Cytotoxic Peptides: Naphthoquinonyl Derivatives of Luteinizing Hormone-Releasing Hormone

In an attempt to produce efficient cytotoxic derivatives of luteinizing hormone-releasing hormone (LH-RH), two novel 1,4-naphthoquinone derivatives of [D-Lys⁶]-LH-RH were synthesized primarily by solid-phase peptide synthesis, in good yield and high purity. The ability of each analog to produce reactive oxygen species using enzymatic reduction, i.e. NADPH-cytochrome P-450 reductase, was evaluated employing electron spin resonance (ESR) spectroscopy and spin-trapping techniques. The ESR results suggest that the novel cytotoxic analogs are extremely effective in generating oxygen radicals.     

Interaction of D-amino acid incorporated analogues of pardaxin with membranes.

The influence of specific L- to D-amino acid substitutions on the interaction of pardaxin, a shark repellent neurotoxin polypeptide, with phospholipid vesicles and human erythrocytes is described. Twelve modified, truncated, or fluorescently labeled [with the fluorophore 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD) at their N-terminal amino acid] analogues of pardaxin were synthesized by a solid-phase method. Fluorescence measurements were used to monitor the interaction of the analogues with membranes [Rapaport, D., & Shai, Y. (1991) J. Biol. Chem. 266, 23769-23775]. Upon titration of solutions containing the NBD-labeled peptides with small unilamellar vesicles, the fluorescent emission spectra of all NBD-labeled peptides displayed similar blue-shifts, in addition to enhanced intensities, upon relocation of the probe to the more apolar environment. Binding isotherms were constructed from which surface partition constants, in the range of 10(4) M-1, were derived. The existence of an aggregation process, suggested by the shape of the binding isotherms, could be associated only with those analogues in which the N-helix (residues 1-9) was not perturbed. The alpha-helical content of the analogues was estimated by circular dichroism (CD) spectroscopy, both before and after binding to vesicles at neutral pH. The ability of the peptides to dissipate a diffusion potential and to cause calcein release, as well as to lyse human erythrocytes, served to functionally characterize the peptides. The results support a two alpha-helix model, with a bend at position 13, as best describing pardaxin in its membrane-bound state.(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.     

Neutralization of pro‐inflammatory monocytes by targeting TLR2 dimerization ameliorates colitis

Monocytes have emerged as critical driving force of acute inflammation. Here, we show that inhibition of Toll‐like receptor 2(TLR2) dimerization by a TLR2 transmembrane peptide (TLR2‐p) ameliorated DSS‐induced colitis by interfering specifically with the activation of Ly6C⁺ monocytes without affecting their recruitment to the colon. We report that TLR2‐p directly interacts with TLR2 within the membrane, leading to inhibition of TLR2–TLR6/1 assembly induced by natural ligands. This was associated with decreased levels of extracellular signal‐regulated kinases (ERK) signaling and reduced secretion of pro‐inflammatory cytokines, such as interleukin (IL)‐6, IL‐23, IL‐12, and IL‐1β. Altogether, our study provides insights into the essential role of TLR2 dimerization in the activation of pathogenic pro‐inflammatory Ly6C^hi monocytes and suggests that inhibition of this aggregation by TLR2‐p might have therapeutic potential in the treatment of acute gut inflammation.     

Dual effects of IkappaB kinase beta-mediated phosphorylation on p105 Fate: SCF(beta-TrCP)-dependent degradation and SCF(beta-TrCP)-independent processing

Processing of the p105 NF-kappaB precursor to yield the p50 active subunit is a unique and rare case in which the ubiquitin system is involved in limited processing rather than in complete destruction of its target. The mechanisms involved in this process are largely unknown, although a glycine repeat in the middle of p105 has been identified as a processing stop signal. IkappaB kinase (IKK)beta-mediated phosphorylation at the C-terminal domain with subsequent recruitment of the SCF(beta-TrCP) ubiquitin ligase leads to accelerated processing and degradation of the precursor, yet the roles that the kinase and ligase play in each of these two processes have not been elucidated. Here we demonstrate that IKKbeta has two distinct functions: (i) stimulation of degradation and (ii) stimulation of processing. IKKbeta-induced degradation is dependent on SCF(beta-TrCP), which acts through multiple lysine residues in the IkappaBgamma domain. In contrast, IKKbeta-induced processing of p105 is beta-transduction repeat-containing protein (beta-TrCP) independent, as it is not affected by expression of a dominant-negative beta-TrCP or following its silencing by small inhibitory RNA. Furthermore, removal of all 30 lysine residues from IkappaBgamma results in complete inhibition of IKK-dependent degradation but has no effect on IKK-dependent processing. Yet processing still requires the activity of the ubiquitin system, as it is inhibited by dominant-negative UbcH5a. We suggest that IKKbeta mediates its two distinct effects by affecting, directly and indirectly, two different E3s.     

Double mutants deficient in cytosolic and thylakoid ascorbate peroxidase reveal a complex mode of interaction between reactive oxygen species, plant development, and response to abiotic stresses

Reactive oxygen species (ROS) play a key signaling role in plants and are controlled in cells by a complex network of ROS metabolizing enzymes found in several different cellular compartments. To study how different ROS signals, generated in different cellular compartments, are integrated in cells, we generated a double mutant lacking thylakoid ascorbate peroxidase (tylapx) and cytosolic ascorbate peroxidase1 (apx1). Our analysis suggests that two different signals are generated in plants lacking cytosolic APX1 or tylAPX. The lack of a chloroplastic hydrogen peroxide removal enzyme triggers a specific signal in cells that results in enhanced tolerance to heat stress, whereas the lack of a cytosolic hydrogen peroxide removal enzyme triggers a different signal, which results in stunted growth and enhanced sensitivity to oxidative stress. When the two signals are coactivated in cells (i.e. tylapx/apx1), a new response is detected, suggesting that the integration of the two different signals results in a new signal that manifests in late flowering, low protein oxidation during light stress, and enhanced accumulation of anthocyanins. Our results demonstrate a high degree of plasticity in ROS signaling in Arabidopsis (Arabidopsis thaliana) and suggest the existence of redundant pathways for ROS protection that compensate for the lack of classical ROS removal enzymes such as cytosolic and chloroplastic APXs. Further investigation of the enhanced heat tolerance in plants lacking tylAPX, using mutants deficient in chloroplast-to-nuclei retrograde signaling, suggests the existence of a chloroplast-generated stress signal that enhances basal thermotolerance in plants.     

植物细胞器间遗传信息转移

真核生物细胞质中有多种执行特定功能的细胞器, 其中线粒体和质体含有独立的基因组, 但细胞器的遗传信息储量有限, 其多数结构和功能蛋白质仍然由核基因组编码.来自植物的相关研究表明, 细胞核与细胞器间不仅在功能上相互依存, 而且遗传信息分子能跨越生物膜屏障, 在细胞核与细胞器间及不同的细胞器间进行传递, 并由此可以引起部分遗传信息在细胞内定位及基因表达等方面的相应改变.细胞器间遗传信息转移机制的研究将为深入认识核质相互作用及真核生物的进化提供重要的线索.