Quantifying agonist activity at G protein-coupled receptors

When an agonist activates a population of G protein-coupled receptors (GPCRs), it elicits a signaling pathway that culminates in the response of the cell or tissue. This process can be analyzed at the level of a single receptor, a population of receptors, or a downstream response. Here we describe how to analyze the downstream response to obtain an estimate of the agonist affinity constant for the active state of single receptors. Receptors behave as quantal switches that alternate between active and inactive states (Figure 1). The active state interacts with specific G proteins or other signaling partners. In the absence of ligands, the inactive state predominates. The binding of agonist increases the probability that the receptor will switch into the active state because its affinity constant for the active state (K(b)) is much greater than that for the inactive state (K(a)). The summation of the random outputs of all of the receptors in the population yields a constant level of receptor activation in time. The reciprocal of the concentration of agonist eliciting half-maximal receptor activation is equivalent to the observed affinity constant (K(obs)), and the fraction of agonist-receptor complexes in the active state is defined as efficacy (ε) (Figure 2). Methods for analyzing the downstream responses of GPCRs have been developed that enable the estimation of the K(obs) and relative efficacy of an agonist. In this report, we show how to modify this analysis to estimate the agonist K(b) value relative to that of another agonist. For assays that exhibit constitutive activity, we show how to estimate K(b) in absolute units of M(-1). Our method of analyzing agonist concentration-response curves consists of global nonlinear regression using the operational model. We describe a procedure using the software application, Prism (GraphPad Software, Inc., San Diego, CA). The analysis yields an estimate of the product of K(obs) and a parameter proportional to efficacy (τ). The estimate of τK(obs) of one agonist, divided by that of another, is a relative measure of K(b) (RA(i)). For any receptor exhibiting constitutive activity, it is possible to estimate a parameter proportional to the efficacy of the free receptor complex (τ(sys)). In this case, the K(b) value of an agonist is equivalent to τK(obs)/τ(sys). Our method is useful for determining the selectivity of an agonist for receptor subtypes and for quantifying agonist-receptor signaling through different G proteins.     

性别与自身免疫性疾病

自身免疫性疾病在人群中感染率5-10%,具有明显的性别差异,女性患者显著高于男性,具体机制仍未研究清楚。研究发现,除了机体自身的遗传易感体质外,雌激素,微嵌合体和性染色体都与自身免疫性疾病发病有关。     

What Users Want and May Need

An increasing number of software tools support designers and other decision makers in making design, production, and purchasing decisions. Some of these tools provide quantitative information on environmental impacts such as climate change, human toxicity, or resource use during the life cycle of these products. Very little is known, however, about how these tools are actually used, what kind of modeling and presentation approaches users really want, or whether the information provided is likely to be used the way the developers intended. A survey of users of one such software tool revealed that although users want more transparency, about half also want an easy-to-use tool and would accept built-in assumptions; that most users prefer modeling of environmental impacts beyond the stressor level, and the largest group of respondents wants results simultaneously on the stressor, impact potential, and damage level; and that although many users look for aggregated information on impacts and costs, a majority do not trust that such an aggregation is valid or believe that there are tradeoffs among impacts. Further, our results show that the temporal and spatial scales of single impact categories explain only about 6% of the variation in the weights between impact categories set by respondents if the weights are set first. If the weights are set after respondents specify temporal and spatial scales, however, these scales explain about 24% of the variation. These results not only help method and tool developers to reconsider some previous assumptions, but also suggest a number of research questions that may need to be addressed in a more focused investigation.     

Measurements on ground or sectioned otoliths: possibilities of bias

Back-calculation usually requires measurements of growth marks revealed on otoliths by specific preparations. The standardization of the grinding (or sectioning) plane is necessary, but difficult, especially along the antero-posterior axis. In order to show the importance of the grinding plane, tetracycline labelling of eel otoliths ( Anguilla anguilla L.) has been used. This marking has a calcio-traumatic effect on otoliths, which can be revealed with staining techniques. Unless the grinding plane is incorrect, the tetracycline labelling and the staining of the ground surface are then superposed.     

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila

Natural selection influences synonymous mutations and synonymouscodon usage in many eukaryotes to improve the efficiency oftranslation in highly expressed genes. Recent studies of genecomposition in eukaryotes have shown that codon usage also variesindependently of expression levels, both among genes and atthe intragenic level. Here, we investigate rates of evolution(Ks) and intensity of selection (_s) on synonymous mutationsin two groups of genes that differ greatly in the length oftheir exons, but with equivalent levels of gene expression andrates of crossing-over in Drosophila melanogaster. We estimate_s using patterns of divergence and polymorphism in 50 Drosophilagenes (100 kb of coding sequence) to take into account possiblevariation in mutation trends across the genome, among genesor among codons. We show that genes with long exons exhibithigher Ks and reduced _s compared to genes with short exons.We also show that Ks and _s vary significantly across long exons,with higher Ks and reduced _s in the central region comparedto flanking regions of the same exons, hence indicating thatthe difference between genes with short and long exons can bemostly attributed to the central region of these long exons.Although amino acid composition can also play a significantrole when estimating Ks and _s, our analyses show that the differencesin Ks and _s between genes with short and long exons and acrosslong exons cannot be explained by differences in protein composition.All these results are consistent with the Interference Selection(IS) model that proposes that the Hill-Robertson (HR) effectcaused by many weakly selected mutations has detectable evolutionaryconsequences at the intragenic level in genomes with recombination.Under the IS model, exon size and exon-intron structure influencethe effectiveness of selection, with long exons showing reducedeffectiveness of selection when compared to small exons andthe central region of long exons showing reduced intensity ofselection compared to flanking coding regions. Finally, ourresults further stress the need to consider selection on synonymousmutations and its variation—among and across genes andexons—in studies of protein evolution.     

Influence of Observer Presence on Pacific Damsel Bug Behavior: Who is Watching Whom?

When direct observations are used to study animal behavior the presence of the observer may alter the animal and hence influence the data being collected, yet few studies have quantified this effect. We conducted direct observation studies in the glasshouse to assess the relative influence of observer presence on the behavior of Pacific damsel bugs, Nabis kinbergii, a potentially important predator of crop pests. Comparisons of predator activity, predator distribution, prey (Helicoverpa armigera) mortality and prey distribution between frequently observed and minimally observed treatments, during diurnal and nocturnal observation sessions showed that the frequency of observer presence had no apparent impact on Pacific damsel bug behavior. This is the first documented test of the impact of observer presence in an insect system. To place our results in context, we reviewed 15 papers on the influence of observer presence in a range of animals. We established that just over half of these papers found evidence for an effect. Nevertheless, direct observations should be useful in further studies of Pacific damsel bug behavior, and researchers using direct observations to study the behavior of other animals should be cognizant of observer effects during design and interpretation of their study.     

Mortality costs of sexual selection and parental care in natural populations of birds

Abstract Is the cost of reproduction different between males and females? On the one hand, males typically compete intensely for mates, thus sexual selection theory predicts higher cost of reproduction for males in species with intense male‐male competition. On the other hand, care provisioning such as incubating the eggs and raising young may also be costly, thus parental care theory predicts higher mortality for the care‐giving sex, which is often the female. We tested both hypotheses of reproductive costs using phylogenetic comparative analyses of sex‐specific adult mortality rates of 194 bird species across 41 families. First, we show that evolutionary increases in male‐male competition were associated with male‐biased mortalities. This relationship is consistent between two measures of mating competition: social mating system and testis size. Second, as predicted by the parental cost hypothesis, females have significantly higher adult mortalities (mean ± SE, 0.364 ± 0.01) than males (0.328 ± 0.01). However, the mortality cost of parental care was only detectable in males, when the influence of mating competition was statistically controlled. Taken together, our results challenge the traditional explanation of female‐biased avian mortalities, because evolutionary changes in female care were unrelated to changes in mortality bias. The interspecific variation in avian mortality bias, as we show here, is driven by males, specifically via the costs of both mating competition and parental care. We also discuss alternative hypotheses for why most birds exhibit female‐biased mortalities, whereas in mammals male‐biased mortalities predominate.     

Nonparametric estimation of ROC curves in the absence of a gold standard

In the evaluation of diagnostic accuracy of tests, a gold standard on the disease status is required. However, in many complex diseases, it is impossible or unethical to obtain such a gold standard. If an imperfect standard is used, the estimated accuracy of the tests would be biased. This type of bias is called imperfect gold standard bias. In this article we develop a nonparametric maximum likelihood method for estimating ROC curves and their areas of ordinal-scale tests in the absence of a gold standard. Our simulation study shows that the proposed estimators for the ROC curve areas have good finite-sample properties in terms of bias and mean squared error. Further simulation studies show that our nonparametric approach is comparable to the binormal parametric method, and is easier to implement. Finally, we illustrate the application of the proposed method in a real clinical study on assessing the accuracy of seven specific pathologists in detecting carcinoma in situ of the uterine cervix.     

Predicting Species Response to Disturbance from Size Class Distributions of Adults and Saplings in a Jamaican Tropical Dry Forest

The diversity of tropical dry forests is poorly described and their regeneration ecology not well understood, however they are under severe threat of conversion and degradation. The Hellshire Hills constitute a dry limestone forest reserve on the south coast of Jamaica that is of high conservation value. In order to describe the structure and composition of this forest and assess the extent to which the population structures of its tree species do characterize their regeneration ecologies, pre-disturbance structure, floristics and seedling populations were compared with post-disturbance species responses in twelve 15 m × 15 m permanent sample plots which were laid out in a blocked design in April 1998, giving a total sample area of 0.27 ha. These plots were subjected to disturbance in April 1999 (cutting) with each of four blocks being assigned with two randomly allocated treatment plots (partially and clear cut) and one control plot (uncut). A total of 1278 trees (≥2 cm DBH) and 7863 seedlings and saplings (0–2 mm and 2–20 mm root collar diameter (RCD) respectively), comprising 60 and 52 species, respectively, were sampled in the plots prior to disturbance. The species-area curve for trees reached a maximum at 0.20 ha, and abundance was widely distributed amongst the species (26 had importance values greater than 1%); four species were notably codominant (with importance values between 7 and 8%). The forest stand structure had a reverse J-shaped curve for tree and for seedling/sapling size-class distributions, which indicated that the forest as a whole was probably regenerating adequately. From an analysis based on adult and sapling size-class distributions (SCDs), 21 species with 15 or more individuals were classified into 3 groups. Many of the species (15 of the 21), had flat adult SCDs that deviate from the whole-community reverse J-shaped SCD. However, sapling SCDs for 6 of the 15 species were strongly positive indicating the potential for their populations to be sustained by recruitment from the saplings present. No general association was found between these SCD species groupings and the actual ability of the species to recover from disturbance. Analysis of post-disturbance response revealed that for only 9 of the 21 species did adult SCDs provide adequate prediction, but for an additional 6 of the species information on sapling SCDs improved the accuracy of prediction if the ‘release’ of saplings or smaller individuals predominated recovery. However in this forest, recovery following disturbance which left stem and roots in place is predominantly by coppice regrowth, and there were no significant correlations found between adult SCDs and the species’ ability to coppice.     

Microsatellite analysis of genetic diversity in the Chinese alligator (<Emphasis Type="Italic">Alligator sinensis</Emphasis>) Changxing captive population

Chinese alligator (Alligator sinensis) is a critically endangered species endemic to China. In this study, the extent of genetic variation in the captive alligators of the Changxing Reserve Center was investigated using microsatellite markers derived from American alligators. Out of 22 loci employed, 21 were successfully amplified in the Chinese alligator. Sequence analysis showed loci in American alligators had a bigger average size than that of the Chinese alligators and the longest allele of an individual locus almost always existed in the species with longer stretch of repeat units. Eight of the 22 loci were found to be polymorphic with a total of 26 alleles present among 32 animals scored, yielding an average of 3.25 alleles per polymorphic locus. The expected heterozygosity (H _E) ranged at a moderate level from 0.4385 to 0.7163 in this population. Compared to that in the American alligators, a lower level of microsatellite diversity existed in the Changxing population as revealed by about 46% fewer alleles per locus and smaller H _E at the homologous loci. The average exclusion power and the ability to detect shared genotypes and multiple paternity were evaluated for those markers. Results suggested that when the polymorphic loci were combined, they could be sensitive markers in genetic diversity study and relatedness inference within the Chinese alligator populations. The level of genetic diversity present in the current Changxing population indicated an important resource to complement reintroductions based on the individuals from the other population. In addition, the microsatellite markers and their associated diversity characterized in this population could be utilized to further investigate the genetic status of this species.