Evolutionary history of vegetative reproduction in Porpidia s. l. (lichen-forming ascomycota)

The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character state reconstructions. The MCMC framework provided confidence estimates for the reconstructions of relationships and ancestral character states, which formed the basis for tests of evolutionary hypotheses. Monophyly tests rejected all hypotheses that predicted any clustering of reproductive modes in extant taxa. In addition, a nearest-neighbor statistic could not reject the hypothesis that the vegetative reproductive mode is randomly distributed throughout the group. These results show that transitions between presence and absence of the vegetative reproductive mode within Porpidia s.l. occurred several times and independently of each other. Likelihood reconstructions of ancestral character states at selected nodes suggest that - contrary to previous thought - the ancestor to Porpidia s.l. already possessed the vegetative reproductive mode. Furthermore, transition rates are reconstructed asymmetrically with the vegetative reproductive mode being gained at a much lower rate than it is lost. A cautious note has to be added, because a simulation study showed that the ancestral character state reconstructions were highly dependent on taxon sampling. However, our central conclusions, particularly the higher rate of change from vegetative reproductive mode present to absent than vice versa within Porpidia s.l., were found to be broadly independent of taxon sampling. [Ancestral character state reconstructions; Ascomycota, Bayesian inference; hypothesis testing; likelihood; MCMC; Porpidia; reproductive systems]

Evolution of micromorphological and chemical characters in the lichen-forming fungal family Pertusariaceae

Micromorphological characters of the fruiting bodies, such as ascus-type and hymenial amyloidity, and secondary chemistry have been widely employed as key characters in Ascomycota classification. However, the evolution of these characters has yet not been studied using molecular phylogenies. We have used a combined Bayesian and maximum likelihood based approach to trace character evolution on a tree inferred from a combined analysis of nuclear and mitochondrial ribosomal DNA sequences. The maximum likelihood aspect overcomes simplifications inherent in maximum parsimony methods, whereas the Markov chain Monte Carlo aspect renders results independent of any particular phylogenetic tree. The results indicate that the evolution of the two chemical characters is quite different, being stable once developed for the medullary lecanoric acid, whereas the cortical chlorinated xanthones appear to have been lost several times. The current ascus-types and the amyloidity of the hymenial gel in Pertusariaceae appear to have been developed within the family. The basal ascus-type of pertusarialean fungi remains unknown. (c) 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89, 615-626.

Response to comment on "On the regulation of populations of mammals, birds, fish, and insects"

Our conclusions are unaffected by removal of the time series identified by Peacock and Garshelis as harvest data. The relationship between a population's growth rate and its size is generally concave in mammals, irrespective of their body sizes. However, our data set includes quality data for only five mammals larger than 20 kilograms, so strong conclusions cannot be made about these animals.

Response to comments on "On the regulation of populations of mammals, birds, fish, and insects"

The technical comments by Getz and Lloyd-Smith, Ross, and Doncaster focus on specific aspects of our analysis and estimation and do not demonstrate any results opposing our key conclusion-that, contrary to what was previously believed, the relation between a population's growth rate (pgr) and its density is generally concave.

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on across-species analyses at identifying known functionally linked proteins. The method shows that protein pairs with at least two to three correlated events of gain or loss are almost certainly functionally linked. Contingent evolution, in which one gene's presence or absence depends upon the presence of another, can also be detected phylogenetically, and may identify genes whose functional significance depends upon its interaction with other genes. Incorporating phylogenetic information improves the prediction of functional linkages. The improvement derives from having a lower rate of false positives and from detecting trends that across-species analyses miss. Phylogenetic methods can easily be incorporated into the screening of large-scale bioinformatics datasets to identify sets of protein links and to characterise gene networks.

On the regulation of populations of mammals, birds, fish, and insects

A key unresolved question in population ecology concerns the relationship between a population's size and its growth rate. We estimated this relationship for 1780 time series of mammals, birds, fish, and insects. We found that rates of population growth are high at low population densities but, contrary to previous predictions, decline rapidly with increasing population size and then flatten out, for all four taxa. This produces a strongly concave relationship between a population's growth rate and its size. These findings have fundamental implications for our understanding of animals' lives, suggesting in particular that many animals in these taxa will be found living at densities above the carrying capacity of their environments.

LVB: parsimony and simulated annealing in the search for phylogenetic trees

Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.

Bayesian estimation of ancestral character states on phylogenies

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods ( BayesMultiState) is available from the authors.

Microglial activation correlates with severity in Huntington disease: a clinical and PET study

Background: Huntington disease ( HD) is characterized by the progressive death of medium spiny dopamine receptor bearing striatal GABAergic neurons. In addition, microglial activation in the areas of neuronal loss has recently been described in postmortem studies. Activated microglia are known to release neurotoxic cytokines, and these may contribute to the pathologic process. Methods: To evaluate in vivo the involvement of microglia activation in HD, the authors studied patients at different stages of the disease using [ C-11]( R)-PK11195 PET, a marker of microglia activation, and [ C-11] raclopride PET, a marker of dopamine D2 receptor binding and hence striatal GABAergic cell function. Results: In HD patients, a significant increase in striatal [ C-11]( R)-PK11195 binding was observed, which significantly correlated with disease severity as reflected by the striatal reduction in [ C-11] raclopride binding, the Unified Huntington's Disease Rating Scale score, and the patients' CAG index. Also detected were significant increases in microglia activation in cortical regions including prefrontal cortex and anterior cingulate. Conclusions: These [ C-11]( R)-PK11195 PET findings show that the level of microglial activation correlates with Huntington disease ( HD) severity. They lend support to the view that microglia contribute to the ongoing neuronal degeneration in HD and indicate that [ C-11]( R)-PK11195 PET provides a valuable marker when monitoring the efficacy of putative neuroprotecting agents in this relentlessly progressive genetic disorder.

Health-related quality of life in Huntington's disease: a comparison of two generic instruments, SF-36 and SIP

Whereas several clinical endpoints in monitoring the response to treatment in patients with Huntington's disease (HD) have been explored, there has been a paucity of research in the quality of life in such patients. The aim of this study was to validate the use of two generic health-related quality of life instruments (the Short Form 36 health survey questionnaire [SF-36] and the Sickness Impact Profile [SIP]) and to evaluate their psychometric properties. We found that both instruments demonstrated acceptable convergent validity and reliability for patients and carers. However, there was an advantage in using the SF-36 because of its more robust construct validity and test-retest reliability; furthermore, motor symptoms appeared to influence some strictly nonmotor dimensions of the SIP. On a pragmatic level, the SF-36 is shorter and quicker to administer and, therefore, easier for patients at various stages of the disease to complete. Thus, the SF-36 would appear to be the recommended instrument of choice for patients with HD and their carers, although further work needs to be done to investigate the sensitivity of this instrument longitudinally. (C) 2004 Movement Disorder Society.

Huntington's disease patients have selective problems with insight

The objective of this study was to determine insight in patients with Huntington's disease (HD) by contrasting patients' ability to rate their own behavior with their ability to rate a person other than themselves. HD patients and carers completed the Dysexecutive Questionnaire (DEX), rating themselves and each other at two time points. The temporal stability of these ratings was initially examined using these two time points since there is no published test-retest reliability of the DEX with this Population to date. This was followed by a comparison of patients' self-ratings and carer's independent ratings of patients by performing correlations with patients' disease variables, and in exploratory factor analysis was conducted on both sets of ratings. The DEX showed good test-retest reliability, with patients consistently and persistently underestimating the degree of their dysexecutive behavior, but not that of their carers. Patients' self-ratings and caters' ratings of patients both showed that dysexecutive behavior in HD can be fractionated into three underlying components (Cognition, Self-regulation, Insight), and the relative ranking of these factors was similar for both data sets. HD patients consistently underestimated the extent of only their own dysexecutive behaviors relative to carers' ratings by 26%, but were similar in ascribing ranks to the components of dysexecutive behavior. (c) 2005 Movement Disorder Society.

Pseudo-neglect in Huntington's disease correlates with decreased angular gyrus density

Visuospatial attentional bias was examined in Huntington's disease (HID) patients with mild disease, asymptomatic gene-positive patients and controls. No group differences were found on the grey scales task (which is a non-motor task of visuospatial attentional bias), although patients' trinucleotide (CAG) repeat length correlated with increasing leftward bias. On the line bisection task, symptomatic patients made significantly larger leftward bisection errors relative to controls, who showed the normal slight degree of leftward error (pseudo-neglect). The asymptomatic group showed a trend for greater leftward error than controls. A subset of participants went on to have structural MRI, which showed a correlation between increased leftward error on the line bisection task and reduced density in the angular gyrus area (BA39) bilaterally. This finding is consistent with recent literature suggesting a critical role for the angular gyrus in the lateralization of visuospatial attention.

Borg's rating of perceived exertion scales: do the verbal anchors mean the same for different clinical groups?

Objective: To examine the interpretation of the verbal anchors used in the Borg rating of perceived exertion (RPE) scales in different clinical groups and a healthy control group. Design: Prospective experimental study. Setting: Rehabilitation center. Participants: Nineteen subjects with brain injury, 16 with chronic low back pain (CLBP), and 20 healthy controls. Interventions: Not applicable. Main Outcome Measures: Subjects used a visual analog scale (VAS) to rate their interpretation of the verbal anchors from the Borg RPE 6-20 and the newer 10-point category ratio scale. Results: All groups placed the verbal anchors in the order that they occur on the scales. There were significant within-group differences (P > .05) between VAS scores for 4 verbal anchors in the control group, 8 in the CLBP group, and 2 in the brain injury group. There was no significant difference in rating of each verbal anchor between the groups (P > .05). Conclusions: All subjects rated the verbal anchors in the order they occur on the scales, but there was less agreement in rating of each verbal anchor among subjects in the brain injury group. Clinicians should consider the possibility of small discrepancies in the meaning of the verbal anchors to subjects, particularly those recovering from brain injury, when they evaluate exercise perceptions.

Wigner Transport models of the electron-phonon kinetics in quantum wires

Two quantum-kinetic models of ultrafast electron transport in quantum wires are derived from the generalized electron-phonon Wigner equation. The various assumptions and approximations allowing one to find closed equations for the reduced electron Wigner function are discussed with an emphasis on their physical relevance. The models correspond to the Levinson and Barker-Ferry equations, now generalized to account for a space-dependent evolution. They are applied to study the quantum effects in the dynamics of an initial packet of highly nonequilibrium carriers, locally generated in the wire. The properties of the two model equations are compared and analyzed.