Bases of motifs for generating repeated patterns with wild cards

Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature: matrices (of letter frequency per position in the motif) and patterns. There is no conclusive evidence in favor of either, and recent work has attempted to integrate the two types into a single model. In this paper, we address the formal issue in relation to motifs as patterns. This is essential to get at a better understanding of motifs in general. In particular, we consider a promising idea that was recently proposed, which attempted to avoid the combinatorial explosion in the number of motifs by means of a generator set for the motifs. Instead of exhibiting a complete list of motifs satisfying some input constraints, what is produced is a basis of such motifs from which all the other ones can be generated. We study the computational cost of determining such a basis of repeated motifs with wild cards in a sequence. We give new upper and lower bounds on such a cost, introducing a notion of basis that is provably contained in (and, thus, smaller) than previously defined ones. Our basis can be computed in less time and space, and is still able to generate the same set of motifs. We also prove that the number of motifs in all bases defined so far grows exponentially with the quorum, that is, with the minimal number of times a motif must appear in a sequence, something unnoticed in previous work. We show that there is no hope to efficiently compute such bases unless the quorum is fixed.     

Sorbitol uptake is regulated by glucose through the hexokinase pathway in vegetative peach-tree buds

In peach trees (Prunus persica L. Batsch cv. Redhaven), sorbitol is a primary photosynthetic product and may play an important role in the budbreak process. Surprisingly, before budbreak (from January to early March), the concentration of sorbitol in the xylem sap decreases, while that of hexoses (glucose and fructose) increases. The aim of this work was to study the control of sorbitol uptake into vegetative buds by hexoses. Sorbitol uptake was selectively inhibited by hexoses at low and physiological concentrations and this effect was both reversible and concentration-dependent. In addition, the active uptake of sorbitol significantly declined in the plasma membrane vesicles-enriched fraction purified from glucose-treated vegetative buds, suggesting that the inhibitory action of glucose was at the membrane level. Finally, among several glucose analogues tested, only hexokinase substrates (2-deoxyglucose and mannose) were able to mimic the glucose effect, which was completely blocked by the hexokinase inhibitor mannoheptulose. These results represent the first steps towards a better understanding of polyol transport control in plants.     

The putative Arabidopsis homolog of yeast vps52p is required for pollen tube elongation, localizes to Golgi, and might be involved in vesicle trafficking

The screening of the Versailles collection of Arabidopsis T-DNA transformants allowed us to identify several male gametophytic mutants, including poky pollen tube (pok). The pok mutant, which could only be isolated as a hemizygous line, exhibits very short pollen tubes, explaining the male-specific transmission defect observed in this line. We show that the POK gene is duplicated in the Arabidopsis genome and that the predicted POK protein sequence is highly conserved from lower to higher eukaryotes. The putative POK homolog in yeast (Saccharomyces cerevisiae), referred to as Vps52p/SAC2, has been shown to be located at the late Golgi and to function in a complex with other proteins, Vps53p, Vps54p, and Vps51p. This complex is involved in retrograde trafficking of vesicles between the early endosomal compartment and the trans-Golgi network. We present the expression patterns of the POK gene and its duplicate P2 in Arabidopsis, and of the putative Arabidopsis homologs of VPS53 and VPS54 of yeast. We show that a POK::GFP fusion protein localizes to Golgi in plant cells, supporting the possibility of a conserved function for Vps52p and POK proteins. These results, together with the expression pattern of the POK::GUS fusion and the lack of plants homozygous for the pok mutation, suggest a more general role for POK in polar growth beyond the pollen tube elongation process.     

Effect of 3D nitrogen, dry mass per area and local irradiance on canopy photosynthesis within leaves of contrasted heterogeneous maize crops

BACKGROUND AND AIMS: Nitrogen partitioning within stands has been described fairly comprehensively, especially for C(3) plants in dense stands where the horizontal heterogeneity of foliage distribution is relatively small. Nitrogen has been shown to be distributed vertically and in parallel to light, maximizing carbon assimilation and stand productivity. Conversely, row crops such as maize (C(4) plants) are characterized by strong horizontal heterogeneity of foliage distribution, and a three-dimensional (3D) approach is required to investigate the combined effect of spatial distribution of nitrogen and light on canopy photosynthesis. MODEL: The 3D geometry of maize canopies was modelled with varying densities and at different developmental stages using plant digitizing under field conditions. For lamina parts, photosynthesis was measured and nitrogen content per unit area (N(a)) was described from analysis of nitrogen content per unit mass (N(m)) and dry mass per unit area (M(a)). Hyperbolic relationships between photosynthesis at irradiance saturation (P(max)) and N(a) were established as well as a linear relationship between dark respiration (R(d)) and N(a), whereas quantum efficiency (alpha) was found to be independent of N(a). KEY RESULTS AND CONCLUSIONS: N(m), M(a) and N(a) were shown to change over time vertically (i.e. between laminae), which has been largely reported previously, and horizontally (i.e. within laminae), which has scarcely been described previously. Even if M(a) played a major role in N(a), a strong relationship between N(a) and M(a) could not be demonstrated, whereas several previous studies have found that N(a) was essentially related to M(a) rather than N(m). From simulations of radiative exchange using a 3D volume-based approach and lamina photosynthesis using a hyperbola, it was shown that real patterns of N(a) partitioning could increase daily crop photosynthesis by up to 8 % compared with uniform patterns of N(a), especially for the earliest stages of stand development.     

A new species of wild mice on the Island of Cyprus

A mitochondrial and nuclear gene analysis allowed us to precise the taxonomical position of the two sympatric species of mice known to be present on Cyprus. One of them is the commensal house mouse M. m. domesticus, and the other revealed to be a new taxon that is a sister species of M. spicilegus and M. macedonicus. The new species is equidistant from each of these, the divergence dating around 0.5-1 Myr. Its origin either results from an ancient accidental colonisation of the island or from a recent transportation by the first epipalaeolithic settlers. In this last eventuality, the new species would also exist somewhere else in Asia Minor.     

Spatio-temporal variation in the genetic composition of wild populations of pearl oyster (Pinctada margaritifera cumingii) in French Polynesia following 10 years of juvenile translocation

Abstract The genetic impact of the cultural practice of spat collection and translocation between genetically distinct stocks of black-lipped pearl oyster, Pinctada margaritifera cumingii, was studied by comparing samples collected in the 1980s and 2000s from seven atolls in French Polynesia. An amova revealed homogenization of the previously genetically distinct wild stocks of Tuamotu-Gambier and Society archipelagos (the indices of genetic differentiation among archipelagos and among populations within archipelagos, respectively, Phi(CT) and Phi(ST), decreased from 0.032* and 0.025*, respectively, to 0.006(NS) and 0.007(NS)). These results suggest high success of spontaneous reproduction in farms, probably due to the very high density of cultivated pearl oysters, and underline the importance of genetic monitoring of future hatchery produced stocks.     

Impaired antibody affinity maturation process characterizes a subset of patients with common variable immunodeficiency

Common variable immunodeficiency (CVID) is an heterogeneous syndrome characterized by decreased levels of serum Ig and recurrent bacterial infection. Here, we were interested to study whether a qualitative defect of the affinity Ab maturation process could be combined to the low level of serum Ig in a cohort of 38 CVID patients. For this, we designed a novel and rapid screening test for the detection of hypomutated V gene expressed by memory B cells. This test delineated a subset of 9/38 (23%) CVID patients with an abnormal pattern of Ig V gene mutation. The mean frequency of V gene mutation of this subset was significantly lower (1.74%) compared with other CVID patients (5.46%) and normal donors (6.5%) (p<0.0001). The mean age of this subgroup was significantly higher than other hypogammaglobulinemic patients with normal levels of V gene mutation (p<0.02), whereas no difference in the duration of symptoms was noted between the two groups. This suggests that hypomutation characterizes patients who began CVID late in life. Recently, it was shown that non-Ig sequences, such as the intronic BCL-6 gene, could be the target of the somatic hypermutation process in normal memory B cells. Our finding of a normal mutation frequency of the BCL-6 gene in two hypomutated CVID point to a defect of the Ig targeting of hypermutation machinery in these cases.     

Five gametophytic mutations affecting pollen development and pollen tube growth in Arabidopsis thaliana

Mutant analysis represents one of the most reliable approaches to identifying genes involved in plant development. The screening of the Versailles collection of Arabidopsis thaliana T-DNA insertion transformants has allowed us to isolate different mutations affecting male gametophytic functions and viability. Among several mutated lines, five have been extensively studied at the genetic, molecular, and cytological levels. For each mutant, several generations of selfing and outcrossing have been carried out, leading to the conclusion that all these mutations are tagged and affect only the male gametophyte. However, only one out of the five mutations is completely penetrant. A variable number of T-DNA copies has integrated in the mutant lines, although all segregate at one mutated locus. Two mutants could be defined as "early mutants": the mutated genes are presumably expressed during pollen grain maturation and their alteration leads to the production of nonfunctional pollen grains. Two other mutants could be defined as "late mutant" since their pollen is able to germinate but pollen tube growth is highly disturbed. Screening for segregation ratio distortions followed by thorough genetic analysis proved to be a powerful tool for identifying gametophytic mutations of all phases of pollen development.