Anti-sense peptide recognition of sense peptides: direct quantitative characterization with the ribonuclease S-peptide system using analytical high-performance affinity chromatography

The ability of peptides coded by the anti-sense strand of DNA to interact specifically with peptides coded by the sense strand has been evaluated. The sense peptide examined, ribonuclease S-peptide, was immobilized on a coated silica affinity chromatographic matrix. Anti-sense peptides were synthesized on the basis of the anti-sense DNA sequence for the S-peptide region in native pancreatic ribonuclease A. The interaction of synthetic anti-sense peptides with sense peptide was quantitated from the degree of retardation during chromatographic elution on the sense peptide affinity matrix in buffers with and without soluble competing sense peptide. Sense/anti-sense peptide interactions were found to occur with significant affinities with each of two anti-sense 20-residue peptides of opposite amino-to-carboxyl orientations and to weaken progressively with decreasing length of anti-sense peptide. The substantial chromatographic retardation of anti-sense peptides was specific, since it decreased as expected with increasing concentration of the soluble competing S-peptide, could not be mimicked by the elution of several control peptides (including S-peptide itself) on the S-peptide matrix, and did not occur with a blank chromatographic matrix (no S-peptide attached). The stoichiometry of anti-sense peptide binding to immobilized sense peptide was found to be far greater than 1:1, and at least 4-5:1, for the two 20-mer anti-sense peptides. In sum, the analytical affinity chromatographic experiments have established quantitatively that anti-sense peptide binding to sense peptides occurs in the ribonuclease S-peptide case and have identified some structural elements that govern these interactions.(ABSTRACT TRUNCATED AT 250 WORDS)     

The Variance of Identity-by-Descent Sharing in the Wright–Fisher Model

Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright–Fisher model. Specifically, using coalescent theory, we calculate the variance of the total sharing between random pairs of individuals. We then investigate the cohort-averaged sharing: the average total sharing between one individual and the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally. Surprisingly, the variance of this distribution does not vanish even for large cohorts, implying the existence of “hypersharing” individuals. The presence of such individuals has consequences for the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD and subsequently in power to detect an association, when individuals are either randomly selected or specifically chosen to be the hypersharing individuals. Using our framework, we also compute the variance of an estimator of the population size that is based on the mean IBD sharing and the variance in the sharing between inbred siblings. Finally, we study IBD sharing in an admixture pulse model and show that in the Ashkenazi Jewish population the admixture fraction is correlated with the cohort-averaged sharing.IN isolated populations, even purported unrelated individuals often share genetic material that is identical-by-descent (IBD). Traditionally, the term IBD sharing referred to coancestry at a single site (or autozygosity, in the case of a diploid individual) and was widely investigated as a measure of the degree of inbreeding in a population (Hartl and Clark 2006). Recent years have brought dramatic increases in the quantity and density of available genetic data and, together with new computational tools, these data have enabled the detection of IBD sharing of entire genomic segments (see, e.g., Purcell et al. 2007; Kong et al. 2008; Albrechtsen et al. 2009; Gusev et al. 2009; Browning and Browning 2011; Carr et al. 2011; Brown et al. 2012). The availability of IBD detection tools that are efficient enough to detect shared segments in large cohorts has resulted in numerous applications, from demographic inference (Davison et al. 2009; Palamara et al. 2012) and characterization of populations (Gusev et al. 2012a) to selection detection (Albrechtsen et al. 2010), relatedness detection and pedigree reconstruction (Huff et al. 2011; Kirkpatrick et al. 2011; Stevens et al. 2011; Henn et al. 2012), prioritization of individuals for sequencing (Gusev et al. 2012b), inference of HLA type (Setty et al. 2011), detection of haplotypes associated with a disease or a trait (Akula et al. 2011; Gusev et al. 2011; Browning and Thompson 2012), imputation (Uricchio et al. 2012), and phasing (Palin et al. 2011).Recently, some of us used coalescent theory to calculate several theoretical quantities of IBD sharing under a number of demographic histories. Then, shared segments were detected in real populations, and their demographic histories were inferred (Palamara et al. 2012). Here, we expand upon Palamara et al. (2012) to investigate additional aspects of the stochastic variation in IBD sharing. Specifically, we provide a precise calculation for the variance of the total sharing in the Wright–Fisher model, either between a random pair of individuals or between one individual and all others in the cohort.Understanding the variation in IBD sharing is an important theoretical characterization of the Wright–Fisher model, and additionally, it has several practical applications. For example, it can be used to calculate the variance of an estimator of the population size that is based on the sharing between random pairs. In a different domain, the variance in IBD sharing is needed to accurately assess strategies for sequencing study design, specifically, in prioritization of individuals to be sequenced. This is because imputation strategies use IBD sharing between sequenced individuals and genotyped, not-sequenced individuals to increase the number of effective sequences analyzed in the association study (Palin et al. 2011; Gusev et al. 2012b; Uricchio et al. 2012).In the remainder of this article, we first review the derivation of the mean fraction of the genome shared between two individuals (Palamara et al. 2012). We then calculate the variance of this quantity, using coalescent theory with recombination. We provide a number of approximations, one of which results in a surprisingly simple expression, which is then generalized to a variable population size and to the sharing of segments in a length range. We also numerically investigate the pairwise sharing distribution and provide an approximate fit. We then turn to the average total sharing between each individual and the entire cohort. We show that this quantity, which we term the cohort-averaged sharing, is approximately normally distributed, but is much wider than naively expected, implying the existence of hypersharing individuals. We consider several applications: the number of individuals needed to be sequenced to achieve a certain imputation power and the implications to disease mapping, inference of the population size based on the total sharing, and the variance of the sharing between siblings. We finally calculate the mean and the variance of the sharing in an admixture pulse model and show numerically that admixture results in a broader than expected cohort-averaged sharing. Therefore, large variance of the cohort-averaged sharing can indicate admixture. In the Ashkenazi Jewish population, we show that the cohort-averaged sharing is strongly anticorrelated with the fraction of European ancestry.     

Feedback from Horizontal Cells to Cones Mediates Color Induction and May Facilitate Color Constancy in Rainbow Trout

Color vision is most beneficial when the visual system is color constant and can correct the excitations of photoreceptors for differences in environmental irradiance. A phenomenon related to color constancy is color induction, where the color of an object shifts away from the color of its surroundings. These two phenomena depend on chromatic spatial integration, which was suggested to originate at the feedback synapse from horizontal cells (HC) to cones. However, the exact retinal site was never determined. Using the electroretinogram and compound action potential recordings, we estimated the spectral sensitivity of the photoresponse of cones, the output of cones, and the optic nerve in rainbow trout. Recordings were performed before and following pharmacological inhibition of HC-cone feedback, and were repeated under two colored backgrounds to estimate the efficiency of color induction. No color induction could be detected in the photoresponse of cones. However, the efficiency of color induction in the cone output and optic nerve was substantial, with the efficiency in the optic nerve being significantly higher than in the cone output. We found that the efficiency of color induction in the cone output and optic nerve decreased significantly with the inhibition of HC-cone feedback. Therefore, our findings suggest not only that color induction originates as a result of HC-cone feedback, but also that this effect of HC-cone feedback is further amplified at downstream retinal elements, possibly through feedback mechanisms at the inner plexiform layer. This study provides evidence for an important role of HC-cone feedback in mediating color induction, and therefore, likely also in mediating color constancy.     

Engineering of Methylation State Specific 3xMBT Domain Using ELISA Screening

The ε-amino group of lysine residues may be mono-, di- or tri-methylated by protein lysine methyltransferases. In the past few years it has been highly considered that methylation of both histone and non-histone proteins has fundamental role in development and progression of various human diseases. Thus, the establishment of tools to study lysine methylation that will distinguish between the different states of methylation is required to elucidate their cellular functions. The 3X malignant brain tumor domain (3XMBT) repeats of the Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1) have been utilized in the past as an affinity reagent for the identification of mono- and di-methylated lysine residues on individual proteins and on a proteomic scale. Here, we have utilized the 3XMBT domain to develop an enzyme-linked immunosorbent assay (ELISA) that allows the high-throughput detection of 3XMBT binding to methylated lysines. We demonstrated that this system allows the detection of methylated peptides, methylated proteins and PKMT activity on both peptides and proteins. We also optimized the assay to detect 3XMBT binding in crude E. coli lysates which facilitated the high throughput screening of 3XMBT mutant libraries. We have utilized protein engineering tools and generated a double site saturation 3XMBT library of residues 361 and 411 that were shown before to be important for binding mono and di-methylated substrates and identified variants that can exclusively recognize only di-methylated peptides. Together, our results demonstrate a powerful new approach that will contribute to deeper understanding of lysine methylation biology and that can be utilized for the engineering of domains for specific binders of other post-translational modifications.     

A biogeographic reversal in sexual size dimorphism along a continental temperature gradient

The magnitude and direction of sexual size dimorphism (SSD) varies greatly across the animal kingdom, reflecting differential selection pressures on the reproductive and/or ecological roles of males and females. If the selection pressures and constraints imposed on body size change along environmental gradients, then SSD will vary geographically in a predictable way. Here, we uncover a biogeographical reversal in SSD of lizards from Central and North America: in warm, low latitude environments, males are larger than females, but at colder, high latitudes, females are larger than males. Comparisons to expectations under a Brownian motion model of SSD evolution indicate that this pattern reflects differences in the evolutionary rates and/or trajectories of sex‐specific body sizes. The SSD gradient we found is strongly related to mean annual temperature, but is independent of species richness and body size differences among species within grid cells, suggesting that the biogeography of SSD reflects gradients in sexual and/or fecundity selection, rather than intersexual niche divergence to minimize intraspecific competition. We demonstrate that the SSD gradient is driven by stronger variation in male size than in female size and is independent of clutch mass. This suggests that gradients in sexual selection and male–male competition, rather than fecundity selection to maximize reproductive output by females in seasonal environments, are predominantly responsible for the gradient.