The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyse multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize species tree estimation errors under various models of gene flow, such as the isolation-migration model, the n-island model, and gene flow between non-sister species or involving ancestral species, and species boundaries crossed by a single gene copy (allelic introgression) or by a single migrant individual. These patterns of gene flow are explored on species trees of different sizes (4 vs. 10 species), at different time scales (shallow vs. deep), and with different migration rates. Species trees are estimated with the multispecies coalescent model using Bayesian methods (BEST and *BEAST) and with a summary statistic approach (MPEST) that facilitates phylogenomic-scale analysis. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can result in overestimates of population sizes (species tree dilation) and underestimates of species divergence times (species tree compression). Signatures of migration events remain present in the distribution of coalescent times for gene trees, and with sufficient data it is possible to identify those loci that have crossed species boundaries. These results highlight the need for careful sampling design in phylogeographic and species delimitation studies as gene flow, introgression, or incorrect sample assignments can bias the estimation of the species tree topology and of parameter estimates such as population sizes and divergence times

Apolipoprotein E delivery by peritoneal implantation of encapsulated recombinant cells improves the hyperlipidaemic profile in apoE-deficient mice

Plasma apolipoprotein E (apoE) is a 34-kDa polymorphic protein which has atheroprotective actions by clearing remnant lipoproteins and sequestering excess cellular cholesterol. Low or dysfunctional apoE is a risk factor for hyperlipidaemia and atherosclerosis, and for restenosis after angioplasty. Here, in short-term studies designed to establish proof-of-principle, we investigate whether encapsulated recombinant Chinese hamster ovary (CHO) cells can secrete wild-type apoE3 protein in vitro and then determine whether peritoneal implantation of the microcapsules into apoE-deficient (apoE(-/-)) mice reduces their hypercholesterolaemia.Recombinant CHO-E3 cells were encapsulated into either alginate poly-L-lysine or alginate polyethyleneimine/polybrene microspheres. After verifying stability and apoE3 secretion, the beads were then implanted into the peritoneal cavity of apoE(-/-) mice; levels of plasma apoE3, cholesterol and lipoproteins were monitored for up to 14 days post-implantation.Encapsulated CHO-E3 cells continued to secrete apoE3 protein throughout a 60-day study period in vitro, though levels declined after 14 days. This cell-derived apoE3 was biologically active. When conditioned medium from encapsulated CHO-E3 cells was incubated with cultured cells pre-labelled with [H-3]-cholesterol, efflux of cholesterol was two to four times greater than with normal medium (at 8 h, for example, 7.4+/-0.3% vs. 2.4+/-0.2% of cellular cholesterol; P<0.001). Moreover, when secreted apoE3 was injected intraperitoneally into apoE(-/-) mice, apoE3 was detected in plasma and the hyperlipidaemia improved. Similarly, when alginate polyethyleneimine/polybrene capsules were implanted into the peritoneum of apoE(-/-) mice, apoE3 was secreted into plasma and at 7 days total cholesterol was reduced, while atheroprotective high-density lipoprotein (HDL) increased. In a second study, apoE was detectable in plasma of five mice treated with alginate poly-L-lysine beads, 4 and 7 days post-implantation, though not at day 14. Furthermore, their hypercholesterolaemia was reduced, while HDL was clearly elevated in all mice at days 4 and 7 (from 18.4+/-6.2% of total lipoproteins to 31.1+/-6.8% at 7 days; P<0.001); however, these had rebounded by day 14, possibly due to the emergence of anti-apoE antibodies.We conclude that microencapsulated apoE-secreting cells have the potential to ameliorate the hyperlipidaemia of apoE deficiency, but that the technology must be improved to become a feasible therapeutic to treat atherosclerosis. (C) 2004 Elsevier B.V. All rights reserved

Estimates of tropical bromoform emissions using an inversion method

Abstract. Bromine plays an important role in ozone chemistry in both the troposphere and stratosphere. When measured by mass, bromoform (CHBr3) is thought to be the largest organic source of bromine to the atmosphere. While seaweed and phytoplankton are known to be dominant sources, the size and the geographical distribution of CHBr3 emissions remains uncertain. Particularly little is known about emissions from the Maritime Continent, which have usually been assumed to be large, and which appear to be especially likely to reach the stratosphere. In this study we aim to reduce this uncertainty by combining the first multi-annual set of CHBr3 measurements from this region, and an inversion process, to investigate systematically the distribution and magnitude of CHBr3 emissions. The novelty of our approach lies in the application of the inversion method to CHBr3. We find that local measurements of a short-lived gas like CHBr3 can be used to constrain emissions from only a relatively small, sub-regional domain. We then obtain detailed estimates of CHBr3 emissions within this area, which appear to be relatively insensitive to the assumptions inherent in the inversion process. We extrapolate this information to produce estimated emissions for the entire tropics (defined as 20° S–20° N) of 225 Gg CHBr3 yr−1. The ocean in the area we base our extrapolations upon is typically somewhat shallower, and more biologically productive, than the tropical average. Despite this, our tropical estimate is lower than most other recent studies, and suggests that CHBr3 emissions in the coastline-rich Maritime Continent may not be stronger than emissions in other parts of the tropics. M. Ashfold thanks the Natural Environment Research Council (NERC) for a research studentship, and is grateful for support through the ERC ACCI project (project number 267760). N. Harris is supported by a NERC Advanced Research Fellowship. This work was supported through the EU SHIVA project, through the NERC OP3 project, and NERC grants NE/F020341/1 and NE/J006246/1. We also acknowledge the Department of Energy and Climate Change for their support in the development of InTEM (contract GA0201). For field site support we thank S.-M. Phang, A. A. Samah and M. S. M. Nadzir of Universiti Malaya, S. Ong and H. E. Ung of Global Satria, Maznorizan Mohamad, L. K. Peng and S. E. Yong of the Malaysian Meteorological Department, the Sabah Foundation, the Danum Valley Field Centre and the Royal Society. This paper constitutes publication no. 613 of the Royal Society South East Asia Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/979/2014/acp-14-979-2014.html

Statistical Shape Analysis using Kernel PCA

©2006 SPIE--The International Society for Optical Engineering. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited. The electronic version of this article is the complete one and can be found online at: http://dx.doi.org/10.1117/12.641417DOI:10.1117/12.641417Presented at Image Processing Algorithms and Systems, Neural Networks, and Machine Learning, 16-18 January 2006, San Jose, California, USA.Mercer kernels are used for a wide range of image and signal processing tasks like de-noising, clustering, discriminant analysis etc. These algorithms construct their solutions in terms of the expansions in a high-dimensional feature space F. However, many applications like kernel PCA (principal component analysis) can be used more effectively if a pre-image of the projection in the feature space is available. In this paper, we propose a novel method to reconstruct a unique approximate pre-image of a feature vector and apply it for statistical shape analysis. We provide some experimental results to demonstrate the advantages of kernel PCA over linear PCA for shape learning, which include, but are not limited to, ability to learn and distinguish multiple geometries of shapes and robustness to occlusions

Subcortical Source and Modulation of the Narrowband Gamma Oscillation in Mouse Visual Cortex

Primary visual cortex exhibits two types of gamma rhythm: broadband activity in the 30-90 Hz range and a narrowband oscillation seen in mice at frequencies close to 60 Hz. We investigated the sources of the narrowband gamma oscillation, the factors modulating its strength, and its relationship to broadband gamma activity. Narrowband and broadband gamma power were uncorrelated. Increasing visual contrast had opposite effects on the two rhythms: it increased broadband activity, but suppressed the narrowband oscillation. The narrowband oscillation was strongest in layer 4 and was mediated primarily by excitatory currents entrained by the synchronous, rhythmic firing of neurons in the lateral geniculate nucleus (LGN). The power and peak frequency of the narrowband gamma oscillation increased with light intensity. Silencing the cortex optogenetically did not abolish the narrowband oscillation in either LGN firing or cortical excitatory currents, suggesting that this oscillation reflects unidirectional flow of signals from thalamus to cortex

The effect of presenting forage in multi-layered haynets and at multiple sites on night time budgets of stabled horses

The aim of this study was to explore the efficacy of multi-layered haynets and multiple presentation of haynets to increase time spent on feed intake behaviour at night (13 hours observation). For preliminary assessment two horses performing the oral stereotypy of crib biting were included. Six horses received the same amount of forage during a 22-day, crossover study where treatment consisted of either forage presentation in a single small-holed haynet (SH) or the forage was divided between 3 haynet combinations hung up simultaneously = multiple haynets (MH). The three haynets presented simultaneously consisted of a) MH single haynet (same as SH), b) MH double layered haynet and c) MH triple layered haynet. Multiple haynets were presented, in random order, on three sides of the stable. Horses were filmed using a video surveillance camera with infrared light source. Behaviour was observed for at least 4 nights per treatment (one night during the acclimatisation period [nights 2-4] and three nights during the end period [nights 7-11]). The observation period commenced at 16:30 - 17.00h (point of haynets being presented) until 06.00h (all horses) or 9.00h (2 crib-biting horses) the next morning. Data was analysed for normal distribution and Anova between haynets, paired t-tests between treatments and Pearson Correlation were used (SPSS. 17.00; 2012). There was a significant effect of type of haynet (p<0.001) on intake time per kg forage (min/kg for SH: 39; MH all (data combined): 51; MH Single: 27; MH Double: 67; MH Triple: 78; overall sem. 8.9). The overall time budget (minutes per observation hour) showed a significant difference between treatments for eating from haynet, standing still, locomotion and drinking. Horses finished eating from SH haynets at around 01:38 am (±1.05 hours s.d.), were last observed at the double net at 03:00 am and at the triple net at 05:12 am (±1.25 hours s.d.). Based on these results, providing 6 kg of forage in 3 double-layered, 2.5 cm haynets spread around the stable could potentially lead to an increased feeding time of 2 hours per night compared to a single 2.5 cm holed haynet containing 6 kg. From the continuous observation data a clear visual difference in crib-biting pattern and therefore motivation to perform crib-biting emerged between the two stereotypic horses

Rapid transport of East Asian pollution to the deep tropics

Abstract. Anthropogenic emissions from East Asia have increased over recent decades, and under the prevailing westerly winds, these increases have led to changes in atmospheric composition as far afield as North America. Here we show that, during Northern Hemisphere (NH) winter, pollution originating in East Asia also directly affects atmospheric composition in the deep tropics. We present observations of marked intra-seasonal variability in the anthropogenic tracer perchloroethene (C2Cl4) collected at two locations in Borneo during the NH winter of 2008/09. We use the NAME trajectory model to show that the observed enhancements in C2Cl4 mixing ratio are caused by rapid meridional transport, in the form of "cold surges", from the relatively polluted East Asian land mass. In these events air masses can move across &gt; 30° of latitude in 4 days. We then present data from the Monitoring Atmospheric Composition and Climate reanalysis which suggests that air masses high in C2Cl4 may also contain levels of the pollutants carbon monoxide and ozone that are approximately double the typical "background" levels in Borneo. Convection in Southeast Asia can be enhanced by cold surges, and further trajectory calculations indicate that the polluted air masses can subsequently be lifted to the tropical upper troposphere. This suggests a potentially important connection between mid-latitude pollution sources and the very low stratosphere. This work was supported by a NERC consortium grant to the OP3 team, by NCAS, by the European Commission through the SCOUT-O3 project (505390-GOCECF2004), though the ERC ACCI project, Project No 267760, and by NERC western Pacific grant number NE/F020341/1 and NERC CAST grant number NE/J006246/1. M. J. Ashfold thanks NERC for a research studentship. A. D. Robinson acknowledges NERC for their support through small grant project NE/D008085/1. N. R. P. Harris is supported by a NERC Advanced Research Fellowship. We thank the Sabah Foundation, Danum Valley Field Centre and the Royal Society (Glen Reynolds) for field site support. This is paper number X of the Royal Society’s South East Asian Rainforest Research Programme. We are grateful for use of data provided by the MACC-II project, funded by the European Union under the 7th Framework Programme. We also acknowledge use of the NAME atmospheric dispersion model and associated NWP meteorological data sets made available to us by the Met O ce. We acknowledge the significant storage resources and analysis facilities made available to us on JASMIN by STFC CEDA along with the corresponding support teams.This is the published version. It first appeared at: http://www.atmos-chem-phys-discuss.net/14/30705/2014/acpd-14-30705-2014.html

Dynamical renormalization group approach to relaxation in quantum field theory

The real time evolution and relaxation of expectation values of quantum fields and of quantum states are computed as initial value problems by implementing the dynamical renormalization group (DRG).Linear response is invoked to set up the renormalized initial value problem to study the dynamics of the expectation value of quantum fields. The perturbative solution of the equations of motion for the field expectation values of quantum fields as well as the evolution of quantum states features secular terms, namely terms that grow in time and invalidate the perturbative expansion for late times. The DRG provides a consistent framework to resum these secular terms and yields a uniform asymptotic expansion at long times. Several relevant cases are studied in detail, including those of threshold infrared divergences which appear in gauge theories at finite temperature and lead to anomalous relaxation. In these cases the DRG is shown to provide a resummation akin to Bloch-Nordsieck but directly in real time and that goes beyond the scope of Bloch-Nordsieck and Dyson resummations. The nature of the resummation program is discussed in several examples. The DRG provides a framework that is consistent, systematic and easy to implement to study the non-equilibrium relaxational dynamics directly in real time that does not rely on the concept of quasiparticle widths.Comment: LaTex, 27 pages, 2 .ps figure

The role of the helper lipid on the DNA transfection efficiency of lipopolyplex formulations.

Multifunctional, lipopolyplex formulations comprising a mixture of cationic liposomes and cationic, receptor-targeting peptides have potential use in gene therapy applications. Lipopolyplex formulations described here are typically far more efficient transfection agents than binary lipoplex or polyplex formulations. It has been shown previously that the peptide component mediates both DNA packaging and targeting of the nanoparticle while in this report we investigate the contribution of the lipid component. We hypothesised that the lipid components synergise with the peptides in the transfection process by promoting endosomal escape after lipid bilayer fusion. Lipopolyplexes were prepared with cationic liposomes comprising DOTAP with either neutral lipid DOPE or DOPC. DOPE promotes fusogenic, inverted hexagonal lipid structures while DOPC promotes more stable laminar structures. Lipopolyplexes containing DOPE showed substantially higher transfection efficiency than those formulated with DOPC, both in vitro and in vivo. DOPE-containing lipopolyplexes showed rapid endosomal trafficking and nuclear accumulation of DNA while DOPC-containing formulations remained within the late endo-lysosomal compartments. These findings are consistent with previous finding for the role of DOPE in lipoplexes and support the hypothesis regarding the function of the lipid components in lipopolyplexes. These findings will help to inform future lipopolyplex design, strategies and clinical development processes