Mapping genes controlling root morphology and root distribution in a doubled-haploid population of rice

 A deep thick root system has been demonstrated to have a positive effect on yield of upland rice under water stress conditions. Molecular-marker-aided selection could be helpful for the improvement of root morphological traits, which are otherwise difficult to score. We studied a doubled-haploid population of 105 lines derived from an indica×japonica cross and mapped the genes controlling root morphology and distribution (root thickness, maximum root length, total root weight, deep root weight, deep root weight per tiller, and deep root to shoot ratio). Most putative QTL activity was concentrated in fairly compact regions on chromosomes 1, 2, 3, 6, 7, 8 and 9, but was widely spread on chromosome 5 and largely absent on chromosomes 4, 10, 11 and 12. Between three and six QTLs were identified on different chromosomes for each trait. Individual QTLs accounted for between 4 and 22% of the variation in the traits. Multiple QTL models accounted for between 14 and 49%. The main QTLs were common between traits, showing that it should be possible to modify several aspects of root morphology simultaneously. There was evidence of interaction between marker locations in determining QTL expression. Interacting locations were mostly on different chromosomes and showed antagonistic effects with magnitudes large enough to mask QTL detection. The comparison of QTL locations with another population showed that one to three common QTLs per trait were recovered, among which the most significant was in one or other population. These results will allow the derivation of isogenic lines introgressed with these common segments, separately in the indica and japonica backgrounds. Received: 12 August 1996 / Accepted: 15 November 1996     

Inhibitory effects of anions and active site amino acid sequence of chicken liver L-2-hydroxyacid oxidase A, a member of the FMN-dependent α-hydroxyacid oxidizing enzyme family

Monocarboxylic acids with aliphatic chains were found to be mixed inhibitors of chicken liver L-2-hydroxyacid oxidase A when L-2-hydroxy-4-methylthiobutanoic acid was used as the substrate. The finding that the binding affinity of the enzyme for monocarboxylic acids was directly proportional to the number of carbon atoms in the chain strongly suggests that in addition to the electrostatic interaction due to the carboxyl moiety, hydrophobic forces may also be involved in the binding affinity of monocarboxylic acids to the enzyme's active site. Oxalate, a dicarboxylic acid, also resulted in a mixed-type inhibition of chicken liver L-2-hydroxyacid oxidase A, and, surprisingly, its binding affinity to the enzyme was found to be quite high as compared with monocarboxylic acids. This is probably due to the fact that the two carboxyl groups of oxalate give rise to electrostatic interactions with the positively charged side chains of two adjacent residues in the polypeptide chain. The inhibitory effects of other dicarboxylic acids was found to decrease as the number of carbon atoms in the chain increased. Oxamate was found however to be a novel type of potent inhibitor of the enzyme. All in all, these kinetic studies and the amino acid sequence determination in the active site region after limited proteolysis of the polypeptide chain definitely establish that chicken liver NADH/FMN containing L-2-hydroxyacid oxidase A is a member of the FMN-dependent α-hydroxyacid oxidizing enzyme family.     

Physiological relationship between the temperate phages lambda and phi80

Summary This work deals with the ability of phage 80 to provide defective mutants of with their missing functions. Functions Involved in Recombination. As shown by others, the Int mechanism of 80 cannot excise prophage . However, 80 efficiently excises recombinants from tandem dilysogens, using its Ter mechanism. Likewise, the nonspecific mechanism Red is interchangeable between 80 and . Maturation of DNA by 80. The Ter recombinants excised by 80 from tandem dilysogens are packaged into a 80 protein coat. This contrasts with the fact, already mentionned by Dove, that 80 is extremely inefficient for packaging phage superinfecting a -lysogen. The latter result is also found when the helper phage is a hybrid with the left arm of (80hy4 or 80hy41 — see Fig. 1). However, the maturation of the superinfecting is much more efficient if the 80hy used as a helper has the att-N region of (like 80hy1). Conversely a with the att-N region of 80 (hy6 — see Fig. 1) is packaged more efficiently by 80 or 80hy4 than by 80hy1. It is suggested that the maturation of chromosome superinfecting an immune cell requires a recombination with the helper phage. Vegetative Functions. Among the replicative functoons O and P, the latter only can be supplied by 80. That N mutants are efficiently helped by 80 does not tell that 80 provides the defective with an active N product; the chromosomes are simply packaged into a 80 coat. This shows that 80 is unable to switch on the late genes of . That neither 80 nor any of the 80hy tested can provide an active N product is shown in a more direct way by their complete failure to help N ^-r₁₄; this phage carries a polar mutation which makes the expression of genes O and P entirely N-dependant. The maturation of a N ^- by 80 contrasts with the fact that mutants affected in late genes (A, F or H) are not efficiently helped by 80. This suggests that the products coded by these genes are not interchangeable between 80 and , and that packaging of DNA into 80 coats is possible but inhibited when late proteins are present in the cell. Activation of the Late Genes. Among the im ₈₀ h ⁺ hybrids tested, only 80hy41 is able to switch on the late genes of a N defective mutant. This hybrid differs from the other hybrids studied here, by the fact that it has the Q-S-R region of (see Fig. 1). The results are consistant with the view that the product of Q gene is sufficient for activating the late genes of a DNA. N would thus control the expression of late genes only indirectly by controlling the expression of gene Q (Couturier & Dambly have independantly reached the same conclusion, 1970). Furthermore the failure of 80 and of the 80hy1 and 80hy4 to activate the late genes of would imply that these phages are unable to provide an Q product active on the chromosome Reciprocally, switches on the late genes of prophage 80hy41, but not of prophages 80hy1 and 80hy4. This suggests that the initiation of late genes expression takes place at a main specific site located in the Q-S-R region of the chromosome. The expression of the late genes would thus be sequential, and proceed through the left arm only when steaky ends cohere. Similar conclusions were reached independantly by Toussaint (1969) and by Herskowitz and Signer (1970).

---

---

Ce travail a été réalisé dans le cadre du contrat d'association Euratom-U. L. B. 007-61-10 ABIB et avec l'aide du Fonds de la Recherche Fondamentale Collective.     

ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis

The tagging‐via‐substrate approach designed for the capture of mammal prenylated proteins was adapted to Arabidopsis cell culture. In this way, proteins are in vivo tagged with an azide‐modified farnesyl moiety and captured thanks to biotin alkyne Click‐iT® chemistry with further streptavidin‐affinity chromatography. Mass spectrometry analyses identified four small GTPases and ASG2 (ALTERED SEED GERMINATION 2), a protein previously associated to the seed germination gene network. ASG2 is a conserved protein in plants and displays a unique feature that associates WD40 domains and tetratricopeptide repeats. Additionally, we show that ASG2 has a C‐terminal CaaX‐box that is farnesylated in vitro. Protoplast transfections using CaaX prenyltransferase mutants show that farnesylation provokes ASG2 nucleus exclusion. Moreover, ASG2 interacts with DDB1 (DAMAGE DNA BINDING protein 1), and the subcellular localization of this complex depends on ASG2 farnesylation status. Finally, germination and root elongation experiments reveal that asg2 and the farnesyltransferase mutant era1 (ENHANCED RESPONSE TO ABSCISIC ACID (ABA) 1) behave in similar manners when exposed to ABA or salt stress. To our knowledge, ASG2 is the first farnesylated DWD (DDB1 binding WD40) protein related to ABA response in Arabidopsis that may be linked to era1 phenotypes.     

Mapping QTLs associated with drought resistance in rice: Progress, problems and prospects

The use of molecular markers in the mapping of traits of agronomic importance holds great promise for speeding the development of improved plant varieties and increasing our understanding of the physiological or molecular mechanisms behind biological phenomena. The technique is now being applied to drought resistance in rice (Oryza sativa L.). Drought is important because a considerable proportion of the world rice area is not irrigated and can be prone to water deficit. A large number of people, particular some of the poorest rice farmers, stand to gain if new varieties which combine high yield and drought resistance can be developed. Rice should be particularly useful for the molecular genetic analysis of drought resistance because of its growing role as a model monocot species and the diversity of drought resistance mechanisms which are found in the germplasm. We briefly review the traits which might be considered important in improving drought resistance in rice, before explaining the molecular mapping approach. We review progress at locating quantitative trait loci (QTLs) for individual mechanisms of drought resistance in controlled environment conditions. This includes a detailed comparison of reported QTLs related to root morphological characters. The search for QTLs associated with field performance under drought stress is analysed and the problems associated with understanding the genetic control of a complex physical and physiological phenomenon under conditions of substantial environmental variation are highlighted. We emphasise that the use of near isogenic lines in overcoming some of the problems offers considerable promise for the future.(seconded from CIRAD-CA, France)     

Reversal of MRP-mediated multidrug resistance in human lung cancer cells by the antiprogestatin drug RU486.

Multidrug resistance-associated protein (MRP) and P-glycoprotein (P-gp) are drug efflux pumps conferring multidrug resistance to tumor cells. RU486, an antiprogestatin drug known to inhibit P-gp function, was examined for its effect on MRP activity in MRP-overexpressing lung tumor GLC4/Sb30 cells. In such cells, the antihormone compound was found to increase intracellular accumulation of calcein, a fluorescent compound transported by MRP, in a dose-dependent manner, through inhibition of cellular export of the dye; in contrast, it did not alter calcein levels in parental GLC4 cells. RU486, when used at 10 microM, a concentration close to plasma concentrations achievable in humans, strongly enhanced the sensitivity of GLC4/Sb30 cells towards two known cytotoxic substrates of MRP, the anticancer drug vincristine and the heavy metal salt potassium antimonyl tartrate. Vincristine accumulation levels were moreover up-regulated in RU486-treated GLC4/Sb30 cells. In addition, such cells were demonstrated to display reduced cellular levels of glutathione which is required for MRP-mediated transport of some anticancer drugs. These findings therefore demonstrate that RU486 can down-modulate MRP-mediated drug resistance, in addition to that linked to P-gp, through inhibition of MRP function.     

Proteolipoprotein gene analysis in 82 patients with sporadic Pelizaeus-Merzbacher Disease: duplications, the major cause of the disease, originate more frequently in male germ cells, but point mutations do not. The Clinical European Network on Brain Dysmyelinating Disease.

Pelizaeus-Merzbacher Disease (PMD) is an X-linked developmental defect of myelination affecting the central nervous system and segregating with the proteolipoprotein (PLP) locus. Investigating 82 strictly selected sporadic cases of PMD, we found PLP mutations in 77%; complete PLP-gene duplications were the most frequent abnormality (62%), whereas point mutations in coding or splice-site regions of the gene were involved less frequently (38%). We analyzed the maternal status of 56 cases to determine the origin of both types of PLP mutation, since this is relevant to genetic counseling. In the 22 point mutations, 68% of mothers were heterozygous for the mutation, a value identical to the two-thirds of carrier mothers that would be expected if there were an equal mutation rate in male and female germ cells. In sharp contrast, among the 34 duplicated cases, 91% of mothers were carriers, a value significantly (chi2=9. 20, P<.01) in favor of a male bias, with an estimation of the male/female mutation frequency (k) of 9.3. Moreover, we observed the occurrence of de novo mutations between parental and grandparental generations in 17 three-generation families, which allowed a direct estimation of the k value (k=11). Again, a significant male mutation imbalance was observed only for the duplications. The mechanism responsible for this strong male bias in the duplications may involve an unequal sister chromatid exchange, since two deletion events, responsible for mild clinical manifestations, have been reported in PLP-related diseases.     

Nonideal nest box selection by tree swallows breeding in farmlands: Evidence for an ecological trap?

Animals are expected to select a breeding habitat using cues that should reflect, directly or not, the fitness outcome of the different habitat options. However, human‐induced environmental changes can alter the relationships between habitat characteristics and their fitness consequences, leading to maladaptive habitat choices. The most severe case of such nonideal habitat selection is the ecological trap, which occurs when individuals prefer to settle in poor‐quality habitats while better ones are available. Here, we studied the adaptiveness of nest box selection in a tree swallow (Tachycineta bicolor) population breeding over a 10‐year period in a network of 400 nest boxes distributed along a gradient of agricultural intensification in southern Québec, Canada. We first examined the effects of multiple environmental and social habitat characteristics on nest box preference to identify potential settlement cues. We then assessed the links between those cues and habitat quality as defined by the reproductive performance of individuals that settled early or late in nest boxes. We found that tree swallows preferred nesting in open habitats with high cover of perennial forage crops, high spring insect biomass, and high density of house sparrows (Passer domesticus), their main competitors for nest sites. They also preferred nesting where the density of breeders and their mean number of fledglings during the previous year were high. However, we detected mismatches between preference and habitat quality for several environmental variables. The density of competitors and conspecific social information showed severe mismatches, as their relationships to preference and breeding success went in opposite direction under certain circumstances. Spring food availability and agricultural landscape context, while related to preferences, were not related to breeding success. Overall, our study emphasizes the complexity of habitat selection behavior and provides evidence that multiple mechanisms may potentially lead to an ecological trap in farmlands.     

Virulence and pathogenicity patterns of Trypanosoma brucei gambiense field isolates in experimentally infected mouse: differences in host immune response modulation by secretome and proteomics

Human African trypanosomiasis is characterised by an important clinical diversity. Although Trypanosoma brucei gambiense field stocks isolated from patients in the same focus did not exhibit apparent genetic variability, they showed marked differences in terms of virulence (capacity to multiply inside a host) and pathogenicity (ability of producing mortality) in experimental murine infections. Two strains exhibiting opposite pathogenic and virulence properties in mouse were further investigated through their host-parasite interactions. In vitro, parasite bloodstream forms or soluble factors (or secretome) from both strains induced macrophage arginase as a function of their virulence. Arginase expression, a hallmark of macrophage alternative activation pathway, favours trypanosome bloodstream forms development. Moreover, a comparative proteomic study of the trypanosome stocks' secretomes evidenced both a differential expression of common molecules and the existence of stock specific molecules. This highlighted the potential involvement of the differential expression of the same genome in the diverse infectious properties of trypanosomes.     

Phage response to CRISPR-encoded resistance in Streptococcus thermophilus

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated genes are linked to a mechanism of acquired resistance against bacteriophages. Bacteria can integrate short stretches of phage-derived sequences (spacers) within CRISPR loci to become phage resistant. In this study, we further characterized the efficiency of CRISPR1 as a phage resistance mechanism in Streptococcus thermophilus. First, we show that CRISPR1 is distinct from previously known phage defense systems and is effective against the two main groups of S. thermophilus phages. Analyses of 30 bacteriophage-insensitive mutants of S. thermophilus indicate that the addition of one new spacer in CRISPR1 is the most frequent outcome of a phage challenge and that the iterative addition of spacers increases the overall phage resistance of the host. The added new spacers have a size of between 29 to 31 nucleotides, with 30 being by far the most frequent. Comparative analysis of 39 newly acquired spacers with the complete genomic sequences of the wild-type phages 2972, 858, and DT1 demonstrated that the newly added spacer must be identical to a region (named proto-spacer) in the phage genome to confer a phage resistance phenotype. Moreover, we found a CRISPR1-specific sequence (NNAGAAW) located downstream of the proto-spacer region that is important for the phage resistance phenotype. Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.