Major groove width variations in RNA structures determined by NMR and impact of <Superscript>13</Superscript>C residual chemical shift anisotropy and <Superscript>1</Superscript>H–<Superscript>13</Superscript>C residual dipolar coupling on refinement

Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by ¹H– ¹H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic ¹H– ¹³C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures.     

Cicada ear geometry: species and sex effects

Many insect species rely on their sense of audition to find a mate, to localize prey or to escape from a predator. Cicadas are particularly known for their loud call and the conspicuous tympanal hearing system located in their abdomen. The vibration pattern of the tympanal membrane (TM) has been investigated recently revealing mechanical properties specific to species and sex. Although TM size and shape is likely to affect these patterns, the geometry of the cicada ear has never been examined per se. Focusing on three Mediterranean cicada species, namely Cicadatra atra, Cicada orni and Lyristes plebejus, we investigated the structure of TM shape variation at two levels, within and across species. Applying an elliptic Fourier analysis to the outlines of both male and female TMs, we estimated sexual dimorphism and species effects. Cicadatra atra showed a large TM compared with its small size, probably as a result of selective constraints related to the role of the TM in sound production. Sexual dimorphism seemed to be greater than interspecific variation, indicating that constraints operating on sex might be more selective than those acting on species identification. In addition, C. orni appeared to be significantly different from the two other species. This morphological peculiarity could be related to the unique vibrational pattern of its membrane. This would establish for the first time a direct link between the shape and mechanism of a hearing organ. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 922–934.     

Synthesis of N-terminally linked protein and peptide dimers by native chemical ligation

Dimerization can be utilized to double the molecular weight of proteins and peptides and potentially increase their avidity of binding to target receptors. These dimerization effects may be utilized to increase in vivo half-lives in a manner similar to PEGylation and may also improve biological activity. In this paper, we report a new strategy for the synthesis of N-terminally linked protein and peptide homodimers utilizing native chemical ligation to conjugate a short dithioester linker to the N-terminal cysteines of protein and peptide monomers to form dimers in a single step. This strategy is general and has been applied to the production of dimers from three recombinantly expressed polypeptides, the IgG binding domain Protein G, an HIV entry inhibitor peptide C37H6, and human interleukin-1 receptor antagonist (IL-1ra). The biological activities of the C37H6 and IL-1ra dimers produced by these methods were retained or even slightly increased when compared to their corresponding monomers.     

Development of a glial network in the olfactory nerve: role of calcium and neuronal activity

In adult olfactory nerves of mammals and moths, a network of glial cells ensheathes small bundles of olfactory receptor axons. In the developing antennal nerve (AN) of the moth Manduca sexta, the axons of olfactory receptor neurons (ORNs) migrate from the olfactory sensory epithelium toward the antennal lobe. Here we explore developmental interactions between ORN axons and AN glial cells. During early stages in AN glial-cell migration, glial cells are highly dye coupled, dividing glia are readily found in the nerve and AN glial cells label strongly for glutamine synthetase. By the end of this period, dye-coupling is rare, glial proliferation has ceased, glutamine synthetase labeling is absent, and glial processes have begun to extend to enwrap bundles of axons, a process that continues throughout the remainder of metamorphic development. Whole-cell and perforated-patch recordings in vivo from AN glia at different stages of network formation revealed two potassium currents and an R-like calcium current. Chronic in vivo exposure to the R-type channel blocker SNX-482 halted or greatly reduced AN glial migration. Chronically blocking spontaneous Na-dependent activity by injection of tetrodotoxin reduced the glial calcium current implicating an activity-dependent interaction between ORNs and glial cells in the development of glial calcium currents.     

Mechanism of human S-adenosylmethionine decarboxylase proenzyme processing as revealed by the structure of the S68A mutant

S-Adenosylmethionine decarboxylase (AdoMetDC) is a pyruvoyl-dependent enzyme that catalyzes the formation of the aminopropyl group donor in the biosynthesis of the polyamines spermidine and spermine. The enzyme is synthesized as a protein precursor and is activated by an autocatalytic serinolysis reaction that creates the pyruvoyl group. The autoprocessing reaction proceeds via an N --> O acyl rearrangement, generating first an oxyoxazolidine anion intermediate followed by an ester intermediate. A similar strategy is utilized in self-catalyzed protein splicing reactions and in autoproteolytic activation of protein precursors. Mutation of Ser68 to alanine in human AdoMetDC prevents processing by removing the serine side chain necessary for nucleophilic attack at the adjacent carbonyl carbon atom. We have determined the X-ray structure of the S68A mutant and have constructed models of the proenzyme and the oxyoxazolidine intermediate. Formation of the oxyoxazolidine intermediate is promoted by a hydrogen bond from Cys82 and stabilized by a hydrogen bond from Ser229. These observations are consistent with mutagenesis studies, which show that the C82S and C82A mutants process slowly and that the S229A mutant does not process at all. Donation of a proton by His243 to the nitrogen atom of the oxyoxazolidine ring converts the oxyoxazolidine anion to the ester intermediate. The absence of a base to activate the hydroxyl group of Ser68 suggests that strain may play a role in the cleavage reaction. Comparison of AdoMetDC with other self-processing proteins shows no common structural features. Comparison to histidine decarboxylase and aspartate decarboxylase shows that these pyruvoyl-dependent enzymes evolved different catalytic strategies for forming the same cofactor.     

Different isoforms of fasciclin II are expressed by a subset of developing olfactory receptor neurons and by olfactory-nerve glial cells during formation of glomeruli in the moth Manduca sexta

During development of the primary olfactory projection, olfactory receptor axons must sort by odor specificity and seek particular sites in the brain in which to create odor-specific glomeruli. In the moth Manduca sexta, we showed previously that fasciclin II, a cell adhesion molecule in the immunoglobulin superfamily, is expressed by the axons of a subset of olfactory receptor neurons during development and that, in a specialized glia-rich "sorting zone," these axons segregate from nonfasciclin II-expressing axons before entering the neuropil of the glomerular layer. The segregation into fasciclin II-positive fascicles is dependent on the presence of the glial cells in the sorting zone. Here, we explore the expression patterns for different isoforms of Manduca fasciclin II in the developing olfactory system. We find that olfactory receptor axons express transmembrane fasciclin II during the period of axonal ingrowth and glomerulus development. Fascicles of TM-fasciclin II+ axons target certain glomeruli and avoid others, such as the sexually dimorphic glomeruli. These results suggest that TM-fasciclin II may play a role in the sorting and guidance of the axons. GPI-linked forms of fasciclin II are expressed weakly by glial cells associated with the receptor axons before they reach the sorting zone, but not by sorting-zone glia. GPI-fasciclin II may, therefore, be involved in axon-glia interactions related to stabilization of axons in the nerve, but probably not related to sorting.     

Theoretical habitat templets, species traits, and species richness: aquatic macrophytes in the Upper Rhône River and its floodplain

• 1 The objective of this study, which is based on forty-two species of hydrophytes and helophytes, is to investigate: (i) relationships among species traits; (ii) habitat utilization by species; (iii) the relationship between species traits and habitat utilization; (iv) trends in species traits in the framework of spatial–temporal habitat variability, and if trends match predictions from the river habitat templet; and (v) trends in species richness in the framework of spatial–temporal habitat variability, and if trends match predictions of the patch dynamics concept.
• 2 Two data sets were used for this analysis: species traits (mainly reproductive and morphological characteristics) were documented from the literature; and species distribution across eight habitat types was from field surveys conducted in the floodplain of the Upper Rhone River, France. This information was structured by a fuzzy coding technique and analysed by ordination methods.
• 3 Several species traits, which are related to disturbances and reflect resistance (e.g. attachment to soil or substrate) or resilience (e.g. potential for regeneration of an individual), are closely related for aquatic macrophytes.
• 4 Habitat utilization by aquatic macrophytes separates the habitat types along a gradient of connectivity with the main channel, which corresponds to a gradient in flood disturbance frequency and the permanence of the different water-bodies.
• 5 The relationship between species traits and habitat utilization is highly significant, indicating that a particular set of habitat types is used by taxa with a particular set of species trait modalities.
• 6 Observations in one habitat templet (in which scaling of the templet is primarily based on water level fluctuations for the temporal variability axis and on substrate characteristics for the spatial variability axis) generally do not support predictions on trends in species traits but do support predictions on trends in species richness.
• 7 Observations in an alternative habitat templet (in which scaling of the templet is based on frequency of flood scouring for the temporal variability axis and on heterogeneity of the substrate for the spatial variability axis) support theoretical predictions on trends for about half of the species traits for which predictions were available. However, trends in species richness in this alternative habitat templet are only partly in agreement with predictions.

     

Ultrastructural examination of the insemination reaction in Drosophila

The insemination reaction is a swelling of the female vagina caused by the male ejaculate. This postmating phenomenon is common among species in the genus Drosophila. It could act as a plug securing male paternity. It is not clear, however, what benefits it provides to the female. The structure formed in the female vagina is expelled in some species and disappears gradually in others suggesting different phenomena. Based on ultrastructural examination of the vaginal contents of five Drosophila species (D. mettleri, D. nigrospiracula, D. melanogaster, D. mojavensis, and D. hexastigma), we propose three terms to describe these vaginal structures: the sperm sac, the mating plug, and the true insemination reaction. Each term describes a distinct structure associated with a specific female postmating behavior. This study questions the concept of the insemination reaction as a single phenomenon and discusses its possible functions from an evolutionary perspective.