The conditional ancestral selection graph with strong balancing selection

Using a heuristic separation-of-time-scales argument, we describe the behavior of the conditional ancestral selection graph with very strong balancing selection between a pair of alleles. In the limit as the strength of selection tends to infinity, we find that the ancestral process converges to a neutral structured coalescent, with two subpopulations representing the two alleles and mutation playing the role of migration. This agrees with a previous result of Kaplan et al., obtained using a different approach. We present the results of computer simulations to support our heuristic mathematical results. We also present a more rigorous demonstration that the neutral conditional ancestral process converges to the Kingman coalescent in the limit as the mutation rate tends to infinity.     

Order‐Restricted Semiparametric Inference for the Power Bias Model

Summary The power bias model, a generalization of length‐biased sampling, is introduced and investigated in detail. In particular, attention is focused on order‐restricted inference. We show that the power bias model is an example of the density ratio model, or in other words, it is a semiparametric model that is specified by assuming that the ratio of several unknown probability density functions has a parametric form. Estimation and testing procedures under constraints are developed in detail. It is shown that the power bias model can be used for testing for, or against, the likelihood ratio ordering among multiple populations without resorting to any parametric assumptions. Examples and real data analysis demonstrate the usefulness of this approach.     

Topologies of the Conditional Ancestral Trees and Full-Likelihood-Based Inference in the General Coalescent Tree Framework

The general coalescent tree framework is a family of models for determining ancestries among random samples of DNA sequences at a nonrecombining locus. The ancestral models included in this framework can be derived under various evolutionary scenarios. Here, a computationally tractable full-likelihood-based inference method for neutral polymorphisms is presented, using the general coalescent tree framework and the infinite-sites model for mutations in DNA sequences. First, an exact sampling scheme is developed to determine the topologies of conditional ancestral trees. However, this scheme has some computational limitations and to overcome these limitations a second scheme based on importance sampling is provided. Next, these schemes are combined with Monte Carlo integrations to estimate the likelihood of full polymorphism data, the ages of mutations in the sample, and the time of the most recent common ancestor. In addition, this article shows how to apply this method for estimating the likelihood of neutral polymorphism data in a sample of DNA sequences completely linked to a mutant allele of interest. This method is illustrated using the data in a sample of DNA sequences at the APOE gene locus.THE interest in analyzing polymorphism data in contemporary samples of DNA sequences under various evolutionary scenarios creates a demand to design computationally tractable full-likelihood-based inference methods. For an evolutionary scenario of interest, an ancestral-mutation model can be used to design such a method. The ancestral-mutation model for a sample of DNA sequences at a nonrecombining locus is a combination of two processes: one is an ancestral process that traces the lineages of the sample back in time until the most recent common ancestor, constructing an ancestral tree for the sample. The second is a mutation process that is superimposed on the ancestral tree. The complexities of ancestral-mutation models make the design of such methods challenging. Full data are used instead of summary statistics, which can result in loss of important information in the data (see Felsenstein 1992; Donnelly and Tavaré 1995). In addition, current methods use specific features of the underlying ancestral-mutation models, so they lose flexibility to be applicable to other ancestral-mutation models.More specifically, Griffiths and Tavaré (1994c, 1995) and Kuhner et al. (1995) developed full-likelihood-based inference methods for neutral polymorphisms at a nonrecombining locus. They used the combinations of the standard coalescent (Kingman 1982a,b,c; Hudson 1983; Tajima 1983) with the finite-sites or infinite-sites (Watterson 1975) models as ancestral-mutation models. Stephens and Donnelly (2000) designed an importance sampling method to estimate the full likelihood of the data using the same settings for the ancestral-mutation models. Hobolth et al. (2008) provided another importance sampling scheme restricted to the infinite-sites model. The last two methods are computationally more efficient than the first two methods, but they lose flexibility to be applicable to ancestral models without standard coalescent features with independent coalescence waiting times, such as the coalescent processes with exponential growth (Slatkin and Hudson 1991; Griffiths and Tavaré 1994b).To incorporate the coalescent processes with exponential growth, Kuhner et al. (1998) and Griffiths and Tavaré (1994a, 1999) extended their previous methods. For example, the method of Griffiths and Tavaré (1994a, 1999) allows one to consider ancestral models based on coalescent processes with variable population sizes. Coop and Griffiths (2004) modified this inference method and made it applicable for analyzing full polymorphism data in a sample of DNA sequences from a nonrecombining locus completely linked to a mutant allele of interest, either neutral or under selection. Additionally, ancestral models have been developed for this type of sample, where the mutant allele is either neutral (Griffiths and Tavaré 1998, 2003; Wiuf and Donnelly 1999; Stephens 2000) or under selection (Slatkin and Rannala 1997; Stephens and Donnelly 2003). The ancestral model of Slatkin and Rannala (1997) is part of a family of ancestral models derived by Thompson (1975), Nee et al. (1994), and Rannala (1997), using a linear birth–death process as an evolutionary process in a population. Although all the ancestral models mentioned above differ in their properties and evolutionary scenarios, they are part of the general coalescent tree framework (Griffiths and Tavaré 1998). Therefore, a computationally tractable full-likelihood-based inference method based on this general framework is of great interest.For a sample of n sequences, an ancestral model in the general coalescent tree framework is described as a bifurcating rooted tree with n − 1 internal nodes and n leaves, where the internal nodes are coalescent events that happen one at a time. The tree is a combination of two independent components: the topology and the branch lengths. The topology of the tree is constructed going backward in time by combining two randomly chosen ancestral lineages of the sample at each node; the branch lengths of the tree are defined by the joint distribution function of the coalescence waiting times. Note that any density function for coalescence waiting times can define an ancestral model in the general coalescent tree framework.The n leaves (and the sequences in the sample) are labeled from 1 to n; and the n − 1 internal nodes of the ancestral tree are labeled from 1 to n − 1 (in order of occurrence of the coalescent events backward in time). Thus, the topology of an ancestral tree is a leaf-labeled bifurcating rooted tree with totally ordered interior vertices. These trees are called topological trees.When using the general coalescent tree framework and the infinite-sites model, an evolutionary process that generates polymorphism data in a sample of DNA sequences can be described in the following way. An ancestral tree is constructed, as described above, and mutations are added independently on different branches of the ancestral tree as Poisson processes with equal rates, θ/2, in which θ is the mutation rate at the locus. Then, at the mutation events, the ancestral sequences of the sample are changed according to the infinite-sites model; that is, each mutation occurs at a site of an ancestral sequence at which no previous mutations occurred. Thus, these changes define polymorphism data.Naively, this probabilistic framework can be used to estimate the likelihood of the full observed data in a sample of n sequences. That is, data sets are simulated independently as described above and each simulated data set is compared to the observed data. The proportion of the simulated data sets that match the observed data is an estimate of the likelihood of the observed data. Although this approach provides an estimate for the likelihood of the observed data, this method is computationally infeasible, because the topologies of the ancestral trees of the generated data sets are sampled from the space of all the possible topological trees with n leaves. This space has size n!(n − 1)!/2ⁿ⁻¹ (Edwards 1970), which is huge for moderate values of n. The topologies of the ancestral trees of the generated data sets that match the observed data represent a small portion of that space. Thus, designing a method that samples topologies of the ancestral trees from this subspace can make the method computationally tractable.On the basis of this idea, I use the general coalescent tree framework with the infinite-sites model to develop a computationally tractable full-likelihood-based inference method for polymorphisms in DNA sequences at a nonrecombining locus. First, an exact sampling scheme for topologies of the conditional ancestral trees is developed. This method has some computational limitations, so to overcome these limitations a second scheme based on an importance sampling is provided. These sampling schemes are combined with Monte Carlo integrations to estimate the likelihood of the full data, the ages of the mutations in the sample, and the time of the most recent common ancestor of the sample. I describe an application of this method for neutral polymorphism data in a sample of DNA sequences at a nonrecombining locus that is completely linked to a mutant allele of interest, either neutral or under selection. The method is illustrated using the data in a sample of DNA sequences at the APOE gene locus from Fullerton et al. (2000).     

Molecular cloning and characterization of UDP-glucose dehydrogenase from the amphibian Xenopus laevis and its involvement in hyaluronan synthesis

UDP-glucose dehydrogenase (UGDH) supplies the cell with UDP-glucuronic acid (UDP-GlcUA), a precursor of glycosaminoglycan and proteoglycan synthesis. Here we reported the cloning and the characterization of the UGDH from the amphibian Xenopus laevis that is one of the model organisms for developmental biology. We found that X. laevis UGDH (xUGDH) maintained a very high degree of similarity with other known UGDH sequences both at the genomic and the protein levels. Also its kinetic parameters are similar to those of UGDH from other species. During X. laevis development, UDGH is always expressed but clearly increases its mRNA levels at the tail bud stage (i.e. 30 h post-fertilization). This result fits well with our previous observation that hyaluronan, a glycosaminoglycan that is synthesized using UDP-GlcUA and UDP-N-acetylglucosamine, is abundantly detected at this developmental stage. The expression of UGDH was found to be related to hyaluronan synthesis. In human smooth muscle cells the overexpression of xUGDH or endogenous abrogation of UGDH modulated hyaluronan synthesis specifically. Our findings were confirmed by in vivo experiments where the silencing of xUGDH in X. laevis embryos decreased glycosaminoglycan synthesis causing severe embryonic malformations because of a defective gastrulation process.     

Effect of anti-TNFalpha treatment on circulating endothelial progenitor cells (EPCs) in rheumatoid arthritis

Rheumatoid arthritis (RA) is associated with increased cardiovascular morbidity and mortality, which may be attenuated by anti-inflammatory treatment. Endothelial progenitor cells (EPCs) have the ability to differentiate into mature endothelium and have a potentially reparative role protecting against ischemia and atherosclerosis. OBJECTIVE: To investigate the effect of treatment with infliximab on the number and functional capacity of endothelial progenitor cells (EPCs) in patients with RA, as a possible mechanism for reducing cardiovascular morbidity in this disorder. METHODS: Patients: Active seropositive RA patients (N = 14) considered candidates for starting infliximab treatment, were recruited. Assessment, based on DAS-28, was performed before treatment and 14 days later. Peripheral blood mononuclear cells were isolated and EPC numbers evaluated by the colony-forming unit (CFU) method. Endothelial phenotyping of CFU was performed by immunofluorescence employing antibodies to Tie-2 VEGF-receptor 2, and CD31. EPC Functional properties were evaluated by fibronectin adherance. RESULTS: A significant 33.4% increase (p < 0.001) in EPC levels was observed after infliximab. A 60% increase was noted in the EPC differentiation scale, (p < 0.002) while a 37.6% increase was observed in mean EPC adhesion (p < 0.001). These changes were associated with a 17.5% decrease in the DAS-28 (p < 0.0001). A significant correlation was observed between the clinical response, reflected by changes in DAS-28 and the degree of increase in EPC CFUs. CONCLUSION: A single dose of infliximab improved the number and functional properties of EPCs, in parallel with an early clinical effect, suggesting a possible mechanism by which anti-inflammatory treatment may reduce cardiovascular risk in RA patients.     

Modification of tree architecture by a gall-forming aphid

Herbivory may substantially alter the architectural structure of plants. Among insects, gall-formers that substantially manipulate host traits may have a profound effect on the plants even at low densities. The aphid, Baizongia pistaciae induces banana-like large galls on the terminal buds of Pistacia palaestina. We hypothesized that these large galls are associated with the shape of the plant which may grow as a tree or a bush. In the natural Mediterranean forest, we monitored the effects of the galls on infested branches. In the year of gall formation, usually (~95%) there is neither elongation nor branching beyond the position of the gall. However, in the following years, galled branches produced more lateral branches (branching) than ungalled branches. This effect persists for at least 2 years. Consequently, galled branches carried more leaves and tended to gain more biomass than ungalled branches. Galling did not affect fruit yield. We suggest that repeated galling by B. pistaciae may promote bush-like architecture in P. palaestina.     

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking

We present a very efficient rigid "unbound" soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the "correct" solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge-bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience.     

Malaria parasites release vesicle subpopulations with signatures of different destinations

Malaria is the most serious mosquito‐borne parasitic disease, caused mainly by the intracellular parasite Plasmodium falciparum. The parasite invades human red blood cells and releases extracellular vesicles (EVs) to alter its host responses. It becomes clear that EVs are generally composed of sub‐populations. Seeking to identify EV subpopulations, we subject malaria‐derived EVs to size‐separation analysis, using asymmetric flow field‐flow fractionation. Multi‐technique analysis reveals surprising characteristics: we identify two distinct EV subpopulations differing in size and protein content. Small EVs are enriched in complement‐system proteins and large EVs in proteasome subunits. We then measure the membrane fusion abilities of each subpopulation with three types of host cellular membranes: plasma, late and early endosome. Remarkably, small EVs fuse to early endosome liposomes at significantly greater levels than large EVs. Atomic force microscope imaging combined with machine‐learning methods further emphasizes the difference in biophysical properties between the two subpopulations. These results shed light on the sophisticated mechanism by which malaria parasites utilize EV subpopulations as a communication tool to target different cellular destinations or host systems.     

Metabolic regulation in Streptomyces parvulus during actinomycin D synthesis, studied with 13C- and 15N-labeled precursors by 13C and 15N nuclear magnetic resonance spectroscopy and by gas chromatography-mass spectrometry.

Recent studies have suggested that the onset of synthesis of actinomycin D in Streptomyces parvulus is due to a release from L-glutamate catabolic repression. In the present investigation we showed that S. parvulus has the capacity to maintain high levels of intracellular glutamate during the synthesis of actinomycin D. The results seem contradictory, since actinomycin D synthesis cannot start before a release from L-glutamate catabolic repression, but a relatively high intracellular pool of glutamate is needed for the synthesis of actinomycin D. Utilizing different labeled precursors, D-[U-13C]fructose and 13C- and 15N-labeled L-glutamate, and nuclear magnetic resonance techniques, we showed that carbon atoms of an intracellular glutamate pool of S. parvulus were not derived biosynthetically from the culture medium glutamate source but rather from D-fructose catabolism. A new intracellular pyrimidine derivative whose nitrogen and carbon skeletons were derived from exogenous L-glutamate was obtained as the main glutamate metabolite. Another new pyrimidine derivative that had a significantly reduced intracellular mobility and that was derived from D-fructose catabolism was identified in the cell extracts of S. parvulus during actinomycin D synthesis. These pyrimidine derivatives may serve as a nitrogen store for actinomycin D synthesis. In the present study, the N-trimethyl group of a choline derivative was observed by 13C nuclear magnetic resonance spectroscopy in growing S. parvulus cells. The choline group, as well as the N-methyl groups of sarcosine, N-methyl-valine, and the methyl groups of an actinomycin D chromophore, arose from D-fructose catabolism. The 13C enrichments found in the peptide moieties of actinomycin D were in accordance with a mechanism of actinomycin D synthesis from L-glutamate and D-fructose.