Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation-with-migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration-divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London

The combined effects of rivers and refugia generate extreme cryptic fragmentation within the common ground skink (Scincella lateralis)

Rivers can act as both islands of mesic refugia for terrestrial organisms during times of aridification and barriers to gene flow, though evidence for long-term isolation by rivers is mixed. Understanding the extent to which riverine barrier effects can be heightened for populations trapped in mesic refugia can help explain maintenance and generation of diversity in the face of Pleistocene climate change. Herein, we implement phylogenetic and population genetic approaches to investigate the phylogeographic structure and history of the ground skink, Scincella lateralis, using mtDNA and eight nuclear loci. We then test several predictions of a river-refugia model of diversification. We recover 14 well-resolved mtDNA lineages distributed east-west along the Gulf Coast with a subset of lineages extending northward. In contrast, ncDNA exhibits limited phylogenetic structure or congruence among loci. However, multilocus population structure is broadly congruent with mtDNA patterns and suggests that deep coalescence rather than differential gene flow is responsible for mtDNA-ncDNA discordance. The observed patterns suggest that most lineages originated from population vicariance due to riverine barriers strengthened during the Plio-Pleistocene by a climate-induced coastal distribution. Diversification due to rivers is likely a special case, contingent upon other environmental or biological factors that reinforce riverine barrier effects. © 2009 The Society for the Study of Evolution

Influence of Container Color, Media Depth, and Subsequent Light Availability on Stem Elongation of Longleaf Pine

Nathan G. Bolner is an undergraduate student in the School of Agricultural Sciences and Forestry at Louisiana Tech University. D. Paul Jackson is an Assistant Professor in the School of Agricultural Sciences and Forestry at Louisiana Tech Universit

Singular electrostatic energy of nanoparticle clusters

The binding of clusters of metal nanoparticles is partly electrostatic. We address difficulties in calculating the electrostatic energy when high charging energies limit the total charge to a single quantum, entailing unequal potentials on the particles. We show that the energy at small separation $h$ has a strong logarithmic dependence on $h$. We give a general law for the strength of this logarithmic correction in terms of a) the energy at contact ignoring the charge quantization effects and b) an adjacency matrix specifying which spheres of the cluster are in contact and which is charged. We verify the theory by comparing the predicted energies for a tetrahedral cluster with an explicit numerical calculation.Comment: 17 pages, 3 figures. Submitted to Phys Rev

Cadherin-26 (CDH26) regulates airway epithelial cell cytoskeletal structure and polarity.

Polarization of the airway epithelial cells (AECs) in the airway lumen is critical to the proper function of the mucociliary escalator and maintenance of lung health, but the cellular requirements for polarization of AECs are poorly understood. Using human AECs and cell lines, we demonstrate that cadherin-26 (CDH26) is abundantly expressed in differentiated AECs, localizes to the cell apices near ciliary membranes, and has functional cadherin domains with homotypic binding. We find a unique and non-redundant role for CDH26, previously uncharacterized in AECs, in regulation of cell-cell contact and cell integrity through maintaining cytoskeletal structures. Overexpression of CDH26 in cells with a fibroblastoid phenotype increases contact inhibition and promotes monolayer formation and cortical actin structures. CDH26 expression is also important for localization of planar cell polarity proteins. Knockdown of CDH26 in AECs results in loss of cortical actin and disruption of CRB3 and other proteins associated with apical polarity. Together, our findings uncover previously unrecognized functions for CDH26 in the maintenance of actin cytoskeleton and apicobasal polarity of AECs

Scattering From a Two Dimensional Array of Flux Tubes: A Study of The Validity of Mean Field Theory

Mean Field Theory has been extensively used in the study of systems of anyons in two spatial dimensions. In this paper we study the physical grounds for the validity of this approximation by considering the Quantum Mechanical scattering of a charged particle from a two dimensional array of magnetic flux tubes. The flux tubes are arranged on a regular lattice which is infinitely long in the ``$y$'' direction but which has a (small) finite number of columns in the ``$x$'' direction. Their physical size is assumed to be infinitesimally small. We develop a method for computing the scattering angle as well as the reflection and transmission coefficients to lowest order in the Aharonov--Bohm interaction. The results of our calculation are compared to the scattering of the same particle from a region of constant magnetic field whose magnitude is equal to the mean field of all the flux tubes. For an incident plane wave, the Mean Field approximation is shown to be valid provided the flux in each tube is much less than a single flux quantum. This is precisely the regime in which Mean Field Theory for anyons is expected to be valid. When the flux per tube becomes of order 1, Mean Field Theory is no longer valid.Comment: 23 pages, University of British Columbia Preprint UBCTP93-01

Teleworking practice in small and medium-sized firms: Management style and worker autonomy

In an empirical study of teleworking practices amongst small and medium-sized enterprises (SMEs) in West London, organisational factors such as management attitudes, worker autonomy and employment flexibility were found to be more critical than technological provision in facilitating successful implementation. Consequently, we argue that telework in most SMEs appears as a marginal activity performed mainly by managers and specialist mobile workers

Results of a randomized, double-blind phase II clinical trial of NY-ESO-1 vaccine with ISCOMATRIX adjuvant versus ISCOMATRIX alone in participants with high-risk resected melanoma.

BACKGROUND: To compare the clinical efficacy of New York Esophageal squamous cell carcinoma-1 (NY-ESO-1) vaccine with ISCOMATRIX adjuvant versus ISCOMATRIX alone in a randomized, double-blind phase II study in participants with fully resected melanoma at high risk of recurrence. METHODS: Participants with resected stage IIc, IIIb, IIIc and IV melanoma expressing NY-ESO-1 were randomized to treatment with three doses of NY-ESO-1/ISCOMATRIX or ISCOMATRIX adjuvant administered intramuscularly at 4-week intervals, followed by a further dose at 6 months. Primary endpoint was the proportion free of relapse at 18 months in the intention-to-treat (ITT) population and two per-protocol populations. Secondary endpoints included relapse-free survival (RFS) and overall survival (OS), safety and NY-ESO-1 immunity. RESULTS: The ITT population comprised 110 participants, with 56 randomized to NY-ESO-1/ISCOMATRIX and 54 to ISCOMATRIX alone. No significant toxicities were observed. There were no differences between the study arms in relapses at 18 months or for median time to relapse; 139 vs 176 days (p=0.296), or relapse rate, 27 (48.2%) vs 26 (48.1%) (HR 0.913; 95% CI 0.402 to 2.231), respectively. RFS and OS were similar between the study arms. Vaccine recipients developed strong positive antibody responses to NY-ESO-1 (p≤0.0001) and NY-ESO-1-specific CD4+ and CD8+ responses. Biopsies following relapse did not demonstrate differences in NY-ESO-1 expression between the study populations although an exploratory study demonstrated reduced (NY-ESO-1)+/Human Leukocyte Antigen (HLA) class I+ double-positive cells in biopsies from vaccine recipients performed on relapse in 19 participants. CONCLUSIONS: The vaccine was well tolerated, however, despite inducing antigen-specific immunity, it did not affect survival endpoints. Immune escape through the downregulation of NY-ESO-1 and/or HLA class I molecules on tumor may have contributed to relapse

Finite covers of random 3-manifolds

A 3-manifold is Haken if it contains a topologically essential surface. The Virtual Haken Conjecture posits that every irreducible 3-manifold with infinite fundamental group has a finite cover which is Haken. In this paper, we study random 3-manifolds and their finite covers in an attempt to shed light on this difficult question. In particular, we consider random Heegaard splittings by gluing two handlebodies by the result of a random walk in the mapping class group of a surface. For this model of random 3-manifold, we are able to compute the probabilities that the resulting manifolds have finite covers of particular kinds. Our results contrast with the analogous probabilities for groups coming from random balanced presentations, giving quantitative theorems to the effect that 3-manifold groups have many more finite quotients than random groups. The next natural question is whether these covers have positive betti number. For abelian covers of a fixed type over 3-manifolds of Heegaard genus 2, we show that the probability of positive betti number is 0. In fact, many of these questions boil down to questions about the mapping class group. We are lead to consider the action of mapping class group of a surface S on the set of quotients pi_1(S) -> Q. If Q is a simple group, we show that if the genus of S is large, then this action is very mixing. In particular, the action factors through the alternating group of each orbit. This is analogous to Goldman's theorem that the action of the mapping class group on the SU(2) character variety is ergodic.Comment: 60 pages; v2: minor changes. v3: minor changes; final versio