Statistical inference from single channel records: two-state Markov model with limited time resolution

Though stochastic models are widely used to describe single ion channel behaviour, statistical inference based on them has received little consideration. This paper describes techniques of statistical inference, in particular likelihood methods, suitable for Markov models incorporating limited time resolution by means of a discrete detection limit. To simplify the analysis, attention is restricted to two-state models, although the methods have more general applicability. Non-uniqueness of the mean open-time and mean closed-time estimators obtained by moment methods based on single exponential approximations to the apparent open-time and apparent closed-time distributions has been reported. The present study clarifies and extends this previous work by proving that, for such approximations, the likelihood equations as well as the moment equations (usually) have multiple solutions. Such non-uniqueness corresponds to non-identifiability of the statistical model for the apparent quantities. By contrast, higher-order approximations yield theoretically identifiable models. Likelihood-based estimation procedures are developed for both single exponential and bi-exponential approximations. The methods and results are illustrated by numerical examples based on literature and simulated data, with consideration given to empirical distributions and model control, likelihood plots, and point estimation and confidence regions.     

tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.     

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae,Conflicting with Current Classification Schemes

Urticaceae is a family with more than 2000 species, which contains remarkable morphological diversity. It has undergone many taxonomic reorganizations, and is currently the subject of further systematic studies. To gain more resolution in systematic studies and to better understand the general patterns of character evolution in Urticaceae, based on our previous phylogeny including 169 accessions comprising 122 species across 47 Urticaceae genera, we examined 19 diagnostic characters, and analysed these employing both maximum-parsimony and maximum-likelihood approaches. Our results revealed that 16 characters exhibited multiple state changes within the family, with ten exhibiting >eight changes and three exhibiting between 28 and 40. Morphological synapomorphies were identified for many clades, but the diagnostic value of these was often limited due to reversals within the clade and/or homoplasies elsewhere. Recognition of the four clades comprising the family at subfamily level can be supported by a small number carefully chosen defining traits for each. Several non-monophyletic genera appear to be defined only by characters that are plesiomorphic within their clades, and more detailed work would be valuable to find defining traits for monophyletic clades within these. Some character evolution may be attributed to adaptive evolution in Urticaceae due to shifts in habitat or vegetation type. This study demonstrated the value of using phylogeny to trace character evolution, and determine the relative importance of morphological traits for classification.     

Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a tertiary relict distribution

Rhododendron subgenus Hymenanthes subsection Pontica is exceptional among Tertiary relict groups in having a high proportion of species (4 of 11) native to SW Eurasia. A phylogeny based on cpDNA matK and trnL-F indicated that multiple Pontica lineages colonised each of SW Eurasia, SE North America, and NE Asia, with little or no speciation within regions thereafter. Therefore, multiple (3-4) Pontica lineages survived the Quaternary in SW Eurasia, in contrast to other Tertiary relict genera. Pontica comprises two major clades, one of which is wholly Eurasian, and paraphyletic with respect to at least some of the remaining 200 species of subgenus Hymenanthes, which are all distributed in SE Asia. The other clade has species from W and SE North America, SW Eurasia, and NE Asia. According to synonymous matK substitution data, the two clades diverged 9-6 million years ago (mya), whereas most divergence within them happened 5-3 mya. Although the phylogeny indicates probable trans-Atlantic migration for one of two America-Eurasia disjunctions in Pontica, the timing supports migration via Beringia for both.     

Helium: visualization of large scale plant pedigrees

Background

Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphological and physiological traits, such as disease resistance and yield that need to be maintained and improved upon if a commercial variety is to be successful. Computational tools that provide the ability to integrate and visualize this data with pedigree structure, will enable breeders to make better decisions on the lines that are used in crossings to meet both the demands for increased yield/production and adaptation to climate change.

Results

We have used a large and unique set of experimental barley (H. vulgare) data to develop a prototype pedigree visualization system. We then used this prototype to perform a subjective user evaluation with domain experts to guide and direct the development of an interactive pedigree visualization tool called Helium.

Conclusions

We show that Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. We have also verified that users were happy with the abstract representation of pedigrees that we have used in our visualization tool.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-259) contains supplementary material, which is available to authorized users.     

The ionic components of normal human oesophageal epithelium.

The distribution of cations and anions in normal human oesophageal epithelium has been investigated with the pyroantimonate and silver-osmium tetroxide techniques. There is a discontinuous distribution of both ions in the intercellular space. The ions are associated with various organelles, as has already been described in the literature. Specifically, in the oesophageal epithelium, there are a few deposits of pyroantimonate and occasional silver in the membrane coating granules, but here is no apparent relationship of either ion with the tonofilaments or glycogen particles. The superficial cells are leaky and contain fewer ions than the deeper functional layer cells.