Maximally selected chi-square statistics for ordinal variables

The association between a binary variable Y and a variable X having an at least ordinal measurement scale might be examined by selecting a cutpoint in the range of X and then performing an association test for the obtained 2 x 2 contingency table using the chi-square statistic. The distribution of the maximally selected chi-square statistic (i.e. the maximal chi-square statistic over all possible cutpoints) under the null-hypothesis of no association between X and Y is different from the known chi-square distribution. In the last decades, this topic has been extensively studied for continuous X variables, but not for non-continuous variables of at least ordinal measurement scale (which include e.g. classical ordinal or discretized continuous variables). In this paper, we suggest an exact method to determine the finite-sample distribution of maximally selected chi-square statistics in this context. This novel approach can be seen as a method to measure the association between a binary variable and variables having an at least ordinal scale of different types (ordinal, discretized continuous, etc). As an illustration, this method is applied to a new data set describing pregnancy and birth for 811 babies.     

Storage oil hydrolysis during early seedling growth

Storage oil breakdown plays an important role in the life cycle of many plants by providing the carbon skeletons that support seedling growth immediately following germination. This metabolic process is initiated by lipases (EC: 3.1.1.3), which catalyze the hydrolysis of triacylglycerols (TAGs) to release free fatty acids and glycerol. A number of lipases have been purified to near homogeneity from seed tissues and analysed for their in vitro activities. Furthermore, several genes encoding lipases have been cloned and characterised from plants. However, only recently has data been presented to establish the molecular identity of a lipase that has been shown to be required for TAG breakdown in seeds. In this review we briefly outline the processes of TAG synthesis and breakdown. We then discuss some of the biochemical literature on seed lipases and describe the cloning and characterisation of a lipase called SUGAR-DEPENDENT1, which is required for TAG breakdown in Arabidopsis thaliana seeds.     

C-terminal Residues Regulate Localization and Function of the Antiapoptotic Protein Bfl-1

Unlike other antiapoptotic members of the Bcl-2 family, Bfl-1 does not contain a well defined C-terminal transmembrane domain, and whether the C-terminal tail of Bfl-1 functions as a membrane anchor is not yet clearly established. The molecular modeling study of the full-length Bfl-1 performed within this work suggests that Bfl-1 may co-exist in two distinct conformational states: one in which its C-terminal helix α9 is inserted in the hydrophobic groove formed by the BH1–3 domains of Bfl-1 and one with its C terminus. Parallel analysis of the subcellular localization of Bfl-1 indicates that even if Bfl-1 may co-exist in two distinct conformational states, most of the endogenous protein is tightly associated with the mitochondria by its C terminus in both healthy and apoptotic peripheral blood lymphocytes as well as in malignant B cell lines. However, the helix α9 of Bfl-1, and therefore the binding of Bfl-1 to mitochondria, is not absolutely required for the antiapoptotic activity of Bfl-1. A particular feature of Bfl-1 is the amphipathic character of its C-terminal helix α9. Our data clearly indicate that this property of helix α9 is required for the anchorage of Bfl-1 to the mitochondria but also regulates the antiapoptotic function Bfl-1.Apoptosis is a highly regulated process that plays a key role in maintaining cellular homeostasis, and a delicate balance between proapoptotic and antiapoptotic regulators of apoptosis pathways ensures the proper survival of cells in a variety of tissues. Imbalance between proapoptotic and antiapoptotic proteins occurs in diseases such as cancer, where an overexpression of antiapoptotic proteins endows cells with a selective survival advantage that promotes malignancy. Bcl-2 family members are essential regulators of the intrinsic apoptotic pathway, which act at the level of mitochondria as initiators of cell death (1). This family comprises nearly 20 proteins divided into three main groups. Antiapoptotic members such as Bcl-2, Bcl-x_L, Bcl-w, Bfl-1, and Mcl-1 promote cell survival, whereas proapoptotic members such as Bax and Bak function as death effectors. The life and death balance is displaced in favor of cell death by proapoptotic BH3-only proteins such as Bim, Bad, Bid, Puma, and Noxa, which interact with antiapoptotic proteins and inactivate their function (2) or directly interact with and activate the Bax-like proteins (3).Distinct subcellular localizations of antiapoptotic members have been reported correlating with the accessibility of their C-terminal tail. The C-terminal tail of the antiapoptotic proteins Bcl-2, Bcl-x_L, and Bcl-w possess a hydrophobic region known to be a membrane anchor domain. Thus, Bcl-2 localizes to mitochondria as well as to the endoplasmic reticulum and nuclear membranes (4, 5, 6), and deletion of its C-terminal amino acids abrogates its targeting to the outer mitochondrial membrane (7). In contrast, in healthy cells, Bcl-x_L and Bcl-w localize mainly in the cytosol because their C-terminal tails are sequestered. Bcl-x_L exists as a homodimer through the exchange of the C-terminal tail bound in the hydrophobic groove of the reciprocal dimer partner (8), whereas the C-terminal tail of Bcl-w occupies its own hydrophobic groove in the monomer form (9, 10). It has been proposed that, following apoptotic stimuli, interaction of the BH3 domain from BH3-only proteins with the hydrophobic groove of Bcl-w or Bcl-x_L liberates their C-terminal tail and then the two proteins translocate to the mitochondria (8, 11).Unlike Bcl-2, Bcl-x_L, and Bcl-w, Bfl-1 and its murine homolog, A1, do not contain a well defined C-terminal transmembrane domain (12, 13). C-terminal ends of these two proteins are similar and contain several hydrophilic residues that interrupt their putative transmembrane hydrophobic domain. Whether the C-terminal tail of Bfl-1 functions as a membrane anchor remains to be clarified. Immunofluorescence analyses in an earlier study have shown that overexpressed human Bfl-1 is predominantly localized in the endoplasmic/nuclear envelope regions (14). Then, recent independent studies, with Bfl-1-overexpressing cells, suggested that Bfl-1 localizes to the mitochondria (15, 16, 17) and that the C-terminal end of Bfl-1 is important for anchoring Bfl-1 to the mitochondria due to GFP-Bfl-1 being associated to the mitochondria, whereas GFP-Bfl-1, devoid of its C-terminal tail, also localizes in the cytosol (16, 18). However, localization of endogenous Bfl-1 has never been investigated. In this study, we present a molecular modeling study of full-length Bfl-1 (FL-Bfl-1), based on the crystal structure of a truncated form of Bfl-1 (residues 1–149) in complex with the BIM-BH3 peptide (Protein Data Bank code 2VM6).⁴ Our model suggests that Bfl-1 may co-exist in two distinct conformational states, the first one with its C-terminal helix α9 (residues 155–175) inserted in the hydrophobic groove formed by the BH1–3 domain of Bfl-1, and the second one with its C-terminal tail. Interestingly, helical wheel projection of the C-terminal helix of Bfl-1 highlights its amphipathic character, a feature of transmembrane helices or membrane anchors. These observations incited the reinvestigation of the subcellular localization of Bfl-1 in both malignant B cell lines and peripheral blood lymphocytes (PBLs).⁵ We demonstrate here that endogenous Bfl-1 is preferentially anchored to the mitochondria in malignant B cell lines but also in healthy PBLs. Moreover, we show that both the anchorage of Bfl-1 to the mitochondria and the anti-apoptotic function of the protein are dependent on the amphipathic nature of the C-terminal helix.     

DLG1/SAP97 modulates transforming growth factor alpha bioavailability

TGFalpha and its receptor EGFR participate in the development of a wide range of tumors including gliomas, the main adult primary brain tumors. TGFalpha soluble form results from the cleavage by the metalloprotease TACE/ADAM17 of the extracellular part of its transmembrane precursor, pro-TGFalpha. To gain insights into the mechanisms underlying TGFalpha bioavailability, a yeast two-hybrid screen was performed to identify proteins interacting with pro-TGFalpha intracellular domain (ICD). DLG1/SAP97 (Discs Large Gene 1 or Synapse Associated Protein 97) was found to interact with both pro-TGFalpha and TACE ICDs through distinct PDZ domains. An in vivo pro-TGFalpha-DLG1-TACE complex was detected in U251 glioma cells and in gliomas-derived tumor initiating cells. Interaction between DLG1 and TACE diminished in response to stimulations promoting pro-TGFalpha shedding. Manipulation of DLG1 levels revealed dual actions of DLG1 on pro-TGFalpha shedding, favoring approximation of pro-TGFalpha and TACE, while limiting TACE full shedding activity. These results show that DLG1 participates in the control of TGFalpha bioavailability through its dynamic interaction with the growth factor precursor and TACE.     

Synthesis and biological activities of new di- and trimeric quinoline derivatives

The synthesis of non-peptidic helix mimetics based on a trimeric quinoline scaffold is described. The ability of these new compounds, as well as their synthetic dimeric intermediates, to bind to various members of the Bcl-2 protein anti-apoptotic group is also evaluated. The most interesting derivative of this new series (compound A) inhibited Bcl-x_L/Bak, Bcl-x_L/Bax and Bcl-x_L/Bid interactions with IC₅₀ values around 25 μM.     

Alien aquatic macroinvertebrates along the lateral dimension of a large floodplain

Floodplains are simultaneously among the most species-rich and the most threatened ecosystems. Alien aquatic macroinvertebrates contribute to this threat but remain scarcely studied in the lateral dimension of floodplains. We modelled the realized ecological niches of the alien species occurring in 24 floodplain channels of the Rhône River. Environmental variables depicting the ecological niches were associated to the lateral hydrological connectivity and light availability, both being modified during floodplain restoration works. Eight alien species were observed and they demonstrated either ubiquity or a restricted niche, with no link to the date of introduction. For most of them, the main river channel appeared as an important dispersal route in the lateral dimension of the floodplain. An increase of both lateral connectivity and light availability favoured most of the modelled species. Consequently, we recommend that sector-scale restoration programmes preserve varying levels of lateral connectivity for floodplain channels to prevent the expansion of alien aquatic macroinvertebrates.     

Drivers of phytoplankton diversity in Lake Tanganyika

In keeping with the theme of this volume, the present article commemorates the 50 years of Hutchinson’s (Am Nat 93:145–159, 1959) famous publication on the ‘very general question of animal diversity’, which obviously leads to the more important question regarding the driving forces of biodiversity and their limitation in various habitats. The study of phytoplankton in large lakes is a challenging task which requires the use of a wide variety of techniques to capture the range of spatial and temporal variations. The analysis of marker pigments may provide an adequate tool for phytoplankton surveys in large water bodies, thanks to automated analysis for processing numerous individual samples, and by achieving sufficient taxonomic resolution for ecological studies. Chlorophylls and carotenoids were analysed by HPLC in water column samples of Lake Tanganyika from 2002 through 2006, at two study sites, off Kigoma (north basin) and off Mpulungu (south basin). Using the CHEMTAX software for calculating contributions of the main algal groups to chlorophyll a, variations of phytoplankton composition and biomass were determined. We also investigated selected samples according to standard taxonomic techniques for elucidating the dominant species composition. Most of the phytoplankton biomass was located in the 0–40 m layer, with maxima at 0 or 20 m, and more rarely at 40 m. Deep chlorophyll maxima (DCM) and surface ‘blooms’ were occasionally observed. The phytoplankton assemblage was essentially dominated by chlorophytes and cyanobacteria, with diatoms developing mainly in the dry season. The dominant cyanobacteria were very small unicells (mostly Synechococcus), which were much more abundant in the southern basin, whereas green algae dominated on average at the northern site. A canonical correspondence analysis (CCA) including the main limnological variables, dissolved nutrients and zooplankton abundance was run to explore environment–phytoplankton relations. The CCA points to physical factors, site and season as key determinants of the phytoplankton assemblage, but also indicates a significant role, depending on the studied site, of calanoid copepods and of nauplii stages. Our data suggest that the factors allowing coexistence of several phytoplankton taxa in the pelagic zone of Lake Tanganyika are likely differential vertical distribution in the water column, which allows spatial partitioning of light and nutrients, and temporal variability (occurring at time scales preventing long-term dominance by a single taxon), along with effects of predation by grazers.