Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis

Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which L-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.     

Effects of carrier, sterilisation method, and incubation on survival of Bradyrhizobium japonicum in soybean (Glycine max L.) inoculants

The production and quality of rhizobial inoculants in many developing countries is limited by the availability of suitable carriers or technological limitations. Experiments were conducted to evaluate the potential of various inexpensive and widely available carrier materials. The carriers, evaluated, were: perlite with pH adjusted with calcium carbonate or charcoal, 1:4 mixtures of perlite and malt residue, sugarcane bagasse, coal, and rice husk. We also contrasted sterilisation procedures (autoclaving or gamma irradiation) and incubation after injection (with or without initial two weeks incubation at 28 °C) for these various carriers. Survival of Bradyrhizobium japonicum strain CB1809 was monitored over a period of 6 months upon storage at 4 °C. Most carriers evaluated, were able to maintain rhizobial populations of more than 1 × 10⁹ rhizobia per gram of inoculant over that time period, with mixtures of perlite with either sugarcane bagasse or malt residue supporting the largest rhizobial populations and a mixture of perlite and rice husk the lowest. All carriers supported rhizobial growth over the 6 months period. Initially, rhizobial populations were greater with gamma irradiation than autoclaving, however after 6 months, this response was significant only with the perlite and sugarcane bagasse mixture. The incubation of the inoculant after injection also ultimately did not benefit rhizobial levels for any of the carriers, tested. Using simple sterilisation procedures and without incubating after injection, perlite based carriers can produce high quality inexpensive inoculants, maintaining bacterial populations of more than 1 × 10⁹/g rhizobia for at least 6 months.     

Effects of genotype on rates of substitution during experimental evolution

Rates of molecular evolution may vary widely between populations, yet the causes of this variation are still incompletely understood. Genetic differences between populations may make an important contribution to variation in rates of evolution, owing to differences in fitness, population size, mutation rates, or in the distribution of fitness effects (DFEs) of available beneficial mutations. By whole genome sequencing of Escherichia coli populations experimentally evolved in the presence of a quinolone antibiotic, we found that rates of substitution varied by genotype, with evidence for a contribution from a genotype's starting fitness. Subsequent targeted sequencing showed that genotypes with high average substitution rates were more likely to undergo the simultaneous fixation of several mutations, consistent with theoretical models of multiple mutation dynamics. Moreover, patterns of substitution were indicative of epistatic relationships between known resistance mutations.     

No band color effects on male courtship rate or body mass in the zebra finch: four experiments and a meta-analysis

Replication of experiments is essential for distinguishing real effects from type 1 errors and idiosyncrasies. One of the most replicated experiments in behavioral ecology is the presumed manipulation of male attractiveness in zebra finches by adding red or green color bands. Red-banded males were found to have higher fitness than green-banded males, and most empirical evidence suggests that this effect is mediated by female mating preferences rather than by male-male competition. A recent study, however, reported that color bands affected male courtship rate and body mass independently of female behavior. If this effect was real, some earlier findings of female preferences and maternal effects on offspring traits could potentially be reinterpreted as being mediated indirectly via effects on male behavior. This new perspective seems appealing also in light of a growing interest in bi-directional feedback mechanisms between endocrinology and ornamentation. However, here we report four independent failures to replicate this effect of color bands on courtship rate and body mass. Combining this new experimental data with all the published evidence in a meta-analysis shows that color bands seem to affect neither male courtship rate (average effect size d?=?0.02) nor male body mass (d?=?-0.07). The present case is a reminder that replication of experiments lies at the heart of distinguishing between real effects and false positive findings.     

In vitro targeting of avidin-expressing glioma cells with biotinylated persistent luminescence nanoparticles

Far red emitting persistent luminescence nanoparticles (PLNP) were synthesized and functionalized with biotin to study their targeting ability toward biotin-binding proteins. First, the interaction of biotin-decorated PLNP with streptavidin, immobilized on a plate, was shown to be highly dependent on the presence of a PEG spacer between the surface of the nanoparticles and the biotin ligand. Second, interaction between biotin-PEG-PLNP and free neutravidin in solution was confirmed by fluorescence microscopy. Finally, in vitro binding study on BT4C cells expressing lodavin fusion protein, bearing the extracellular avidin moiety, showed that such biotin-covered PLNP could successfully be targeted to malignant glioma cells through a specific biotin-avidin interaction. The influence of nanoparticle core diameter, incubation time, and PLNP concentration on the efficiency of targeting is discussed.     

Lipopolythiourea transfecting agents: lysine thiourea derivatives

Synthetic vectors represent an alternative to recombinant viruses for gene transfer. We have recently explored the transfection potential of a class of noncationic lipids bearing thiourea moieties as DNA-associating headgroups. The encouraging results obtained with lipopolythioureas derived from serinol prompted us to further investigate this family of vectors. In the present study, we considered the transfection properties of a series of derivatives based on a different thiourea polar headgroup bearing a lysine scaffold. The synthesis of these compounds could be readily achieved in three steps with good yields. We found that these lipopolythioureas (LPT) might be considered as alternative systems for gene transfection since their activity reached the same magnitude range as that of cationic vectors in the presence of serum. LPT with 14-carbon length chains appeared to be more efficient as a transfecting agent than the ones with shorter chains. Toxicity studies proved that the hydration film method led to particles well tolerated both by the cells in vitro and by the mice in vivo. The ability to induce gene expression in vivo was demonstrated by intratumoral injection. Finally, biodistribution studies showed that the quantity recovered in blood circulation, 2 h after systemic injection, was improved as compared to that in cationic lipids.     

Impact of Storage Time on the Juice and Sugars Extracted from Chopped and Whole Stalk Sweet Pearl Millet and Sweet Sorghum Biomass

Since they have a high concentrations of fermentable sugars, sweet pearl millet and sweet sorghum are two interesting crops for bioethanol production. However, if the juice is not extracted from the biomass immediately after harvest, the biomass has to be transported and stored for further juice extraction. This delay could affect the amount of juice extracted and its sugar concentration. This paper presents the results of 3 years of experiments where different storage modes (chopped and whole stalks) and various storage time (0 to 14 days) were applied on two different crop species (sweet pearl millet and sweet sorghum). Storing sweet pearl millet as whole stalks for 2 weeks resulted in a water-soluble carbohydrate (WSC) concentration decrease of 52 %, while no significant decrease of the WSC concentration was observed for sweet sorghum. Whole stalks storage is much more efficient than storing the biomass chopped to avoid a rapid sugar loss. However, more juice can be extracted from stored chopped biomass than from stored whole stalks biomass. If the juice cannot be extracted quickly after the harvest, the biomass can be stored as whole stalks to avoid rapid sugar deterioration, especially for sweet sorghum.     

Ribosomal DNA variations in wild and cultivated rubber tree (Hevea brasiliensis).

Ribosomal DNA variations were surveyed to assess the genetic variability among Hevea brasiliensis genetic resources. One hundred and sixty-eight individuals, including 73 cultivated Wickham clones and 95 wild clones from a prospection, were analyzed. Restriction mapping of rDNA units showed that RFLP variations are the result of both length and site (EcoRI) variations in the intergenic spacer (IGS). These variations can be revealed between as well as within individuals. A total of 12 spacer length variants is scored in the whole population, as well as two different ribosomal units (refered as type I and type II), defined by the presence or absence of an EcoRI site. Particular associations between spacer length variants and unit types can be revealed, leading to complex RFLP patterns. Cultivated clones appear to be less variable than prospections but show, however, a relatively high level of variability despite their narrow genetic base. Furthermore, IGS variations allowed a structuring within wild clones to be drawn, based mainly on their geographical origin. Some interesting discrepancies with previous work on isozyme variations are discussed and show the interest of surveying different genetic markers for diversity studies.     

Homoeology and phylogeny of the A,S, and D genomes of the triticinae

Summary Two-dimensional gel electrophoresis of seedling proteins has been undertaken on diploid representatives of the A, S, and DTriticum genomes. The 457 reproducible spots of the hexaploid Chinese Spring were taken into account in the comparisons. More than 82% of the hexaploid spots were found among the representatives of each of the three genomes. Thus, it was proposed that the homoeologous structural loci, on the three homoeologous genomes, can be present in the same allelic forms and that from 72% to 86% of the spots of the hexaploid pattern are in two or three doses. The dendrogram, deduced from the similarity indices computed between the 16 diploid accessions, was very consistent with our present knowledge of the genetic relationships in theTriticum genus. This result, in addition to previous ones, shows that the comparison of two-dimensional protein patterns represents a novel experimental approach for studying the phylogenetic relationships in theTriticinae.     

Corpus luteum function and pregnancy rate in lactating dairy cows given human chorionic gonadotropin at middiestrus

The effect of human chorionic gonadotropin (HCG) on corpus luteum (CL) function in lactating dairy cows and its subsequent effect on pregnancy rates achieved with artificial insemination was studied in two parts. In Part 1, four IM injections at intervals of seven days or two IM injections at a 14 day interval of HCG (10,000 IU) were given to two groups of six cows each, groups A and B respectively, beginning on days 9, 10 or 11 of the estrous cycle. Ten control cows were given 10 ml of isotonic saline solution on days 9, 10 or 11. Interestrous intervals were prolonged by an average of 8.1 and 3.4 days for groups A and B respectively over controls. In Part 2, 200 lactating dairy cows on nine farms were assigned, on an alternate basis at insemination, to control or treatment groups to study the effect of CL prolongation via HCG on pregnancy rate. A single injection of HCG (10,000 IU) was given 10, 11 or 12 days after a first or second insemination. Pregnancy rates for control and treated cows were similar (64 101 = 63% and 58 99 = 59% respectively). Interestrous intervals of treated nonpregnant cows were prolonged by approximately five days. Providing additional time for developing embryos to become established in utero by delaying luteolysis did not improve pregnancy rates achieved with artificial insemination in lactating dairy cows.