Netropsin binding in five duplex-dimer DNA constructs as a function of size and distance between binding sites: circular dichroism and absorption spectroscopy

The optical activity induced on binding the drug netrospin (NET) in the minor groove of DNA is studied in five oligonucleotides (OGNs) as a function of (1) the size of the binding site in (5′-(GC)₂AATT(GC)₂-3′)₂ (OGN 1a) versus (5′-(GC)₂AAATTT(GC)₂-3′)₂ (OGN 1b) and (2) the distance between two AATT binding sites in (5′-(GC)₂AATT(GC) _x AATT(GC)₂-3′)₂, with x = 1, 2, or 3 (OGNs 2a, b, c, respectively). NET binding is monitored via the induced circular dichroism (CD) at ~315 nm, where the nucleic acids are optically inactive. The CD titrations, fit to a tight binding model, yield lower limits for the binding constant, K_a, ≥8 × 10⁷ M⁻¹ for OGN 1a and ≥2 × 10⁸ M⁻¹ for OGNs 2a, b, c in 1 mM buffer. In 100 mM buffer, tight binding occurs in all five OGNs with K_a ≥ 8 × 10⁷ M⁻¹ for OGN 1a and ≥1 × 10⁸ M⁻¹ for OGNs 1b and 2a, b, c. In contrast, the elongated AAATTT binding site of OGN 1b results in weak binding of NET in 1 mM buffer, where competing electrostatic interactions with the solvent environment are lower. In the constructs with two binding sites, the increase in flexibility introduced by intervening GC base pairs does not induce co-operative binding, although differences in the number of binding sites, n (2.05–2.65), indicate that there may be differences in the way NET is bound in OGNs 2a, b, c. In addition, the large shifts in the absorption spectra induced in bound versus free NET, and effects on the CD spectral bands at higher energy, are discussed in terms of electrostatic and excitonic interactions.     

Predator dietary response to prey density variation and consequences for cestode transmission

The functional response of predators to prey density variations has previously been investigated in order to understand predation patterns. However, the consequences of functional response on parasite transmission remain largely unexplored. The rodents Microtus arvalis and Arvicola terrestris are the main prey of the red fox Vulpes vulpes in eastern France. These species are intermediate and definitive hosts of the cestode Echinococcus multilocularis. We explored the dietary and contamination responses of the red fox to variations in prey density. The dietary response differed between the two prey species: no response for M. arvalis and a type III-like (sigmoidal) response for A. terrestris that shows possible interference with M. arvalis. The fox contamination response followed a type II shape (asymptotic) for both species. We conclude that fox predation is species specific and E. multilocularis transmission is likely to be regulated by a complex combination of predation and immunologic factors. These results should provide a better understanding of the biological and ecological mechanisms involved in the transmission dynamics of trophically transmitted parasites when multiple hosts are involved. The relevance of the models of parasite transmission should be enhanced if non-linear patterns are taken into account.     

(35)S]GTPgammaS binding stimulated by endomorphin-2 and morphiceptin analogs

The ability of several mu-selective opioid peptides to activate G-proteins was measured in rat thalamus membrane preparations. The mu-selective ligands used in this study were three structurally related peptides, endomorphin-1, endomorphin-2 and morphiceptin, and their analogs modified in position 3 or 4 by introducing 3-(1-naphthyl)-d-alanine (d-1-Nal) or 3-(2-naphthyl)-d-alanine (d-2-Nal). The results obtained for these peptides in [(35)S]GTPgammaS binding assay were compared with those obtained for a standard mu-opioid agonist DAMGO. [d-1-Nal(3)]Morphiceptin was more potent in G-protein activation (EC(50) value of 82.5+/-4.5 nM) than DAMGO (EC(50)=105+/-9 nM). [d-2-Nal(3)]Morphiceptin, as well as endomorphin-2 analogs substituted in position 4 by either d-1-Nal or d-2-Nal failed to stimulate [(35)S]GTPgammaS binding and were shown to be potent antagonists against DAMGO. It seems that the topographical location of the aromatic ring of position 3 and 4 amino acid residues can result in a completely different mode of action, producing either agonists or antagonists.     

Glucose acutely decreases pH of secretory granules in mouse pancreatic islets. Mechanisms and influence on insulin secretion

Glucose-induced insulin secretion requires a rise in beta-cell cytosolic Ca2+ ([Ca2+]c) that triggers exocytosis and a mechanistically unexplained amplification of the action of [Ca2+]c. Insulin granules are kept acidic by luminal pumping of protons with simultaneous Cl- uptake to maintain electroneutrality. Experiments using patched, dialyzed beta-cells prompted the suggestion that acute granule acidification by glucose underlies amplification of insulin secretion. However, others found glucose to increase granular pH in intact islets. In this study, we measured islet granular pH with Lysosensor DND-160, a fluorescent dye that permits ratiometric determination of pH < 6 in acidic compartments. Stimulation of mouse islets with glucose reversibly decreased granular pH by mechanisms that are dependent on metabolism and Cl- ions but independent of changes in [Ca2+]c and protein kinase A or C activity. Granular pH was increased by concanamycin (blocker of the vesicular type H+-ATPase) > methylamine (weak base) > Cl- omission. Concanamycin and methylamine did not alter glucose-induced [Ca2+]c increase in islets but strongly inhibited the two phases of insulin secretion. Omission of Cl- did not affect the first phase but decreased the second phase of both [Ca2+]c and insulin responses. Neither experimental condition affected the [Ca2+]c rise induced by 30 mM KCl, but the insulin responses were inhibited by concanamycin > methylamine and not affected by Cl- omission. The amplification of insulin secretion by glucose was not suppressed. We conclude that an acidic granular pH is important for insulin secretion but that the acute further acidification produced by glucose is not essential for the augmentation of secretion via the amplifying pathway.     

Zooplankton of Lake Kivu, East Africa, half a century after the Tanganyika sardine introduction

The introduction into Lake Kivu of the planktivorous fish Limnothrissamiodon at the end of the 1950s raised major concern about thefate of mesozooplankton, but few data were available to assessthe impact of predation. In this study, we followed zooplanktonvariations in Lake Kivu for 3.5 years. Present Lake Kivu mesozooplanktonis dominated by cyclopoid copepods (Thermocyclops consimilis,Mesocyclops aequatorialis and Tropocyclops confinis), but cladoceransand rotifers are also present. Each year, total crustacean abundancein the plankton increased to a distinct seasonal maximum followinga rise of phytoplankton production associated with a deep epilimneticmixing in the dry season (August–September). This dependenceon phytoplankton resource suggests that mesozooplankton dynamicsin Lake Kivu is mainly bottom-up controlled, contrary to expectationsfrom the food web structure. However, measurements of body sizeindicate that sardine predation affects the cladoceran Diaphanosomaexcisum, whereas the larger copepods may efficiently escapepredation by migration in the deep mixolimnion at daytime. Totalbiomass of mesozooplankton in Lake Kivu is lower than in lakesTanganyika and Malawi. This may be related to the disappearanceof a large grazer that existed before the sardine introduction,whereas the large lakes of the same region have a more complexpelagic food web, with piscivorous fish, and with calanoid copepods,which can more efficiently exploit phytoplankton production.     

Two highly divergent alcohol dehydrogenases of melon exhibit fruit ripening-specific expression and distinct biochemical characteristics

Alcohol dehydrogenases (ADH) participate in the biosynthetic pathway of aroma volatiles in fruit by interconverting aldehydes to alcohols and providing substrates for the formation of esters. Two highly divergent ADH genes (15% identity at the amino acid level) of Cantaloupe Charentais melon (Cucumis melo var. Cantalupensis) have been isolated. Cm-ADH1 belongs to the medium-chain zinc-binding type of ADHs and is highly similar to all ADH genes expressed in fruit isolated so far. Cm-ADH2 belongs to the short-chain type of ADHs. The two encoded proteins are enzymatically active upon expression in yeast. Cm-ADH1 has strong preference for NAPDH as a co-factor, whereas Cm-ADH2 preferentially uses NADH. Both Cm-ADH proteins are much more active as reductases with K _ms 10–20 times lower for the conversion of aldehydes to alcohols than for the dehydrogenation of alcohols to aldehydes. They both show strong preference for aliphatic aldehydes but Cm-ADH1 is capable of reducing branched aldehydes such as 3-methylbutyraldehyde, whereas Cm-ADH2 cannot. Both Cm-ADH genes are expressed specifically in fruit and up-regulated during ripening. Gene expression as well as total ADH activity are strongly inhibited in antisense ACC oxidase melons and in melon fruit treated with the ethylene antagonist 1-methylcyclopropene (1-MCP), indicating a positive regulation by ethylene. These data suggest that each of the Cm-ADH protein plays a specific role in the regulation of aroma biosynthesis in melon fruit. Daniel Manríquez and Islam El-Sharkawy contributed equally to the work. Accession numbers for Cm-ADH1 (ABC02081), and Cm-ADH2 (ABC02082).     

Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate

One alternative to mineral fertilization is to use organic fertilizers. Our aim was to compare the impacts of 7-year applications of composted pig manure and ammonium nitrate on the structure and activity of the denitrifying community. Mineralization and organization of N, denitrification rates and N2O/N2 ratio were also investigated. Fourteen months after the last application, the potential denitrifying activity (+319%), N mineralization (+110%) and organization (+112%) were higher under pig compost than under ammonium nitrate fertilization. On the other hand, the N2O/(N2O+N2) ratio was lower (P<0.05, n=5) under organic fertilization. These effects of organic fertilization were in accordance with its higher total carbon content and microbial biomass. Fingerprints and clone library analyses showed that the structure of the denitrifying community was affected by the fertilization regime. Our results reveal that organic or mineral fertilizer applications could affect both structure and activity of the denitrifying community, with a possible influence on in situ N2O fluxes. These effects of the fertilization regime persisted for at least 14 months after the last application.     

Structure and functions of the novel hypothalamic RFamide neuropeptides R-RFa and 26RFa in vertebrates

A number of RFamide peptides have been characterized in invertebrate species and these peptides have been found to exert a broad spectrum of biological activities. In contrast, in vertebrates, our knowledge on RFamide peptides is far more limited and only a few members of the RFamide peptide family have been identified in various vertebrate classes during the last years. The present review focuses on two novel RFamide peptides, Rana RFamide (R-RFa) and 26RFa, that have been recently isolated from the amphibian brain. R-RFa shares the C-terminal LPLRFamide motif with other RFamide peptides previously identified in mammals, birds and fish. The distribution of R-RFa in the frog brain exhibits strong similarities with those of other LPLRFamide peptides, notably in the periventricular region of the hypothalamus. There is also evidence that the physiological functions of R-RFa and other LPLRFamide peptides have been conserved from fish to mammals; in particular, all these peptides appear to be involved in the control of pituitary hormone secretion. 26RFa does not exhibit any significant structural identity with other RFamide peptides and this peptide is the only member of the family that possesses an FRFamide motif at its C-terminus. The strong conservation of the primary structure of 26RFa from amphibians to mammals suggests that this RFamide peptide is involved in important biological functions in vertebrates. As for several other RFamide peptides, 26RFa-containing neurons are present in the hypothalamus, notably in two nuclei involved in the control of feeding behavior. Indeed, 26RFa is a potent stimulator of appetite in mammals. Concurrently, recent data suggest that 26RFa exerts various neuroendocrine regulatory activities at the pituitary and adrenal level.     

A genomewide screen for suppressors of par-2 uncovers potential regulators of PAR protein-dependent cell polarity in Caenorhabditis elegans

The PAR proteins play an essential role in establishing and maintaining cell polarity. While their function is conserved across species, little is known about their regulators and effectors. Here we report the identification of 13 potential components of the C. elegans PAR polarity pathway, identified in an RNAi-based, systematic screen to find suppressors of par-2(it5ts) lethality. Most of these genes are conserved in other species. Phenotypic analysis of double-mutant animals revealed that some of the suppressors can suppress lethality associated with the strong loss-of-function allele par-2(lw32), indicating that they might impinge on the PAR pathway independently of the PAR-2 protein. One of these is the gene nos-3, which encodes a homolog of Drosophila Nanos. We find that nos-3 suppresses most of the phenotypes associated with loss of par-2 function, including early cell division defects and maternal-effect sterility. Strikingly, while PAR-1 activity was essential in nos-3; par-2 double mutants, its asymmetric localization at the posterior cortex was not restored, suggesting that the function of PAR-1 is independent of its cortical localization. Taken together, our results identify conserved components that regulate PAR protein function and also suggest a role for NOS-3 in PAR protein-dependent cell polarity.     

The Near-bottom Layer as an Ecological Boundary in Marine Ecosystems: Diversity, Taxonomic Composition and Community Definitions

The near-bottom layer of the ocean represents a boundary between two oceanic biotopes (pelagial and benthal), and as a result, the animal populations living in this habitat belong to various diverse ecological groups. There is a profusion of terms to designate the organisms which live near the sea bottom, both in relation to their behaviour and to boundary-layer hydrodynamics. Do the fauna living above the sea bottom form a true community? Should the fauna in this habitat be considered as a true community or a mixed assemblage comprised of benthic and pelagic organisms? Between 1988 and 1996, more than 500 suprabenthic hauls were taken with a modified Macer-GIROQ sledge at 15 sites in the English Channel and the Seine Estuary (5–70 m), at 13 sites on the southern edge of the Cap Ferret Canyon (Bay of Biscay, 350–1100 m), and at 8 sites on the Atlantic seamounts south of the Azores (260–2235 m). This intensive sampling permitted the collection of more than several hundred species and will serve to facilitate discussion concerning the biodiversity of the fauna collected near the sea bottom. This paper proposes that in the estuary, the near-bottom layer is colonized by a mixed assemblage of both pelagic and benthic organisms, while in the coastal and in the bathyal zones, the response to the gradual extinction of light and the decreasing benthic resuspension at near-bottom depths leads to an ecocline.