Binding mode of 6ECDCA,a potent bile acid agonist of the farnesoid X receptor (FXR)

Based on the folding conservation across the nuclear receptor superfamily and the sequence homology with RAR-gamma, we report the construction of a three dimensional model of the ligand binding domain of FXR. The model is exploited for the elucidation of the binding mode of 6alpha-ethyl-chenodeoxycholic acid. The results of the docking experiments give quite clear indications that the bile acid derivative would bind the receptor in a mode significantly different than that observed for agonists of other nuclear receptor superfamily.     

Methyl jasmonate vapor increases the developmentally controlled synthesis of alkaloids in Catharanthus and Cinchona seedlings

Shortly after germination, alkaloids are rapidly synthesized in seedlings of both Catharanthus roseus L.G. Don and Cinchona ledgeriana Moens. The effect of low-level, atmospheric methyl jasmonate on this developmentally controlled process was studied. In both species, about 1 p.p.m. of methyl jasmonate vapor significantly enhanced alkaloid synthesis during germination, resulting in a doubling of alkaloid content in seedlings. Treatment with methyl jasmonate resulted in increased allocation of alkaloid precursors and in enhanced enzyme activities in alkaloid biosynthesis. The ability of methyl jasmonate to increase alkaloid biosynthesis decreased with age of the seedlings. Susceptibility of the process to methyl jasmonate was confined to a narrow time interval where the developmentally regulated onset of alkaloid synthesis occurred. When methyl jasmonate was applied at later developmental stages, its ability to enhance alkaloid content in the seedlings declined sharply.     

Open field trial of genetically modified parthenocarpic tomato: seedlessness and fruit quality

Background

Precise analysis of expression-regulating elements, such as enhancers and insulators, requires that they be tested under reproducible, isogenic conditions. The commonly used methods of transfecting DNA into cell lines and selecting for drug resistance lack the requisite precision, as they yield cell lines in which varying numbers of gene copies have inserted at varying and undefined sites. By contrast, recombination-mediated cassette exchange (RMCE), by which a site-specific recombinase is used to place a single copy of a transgene at a constant chromosomal site of a cell line, offers the necessary precision. Although RMCE is generally applicable, many regulatory elements of interest are tissue-specific in their function and so require cell lines in the appropriate ontogenetic state.

Results

As reported here, we have used RMCE in a mouse B hybridoma cell line to establish a system with several additional advantages. To avoid the non-physiological features of prokaryotic DNA, this system uses the immunoglobulin μ heavy chain (IgH) gene from the hybridoma as the reporter. Expression can be measured simply by bulk culture assays (ELISA, Northern blot) and single cell assays (flow cytometry). Expression of the IgH reporter gene varies only 1.5 fold among independent transfectants, and expression is greatly (> 50 fold) increased by inclusion of the IgH intronic enhancer.

Conclusion

This system is suitable for precise analysis of the regulatory elements of the immunoglobulin loci.     

Apoptotic responses to hindlimb suspension in gastrocnemius muscles from young adult and aged rats

Although apoptosis has been demonstrated in soleus during hindlimb suspension (HS), it is not known whether apoptosis is also involved in the loss of muscles dominated by mixed fibers. Therefore, we examined the apoptotic responses in gastrocnemius muscles of young adult and aged Fischer 344 x Brown Norway rats after 14 days of HS. The medial gastrocnemius muscle wet weight significantly decreased by 30 and 32%, and muscle wet weight normalized to the animal body weight decreased by 11 and 15% in young adult and aged animals, respectively, after HS. The extent of apoptotic DNA fragmentation increased by 119 and 61% in suspended muscles from young and aged rats, respectively. Bax mRNA increased by 73% in young muscles after HS. Bax and Bcl-2 protein levels were greater in suspended muscles relative to control muscles in both age groups. The level of cytosolic mitochondria-housed apoptotic factor cytochrome c was significantly increased in the mitochondria-free cytosol of suspended muscles from young and aged rats. In contrast, the release/accumulation of AIF, a caspase-independent apoptogenic factor, was exclusively expressed in the suspended muscles from aged rats. Our data also show that aging favors the proapoptotic signaling in skeletal muscle by altering the contents of Bax, Bcl-2, Apaf-1, AIF, caspases, XIAP, Smac/DIABLO, and cytochrome c. Furthermore, these results indicate that apoptosis occurs not only in slow-twitch soleus muscle but also in the mixed-fiber (predominately fast fibered) gastrocnemius muscle. Our data are consistent with the hypothesis that apoptotic signaling differs in young adult and aged gastrocnemius muscles during HS.     

Induction of antimicrobial 3-deoxyflavonoids in pome fruit trees controls fire blight

Fire blight, a devastating bacterial disease in pome fruits, causes severe economic losses worldwide. Hitherto, an effective control could only be achieved by using antibiotics, but this implies potential risks for human health, livestock and environment. A new approach allows transient inhibition of a step in the flavonoid pathway, thereby inducing the formation of a novel antimicrobial 3-deoxyflavonoid controlling fire blight in apple and pear leaves. This compound is closely related to natural phytoalexins in sorghum. The approach does not only provide a safe method to control fire blight: Resistance against different pathogens is also induced in other crop plants.     

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues

Detection of homologous proteins with low-sequence identity to a given target (remote homologues) is routinely performed with alignment algorithms that take advantage of sequence profile. In this article, we investigate the efficacy of different alignment procedures for the task at hand on a set of 185 protein pairs with similar structures but low-sequence similarity. Criteria based on the SCOP label detection and MaxSub scores are adopted to score the results. We investigate the efficacy of alignments based on sequence-sequence, sequence-profile, and profile-profile information. We confirm that with profile-profile alignments the results are better than with other procedures. In addition, we report, and this is novel, that the selection of the results of the profile-profile alignments can be improved by using Shannon entropy, indicating that this parameter is important to recognize good profile-profile alignments among a plethora of meaningless pairs. By this, we enhance the global search accuracy without losing sensitivity and filter out most of the erroneous alignments. We also show that when the entropy filtering is adopted, the quality of the resulting alignments is comparable to that computed for the target and template structures with CE, a structural alignment program.     

Investigating the allosteric reverse signalling of PARP inhibitors with microsecond molecular dynamic simulations and fluorescence anisotropy

The inhibition of the poly(ADP-ribose) polymerase (PARP) family members is a strategy pursued for the development of novel therapeutic agents in a range of diseases, including stroke, cardiac ischemia, cancer, inflammation and diabetes. Even though some PARP-1 inhibitors have advanced to clinical setting for cancer therapy, a great deal of attention is being devoted to understand the polypharmacology of current PARP inhibitors. Besides blocking the catalytic activity, recent works have shown that some PARP inhibitors exhibit a poisoning activity, by trapping the enzyme at damaged sites of DNA and forming cytotoxic complexes.     

Validation of Self-Reported Information on Dental Caries in a Birth Cohort at 18 Years of Age

Objective

Estimate the prevalence of dental caries based on clinical examinations and self-reports and compare differences in the prevalence and effect measures between the two methods among 18-year-olds belonging to a 1993 birth cohort in the city of Pelotas, Brazil.

Method

Data on self-reported caries, socio-demographic aspects and oral health behaviour were collected using a questionnaire administered to adolescents aged 18 years (n = 4041). Clinical caries was evaluated (n = 1014) by a dentist who had undergone training and calibration exercises. Prevalence rates of clinical and self-reported caries, sensitivity, specificity, positive and negative predictive values, absolute and relative bias, and inflation factors were calculated. Prevalence ratios of dental caries were estimated for each risk factor.

Results

The prevalence of clinical and self-reported caries (DMFT>1) was 66.5% (95%CI: 63.6%–69.3%) and 60.3% (95%CI: 58.8%–61.8%), respectively. Self-reports underestimated the prevalence of dental caries by 9.3% in comparison to clinical evaluations. The analysis of the validity of self-reports regarding the DMFT index indicated high sensitivity (81.8%; 95%CI: 78.7%–84.7%) and specificity (78.1%; 95%CI: 73.3%–82.4%) in relation to the gold standard (clinical evaluation). Both the clinical and self-reported evaluations were associated with gender, schooling and self-rated oral health. Clinical dental caries was associated with visits to the dentist in the previous year. Self-reported dental caries was associated with daily tooth brushing frequency.

Conclusions

Based on the present findings, self-reported information on dental caries using the DMFT index requires further studies prior to its use in the analysis of risk factors, but is valid for population-based health surveys with the aim of planning and monitoring oral health actions directed at adolescents.