RANDNA: a random DNA sequence generator

Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.     

Uptake of n-butyl-β-carboline-3-carboxylate by rat cerebral cortex

The existence of transport of butyl-β-carboline-3-carboxylate (βCCB) into rat cerebral cortex was examined in vitro. Accumulation of βCCB was observed within fragments of rat cerebral cortex at 37°C, reaching levels of 9200 pmol βCCB/mg of protein in 30 min. In crude synaptosomal fraction the uptake was rapid, reaching equilibration after 2 min. Kinetic analyses demonstrated that the mechanism was saturable with an estimated K_M of 30 μM and a maximum influx of 2680 pmol/mg of protein/min. The transported material was accumulated inside the synaptosomal vesicles and was identified as βCCB by HPLC. Under our experimental conditions the βCCB uptake was not Na⁺-dependent. The cellular uptake of βCCB in brain tissue supports the hypothesis that this molecule may play a functional role in the brain.     

Sharing N resources in the early growth of rapeseed intercropped with faba bean: does N transfer matter?

Background and aims

Legume-brassica intercrops may help to reduce N fertilizer input. We tested whether (i) intercropping with faba bean can improve N status of rapeseed, and (ii) root complementarity and/or N transfer is involved in such performance.

Methods

Pre-germinated rapeseed and faba bean were grown either together or in monospecific rhizotrons (2 plants per rhizotron). Root growth was recorded. N rhizodeposition of the crops and N transferred between species were assessed using a ¹⁵N stem-labelling method.

Results

Intercropped rapeseeds accumulated 20 % higher amounts of N per plant than monocultures. Up to 32 days after sowing, root distribution in the rhizotrons was favourable to physical sharing of the soil N: 64 % of faba bean root length was located in the upper part, as 70 % was in the lower part for rapeseed. At late flowering of the faba bean (52 days after sowing), N rhizodeposition of the two crops were similar and reached 8 to 9 % of the plant N. N transferred from the faba bean to the rapeseed was similar to that transferred from the rapeseed to the faba bean.

Conclusions

Niche complementarity benefits more intercropped rapeseed than net N fluxes between species in the early growth.     

Two independent activities define Ccm1p as a moonlighting protein in Saccharomyces cerevisiae

Ccm1p is a nuclear-encoded PPR (pentatricopeptide repeat) protein that localizes into mitochondria of Saccharomyces cerevisiae. It was first defined as an essential factor to remove the bI4 [COB (cytochrome b) fourth intron)] and aI4 [COX1 (cytochrome c oxidase subunit 1) fourth intron] of pre-mRNAs, along with bI4 maturase, a protein encoded by part of bI4 and preceding exons that removes the intronic RNA sequence that codes for it. Later on, Ccm1p was described as key to maintain the steady-state levels of the mitoribosome small subunit RNA (15S rRNA). bI4 maturase is produced inside the mitochondria and therefore its activity depends on the functionality of mitochondrial translation. This report addresses the dilemma of whether Ccm1p supports bI4 maturase activity by keeping steady-state levels of 15S rRNA or separately and directly supports bI4 maturase activity per se. Experiments involving loss of Ccm1p, SMDC (sudden mitochondrial deprivation of Ccm1p) and mutations in one of the PPR (pentatricopeptide repeat) motifs revealed that the failure of bI4 maturase activity in CCM1 deletion mutants was not due to a malfunction of the translational machinery. Both functions were found to be independent, defining Ccm1p as a moonlighting protein. bI4 maturase activity was significantly more dependent on Ccm1p levels than the maintenance of 15S rRNA. The novel strategy of SMDC described here allowed the study of immediate short-term effects, before the mutant phenotype was definitively established. This approach can be also applied for further studies on 15S rRNA stability and mitoribosome assembly.     

Further evidence that gonadal steroids do not modulate brain opiate receptors in male rats

It is still unclear whether, in the male rat, castration and androgen replacement affect the binding characteristics of brain opiate receptors. To clarify this issue, the effects exerted by orchidectomy and testosterone (T) replacement on the subpopulation of brain mu opiate receptors were studied in male rats; testosterone was administered via subcutaneous Silastic capsules. Utilizing 3H-dihydromorphine (a mu receptor ligand) it has been shown that the affinity constant (Ka) of brain mu opiate binding sites, measured in plasma membrane preparations, is not affected by castration. When mu receptor concentrations were measured in individual brains, it was found that gonadectomy and T replacement failed to produce any change in the number of mu opiate receptors. These data suggest that, in male rats, gonadal steroids do not develop their central feedback effects by affecting brain mu opiate receptors.     

Effect of oestrus cyclicity on the number of brain opioid mu receptors in the rat

The present experiments have been performed in order to analyse whether the binding characteristics of brain opioid receptors of the mu type vary during the different phases of the oestrous cycle in the female rat. To this purpose different groups of females with a regular 4-day oestrous cycle were killed by decapitation in different phases of their oestrous cycle, i.e. at 10.00 and 16.00 h of the first and second day of dioestrus, at 10.00, 12.00, 14.00, 16.00 18.00 and 20.00 of the day of pro-oestrus, and at 10.00, 12.00 14.00, 16.00 and 18.00 of the day of oestrus. The total brains, after discarding the cerebellum, were homogenized and crude membrane preparations were obtained. On these preparations the maximal binding capacity (Bmax, index of the number of receptors) and the constant of affinity (Ka) for dihydromorphine, a typical ligand of mu opioid receptors were evaluated. Serum concentrations of luteinizing hormone (LH), follicle-stimulating hormone (FSH) and prolactin were measured by specific radioimmunoassays in order to exactly ascertain the different phases of the oestrous cycle. The results obtained show that the number of mu opioid receptors in the whole brain presents significant changes during the different phases of the oestrous cycle. In particular, an increase in the concentration of these receptors was observed at 12.00 h of the day of pro-oestrus and at 18.00 h of the day of oestrus; these fluctuations of the number of mu receptors were not accompanied by any change of their affinity for the ligand.(ABSTRACT TRUNCATED AT 250 WORDS)