RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

A number of approaches for studying macroevolution using phylogenetic trees have been developed in the last few years. Here, we present RPANDA, an R package that implements model‐free and model‐based phylogenetic comparative methods for macroevolutionary analyses. The model‐free approaches implemented in RPANDA are recently developed approaches stemming from graph theory that allow summarizing the information contained in phylogenetic trees, computing distances between trees, and clustering them accordingly. They also allow identifying distinct branching patterns within single trees. RPANDA also implements likelihood‐based models for fitting various diversification models to phylogenetic trees. It includes birth–death models with i) constant, ii) time‐dependent and iii) environmental‐dependent speciation and extinction rates. It also includes models with equilibrium diversity derived from the coalescent process, as well as a likelihood‐based inference framework to fit the individual‐based model of Speciation by Genetic Differentiation, which is an extension of Hubbell's neutral theory of biodiversity. RPANDA can be used to (i) characterize trees by plotting their spectral density profiles (ii) compare trees and cluster them according to their similarities, (iii) identify and plot distinct branching patterns within trees, (iv) compare the fit of alternative diversification models to phylogenetic trees, (v) estimate rates of speciation and extinction, (vi) estimate and plot how these rates have varied with time and environmental variables and (vii) deduce and plot estimates of species richness through geological time. RPANDA provides investigators with a set of tools for exploring patterns in phylogenetic trees and fitting various models to these trees, thereby contributing to the ongoing development of phylogenetics in the life sciences

O Mapa das Cortes: perspectivas cartográficas

O presente trabalho realiza uma análise exaustiva do Mapa das Cortes, aplicando critérios da cartografia, em particular da cartografia matemática. Assim, analisam-se: autor, escala, projeção, meridiano de origem, cores, convenções, simbologia e outros. Após uma análise morfológica qualitativa, passa-se a um exame quantitativo, comparando esse mapa com um atual, bastante preciso: com o auxílio de um programa de cartografia digital e uma planilha eletrônica foram comparadas as coordenadas geográficas (latitude e longitude) de mais de 430 pontos. A quantificação sistemática e detalhada dos erros em diferentes regiões, da costa atlântica à região amazônica, mostrou aspectos surpreendentes de como o Mapa das Cortes (MC) foi habilmente construído. Essa análise permitiu quantificar de maneira mais precisa as distorções, identificando em que locais foram introduzidas e seu caráter indubitavelmente proposital.In this paper, we present a thorough analysis of the Map of the Courts based on criteria used in cartography, particularly mathematical cartography. As such, it takes into account the following elements: author, scale, projection, the prime meridian, colors, conventions, symbology, and other. After a qualitative morphological analysis, we move on to a quantitative examination by comparing the said map with a quite accurate present-day chart, using a digital cartography software application and spreadsheet to match the geographic coordinates (latitude and longitude) of over 430 points. The systematic and detailed quantification of errors in various areas, from the Atlantic coast to the Amazon region, revealed surprising aspects as to how skillfully the Map of the Courts was constructed. This analysis enabled us to quantify the distortions more accurately and thus identify the locations where they were introduced as well their unquestionable intentional character

Cryptands and bismacrocycles with cyanuric and isocyanuric units: synthesis and structural investigations

Hay synthesis of cryptands and bismacrocycles starting from tripodands with cyanuric and isocyanuric cores is reported. The structure of the compounds is revealed by X-ray diffraction, NMR spectrometry and MS investigations. DNMR experiments carried out with bismacrocycles indicated the flipping of the rings and the free-energy barrier for the conformational process could be determined in one case. (C) 2012 Elsevier Ltd. All rights reserved

Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise

BACKGROUND: Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na(+ )compared to Maythorpe when growing under saline conditions. This study focused on elucidating the genetic basis and mechanisms involved in this difference. RESULTS: The level of polymorphism between the two genotypes was explored using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected between the two genotypes. CONCLUSION: The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different

Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant

The Elbow-EpiTrainer : A method of delivering graded resistance to the extensor carpi radialis brevis. Effectiveness of a prototype device in a healthy population

This document is the Accepted Manuscript version of the following article: Navsaria R, Ryder DM, Lewis JS, et al, 'The Elbow-EpiTrainer: a method of delivering graded resistance to the extensor carpi radialis brevi:. Effectiveness of a prototype device in a healthy population', British Journal of Sports Medicine, Vol. 49(5):318-322, March 2015, available online at: http://bjsm.bmj.com/content/49/5/318. Published by the BMJ Publishing Group Limited.Background: Tennis elbow or lateral epicondylopathy (LE) is experienced as the lateral elbow has a reported prevalence of 1.3%, with symptoms lasting up to 18 months. LE is most commonly attributed to tendinopathy involving the extensor carpi radialis brevis (ECRB) tendon. The aim of tendinopathy management is to alleviate symptoms and restore function that initially involves relative rest followed by progressive therapeutic exercise. Objective: To assess the effectiveness of two prototype exercises using commonly available clinical equipment to progressively increase resistance and activity of the ECRB. Method: Eighteen healthy participants undertook two exercise progressions. Surface electromyography was used to record ECRB activity during the two progressions, involving eccentric exercises of the wrist extensors and elbow pronation exercises using a prototype device. The two progressions were assessed for their linearity of progression using repeated ANOVA and linear regression analysis. Five participants repeated the study to assess reliability. Results: The exercise progressions led to an increase in ECRB electromyographic (EMG) activity (p0.7) between the first and second tests for five participants. Conclusions: Manipulation of resistance and leverage with the prototype exercises was effective in creating significant increases of ECRB normalised EMG activity in a linear manner that may, with future research, become useful to clinicians treating LE. In addition, between trial reliability for the device to generate a consistent load was acceptable.Peer reviewe

An improved method to identify BAC clones using pooled overgos

Hybridization using overgo probes is an established approach for screening arrayed bacterial artificial chromosome (BAC) libraries. We have improved the use of overgos by increasing the yield of positive clones using reduced levels of radioisotopes and enzyme. The strategy involves labeling with all four radiolabeled nucleotides in a hot pulse followed by a cold nucleotide chase and then extending the exposure time to compensate for reduced specific activity of the probes. The resulting cost savings and reduced human exposure to radiation make the use of highly pooled overgo probes a more attractive approach for screening of BAC libraries from organisms with large genomes

Development and implementation of high-throughput SNP genotyping in barley

<p>Abstract</p> <p>Background</p> <p>High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource.</p> <p>Results</p> <p>Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM.</p> <p>Conclusion</p> <p>The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.</p