Preferential Pairing Research Articles

The paired preference test and the ‘No Preference’ option: was Odesky correct?

After experimenting with questionnaires, Odesky had recommendations for eliminating ‘No Preference’ responses in a paired preference test. He concluded that, judges who had chosen the ‘No Preference’ option would, if forced to choose, express preferences in the same pattern as those who had actually expressed a preference. Using questionnaire, food and personal product stimuli, this conclusion was found to be commonly violated. Odesky’s recommendation, to ignore or distribute ‘No Preference’ responses in the same proportion as expressed preferences was sometimes seen to distort data, sometimes not, depending on relative response frequencies and extent of violation of his conclusion regarding forced preferences. When the number of ‘No Preference’ responses is not insignificantly small, to eliminate them, runs the risk of distortion of the overall pattern of preferences.

Hydrophobic core repacking in a coiled-coil dimer via phage display: insights into plasticity and specificity at a protein-protein interface.

The coiled-coil, which consists of two or more interwoven amphiphilic alpha-helices, is formed by sequences that have a characteristic heptad repeat (abcdefg) where a and d are hydrophobic residues. Most efforts to elucidate the origins of coiled-coil pairing selectivity have focused on electrostatic interactions among side chains that flank the core (positions e and g) and on polar side chains that occur occasionally at core positions. We have used phage display to explore another source of coiled-coil specificity: steric matching among nonpolar side chains in the core. We introduced a destabilizing Leu-->Ala mutation into the core of one helix in a known heterodimer and then screened a phage-based library of potential partner helices in search of compensating mutations. We identified a new heterodimer pair (30 residues/helix) that is comparable in stability to the GCN4-p1 homodimer (33 residues/helix). Furthermore, the Leu-->Ala mutant shows specificity for its phage-derived partner over the original partner despite their similar sequences. These results show that a phage-based approach can provide unique insights on coiled-coil pairing preferences that should facilitate both the analysis of natural sequences and the development of specific dimerization motifs that are orthogonal to one another.

A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design

Based on how chromosomes pair at meiosis, the nature of polyploids can be described by bivalent polyploids, multivalent polyploids, and mixed polyploids. In bivalent polyploids, only two chromosomes pair, during which two more similar chromosomes have a higher pairing probability (preferential pairing) than two less similar chromosomes, whereas in multivalent polyploids more than two chromosomes pair at a time, which results in double reduction. Preferential chromosome pairings and double reduction affect the frequencies of gamete formation and, therefore, linkage analysis of polymorphic markers in bivalent and multivalent polyploids, respectively. For mixed polyploids, in which both bivalent and multivalent formations occur simultaneously, linkage analysis is affected by both preferential pairings and double reduction. In this study, we develop a hierarchical maximum likelihood model for discerning gamete genotypes derived from different pairing mechanisms and different formation modes. The first-stage model in the hierarchy is formulated to characterize the relative frequencies of bivalent and multivalent pairing configurations in terms of the preferential pairing factor. The second-stage model is derived to rule out identical gamete genotypes into their different formation modes with relative probabilities determined by the recombination fraction. The first-stage pairing mechanism and second-stage formation mode are integrated to provide the simultaneous maximum likelihood estimates of the preferential pairing factor, the frequency of double reduction, and the recombination fraction, by implementing the EM algorithm. We performed extensive simulation studies to demonstrate the statistical properties of our hierarchical model for linkage analysis in tetraploids. The implications of our model for polyploid linkage mapping are discussed.

Estimating a “consumer rejection threshold” for cork taint in white wine

Cork taint in wine produced by 2,4,6-trichloroanisole (TCA) is characterised by generally unacceptable musty or earthy odours. Estimates of TCA threshold in wine have been reported in the low parts per trillion (ppt) range, although it is not clear at what levels TCA begins to render a wine unacceptable. We conducted two studies to address this question by using a method that combined a paired preference test with a method of constant stimuli threshold procedure. The aim was to determine the point at which wine consumers would begin to reject a wine containing TCA, which we termed the consumer rejection threshold (CRT). Regular white wine consumers (Ss) received pairs of samples of white wine––one spiked with TCA in eight ascending concentrations––and were asked to indicate which of the samples was preferred. Detection thresholds (DT) for TCA in wine were also determined using triangle tests. The CRT and DT were 3.1 and 2.1 ppt, respectively. CRT and DT were significantly positively correlated with one another, and negatively correlated with TCA knowledge. A replication provided a similar CRT value, and suggested that a percentage of consumers are either highly insensitive to TCA or do not find it objectionable. These results suggest that the use of this method may provide a rational basis on which to assess the real impact of TCA in white wine.

A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design

Based on how chromosomes pair at meiosis, the nature of polyploids can be described by bivalent polyploids, multivalent polyploids, and mixed polyploids. In bivalent polyploids, only two chromosomes pair, during which two more similar chromosomes have a higher pairing probability (preferential pairing) than two less similar chromosomes, whereas in multivalent polyploids more than two chromosomes pair at a time, which results in double reduction. Preferential chromosome pairings and double reduction affect the frequencies of gamete formation and, therefore, linkage analysis of polymorphic markers in bivalent and multivalent polyploids, respectively. For mixed polyploids, in which both bivalent and multivalent formations occur simultaneously, linkage analysis is affected by both preferential pairings and double reduction. In this study, we develop a hierarchical maximum likelihood model for discerning gamete genotypes derived from different pairing mechanisms and different formation modes. The first-stage model in the hierarchy is formulated to characterize the relative frequencies of bivalent and multivalent pairing configurations in terms of the preferential pairing factor. The second-stage model is derived to rule out identical gamete genotypes into their different formation modes with relative probabilities determined by the recombination fraction. The first-stage pairing mechanism and second-stage formation mode are integrated to provide the simultaneous maximum likelihood estimates of the preferential pairing factor, the frequency of double reduction, and the recombination fraction, by implementing the EM algorithm. We performed extensive simulation studies to demonstrate the statistical properties of our hierarchical model for linkage analysis in tetraploids. The implications of our model for polyploid linkage mapping are discussed.

Genomic context of paralogous recombination hotspots mediating recurrent NF1 region microdeletion.

Recombination between paralogs that flank the NF1 gene at 17q11.2 typically results in a 1.5-Mb microdeletion that includes NF1 and at least 13 other genes. We show that the principal sequences responsible are two 51-kb blocks with 97.5% sequence identity (NF1REP-P1-51 and NF1REP-M-51). These blocks belong to a complex group of paralogs with three components on 17q11.2 and another on 19p13.13. Breakpoint sequencing of deleted chromosomes from multiple patients revealed two paralogous recombination hot spots within the 51-kb blocks. Lack of sequence similarity between these sites failed to suggest or corroborate any putative cis-acting recombinogenic motifs. However, the NF1 REPs showed relatively high alignment mismatch between recombining paralogs, and we note that the NF1REP hot spots were regions of good alignment bordered by relatively large alignment gaps. Statistical tests for gene conversion detected a single significant tract of perfect match between the NF1REPs that was 700 bp long and coincided with PRS2, the predominant recombination hot spot. Tracts of perfect match occurring by chance may contribute to breakpoint localization, but our result suggests that perfect tracts at recombination hot spots may be a result of gene conversion at sites at which preferential pairing occurs for other, as-yet-unknown reasons.

On the consistency of liking scores: insights from a study including 917 consumers from 10 to 80 years old

Preference for 7 orange juices was recorded monadically. Three of the samples were replicates of the same juice (RJ). The 4 other samples were RJ slightly spiked with either sucrose, or citric acid, or quinine or an orange flavor. Each subject then performed a paired preference test composed of RJ and the modified juice whose score was the furthest from the RJ score. Finally, subjects were asked to choose one among 8 reasons why they preferred that sample. A number of individual statistics were computed in order to compare the consistency of liking scores within session, across ages and between genders. Women were slightly more consistent than men. However, no significant effect of age nor gender was found in the coherence between the first hedonic test and the paired preference test. Moreover, children and seniors found it more difficult than other consumers to identify the reason for their preference.

Genome Analysis of Triploids Using Mathematical Models

Meiotic pairing was analysed in Aegilops variabilis×Secale cereale hybrids. Genome affinity between the U, S, and R genomes was estimated in meiotic metaphase I either by using C-banding or by applying theoretical models. The obtained results were contradictory and opposing: a preferential pairing between the U and the S genomes was detected by C-banding, whereas theoretical models predicted random pairing. This disagreement can be explained as the result of translocations not detected with conventional chromosome staining techniques. Begona Fernandez-Calvin, Departamento de Genetica, ETSI Agronomos, Universidad Politecnica de Madrid, 28040 Madrid, SpainThe interest in the analysis of pairing in interspecific hybrids is not only intended to establish the evolutionary origin of the genomes of a polyploid, but has also practical implications in plant breeding, since it could be used to determine the possibility of introduction of alien genes from one species into another related one. This last aspect gains a special relevance in cereal crops because of their economic importance.

Preferential Pairing of Sex Chromosomes in the Tetraploid Silkworms (Bombyx Mori)

In the oocytes of the silkworm, Bombyx mori, only the sex chromosome bivalent (ZW) can be identified among the 28 bivalents, when we use the females of the sex-limited yellow cocoon (Sy) strain, in which the W carries a long fragment of the second chromosome. Autotetraploid silkwonns were induced from Sy females, in order to investigate whether preferential pairing between Z and Z as well as W and W occurs in the 4n oocytes. Two types of pairing patterns, (ZZ + WW) and (ZW +ZW), were observed in the oocytes, and the ratio of the pairing patterns, (ZZ+WW): (ZW + ZW), was 34:21 in Sy4n (Sy♂× Sy♀), while 16:2 in Syr4n (Sy♂× re9♀). Sex chromosome formulae of the eggs formed by the tetraploid can he confirmed when tetraploid females are crossed with sch males (sex-linked chocolate larva). The triploid off spring from Syr4n females mated with sch males, showed ZW gametes and ZZ gemetes produced in a 22:l ratio, which coincides with the ratio calculated from the pairing pattern ratio, 16:2. The results indicated preferential pairing of Z with Z and of W with W in tetraploid oocytes.

Chromosomal Rearrangement in Autotetraploid Plants of Arabidopsis Thaliana

Recent development of cytogenetic techniques has facilitated significant progress in Arabidopsis thaliana karyotype studies. Double-target FISH with rRNA genes provides makers that allow individual chromosome in the genome to be distinguished. Those studies have revealed that the number and position of rDNA loci is ecotype-specific. Arabidopsis is believed to be a true diploid (x = 5) with numerous ecotypes (accessions) and only a very few natural polyploid populations reported. Few studies were undertaken to induce polyploidy in Arabidopsis, however none of those gave the cytogenetic characteristics of polyploid plants. Our analysis of chromosome pairing of colchicine-induced autotetraploid Arabidopsis (Wilna ecotype) revealed preferential bivalent pairing in PMCs (pollen mother cells). In order to attempt to explain this phenomenon, first of all more detailed cytogenetic studies of autopolyploid plants have been undertaken. The localization of 45S and 5S rDNA loci in the diploid and autotetraploid plants revealed that Wilna ecotypes belongs to the group of Arabidopsis accessions with only two 5S rDNA loci present in a genome. Furthermore, the rearrangement of 45S rDNA locus in autopolyploid, when compared to the diploid plants of the same ecotype, was revealed. These results are interesting also in the context of the recently emphasised role of polyploidy in plant evolution and speciation. Arabidopsis, despite having small chromosomes, is a good system to study chromosome behaviour in relation to diploidization of autopolyploids and to evaluate the degree of chromosomal rearrangements during this process.

Sensory Preference and Discrimination of Wild-caught and Cultured Yellow Perch (Perca flavescens )

: Wild-caught and cultured yellow perch (Perca flavescens) were compared for overall difference and preference. Judges (n= 52) completed 2 replications each of both a paired preference and a triangle test. Results were analyzed using the p-binomial model. Findings indicate that samples were significantly different from each other (P= 0.0001) but there was no significant preference for either sample (P= 0.1167). For both tests, overdispersion, or panelist variability was very low, indicating judges were acting similarly and the binomial model better fit the data. Judges' comments were contradictory and inconsistent, making it impossible to determine the exact nature of the difference.

Utilization of Dried Apple Pomace as a Press Aid to Improve the Quality of Strawberry, Raspberry, and Blueberry Juices

ABSTRACT: We analyzed the effects of press aids on strawberry, raspberry, and blueberry juice quality and evaluated the effectiveness of dried apple pomace as an alternative press aid. Juice yields with apple pomace were similar to the yields from using rice hulls and paper. Triangle difference tests showed that there were differences between the berry juices pressed with conventional press aid to the berry juices pressed with apple pomace press aid, and paired comparison preference tests showed that the berry juices pressed with apple pomace were preferred. Flavor analysis using gas chromatography-olfactometry indicated possible off-flavors being extracted from rice hulls, such as indole and 4-vinylguaical, and from paper, such as (Z)-2-octenal and 2-nonenal, into the berry juices.

Probing Ionic Association on Metal Oxide Clusters by Pulsed Field Gradient NMR Spectroscopy: The Example of Sn12–Oxo Clusters

Pulsed field gradient (1)H NMR spectroscopy has been applied to investigate the association behavior of the Sn(12)-oxo cluster macrocation [(BuSn)(12)O(14)(OH)(6)](2+) with two different and smaller anions, p-toluenesulfonate (PTS(-)) and diphenylphosphinate (Ph(2)PO(2) (-)). By monitoring the translational diffusion coefficients of the various species involved, it is shown that the association depends on the anion involved and on the solvent used. Moreover, the possibility to individually monitor the diffusion characteristics of multiple anionic and cationic species in mixtures, by virtue of resolved (1)H resonances available from each species, allows us to evidence the occurrence of ion exchange in such systems. Thus when [(BuSn)(12)O(14)(OH)(6)](PTS)(2) is mixed with two equivalents of Ph(2)PO(2)NMe(4), PTS(-) is displaced by Ph(2)PO(2) (-), highlighting the greater affinity of the organotin macrocation for the diphenylphosphinate. This example clearly illustrates the potential of pulsed field gradient (1)H NMR spectroscopy in inorganic/organometallic chemistry, to follow preferential ion pairing in multi-ion systems at the level of each individually charged species.

Correct estimation of preferential chromosome pairing in autotetraploids.

In recent work, a statistical model was proposed for the purpose of estimating parameters associated with quantitative trait locus (QTL) mapping and preferential pairing within a polyploidy framework. The statistical model contained several parameters that, when estimated from experimental data, supplied information about QTL, including a preferential pairing factor. Among the results reported were estimates of preferential pairing, many of which indicated high levels of preferential pairing (p = 0.60) that were inconsistent with biological expectations. By using the biological inconsistencies as our motivation, we present a reformulated statistical method for estimating preferential pairing, and use this method to reanalyze the same autotetraploid alfalfa data and to conduct a simulation study. Our results directly contradict the current findings of significant preferential pairing and affirm the traditional view of random chromosome segregation in alfalfa.

A bivalent polyploid model for mapping quantitative trait loci in outcrossing tetraploids.

Two major aspects have made the genetic and genomic study of polyploids extremely difficult. First, increased allelic or nonallelic combinations due to multiple alleles result in complex gene actions and interactions for quantitative trait loci (QTL) in polyploids. Second, meiotic configurations in polyploids undergo a complex biological process including either bivalent or multivalent formation, or both. For bivalent polyploids, different degrees of preferential chromosome pairings may occur during meiosis. In this article, we develop a maximum-likelihood-based model for mapping QTL in tetraploids by considering the quantitative inheritance and meiotic mechanism of bivalent polyploids. This bivalent polyploid model is implemented with the EM algorithm to simultaneously estimate QTL position, QTL effects, and QTL-marker linkage phases by incorporating the impact of a cytological parameter determining bivalent chromosome pairings (the preferential pairing factor). Simulation studies are performed to investigate the performance and robustness of our statistical method for parameter estimation. The implication and extension of the bivalent polyploid model are discussed.

Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC.

According to previous cytological evidence, the hemisexual dog-rose species, Rosa sect. Caninae, transmit only seven chromosomes (derived from seven bivalents) through their pollen grains, whereas egg cells contain 21, 28 or 35 chromosomes (derived from seven bivalents and 14, 21 or 28 univalents) depending on ploidy level. Two sets of reciprocal pairwise interspecific crosses involving the pentaploid species pair R. dumalis and R. rubiginosa, and the pentaploid/tetraploid species pair R. sherardii and R. villosa, were analysed for 13 and 12 microsatellite DNA loci, respectively. Single loci were represented by a maximum of three simultaneously occurring alleles in R. villosa, and four alleles in the other three parental plants. In the experimentally derived offspring, the theoretical maximum of five alleles was found for only one locus in the pentaploid progenies. Microsatellite DNA allele composition was identical with that of the maternal parent in 10 offspring plants, which were probably derived through apomixis. Almost all microsatellite DNA alleles were shared with the maternal parent also in the remaining offspring, but 1-4 alleles shared only with the paternal parent, indicating sexual seed formation. Analysis of quantitative peak differences allowed a tentative estimation of allelic configuration in the individual plants, and suggested that bivalent formation preferentially takes place between chromosomes that consistently share the same microsatellite alleles and therefore appear to be highly homologous. Moreover, alleles that were shared between the species in each cross combination comparatively often appear to reside on the bivalent-forming chromosomes, whereas species-specific alleles instead occur comparatively often on the univalent-forming chromosomes and are therefore inherited through the maternal parent only. Recombination then takes place between very similar genomes also in interspecific crosses, resulting in a reproduction system that is essentially a mixture between apomixis and selfing.

CONSUMERS REPORT PREFERENCES WHEN THEY SHOULD NOT: A CROSS‐CULTURAL STUDY

ABSTRACTIf a chi‐squared analysis were to be performed to determine whether preferences were significant in a paired preference test, the appropriate expected frequencies in the analysis would represent those that would occur should the consumers have no preference. One way of determining these ‘no preference’frequencies, for a particular test situation, would be to note the preference responses obtained when the stimuli were putatively identical. Over 2000 consumers were given paired preference tests in which the stimuli were putatively identical. Response conditions and consumer groups were varied and the proportions of preference and no preference responses were noted. In a preliminary experiment, further research was seen to be justified when for putatively identical stimuli, judges did not exclusively express lack of preference; many expressed a preference for one or other of the stimuli. Further experiments were conducted using a written response condition and putatively identical potato chips (potato crisps) as stimuli. Using a single ‘no preference’option, variation in the placement of this option at either first, second or third place on the response sheet had no significant effect on the response frequencies. The proportion of ‘no preference’responses was approximately 30% in all cases. A previously reported 40‐20‐40 distribution was not always confirmed. The experiment was repeated with Korean consumers; these had fewer ‘no preference’responses. Deriving preferences from hedonic scales, rather than having judges respond to preference options, increased the proportion of ‘no preference’responses, with American judges still having more than Korean judges. Yet there are logical objections to extracting preference data from hedonic scales. Increasing the number of ‘no preference’options to two or three, had the effect of increasing the number of ‘no preference’responses up to as much as approximately 60%. Extending the results to Koreans, using two ‘no preference’options, it was seen that only the judges in an anonymous response condition had significantly fewer ‘no preference’responses than Americans. The use of these response frequencies as expected frequencies in chi squared analyses was illustrated, after adjustments for counterbalancing.

Exploring the sequence patterns in the alpha-helices of proteins.

This paper reports an extensive sequence analysis of the alpha-helices of proteins. alpha-Helices were extracted from the Protein Data Bank (PDB) and were divided into groups according to their sizes. It was found that some amino acids had differential propensity values for adopting helical conformation in short, medium and long alpha-helices. Pro and Trp had a significantly higher propensity for helical conformation in short helices than in medium and long helices. Trp was the strongest helix conformer in short helices. Sequence patterns favoring helical conformation were derived from a neighbor-dependent sequence analysis of proteins, which calculated the effect of neighboring amino acid type on the propensity of residues for adopting a particular secondary structure in proteins. This method produced an enhanced statistical significance scale that allowed us to explore the positional preference of amino acids for alpha-helical conformations. It was shown that the amino acid pair preference for alpha-helix had a unique pattern and this pattern was not always predictable by assuming proportional contributions from the individual propensity values of the amino acids. Our analysis also yielded a series of amino acid dyads that showed preference for alpha-helix conformation. The data presented in this study, along with our previous study on loop sequences of proteins, should prove useful for developing potential 'codes' for recognizing sequence patterns that are favorable for specific secondary structural elements in proteins.

Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare(L.) Link syn.Cenchrus ciliarisL.) as revealed by genome mapping

Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.

Chromosome Homology in Tetraploid Southern Highbush × Vaccinium elliottii Hybrids

A yellow-leaf seedling marker, r, was used to determine if there was preferential chromosome pairing in a group of tetraploid southern highbush blueberry hybrids. Plants with four copies of r (no copies of R) fail to develop anthocyanins, and cotyledons, hypocotyls, leaves, stems, and other vegetative tissues have a bright yellow-green color. In the hybrids that were studied, two genomes were from the diploid wild species, V. elliottii Chapman, and both carried the recessive marker r. The other two genomes were from southern highbush cultivars and both carried the dominant wildtype allele, R. When RRrr hybrids were intercrossed or crossed to rrrr yellow-leaf plants, the number of yellowleaf rrrr seedlings obtained usually equalled or exceeded the number predicted from nonpreferential chromosome pairing. Since rr gametes can only be produced by RRrr plants when R and r chromosomes pair at Meiosis I, there was no evidence that the chromosomes derived from V. elliottii were pairing at a higher-than-random rate.