Mapping characters on a tree with or without the outgroups

A character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non‐exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest. © The Willi Hennig Society 2004.     

Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)

An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds. © The Willi Hennig Society 2004.     

Explorations cardiologiques nucléaires dans la cardiomyopathie de Takotsubo

Transient left ventricular apical ballooning syndrome, also known as Takotsubo cardiomyopathy (TTC) was described for the first time in Japan in the earliest nineties. It represents 1 to 2 % of acute cardiac events and mimics closely acute myocardial infarction. The aim of this study was to investigate ^99mTc-tetrofosmine or ²⁰¹Thallium myocardial Single Photon Emission Computed Tomography (SPECT), ¹²³I-metaIodoBenzylGuanidine (¹²³I-mIBG) myocardial SPECT and myocardial Positron Emission Tomography using ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) in patients with TTC, assessing respectively left ventricular perfusion, innervation and metabolism. We studied four patients (three females) with TTC. We performed two weeks after acute phase (subacute phase) myocardial perfusion SPECT and ¹²³I-mIBG myocardial SPECT for each patient. Two of them underwent myocardial PET with FDG. Then, we assessed left ventricular innervation and metabolism three months (chronic phase I) and more than six months (chronic phase II) after the acute phase. We compared the discrepancies between radionuclides uptake in the left ventricular apical region during a follow-up period of more than six months. In subacute phase, perfusion SPECT was normal for each patient. Conversely, ¹²³I-mIBG SPECT and FDG-PET showed concordant apical uptake defect. This perfusion-metabolism pattern called “inverse flow-metabolism mismatch” is the metabolic state of stunned myocardium. After three months, we found improvement of apical tracer uptake in both FDG-PET and ¹²³I-mIBG SPECT. These findings suggest that TTC is characterized by myocardial apical stunning which is related to a disturbance of cardiac sympathetic innervation. ¹²³I-mIBG SPECT might be useful to diagnose earlier this pathology and to rule out acute myocardial infarction.     

Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects

Hexapoda includes 33 commonly recognized orders, most of them insects. Ongoing controversy concerns the grouping of Protura and Collembola as a taxon Ellipura, the monophyly of Diplura, a single or multiple origins of entognathy, and the monophyly or paraphyly of the silverfish (Lepidotrichidae and Zygentoma s.s.) with respect to other dicondylous insects. Here we analyze relationships among basal hexapod orders via a cladistic analysis of sequence data for five molecular markers and 189 morphological characters in a simultaneous analysis framework using myriapod and crustacean outgroups. Using a sensitivity analysis approach and testing for stability, the most congruent parameters resolve Tricholepidion as sister group to the remaining Dicondylia, whereas most suboptimal parameter sets group Tricholepidion with Zygentoma. Stable hypotheses include the monophyly of Diplura, and a sister group relationship between Diplura and Protura, contradicting the Ellipura hypothesis. Hexapod monophyly is contradicted by an alliance between Collembola, Crustacea and Ectognatha (i.e., exclusive of Diplura and Protura) in molecular and combined analyses.     

Kinetics and metabolic specificities of Vero cells in bioreactor cultures with serum-free medium

The aim of this study was to understand the metabolism kinetics of Vero cells grown on microcarriers in bioreactors in serum-free medium (SFM). We sought to determine what nutrients are essential for Vero cells and how they are consumed. Contrary to glucose and to most of the amino acids, glutamine and serine were very quickly depleted in this medium and can be supposed to be responsible for cell apoptosis. Lactate and ammonium ions did not reach toxic levels for Vero cells. We payed more attention to the lactate metabolism. Usually we observed that after about 2 days lactate was consumed in serum-containing media, but its concentration plateaud in SFM. Moreover, the addition of serum in SFM provoked lactate consumption and the rate of glucose and glutamine consumption was twice as high as in the SFM not supplemented with serum. The depletion of glutamine and serine and the metabolic deviations leading to a shortage of intermediate products required for other metabolic pathways probably contribute to the lower cell yield and higher cell death rate in SFM. This revised version was published online in July 2006 with corrections to the Cover Date.     

The glycerol channel Fps1p mediates the uptake of arsenite and antimonite in Saccharomyces cerevisiae

The Saccharomyces cerevisiae FPS1 gene encodes a glycerol channel protein involved in osmoregulation. We present evidence that Fps1p mediates influx of the trivalent metalloids arsenite and antimonite in yeast. Deletion of FPS1 improves tolerance to arsenite and potassium antimonyl tartrate. Under high osmolarity conditions, when the Fps1p channel is closed, wild-type cells show the same degree of As(III) and Sb(III) tolerance as the fps1Delta mutant. Additional deletion of FPS1 in mutants defective in arsenite and antimonite detoxification partially suppresses their hypersensitivity to metalloid salts. Cells expressing a constitutively open form of the Fps1p channel are highly sensitive to both arsenite and antimonite. We also show by direct transport assays that arsenite uptake is mediated by Fps1p. Yeast cells appear to control the Fps1p-mediated pathway of metalloid uptake, as expression of the FPS1 gene is repressed upon As(III) and Sb(III) addition. To our knowledge, this is the first report describing a eukaryotic uptake mechanism for arsenite and antimonite and its involvement in metalloid tolerance.     

The flexibility of Apicomplexa parasites in lipid metabolism

Apicomplexa are obligate intracellular parasites responsible for major human infectious diseases such as toxoplasmosis and malaria, which pose social and economic burdens around the world. To survive and propagate, these parasites need to acquire a significant number of essential biomolecules from their hosts. Among these biomolecules, lipids are a key metabolite required for parasite membrane biogenesis, signaling events, and energy storage. Parasites can either scavenge lipids from their host or synthesize them de novo in a relict plastid, the apicoplast. During their complex life cycle (sexual/asexual/dormant), Apicomplexa infect a large variety of cells and their metabolic flexibility allows them to adapt to different host environments such as low/high fat content or low/high sugar levels. In this review, we discuss the role of lipids in Apicomplexa parasites and summarize recent findings on the metabolic mechanisms in host nutrient adaptation.     

Disrupting the plastidic iron-sulfur cluster biogenesis pathway in Toxoplasma gondii has pleiotropic effects irreversibly impacting parasite viability

Like many other apicomplexan parasites, Toxoplasma gondii contains a plastid harboring key metabolic pathways, including the sulfur utilization factor (SUF) pathway that is involved in the biosynthesis of iron-sulfur clusters. These cofactors are crucial for a variety of proteins involved in important metabolic reactions, potentially including plastidic pathways for the synthesis of isoprenoid and fatty acids. It was shown previously that impairing the NFS2 cysteine desulfurase, involved in the first step of the SUF pathway, leads to an irreversible killing of intracellular parasites. However, the metabolic impact of disrupting the pathway remained unexplored. Here, we generated another mutant of this pathway, deficient in the SUFC ATPase, and investigated in details the phenotypic consequences of TgNFS2 and TgSUFC depletion on the parasites. Our analysis confirms that Toxoplasma SUF mutants are severely and irreversibly impacted in division and membrane homeostasis, and suggests a defect in apicoplast-generated fatty acids. However, we show that increased scavenging from the host or supplementation with exogenous fatty acids do not fully restore parasite growth, suggesting that this is not the primary cause for the demise of the parasites and that other important cellular functions were affected. For instance, we also show that the SUF pathway is key for generating the isoprenoid-derived precursors necessary for the proper targeting of GPI-anchored proteins and for parasite motility. Thus, we conclude plastid-generated iron-sulfur clusters support the functions of proteins involved in several vital downstream cellular pathways, which implies the SUF machinery may be explored for new potential anti-Toxoplasma targets.     

The geometric mean length, a new statistic to describe the distribution of character steps on a tree

The geometric mean length (GML) is proposed as a new statistic aimed at describing the evenness of character changes on a tree for a given set of character optimizations. It is the geometric mean of the number of steps on each branch of the tree, varying between a maximum value when all branch lengths are equal, and a minimum value when all branches but one have only one character step. It can be scaled according to its theoretical maximum value, thus indicating a relative GML that allows a comparison of the evenness of character steps between different tree topologies.     

The PhysioFlow Thoracic Impedancemeter Is Not Valid for the Measurements of Cardiac Hemodynamic Parameters in Chronic Anemic Patients

The aim of the present study was to test the validity of the transthoracic electrical bioimpedance method PhysioFlow® to measure stroke volume in patients with chronic anemia. Stroke volume index (SVI), as well as cardiac index (CI) obtained by transthoracic electrical bioimpedance method and doppler echocardiography were compared in healthy subjects (n = 25) and patients with chronic anemia (i.e. mainly with sickle cell anemia; n = 32), at rest. While doppler echocardiography was able to detect difference in SVI between the two populations, the Physioflow® failed to detect any difference. Bland & Altman analyses have demonstrated no interchangeability between the two methods to assess CI and SVI in anemic patients and healthy subjects. While doppler echocardiography displayed a good concordance for SVI results with those obtained in the literature for anemic patients, the Physioflow® did not. Finally, in contrast to doppler echocardiography: 1) the CI obtained with the Physioflow® was not correlated with the hemoglobin level and 2) the stroke volume determined by the Physioflow® was highly influenced by body surface area. In conclusion, our findings indicate that the Physioflow® device is inaccurate for the measurement of SVI and CI in patients with chronic anemia and has a poor accuracy for the measurement of these parameters in African healthy subjects.