Photochemical cross-linking of Escherichia coli Fpg protein to DNA duplexes containing phenyl(trifluoromethyl)diazirine groups.

Formamidopyrimidine-DNA glycosylase (Fpg protein) of Escherichia coli is a DNA repair enzyme that excises oxidized purine bases, most notably the mutagenic 7-hydro-8-oxoguanine, from damaged DNA. In order to identify specific contacts between nucleobases of DNA and amino acids from the E. coli Fpg protein, photochemical cross-linking was employed using new reactive DNA duplexes containing 5-[4-[3-(trifluoromethyl)-3H-diazirin-3-yl]phenyl]-2'-deoxyuridine dU* residues near the 7-hydro-8-oxoguanosine (oxoG) lesion. The Fpg protein was found to bind specifically and tightly to the modified DNA duplexes and to incise them. The nicking efficiency of the DNA duplex containing a dU* residue 5' to the oxoG was higher as compared to oxidized native DNA. The conditions for the photochemical cross-linking of the reactive DNA duplexes and the Fpg protein have been optimized to yield as high as 10% of the cross-linked product. Our results suggest that the Fpg protein forms contacts with two nucleosides, one 5' adjacent to oxoG and the other 5' adjacent to the cytidine residue pairing with oxoG in the other strand. The approaches developed may be applicable to pro- and eukaryotic homologues of the E. coli Fpg protein as well as to other repair enzymes.     

Synthetic activity of isolated rat liver nuclei : I. Ultrastructural study at various steps of isolation

The incorporation of labelled amino acids into hot TCA-insoluble material was used as a measure of protein elaboration in nuclear fractions and compared with the kinetics and distribution of labelling by means of electronmicroscope autoradiography.The method of isolation and the various controls were designed in order to exclude reasonably that this incorporation could be due to cytoplasmic contamination.The pattern of incorporation was found to be characteristic, as compared with microsomal systems. It was insensitive to RNAse and did not require a cytoplasmic pH 5 fraction or an exogenous energy-yielding system.The localization of the activity in the autoradiographs was not random, but clearly associated with definite regions of the nucleus. The nucleolus was 3 times as radioactive as the rest of the nucleus.These results can be interpreted in favor of the concept that protein synthesis occurs in the nucleus. The theoretical limitations of this conclusion are discussed.     

Is genome size of Lepidoptera linked to host plant range?

Genome size varies considerably among organisms, largely as the result of differences in the content of non‐coding and/or repetitive DNA, such as introns, pseudogenes, or transposable elements, as well as whole‐genome duplications. Genome size is known to correlate with metabolic rates. Because polyphagy also affects the metabolism, a correlation between diet specialization and genome size can be expected. To test this hypothesis, a study was undertaken with five closely related species of stem borers which are easy to rear under artificial conditions, namely Busseola fusca (Fuller), Busseola segeta (Bowden), Busseola nairobica Le Ru, Sesamia calamistis Hampson, and Sesamia nonagrioides Lefebvre (all Lepidoptera: Noctuidae). However, as the number of species was too low for correlating diet with genome size in Lepidoptera in general, literature data from 16 Lepidoptera species were used in addition. The results pointed to a relationship between genome size and the insect's host plant range in Lepidoptera, but below the family level only, with larger genomes in polyphagous compared to specialist species. In addition, the genome size appeared to be influenced not only by host plant range but also by environmental/climatic conditions. Studies to test this hypothesis should be done strictly below the family level.     

Temporal distribution of PBAN‐like immunoreactivity in the hemolymph of Mamestra brassicae females in relation to sex pheromone production and calling behavior

A direct enzyme‐linked immunosorbent assay has been developed and applied to the analysis of PBAN immunoreactivity in female hemolymph of the cabbage armyworm, Mamestra brassicae. PBAN‐IR determinations have been carried out with third scotophase insects at different times of the photoperiod. The rhythm of calling and the pattern of pheromone production by third scotophase females at different times of the photoperiod have also been determined. PBAN‐IR and calling are well correlated. However, whereas pheromone titers decrease, both PBAN‐IR levels and percentage of calling females remain high in the last hours of the scotophase. These results are discussed in the context of the regulation of sex pheromone biosynthesis in M. brassicae. Arch. Insect Biochem. Physiol. 40:80–87, 1999. © 1999 Wiley‐Liss, Inc.     

Excision of uracil residues in DNA: mechanism of action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases.

Various octadeoxynucleotides containing uracil at different positions were synthesized and submitted to the action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases. A uracil residue situated at the 5'-end was excised by the M.luteus enzyme but not by the E.coli one. Uracil residues located at the ultimate and penultimate positions at the 3'-end were not cleaved by either enzymes. At the other central positions, uracil was eliminated with different initial velocities. Single stranded phi X 174 DNA fragments were used to study the influence of the sequence. Cytosine bases were deaminated to give uracil by bisulfite treatment. It was shown that the initial excision velocity of two vicinal uracil residues was decreased. The same observation was made for two uracils separated by one base. A hypothetical scheme is suggested to explain the mechanism of action of uracil-DNA glycosylases.     

Genetic diversity and trait genomic prediction in a pea diversity panel

Background

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection.

Results

A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted.

Conclusion

The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1266-1) contains supplementary material, which is available to authorized users.     

Analyses archéométriques dans la grotte ornée Mayenne-Sciences (Thorigné-en-Charnie, Mayenne)

Since 1998, a multidisciplinary team works on the study of the representations in the cave Mayenne-Sciences (Thorigné-en-Charnie, Mayenne). Particularly, there are trials for U-TH (TIMH) datations of the speleothems recovering the drawings and fossils of the bats; this would help to know at what date the decorated cave was closed. The studies already allowed to know better the black drawings, executed with a wooden charcoal crayon. Thus, it was possible to make removals which gave two dates from the Gravettian phase; this feeds again the discussion about the chronocultural position of this cave, on of the most septentrional caves we know.     

Eumelanin‐based colouration reflects local survival of juvenile feral pigeons in an urban pigeon house

Urbanisation introduces deep changes in habitats, eventually creating new urban ecosystems where ecological functions are driven by human activities. The higher frequency of some phenotypes in urban vs rural/wild areas has led to the assumption that directional selection in urban habitats occurs, which may thereby favour some behavioural and physiological traits in urban animal populations compared to rural ones. However, empirical evidence of directional selection on phenotypic traits in urban areas remains scarce. In this study we tested whether eumelanin‐based colouration could be linked to survival in two urban populations of the feral pigeon Columba livia. A number of studies in different cities pointed out a higher frequency of darker individuals in more urbanised areas compared to rural ones. To investigate whether directional selection through survival on this highly heritable trait could explain such patterns, we conducted mark–recapture studies on two populations of feral pigeons in highly urbanized areas. We predicted that darker coloured individuals would exhibit higher survival and/or philopatry (integrated into ‘local survival’) than paler coloured ones. No difference in local survival was found between adults of different colouration intensities. However, on one site, we found that darker juveniles had a higher local survival probability than light ones. Juvenile local survival on that site was also negatively correlated with the number of chicks born. This suggests the existence of colour‐ and/or density‐dependent selection processes acting on juvenile feral pigeons in urban environments, acting through differential mortality and/or dispersal.