Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brad

Proof techniques for CCS

Proofs of observational equivalence of behaviour expressions in Milner's Calculus of Communicating Systems can be quite lengthy, and as larger and more practical systems of agents are considered the need for shorter proof techniques becomes more important. In this thesis a number of results about the calculus are proved which give rise to give more natural techniques. Three principal areas of research are presented:(i) A study of strong confluence and determinacy is made, extending Hilner's work to the whole calculus - the appropriate modifications to take value-passing into account are motivated and defined, and a strong confluence theorem is proved. It is shown that a useful subcalculus of CCS is strongly confluent.(ii) An investigation into criteria for uniqueness of solution of equations pf the form b = Fib] is performed. To do this a concept of derivations of an agent A "causing" derivations of FlAl is defined; using this, conditions are imposed on F which imply uniqueness, and a study follows of how these conditions relate to the structure of F.(iii) By using an alternative, stronger, definition of observational equivalence as a maximal fixed point it is found that equivalences can be demonstrated by constructing bisimulations between agents, and results leading to an algorithm for such constructions are presented. Also, using this alternative definition a weaker form of confluence can be defined very easily, and this is investigated.The theoretical material in this thesis is supplemented by examples demonstrating how the results proved can be applied to give proof techniques for use within the calculus

Loading fluorescent Ca²⁺ indicators into living cells

Small-molecule fluorescent Ca2+ reporters are the most widely used tools in the field of Ca2+ signaling. The excellent spatial and temporal resolution afforded by fluorescent reporters has driven the understanding of Ca2+ as a messenger in many different cell types. In many situations, the cellular loading and monitoring of fluorescent Ca2+ indicators is quite trivial. However, there are numerous pitfalls that require consideration to ensure that optimal data are recorded. Fluorescent Ca2+ indicators have carboxylic acid groups for binding of Ca2+. Because these “free-acid” forms of the indicators are hydrophilic they cannot readily cross cell membranes and need to be introduced into cells using techniques such as microinjection, pinocytosis, or diffusion from a patch pipette. However, the most convenient and widely used method for loading indicators into cells is as hydrophobic compounds in which the carboxylic acid groups are esterified (commonly as acetoxymethyl [AM] or acetate esters). The ester versions of the indicators permeate the plasma membrane. The Ca2+-sensitive, free-acid form of the indicator is liberated following hydrolysis of the ester groups by intracellular esterases

Predictive habitat modelling as a tool to assess the change in distribution and extent of an OSPAR priority habitat under an increased ocean temperature scenario:consequences for marine protected area networks and management

The aims of this study were to determine the extent and distribution of an OSPAR priority habitat under current baseline ocean temperatures; to illustrate the prospect for habitat loss under a changing ocean temperature scenario; and to demonstrate the potential application of predictive habitat mapping in "future-proofing" conservation and biodiversity management. Maxent modelling and GIS environmental envelope analysis of the biogenic bed forming species, Modiolus modiolus was carried out. The Maxent model was tested and validated using 75%/25% training/test occurrence records and validated against two sampling biases (the whole study area and a 20km buffer). The model was compared to the envelope analysis and the area under the receiver operating characteristic curve (Area Under the curve; AUC) was evaluated. The performance of the Maxent model was rated as 'good' to 'excellent' on all replicated runs and low variation in the runs was recorded from the AUC values. The extent of "most suitable", "less suitable" and "unsuitable" habitat was calculated for the baseline year (2009) and the projected increased ocean temperature scenarios (2030, 2050, 2080 and 2100). A loss of 100% of "most suitable" habitat was reported by 2080. Maintaining a suitable level of protection of marine habitats/species of conservation importance may require management of the decline and migration rather than maintenance of present extent. Methods applied in this study provide the initial application of a plausible "conservation management tool"

Adaptive management, international co-operation and planning for marine conservation hotspots in a changing climate

Acknowledgements This work received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (Grant reference HR09011) and contributing institutions.Peer reviewedPublisher PD

Testing a global city hypothesis : an assessment of polarization across US cities

Social polarization is perhaps most evident within the world's large cities where we can easily observe stark contrasts between wealth and poverty. A world city theoretical perspective has emerged that associates large cities importance in a global network of cities to the degree of internal polarization within these cities. The research reported here locates 57 large US cities within this world city hierarchy and then empirically examines the hypothesized positive association between global centrality and social polarization using a multivariate, cross-city analysis. The findings are mixed, with some evidence that global centrality increases income polarization, but only in the context of higher levels of immigration. There is no evidence that a city's centrality affects occupational polarization. We conclude by suggesting implications for the world city literature and future research

Acetylcholine-induced Calcium Signaling and Contraction of Airway Smooth Muscle Cells in Lung Slices

The Ca2+ signaling and contractility of airway smooth muscle cells (SMCs) were investigated with confocal microscopy in murine lung slices (∼75-μm thick) that maintained the in situ organization of the airways and the contractility of the SMCs for at least 5 d. 10–500 nM acetylcholine (ACH) induced a contraction of the airway lumen and a transient increase in [Ca2+]i in individual SMCs that subsequently declined to initiate multiple intracellular Ca2+ oscillations. These Ca2+ oscillations spread as Ca2+ waves through the SMCs at ∼48 μm/s. The magnitude of the airway contraction, the initial Ca2+ transient, and the frequency of the subsequent Ca2+ oscillations were all concentration-dependent. In a Ca2+-free solution, ACH induced a similar Ca2+ response, except that the Ca2+ oscillations ceased after 1–1.5 min. Incubation with thapsigargin, xestospongin, or ryanodine inhibited the ACH-induced Ca2+ signaling. A comparison of airway contraction with the ACH-induced Ca2+ response of the SMCs revealed that the onset of airway contraction correlated with the initial Ca2+ transient, and that sustained airway contraction correlated with the occurrence of the Ca2+ oscillations. Buffering intracellular Ca2+ with BAPTA prohibited Ca2+ signaling and airway contraction, indicating a Ca2+-dependent pathway. Cessation of the Ca2+ oscillations, induced by ACH-esterase, halothane, or the absence of extracellular Ca2+ resulted in a relaxation of the airway. The concentration dependence of the airway contraction matched the concentration dependence of the increased frequency of the Ca2+ oscillations. These results indicate that Ca2+ oscillations, induced by ACH in murine bronchial SMCs, are generated by Ca2+ release from the SR involving IP3- and ryanodine receptors, and are required to maintain airway contraction