Phylogenetic information complexity: Is testing a tree easier than finding it?

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following question: is the amount of sequence data required to accurately reconstruct a tree significantly more than the amount required to test whether or not a candidate tree was the `true' tree? By `significantly', we mean that the two quantities behave the same way as a function of the number of species being considered. We prove that, for a certain type of model, the amount of information required is not significantly different; while for another type of model, the information required to test a tree is independent of the number of leaves, while that required to reconstruct it grows with this number. Our results combine probabilistic and combinatorial arguments.Comment: 15 pages, 3 figure

Ebola virus infection inversely correlates with the overall expression levels of promyelocytic leukaemia (PML) protein in cultured cells

BACKGROUND: Ebola virus causes severe, often fatal hemorrhagic fever in humans. The mechanism of escape from cellular anti-viral mechanisms is not yet fully understood. The promyelocytic leukaemia (PML) associated nuclear body is part of the interferon inducible cellular defense system. Several RNA viruses have been found to interfere with the anti-viral function of the PML body. The possible interaction between Ebola virus and the PML bodies has not yet been explored. RESULTS: We found that two cell lines, Vero E6 and MCF7, support virus production at high and low levels respectively. The expression of viral proteins was visualized and quantified using high resolution immunofluorescence microscopy. Ebola encoded NP and VP35 accumulated in cytoplasmic inclusion bodies whereas VP40 was mainly membrane associated but it was also present diffusely in the cytoplasm as well as in the euchromatic areas of the nucleus. The anti-VP40 antibody also allowed the detection of extracellular virions. Interferon-alpha treatment decreased the production of all three viral proteins and delayed the development of cytopathic effects in both cell lines. Virus infection and interferon-alpha treatment induced high levels of PML protein expression in MCF7 but much less in Vero E6 cells. No disruption of PML bodies, a common phenomenon induced by a variety of different viruses, was observed. CONCLUSION: We have established a simple fixation and immunofluorescence staining procedure that allows specific co-detection and precise sub-cellular localization of the PML nuclear bodies and the Ebola virus encoded proteins NP, VP35 and VP40 in formaldehyde treated cells. Interferon-alpha treatment delays virus production in vitro. Intact PML bodies may play an anti-viral role in Ebola infected cells

Multi-Dimensional Laser Confocal Microscopy on Live Cells in Submicroliter Volumes Using Glass Capillaries

Imaging live cells using laser confocal microscopy requires the use of complex and rather cumbersome incubation chamber systems in order to maintain the correct physiological conditions. The volume of these chambers is in the range of a few hundred microliters. Here we present an easy and convenient alternative in the form of glass capillaries that accommodate volumes of 0.2–10 microliters. The capillaries can be loaded with both suspension and adherent cells. The loaded capillaries are taped on microscope slides and submerged into the immersion oil that covers the objective. The correct temperature is maintained using a thermostat-controlled objective heater. We demonstrate that using microlens enhanced ­rotating Nipkow disc based confocal illumination, in combination with cold CCD cameras, maximum resolution multicolor time lapse fluorescence images can be obtained from live cells. The images obtained are free from disturbing optical distortions. Imaging in submicroliter volumes allows for fluorescence visualization of very rare cell types isolated using flow or affinity sorting or obtained by fine needle biopsies