Efficiency clustering for low-density microarrays and its application to QPCR

Background  

Pathway-targeted or low-density arrays are used more and more frequently in biomedical research, particularly those arrays that are based on quantitative real-time PCR. Typical QPCR arrays contain 96-1024 primer pairs or probes, and they bring with it the promise of being able to reliably measure differences in target levels without the need to establish absolute standard curves for each and every target. To achieve reliable quantification all primer pairs or array probes must perform with the same efficiency.     

Visual sensitivity in search tasks depends on the response requirement

This paper reports a comparison between two tasks of visual search. Two observers carried out, in separate blocks, a saccade-to-target task and a manual-target-detection task. The displays, which were identical for the two tasks, consisted of a ring of eight equally spaced Gabor patches. The target could be defined by a difference from the distractors along four possible dimensions: orientation, spatial frequency, contrast or size. These four dimensions were used as variables in separate experiments. In each experiment, performance was measured over an extensive range of values of the particular dimension. Thresholds were thus obtained for the saccade and the manual response tasks. The nature of the response was found to modify the relative visual sensitivity. For orientation differences, manual response performance was better than saccade-to-target performance. The reverse was true for spatial frequency and contrast differences, where saccade-to-target performance was better than manual response performance. We conclude that saccade-selection in a search task draws on different visual information from that used for manual responding in the equivalent task. The two tasks thus differ in more than the different response systems used: the results suggest the action of different underlying neural visual mechanisms as well as different neural motor mechanisms.     

Comparative analysis of the zeta-crystallin/quinone reductase gene in guinea pig and mouse

zeta-Crystallin is a novel nicotinamide adenine dinucleotide phosphate:quinone reductase, present at enzymatic levels in various tissues of different species, which is highly expressed in the lens of some hystricomorph rodents and camelids. We report here the complementary DNA (cDNA) cloning of zeta-crystallin from liver libraries in guinea pig (Cavia porcellus), where zeta-crystallin is highly expressed in the lens, and in the laboratory mouse (Mus musculus), where expression in the lens occurs only at enzymatic levels. A 5' untranslated sequence different from the one previously reported for the guinea pig lens cDNA was found in these clones. We also report the isolation of genomic clones including the complete guinea pig zeta-crystallin gene and the 5' region of this gene in mouse. These results show the presence of two promoters in the guinea pig zeta-crystallin gene, one responsible for expression at enzymatic levels and the other responsible for the high expression in the lens. The guinea pig lens promoter is not present in the mouse gene. This is the first example in which the recruitment of an enzyme as a lens crystallin can be explained by the acquisition of an alternative lens- specific promoter.      

An exact form of the breeder's equation for the evolution of a quantitative trait under natural selection

Starting with the Price equation, I show that the total evolutionary change in mean phenotype that occurs in the presence of fitness variation can be partitioned exactly into five components representing logically distinct processes. One component is the linear response to selection, as represented by the breeder's equation of quantitative genetics, but with heritability defined as the linear regression coefficient of mean offspring phenotype on parent phenotype. The other components are identified as constitutive transmission bias, two types of induced transmission bias, and a spurious response to selection caused by a covariance between parental fitness and offspring phenotype that cannot be predicted from parental phenotypes. The partitioning can be accomplished in two ways, one with heritability measured before (in the absence of) selection, and the other with heritability measured after (in the presence of) selection. Measuring heritability after selection, though unconventional, yields a representation for the linear response to selection that is most consistent with Darwinian evolution by natural selection because the response to selection is determined by the reproductive features of the selected group, not of the parent population as a whole. The analysis of an explicitly Mendelian model shows that the relative contributions of the five terms to the total evolutionary change depends on the level of organization (gene, individual, or mated pair) at which the parent population is divided into phenotypes, with each frame of reference providing unique insight. It is shown that all five components of phenotypic evolution will generally have nonzero values as a result of various combinations of the normal features of Mendelian populations, including biparental sex, allelic dominance, inbreeding, epistasis, linkage disequilibrium, and environmental covariances between traits. Additive genetic variance can be a poor predictor of the adaptive response to selection in these models. The narrow-sense heritability sigma2A/sigma2P should be viewed as an approximation to the offspring-parent linear regression rather than the other way around.     

Prolonged in vivo residence times of antibody fragments associated with albumin

Antibody fragments can be expressed at a high level in microbial systems, but they may have limited therapeutic value because they are rapidly eliminated from the body. We demonstrate here that site-specific conjugation or binding of bacterially derived Fab' to the long-lived protein serum albumin allows full retention of the antibody's binding characteristics while imparting the albumin's longevity in vivo. In rats the area under the curve for Fab' conjugated to rat serum albumin was 17-fold greater than for the control of Fab' conjugated to cysteine. Again, a bispecific F(ab')(2) with specificity for rat serum albumin showed an area under the curve about 8-fold greater than did a F(ab')(2) without specificity to albumin. Genetic fusions of scFv to albumin were similarly long-lived and could be expressed in yeast to provide the basis of a cost-effective production system.     

Pollination limitation to reproductive success in the Missouri evening primrose, Oenothera macrocarpa (Onagraceae)

Habitat fragmentation may result in plant populations that are less attractive to pollinators and thus susceptible to reduced reproductive output due to pollination limitation. Pollination limitation was investigated in three Missouri populations of Oenothera macrocarpa, a hawk-moth-pollinated, perennial herb. The populations represented extremes in size and habitat quality. Following supplemental pollination, mean fertilization success (proportion of ovules fertilized) across populations increased from 24.3 to 44.8% and mean seed set (proportion of ovules that matured into seed) increased from 14.7 to 27.9%. These increases were statistically significant in two of the three populations. Failure to achieve 100% fertilization and seed set following supplementation indicates that other factors, in addition to pollination, were limiting to female reproductive success. Fruit set was pollination limited in only one population. Fruits matured with as few as one seed, suggesting that fruit set was not resource limited. The degree of pollination limitation was greatest in the most disturbed population. The population located in the highest-quality habitat was not significantly pollination limited. This suggests that pollination limitation is occurring, at least in part, because of reduced pollinator activity in degraded habitats.     

INTRACELLULAR BACTERIA IN GONYOSTOMUM SEMEN (CHLOROMONADOPHYCEAE)1,2

Intracellular bacteria occur in ca. 5–10% of Gonyostomum semen Diesing cells. Bacteria are rod-shaped and are present in localized regions of the cytoplasm. This is the first report of intracellular bacteria in the Chloromonadophyceae.