Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines

Parallel-stranded hairpins with a polypyrimidine sequence linked to a complementary purine carrying 8-aminopurines such as 8-aminoadenine, 8-aminoguanine and 8-aminohypoxanthine bind polypyrimidine sequences complementary (in an antiparallel sense) to the purine part by a triple helix. The relative stabilities of triplexes were assessed by UV-absorption melting experiments as a function of pH and salt concentration. Hairpins carrying 8-aminopurines give very stable triple helical structures even at neutral pH, as confirmed by gel-shift experiments, circular dichroism and nuclear magnetic resonance spectroscopy. The modified hairpins may be redesigned to cope with small interruptions in the polypyrimidine target sequence.     

Combined effects of air and soil pollution by fluoride emissions on Tibouchina pulchra Cogn., at Cubatão,SE Brazil,and their relations with aluminium

High deposition of gaseous/particulate fluorides and other air pollutants has resulted in an acidification and probable formation of soluble AlF_x complexes in the soil in the vicinity of the industrial complex of Cubatão, SE Brazil. With the present field study we aimed at determining the contribution of F and Al uptake from fluoride-contaminated soil, supposedly as AlF_x complexes, to the increase of foliar F and Al contents in saplings of an Al-accumulator tree species (Tibouchina pulchra) which were concomitantly exposed to fluoride-contaminated air and also the proportional contribution of both air and soil contamination to the mentioned foliar accumulation of these elements. The seasonal variations in F and Al accumulation and possible metabolic changes in the plants due to F and Al accumulation were also investigated. The saplings were exposed during three consecutive periods of 16 weeks to: (a) air and soil from a reference site (PV_noF); (b) air or soil from two polluted sites (CM-high air pollution, low F and MV-high air pollution, high F); and (c) both air and soil from these polluted sites. After exposure, the changes in the foliar concentrations of F and Al, the relations between both element contents and their relationships with oxidative stress indicators were determined. The data were grouped in three matrices: PV_noF–CM_lwF and PV_noF–MV_hgF, taking in account the possible air/soil exposure combinations in each, and soil/air from all sites. The slight F accumulation in plants of PV_noF–CM_lwF matrix was a result of higher uptake from soil than from air (54 and 46%, respectively). At PV_noF–MV_hgF matrix, the extremely high F accumulation in leaves of T. pulchra could be attributed to the combination of both air and soil contamination (83 and 17%, respectively). T. pulchra always showed higher foliar Al concentrations than 1000 g g^–1 dry mass, mainly after exposure to air and soil of both polluted sites (CM_lwF and MV_hgF). A highly significant linear regression was estimated between molar Al and F contents, taking in account the data obtained for saplings of T. pulchra cultivated in the different soils and exposed to ambient air of PV_noF, suggesting that both elements were taken as Al–F complexes from soil. The uptake of fluorides from air and/or soil of MV_hgF caused significant metabolic changes in T. pulchra, but visible injury supposedly induced by fluorides were observed only when the foliar F contents surpassed 700 g g^–1 dry mass. On the contrary, Al did not cause any metabolic stress to the plants.     

Tyrosine hydroxylase activity in the endocrine pancreas: changes induced by short-term dietary manipulation

BACKGROUND: Tyrosine hydroxylase (TH) activity and its possible participation in the control of insulin secretion were studied in pancreatic islets of adult Wistar rats fed a standard commercial diet (SD) or carbohydrates alone (CHD) for one week. TH activity, norepinephrine (NE) content, and glucose-induced insulin secretion were assessed. Blood glucose and insulin levels were measured at the time of sacrifice. RESULTS: CHD rats had significantly higher blood glucose and lower insulin levels than SD rats (114.5 PlusMinus; 6.7 vs 80.7 PlusMinus; 7.25 mg/dl, p < 0.001; 20.25 PlusMinus; 2.45 vs 42.5 PlusMinus; 4.99 &mgr;U/ml, p < 0.01, respectively). Whereas TH activity was significantly higher in CHD isolated islets (600 PlusMinus; 60 vs 330 PlusMinus; 40 pmol/mg protein/h; p < 0.001), NE content was significantly lower (18 PlusMinus; 1 vs 31 PlusMinus; 5 pmol/mg protein), suggesting that TH activity would be inhibited by the end-products of catecholamines (CAs) biosynthetic pathway. A similar TH activity was found in control and solarectomized rats (330 PlusMinus; 40 vs 300 PlusMinus; 80 pmol/mg protein/h), suggesting an endogenous rather than a neural origin of TH activity. CHD islets released significantly less insulin in response to glucose than SD islets (7.4 PlusMinus; 0.9 vs 11.4 PlusMinus; 1.1 ng/islet/h; p < 0.02). CONCLUSIONS: TH activity is present in islet cells; dietary manipulation simultaneously induces an increase in this activity together with a decrease in glucose-induced insulin secretion in rat islets. TH activity - and the consequent endogenous CAs turnover - would participate in the paracrine control of insulin secretion.     

Molecular Modeling of the NPY Binding Site on the Y1 Receptor

A three-dimensional model of the neuropeptide Y (NPY) - rat Y₁ (rY₁) receptor complex and of the NPY _13-36 - rY₁ receptor complex was constructed by molecular modeling based on the electron density projection map of rhodopsin and on site-directed mutagenesis studies of neuropeptide receptors. In order to further guide the modeling, the nucleotide sequences encoding Trp287, Cys295 and His297 in the third extracellular loop of the rY₁ receptor, were altered by site-directed mutagenesis experiments. Single-point mutated receptors were expressed in COS-7 cells, and tested for their ability to bind radio labelled NPY (³H-NPY). Mutations of Trp287 and His297 completely abolished binding of ³H-NPY. The Cys295Ser mutation only slightly decreased the binding of ³H-NPY, suggesting that the involvement of Cys295 in a disulphide bond is not essential for maintaining the correct three-dimensional structure of the binding site for NPY. Molecular dynamics simulations of NPY-rY₁ receptor interactions suggested that Asp199, Asp103 and Asp286 in the receptor interact, respectively, with Lys4, Arg33 and Arg35 of NPY. The simulations also suggested that His297 acts as a hydrogen acceptor from Arg35 in NPY, and that Tyr1 of NPY interacts with a binding pocket on the receptor formed by Asn115, Asp286, Trp287 and His297. Tyr36 in NPY interacted both with Thr41 and Tyr99 via hydrogen bonds, and also with Asn296, His297 and Phe301. The present study suggests that amino acid residues at the extracellular end of the transmembrane helices and in the extracellular loops are strongly involved in binding to NPY and NPY_13-36.Electronic Supplementary Material available.     

Rho GTPase-activating bacterial toxins: from bacterial virulence regulation to eukaryotic cell biology

Studies on the interactions of bacterial pathogens with their host have provided an invaluable source of information on the major functions of eukaryotic and prokaryotic cell biology. In addition, this expanding field of research, known as cellular microbiology, has revealed fascinating examples of trans-kingdom functional interplay. Bacterial factors actually exploit eukaryotic cell machineries using refined molecular strategies to promote invasion and proliferation within their host. Here, we review a family of bacterial toxins that modulate their activity in eukaryotic cells by activating Rho GTPases and exploiting the ubiquitin/proteasome machineries. This family, found in human and animal pathogenic Gram-negative bacteria, encompasses the cytotoxic necrotizing factors (CNFs) from Escherichia coli and Yersinia species as well as dermonecrotic toxins from Bordetella species. We survey the genetics, biochemistry, molecular and cellular biology of these bacterial factors from the standpoint of the CNF1 toxin, the paradigm of Rho GTPase-activating toxins produced by urinary tract infections causing pathogenic Escherichia coli. Because it reveals important connections between bacterial invasion and the host inflammatory response, the mode of action of CNF1 and its related Rho GTPase-targetting toxins addresses major issues of basic and medical research and constitutes a privileged experimental model for host-pathogen interaction.     

A mixed-age classed ‘pelycosaur’ aggregation from South Africa: earliest evidence of parental care in amniotes?

Living species of mammals, crocodiles and most species of birds exhibit parental care, but evidence of this behaviour is extremely rare in the fossil record. Here, we present a new specimen of varanopid 'pelycosaur' from the Middle Permian of South Africa. The specimen is an aggregation, consisting of five articulated individuals preserved in undisturbed, close, lifelike, dorsal-up, subparallel positions, indicating burial in 'life position'. Two size classes are represented. One is 50% larger than the others, is well ossified, has fused neurocentral sutures and is distinguished by a coat of dermal ossifications that covers the neck and shoulder regions. We regard this individual to be an adult. The remaining four skeletons are considered to be juveniles as they are approximately the same size, are poorly ossified, have open neurocentral sutures and lack dermal ossifications. Aggregates of juvenile amniotes are usually siblings. Extant analogues of adult and juvenile groupings suggest that the adult is one of the parents, leading us to regard the aggregation as a family group. The Late Middle Permian age of the varanopid family predates the previously known oldest fossil evidence of parental care in terrestrial vertebrates by 140 Myr.     

Thorough validation of protein normal mode analysis: a comparative study with essential dynamics

The deformation patterns of a large set of representative proteins determined by essential dynamics extracted from atomistic simulations and coarse-grained normal mode analysis are compared. Our analysis shows that the deformational space obtained with both approaches is quite similar when taking into account a representative number of modes. The results provide not only a comprehensive validation of the use of a low-frequency modal spectrum to describe protein flexibility, but also a complete picture of normal mode limitations.     

Development and pilot evaluation of novel genetic educational materials designed for an underserved patient population

Genetic counseling for BRCA1 and BRCA2 mutations involves teaching about hereditary cancer, genetics and risk, subjects that are difficult to grasp and are routinely misunderstood. Supported by a grant from the Avon Foundation, the UCSF Cancer Risk Program started the first genetic testing and counseling service for a population of traditionally underserved women of varied ethnic and social backgrounds at the San Francisco General Hospital (SFGH). Informed by educational theory and clinical experience, we devised and piloted two simplified explanations of heredity and genetic risk, with the aim of uncovering how to best communicate genetics and risk to this underserved population. A "conventional" version comprised pictures of genes, pedigrees, and quantitative representations of risk. A "colloquial" pictorial version used an analogy of the "information book" of genes, family stories and vignettes, and visual representations of risk, without using scientific words such as genes or chromosomes. A verbal narrative accompanied each picture. We presented these modules to four focus groups of five to eight women recruited from the SFGH Family Practice Clinic. Overall, women preferred a picture-based approach and commented that additional text would have been distracting. The majority of women preferred the colloquial version because it was easier to understand and better conveyed a sense of comfort and hope. We conclude that simplicity, analogies, and familiarity support comprehension while vignettes, family stories, and photos of real people provide comfort and hope. These elements may promote understanding of complex scientific topics in healthcare, particularly when communicating with patients who come from disadvantaged backgrounds.