Circularity and Independence in Phylogenetic Tests of Ecological Hypotheses

It has been asserted that in order to avoid circularity in phylogenetic tests of ecological hypotheses, one must exclude from the cladistic analysis any characters that might be correlated with that hypothesis. The argument assumes that selective correlation leads to lack of independence among characters and may thus bias the analysis. This argument conflates the idea of independence between the ecological hypothesis and the phylogeny with independence among characters used to construct the tree. We argue that adaptation or selection does not necessarily result in the non-independence of characters, and that characters for a cladistic analysis should be evaluated as homology statements rather than functional ones. As with any partitioning of data, character exclusion may lead to weaker phylogenetic hypotheses, and the practice of mapping characters onto a tree, rather than including them in the analysis, should be avoided. Examples from pollination biology are used to illustrate some of the theoretical and practical problems inherent in character exclusion.     

Phylogenetic analysis of a polyphyletic African genus of Caesalpinioideae (Leguminosae): Monopetalanthus Harms

 To assess the new taxonomy of Monopetalanthus proposed by Wieringa, a phylogenetic study was performed using the chloroplast trnL intron and psbA-trnH spacer, and the nuclear ITS region of the 18-26S rDNA. The phylogeny clearly indicates the polyphyletic nature of Monopetalanthus. The molecular data support the transfer of M. longiracemosus to Tetraberlinia and the newly defined Aphanocalyx, which now includes all the previous Monopetalanthus species having leaflets with a marginal vein. Our analyses do not support the monophyly of the newly described genus Bikinia, which includes four new species and six species transferred from Monopetalanthus. Bikinia occurs either as paraphyletic with Tetraberlinia (chloroplast DNA data) or as a monophyletic group that also includes the new monotypic genus Icuria sister to Tetraberlinia (ITS data). Nonetheless, the molecular phylogeny generally supports the taxonomy of Wieringa in subdividing the genus Monopetalanthus into distinct groups, none of which retains the name Monopetalanthus. Received May 28, 2001; accepted July 6, 2002 Published online: November 20, 2002 Address of the authors: G. Y. Fannie Gervais, Anne Bruneau (e-mail: bruneaua@irbv.umontreal. ca), Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, Québec, Canada, H1X2B2.     

Patterns of Hepatitis C Virus RNA Levels during Acute Infection: The InC3 Study

Background

Understanding the patterns of HCV RNA levels during acute hepatitis C virus (HCV) infection provides insights into immunopathogenesis and is important for vaccine design. This study evaluated patterns of HCV RNA levels and associated factors among individuals with acute infection.

Methods

Data were from an international collaboration of nine prospective cohorts of acute HCV (InC³ Study). Participants with well-characterized acute HCV infection (detected within three months post-infection and interval between the peak and subsequent HCV RNA levels≤120 days) were categorised by a priori-defined patterns of HCV RNA levels: i) spontaneous clearance, ii) partial viral control with persistence (≥1 log IU/mL decline in HCV RNA levels following peak) and iii) viral plateau with persistence (increase or <1 log IU/mL decline in HCV RNA levels following peak). Factors associated with HCV RNA patterns were assessed using multinomial logistic regression.

Results

Among 643 individuals with acute HCV, 162 with well-characterized acute HCV were identified: spontaneous clearance (32%), partial viral control with persistence (27%), and viral plateau with persistence (41%). HCV RNA levels reached a high viraemic phase within two months following infection, with higher levels in the spontaneous clearance and partial viral control groups, compared to the viral plateau group (median: 6.0, 6.2, 5.3 log IU/mL, respectively; P=0.018). In the two groups with persistence, Interferon lambda 3 (IFNL3) CC genotype was independently associated with partial viral control compared to viral plateau (adjusted odds ratio [AOR]: 2.75; 95%CI: 1.08, 7.02). In the two groups with viral control, female sex was independently associated with spontaneous clearance compared to partial viral control (AOR: 2.86; 95%CI: 1.04, 7.83).

Conclusions

Among individuals with acute HCV, a spectrum of HCV RNA patterns is evident. IFNL3 CC genotype is associated with initial viral control, while female sex is associated with ultimate spontaneous clearance.     

The heart's Da Vinci code: a Renaissance at Keystone

At a recent Keystone symposium on "Molecular Pathways in Cardiac Development and Disease" in Colorado, significant advances in the understanding of heart development were discussed. The identification and isolation of cardiovascular progenitors, their modulation by secreted factors, and some tantalizing insights into cardiac regeneration were some of the highlights of what was characterized by some as a renaissance in cardiovascular development.     

Effect of interleukin-1 receptor antagonist (IL-1RA) on histamine and serotonin release by rat basophilic leukemia cells (RBL-2H3) and peritoneal mast cells

Recently, it has been appreciated that cultured mast cells are significant sources of cytokines. However, the role of interkeukin-1 (IL-1) on mast cells and/or basophil degranulation is still unclear. In this report we provide evidence that rat basophilic leukemia cells (RBLC) cultured with a natural inhibitor of IL-1, interleukin-1 receptor antagonist (IL-1RA) (500 ng/ml) for 48 h, strongly inhibited the spontaneous release of serotonin (5HT) and histamine (from 22.50 to 43.49%), compared to untreated cells (control). When IL-1RA-treated and untreated RBLC were stimulated with a secretagogue (anti-IgE), no difference was found in the percent of 5HT and histamine release. Moreover, in another set of experiments using rat peritoneal mast cells (RPMC) treated and untreated with IL-1RA, we found that IL-1RA did not affect the release of 5HT or histamine, even when the secretagogue anti-IgE or compound 48/80 (C48/80) were used. The present studies describe an additional biological activity of IL-1RA, inhibiting histamine and 5HT release from RBLC cultures.Abbreviations IL-1 interleukin-1 - RA receptor antagonist - 5HT serotonin - RBLC rat basophilic leukemia cells - RPMC rat peritoneal mast cells - IgE immunoglobulin E - Fc immunoglobulin E receptor - CPM counts per minute - BSA bovine serum albumin - C48/80 compound 48/80 - TNF tumor necrosis factor     

Localization of the preprosomatostatin-mRNA by in situ hybridization in the ewe hypothalamus

The peptidergic neurohormone somatostatin (SRIF) derives from a precursor called preprosomatostatin (PPS) by proteolysis. We have isolated by RT-PCR and sequenced a partial cDNA coding for the ovine PPS. It contains a 348 base pairs coding sequence that shares strong similarities with previously cloned mammalian cDNAs. The ovine cDNA was used to synthesize radiolabeled cRNA to probe the PPS mRNA in the ewe hypothalamus by in situ hybridization. The PPS mRNA-containing cells are widely distributed in the hypothalamus. According to the number of silver grains over a cell, they show various staining intensities. The distribution of the PPS mRNA is in good agreement with that of the peptide previously determined using immunohistochemistry. The strongest labeled areas include the periventricular region of the paraventricular nucleus and the lateral division of the ventromedial nucleus. The difference in labeling intensity observed in the diverse populations of labeled neurons could reflect various levels of neuronal activity.