal behavioural plasticities has surged in recent years, but research in this area has been hampered by semantic confusion as different investigators use the same terms (e.g. plasticity, flexibility, responsiveness) to refer to different phenomena. The first goal of this review is to suggest a framework for categorizing the many different types of behavioural plasticities, describe examples of each, and indicate why using reversibility as a criterion for categorizing behavioural plasticities is problematic. This framework is then used to address a number of timely questions about individual differences in behavioural plasticities. One set of questions concerns the experimental designs that can be used to study individual differences in various types of behavioural plasticities. Although within‐individual designs are the default option for empirical studies of many types of behavioural plasticities, in some situations (e.g. when experience at an early age affects the behaviour expressed at subsequent ages), ‘replicate individual’ designs can provide useful insights into individual differences in behavioural plasticities. To date, researchers using within‐individual and replicate individual designs have documented individual differences in all of the major categories of behavioural plasticities described herein. Another important question is whether and how different types of behavioural plasticities are related to one another. Currently there is empirical evidence that many behavioural plasticities [e.g. contextual plasticity, learning rates, IIV (intra‐individual variability), endogenous plasticities, ontogenetic plasticities) can themselves vary as a function of experiences earlier in life, that is, many types of behavioural plasticity are themselves developmentally plastic. These findings support the assumption that differences among individuals in prior experiences may contribute to individual differences in behavioural plasticities observed at a given age. Several authors have predicted correlations across individuals between different types of behavioural plasticities, i.e. that some individuals will be generally more plastic than others. However, empirical support for most of these predictions, including indirect evidence from studies of relationships between personality traits and plasticities, is currently sparse and equivocal. The final section of this review suggests how an appreciation of the similarities and differences between different types of behavioural plasticities may help theoreticians formulate testable models to explain the evolution of individual differences in behavioural plasticities and the evolutionary and ecological consequences of individual differences in behavioural plasticities.     

FREE-CHOICE PROFILING OF MILKS AND OTHER PRODUCTS PREPARED WITH MILKS OF DIFFERENT FAT CONTENTS

Free-choice profiling was used to develop a sensory profile of milks of different fat content and a range of food products prepared from them. The products were cornflakes, flavored milk, instant coffee, oat cereal, savory sauce, tea, and whipped dessert. The aim of the work was to investigate whether or not sensory differences brought about by using milk with a different fat content are noticeable in the context of use, and, if so how the differences can best be described. The milks of different fat content, the flavored milk and the cornflakes, savory sauce, and tea to which milk was added were significantly different from each other but the instant coffee, oat cereal, and whipped desserts were not. The differences found between the samples of different fat content were most often described with mouthfeel terms pertaining to viscosity, i.e., “thin/watery,”“buttery/fatty/ greasy/oily,”“coating/clinging,” and “creamy/rich.”     

A map of pheromone receptor activation in the mammalian brain

In mammals, the detection of pheromones is mediated by the vomeronasal system. We have employed gene targeting to visualize the pattern of projections of axons from vomeronasal sensory neurons in the accessory olfactory bulb. Neurons expressing a specific receptor project to multiple glomeruli that reside within spatially restricted domains. The formation of this sensory map in the accessory olfactory bulb and the survival of vomeronasal organ sensory neurons require the expression of pheromone receptors. In addition, we observe individual glomeruli in the accessory olfactory bulb that receive input from more than one type of sensory neuron. These observations indicate that the organization of the vomeronasal sensory afferents is dramatically different from that of the main olfactory system, and these differences have important implications for the logic of olfactory coding in the vomeronasal organ.     

Application of cDNA arrays to monitor mRNA profiles in single preimplantation mouse embryos

Array technology is a widely used tool for gene expression profiling in various biological systems. However, the application of this method to mammalian preimplantation embryos is limited by the small amount of mRNA that can be extracted from a single embryo, which is not sufficient for array analysis. Here we report a protocolfor the rapid global amplification of embryonic mRNA that permits the generation of expression profiles from single murine blastocysts. The approach combines global PCR and 77 RNA polymerase amplification and allows the preparation of labeled, amplified RNA for array hybridization from single murine blastocysts containing approximately 1.5 pg mRNA in less than 12 h. We demonstrate that this amplification procedure is highly reproducible and does not bias original relative mRNA levels. Signal patterns from various embryonic stages of murine development revealed marked differences in mRNA expression that were in accordance with previously published data. We found genes known to be involved in embryonic apoptosis expressed at different levels in individual murine day 3.5 blastocysts. This technique can thus be used to assess embryonic viability and investigate molecular mechanisms of embryonic development.     

Genome-wide mRNA profiling: impact on compound evaluation and target identification in anti-bacterial research

Array-based mRNA profiling offers a variety of opportunities to address different issues relevant to anti-bacterial research. The technique can be used to investigate the mode of action of antibiotics, bacterial resistance mechanisms and virulence factors, and to identify novel targets. This review discusses recent developments of this highly innovative field of technology with respect to technical requirements and experimental design. Several applications are described in which bacterial mRNA profiling has already been successfully performed, illustrating how the generation of large numbers of diverse datasets can be used as a powerful tool for evaluating anti-bacterial compounds and consequent counteracting mechanisms in the cell.     

Transforming bottom-up topographic representations with top-down signals in the brain

There has been considerable success in allocating function to the different parts of the brain. We also know much about brain organisation in different regions of the brain and how different brain regions connect to one another. One of the most important next steps for modern neuroscience is to work out how different areas of the brain interact with one another. In particular we need to know how sensory regions communicate with association areas and vice versa. This article explores how top-down signals originating from association areas may be used to process and transform bottom-up representations originating from sensory areas of the brain. Simple models of networks containing topographically organised ensembles of neurons used to integrate and process information are described. The different models can be used to process information in a variety of different ways that could be used as the starting point for a variety of cognitive operations, in particular the extraction of abstract information from sensory representations.     

Transforming bottom-up topographic representations with top-down signals in the brain

There has been considerable success in allocating function to the different parts of the brain. We also know much about brain organisation in different regions of the brain and how different brain regions connect to one another. One of the most important next steps for modern neuroscience is to work out how different areas of the brain interact with one another. In particular we need to know how sensory regions communicate with association areas and vice versa. This article explores how top-down signals originating from association areas may be used to process and transform bottom-up representations originating from sensory areas of the brain. Simple models of networks containing topographically organised ensembles of neurons used to integrate and process information are described. The different models can be used to process information in a variety of different ways that could be used as the starting point for a variety of cognitive operations, in particular the extraction of abstract information from sensory representations.     

Identification of thermosensory and olfactory neuron-specific genes via expression profiling of single neuron types

Most C. elegans sensory neuron types consist of a single bilateral pair of neurons, and respond to a unique set of sensory stimuli. Although genes required for the development and function of individual sensory neuron types have been identified in forward genetic screens, these approaches are unlikely to identify genes that when mutated result in subtle or pleiotropic phenotypes. Here, we describe a complementary approach to identify sensory neuron type-specific genes via microarray analysis using RNA from sorted AWB olfactory and AFD thermosensory neurons. The expression patterns of subsets of these genes were further verified in vivo. Genes identified by this analysis encode 7-transmembrane receptors, kinases, and nuclear factors including dac-1, which encodes a homolog of the highly conserved Dachshund protein. dac-1 is expressed in a subset of sensory neurons including the AFD neurons and is regulated by the TTX-1 OTX homeodomain protein. On thermal gradients, dac-1 mutants fail to suppress a cryophilic drive but continue to track isotherms at the cultivation temperature, representing the first genetic separation of these AFD-mediated behaviors. Expression profiling of single neuron types provides a rapid, powerful, and unbiased method for identifying neuron-specific genes whose functions can then be investigated in vivo.     

Ontogenetic and interspecific organ weight allometry in Old World monkeys

The importance of allometry as an analytic tool is well recognized in the literature of primate morphology. However, a number of recent studies have illustrated how interpretive difficulties can arise when researchers confound different types of allometric data. Such confusion is due less to carelessness than to uncertainty about how different types of allometry are related. The present study examines the relationship between two types—ontogenetic and interspecific allometry–in the case of organ weight scaling in six species of Old World monkeys. Accepting the interpretation of interspecific allometry as a reflection of functional scaling constraints, the results of this analysis indicate how ontogenetic patterns have been modified in different-sized species to maintain compliance with these constraints. Specifically, for the heart and lungs it appears that vertical transpositions of individual species' ontogenies are dictated by isometric interspecific allometry, while in the case of the kidneys and liver, the relation of negative allometry across species entails alteration of the relative growth coefficients of the individual species. While these conclusions can at present only be applied to organ weight scaling, the approach of examining interspecific patterns in light of developmental differences between species should prove very helpful in our efforts to understand the phenomena of size and scaling.     

Expression profiling of single cells using 3 prime end amplification (TPEA) PCR.

The ability to relate the physiological status of individual cells to the complement of genes they express is limited by current methodological approaches for performing these analyses. We report here the development of a robust and reproducible method for amplifying 3' sequences of mRNA derived from single cells and demonstrate that the amplified cDNA, derived from individual human lymphoblastoma cells, can be used for the expression profiling of up to 40 different genes per cell. In addition, we show that 3 prime end amplification (TPEA) PCR can be used to enable the detection of both high and low abundance mRNA species in samples harvested from live neurons in rat brain slices. This procedure will facilitate the study of complex tissue function at the cellular level.     

RELATIONSHIP BETWEEN ORAL AND NONORAL EVALUATION OF TEXTURE IN ACID MILK GELS

The objectives of this study were to compare oral and nonoral sensory evaluation for discrimination of texture of acid skim milk gels and to establish whether nonoral attributes could be correlated to the oral perception of texture. Trained panelists (n = 13) identified 11 nonoral (visual and in-hand) and 4 oral attributes during a preliminary profiling session that could be used to discriminate textures (P < 0.001) in a range of acid gels prepared with different solid contents and heat treatment of the milks. Both methods of sensory appraisal were found to discriminate between gels. Correlation analysis showed high interrelationship between individual oral and nonoral attributes (P < 0.01). Principal component analysis revealed that all 4 oral attributes could be combined into one single attribute (PC1), with equal relative importance of the individual attributes in explaining the variance in the oral sensory data set. Canonical correlation analysis revealed good correlation between the oral and nonoral set of attributes (R² > 87.5%).     

Laser capture microdissection of cells from plant tissues

Laser capture microdissection (LCM) is a technique by which individual cells can be harvested from tissue sections while they are viewed under the microscope, by tacking selected cells to an adhesive film with a laser beam. Harvested cells can provide DNA, RNA, and protein for the profiling of genomic characteristics, gene expression, and protein spectra from individual cell types. We have optimized LCM for a variety of plant tissues and species, permitting the harvesting of cells from paraffin sections that maintain histological detail. We show that RNA can be extracted from LCM-harvested plant cells in amount and quality that are sufficient for the comparison of RNAs among individual cell types. The linear amplification of LCM-captured RNA should permit the expression profiling of plant cell types.     

Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types

Using environmental DNA (eDNA) to assess the distribution of micro‐ and macroorganisms is becoming increasingly popular. However, the comparability and reliability of these studies is not well understood as we lack evidence on how different DNA extraction methods affect the detection of different organisms, and how this varies among sample types. Our aim was to quantify biases associated with six DNA extraction methods and identify one which is optimal for eDNA research targeting multiple organisms and sample types. We assessed each methods’ ability to simultaneously extract bacterial, fungal, plant, animal and fish DNA from soil, leaf litter, stream water, stream sediment, stream biofilm and kick‐net samples, as well as from mock communities. Method choice affected alpha‐diversity for several combinations of taxon and sample type, with the majority of the differences occurring in the bacterial communities. While a single method performed optimally for the extraction of DNA from bacterial, fungal and plant mock communities, different methods performed best for invertebrate and fish mock communities. The consistency of methods, as measured by the similarity of community compositions resulting from replicate extractions, varied and was lowest for the animal communities. Collectively, these data provide the first comprehensive assessment of the biases associated with DNA extraction for both different sample types and taxa types, allowing us to identify DNeasy PowerSoil as a universal DNA extraction method. The adoption of standardized approaches for eDNA extraction will ensure that results can be more reliably compared, and biases quantified, thereby advancing eDNA as an ecological research tool.     

EVALUATION AND APPLICATIONS OF ODOR PROFILING

An odor profiling procedure was developed based on the ASTM odor profiling method. This modified procedure involved using approximately twenty panelists. Panel sessions and data collection were controlled by computer. The results obtained by this panel compared favorably to results obtained by the ASTM panel for which 150 panelists evaluated each compound, indicating that a small panel can be used to produce replicable results. Statistical methods of finding similarities and dissimilarities among compounds using profile data are discussed and compared to results from a multidimensional scaling (MDS) study in which degrees of differences among compounds were judged directly. These results indicate that profile data can be used to define and map the degree of similarity/dissimilarity among compounds, as well as to define the sensory dimensions on which these compounds differ. The use of factor analysis to study the underlying sensory dimensions of the odor space is also discussed. It is hoped that this type of research will lead to a better understanding of the underlying dimensions used to describe odorants.     

Sensory Perception: Lessons from Synesthesia: Using Synesthesia to Inform the Understanding of Sensory Perception

Synesthesia, the conscious, idiosyncratic, repeatable, and involuntary sensation of one sensory modality in response to another, is a condition that has puzzled both researchers and philosophers for centuries. Much time has been spent proving the condition’s existence as well as investigating its etiology, but what can be learned from synesthesia remains a poorly discussed topic. Here, synaesthesia is presented as a possible answer rather than a question to the current gaps in our understanding of sensory perception. By first appreciating the similarities between normal sensory perception and synesthesia, one can use what is known about synaesthesia, from behavioral and imaging studies, to inform our understanding of “normal” sensory perception. In particular, in considering synesthesia, one can better understand how and where the different sensory modalities interact in the brain, how different sensory modalities can interact without confusion ― the binding problem ― as well as how sensory perception develops.     

Processing of tactile information in neuronal networks controlling leg movements of the Locust

The successful, coordinated, posture and locomotion of any animal requires a precise and continuous adjustment of limb movements by sensory feedback from extero- and proprioceptors associated with the legs. We here review the recent advances in our understanding of how specific local adjustments of the hind legs of the desert locust, Schistocerca gregaria, are made in response to tactile signals from two different classes of exteroceptor on a leg. The aim is to understand particular features of the organization of neuronal networks and how different types of constituent interneurones contribute to the processing of sensory signals. This information can then be used to define the design principles that govern the organization of sensory-motor networks.     

Essential role for gene profiling analysis in the authentication of human cell lines

Cross-contamination between cultured cell lines can result in the generation of erroneous scientific data. Hence, it is very important to eliminate cell lines that are of an origin different from that being claimed. Inter-species contamination can be detected by various established methods, such as karyotype and isozyme analyses. However, it has been impossible to detect intraspecies cross-contamination prior to the development of technology to detect differences between cell lines at the molecular level. Recently, profiling of short tandem repeat (STR) polymorphisms has been established as a method for the analyses of gene polymorphism. Gene profiling by STR polymorphism (STR profiling) is a simple and reliable method to identify individual cell lines. Each human cell line currently provided by the Cell Engineering Division of the RIKEN BioResource Center was analyzed by STR profiling to authenticate its identity. We found that more than 10 human cell lines out of approximately 400 were in fact identical to a different cell line deposited in the collection, and therefore had been misidentified. We conclude that STR profiling is a useful and powerful method for eliminating cell lines that have been misidentified by cross-contamination or by other causes. Hence, STR profiling of human cell lines used in published research will likely be a prerequisite for publication in the future, so that the problem of misidentification of cell lines can be eliminated.