Identification of air phase retronasal and orthonasal odorant pairs

Identifications (IDs) of paired retronasal and orthonasal odorants were studied, with stimuli limited to air phase. Odorants were liquid extracts of plant materials, sold as food flavorings, matched by each subject both for retronasal-only and orthonasal-only air phase intensities and then learned to 100% correct veridical name retronasal-only and orthonasal-only IDs. Subjects were tested for ID of (a) retronasal-only and orthonasal-only odorants, (b) homogeneously paired odorant (the same odorant in retronasal and orthonasal locations), and (c) heterogeneously paired odorants (different odorants in retronasal and orthonasal locations). Paired odorants were presented in two different sequences: retronasal location odorant smelled first or orthonasal location odorant smelled first. IDs were reported after odorants were removed. Results were as follows: (a) no significant differences between correct ID of odorants when in retronasal-only versus orthonasal-only locations, although percent correct IDs were lower for half the retronasal-only location odorants; (b) correct ID of a homogeneously paired odorant equaled or exceeded its unpaired ID, with two successive, identical IDs reported on the majority of its trials; (c) with heterogeneous pairs, for all odorants when in the orthonasal location of a pair, correct ID occurred less often than when these odorants were presented orthonasal-only, but for odorants in the retronasal location, correct ID equaled or exceeded retronasal-only correct ID; and (d) perceived order of presentation of heterogeneous pairs was the reverse of the physically presented sequence for both retronasal-first and orthonasal-first conditions. The heterogeneous odorant ID outcome supports the concept that processing of retronasal and orthonasal odorants differ, and the perceived reversal of the presented sequence is in agreement with the importance of recency in odorant memory.     

Structure of the cytochrome <Emphasis Type="Italic">b</Emphasis><Subscript>6</Subscript><Emphasis Type="Italic">f</Emphasis> complex: new prosthetic groups,Q-space,and the ‘hors d’oeuvres hypothesis’ for assembly of the complex

3-Å crystal structures of the cytochrome b₆f complex have provided a structural framework for the photosynthetic electron transport chain. The structures of the 220,000 molecular weight dimeric cytochrome b₆f complex from the thermophilic cyanobacterium, Mastigocladis laminosus (Kurisu et al. 2003, Science 302: 1009–1014), and the green alga, Chlamydomonas reinhardtii (Stroebel et al. 2003, Nature 426: 413–418), are very similar. The latter is the first structure of a integral membrane photosynthetic electron transport complex from a eukaryotic source. The M. laminosus and C. reinhardtii structures have provided structural information and experimental insights to the properties and functions of three native and novel prosthetic groups, a chlorophyll a, a -carotene, and a unique heme x, one copy of which is found in each monomer of the cytochrome b₆f complex, but not the cytochrome bc₁ complex from the mitochondrial respiratory chain of animals and yeast. Several functional insights have emerged from the structures including the function of the dimer; the properties of heme x; the function of the inter-monomer quinone-exchange cavity; a quinone diffusion pathway through relatively narrow crevices or portals; a modified reaction scheme for n-side quinone redox reactions; a necessarily novel mechanism for quenching of the bound chlorophyll triplet state; a possible role for the bound chlorophyll a in activation of the LHC kinase; and a structural and assembly role for the four small PetG, L, M, and N subunits. An hors doeuvres hypothesis for assembly of the complex is proposed for the small hydrophobic stick or picket fence polypeptides at the periphery of the complex, based on the cis-positive orientation of the small hydrophobic subunits and the toothpick binding mode of the -carotene.     

Folding behavior of chaperonin-mediated substrate protein

Chaperonin-mediated protein folding is complex. There have been diverse results on folding behavior, and the chaperonin molecules have been investigated as enhancing or retarding the folding rate. To understand the diversity of chaperonin-mediated protein folding, we report a study based on simulations using a simplified Gō-type model. By considering effects of affinity between the substrate protein and the chaperonin wall and spatial confinement of the chaperonin cavity, we study the thermodynamics and kinetics of folding of an unfrustrated substrate protein encapsulated in a chaperonin cavity. The affinity makes the hydrophobic residues of the protein bind to the chaperonin wall, and a strong (or weak) affinity results in a large (or small) effect of binding. Compared with the folding in bulk, the folding in chaperonin cavity with different strengths of affinity shows two kinds of behaviors: one with less dependence on the affinity but more reliance on the spatial confinement effect and the other relying strongly on the affinity. It is found that the enhancement or retardation of the folding rate depends on the competition between the spatial confinement and the affinity due to the chaperonin cavity, and a strong affinity produces a slow folding while a weak affinity induces a fast folding. The crossover between two kinds of folding behaviors happens in the case that the favorable effect of confinement is balanced by the unfavorable effect of the affinity, and a critical affinity strength is roughly defined. By analyzing the contacts formed between the residues of the protein and the chaperonin wall and between the residues of the protein themselves, the role of the affinity in the folding processes is studied. The binding of the residues with the chaperonin wall reduces the formation of both native contacts and nonnative contact or mis-contacts, providing a loose structure for further folding after allosteric change of the chaperonin cavity. In addition, 15 single-site-mutated mutants are simulated in order to test the validity of our model and to investigate the importance of affinity. Inspiringly, our results of the folding rates have a good correlation with those obtained from experiments. The folding rates are inversely correlated with the strength of the binding interactions, i.e., the weaker the binding, the faster the folding. We also find that the inner hydrophobic residues have larger effects on the folding kinetics than those of the exterior hydrophobic residues. We suggest that, besides the confinement effect, the affinity acts as another important factor to affect the folding of the substrate proteins in chaperonin systems, providing an understanding of the folding mechanism of the molecular chaperonin systems.     

Odorant binding initially occurring at the central pocket in bovine odorant-binding protein

Why bovine odorant-binding protein (OBPb), among OBP family, assumes a dimeric structure has been unclear. Here we clarified, by measuring the fluorescence of intrinsic tryptophan and tyrosine residues of intact OBPb and OBPb whose C-terminal 10 amino acids were deleted, that odorant enters the central pocket formed by the dimerization when OBPb first encounters odorant, and odorant with high affinity with OBPb subsequently enters the internal cavity (suggested binding site), releasing the pre-bound odorant. The internal cavity-bound odorant can be released by the binding of other odorants at another internal cavity or at the central pocket, depending on the binding odorants. Due to this mechanism enabled by the dimerization, OBPb is more reactive than other monomeric OBPs.     

Control of retinoic acid synthesis and FGF expression in the nasal pit is required to pattern the craniofacial skeleton

Endogenous retinoids are important for patterning many aspects of the embryo including the branchial arches and frontonasal region of the embryonic face. The nasal placodes express retinaldehyde dehydrogenase-3 (RALDH3) and thus retinoids from the placode are a potential patterning influence on the developing face. We have carried out experiments that have used Citral, a RALDH antagonist, to address the function of retinoid signaling from the nasal pit in a whole embryo model. When Citral-soaked beads were implanted into the nasal pit of stage 20 chicken embryos, the result was a specific loss of derivatives from the lateral nasal prominences. Providing exogenous retinoic acid residue development of the beak demonstrating that most Citral-induced defects were produced by the specific blocking of RA synthesis. The mechanism of Citral effects was a specific increase in programmed cell death on the lateral (lateral nasal prominence) but not the medial side (frontonasal mass) of the nasal pit. Gene expression studies were focused on the Bone Morphogenetic Protein (BMP) pathway, which has a well-established role in programmed cell death. Unexpectedly, blocking RA synthesis decreased rather than increased Msx1, Msx2, and Bmp4 expression. We also examined cell survival genes, the most relevant of which was Fgf8, which is expressed around the nasal pit and in the frontonasal mass. We found that Fgf8 was not initially expressed along the lateral side of the nasal pit at the start of our experiments, whereas it was expressed on the medial side. Citral prevented upregulation of Fgf8 along the lateral edge and this may have contributed to the specific increase in programmed cell death in the lateral nasal prominence. Consistent with this idea, exogenous FGF8 was able to prevent cell death, rescue most of the morphological defects and was able to prevent a decrease in retinoic acid receptorbeta (Rarbeta) expression caused by Citral. Together, our results demonstrate that endogenous retinoids act upstream of FGF8 and the balance of these two factors is critical for regulating programmed cell death and morphogenesis in the face. In addition, our data suggest a novel role for endogenous retinoids from the nasal pit in controlling the precise downregulation of FGF in the center of the frontonasal mass observed during normal vertebrate development.     

House dust mite extract activates apical Cl− channels through protease‐activated receptor 2 in human airway epithelia

Adequate fluid secretion from airway mucosa is essential for maintaining mucociliary clearance, and fluid hypersecretion is a prominent feature of inflammatory airway diseases such as allergic rhinitis. House dust mite extract (HDM) has been reported to activate protease‐activated receptors (PARs), which play various roles in airway epithelia. However, the role of HDM in regulating ion transporters and fluid secretion has not been investigated. We examined the effect of HDM on ion transport in human primary nasal epithelial cells. The Ca²⁺‐sensitive dye Fura2‐AM was used to determine intracellular Ca²⁺ concentration ([Ca²⁺]_i) by means of spectrofluorometry in human normal nasal epithelial cells (NHNE). Short‐circuit current (Isc) was measured using Ussing chambers. Fluid secretion from porcine airway mucosa was observed by optical measurement. HDM extract (10 µg/Ml) effectively cleaved the PAR‐2 peptide and induced an increase of [Ca²⁺]_i that was abolished by desensitization with trypsin, but not with thrombin. Apical application of HDM‐induced Isc sensitive to both a cystic fibrosis transmembrane conductance regulator (CFTR) inhibitor and a Ca²⁺‐activated Cl^? channel (CaCC) inhibitor. HDM extract also stimulated fluid secretion from porcine airway mucosa. HDM extract activated PAR‐2 and apical Cl^? secretion via CaCC and CFTR, and HDM‐induced fluid secretion in porcine airway mucosa. Our results suggest a role for PAR‐2 in mucociliary clearance and fluid hypersecretion of airway mucosa in response to air‐borne allergens such as HDM. J. Cell. Biochem. 109: 1254–1263, 2010. © 2010 Wiley‐Liss, Inc.     

Pump out the volume—The effect of tracheal and subelytral pressure pulses on convective gas exchange in a dung beetle, Circellium bacchus (Fabricus)

Many flightless beetles like the large apterous dung beetle Circellium bacchus, possess a subelytral cavity (SEC) providing an extra air space below the elytra which connects to the tracheal system (TS) via metathoracic and abdominal spiracles. By measuring subelytral and intratracheal pressure as well as body movements and gas exchange simultaneously in a flow-through setup, we investigated the contribution of convection on Circellium respiratory gas exchange.No constriction phase was observed. TS and SEC pressures were always around atmospheric values. During interburst phase open abdominal spiracles and a leaky SEC led to small CO₂-peaks on a continuous CO₂ baseline, driven by intermittent positive tracheal pressure peaks in anti-phase with small negative subelytral pressure peaks caused by dorso-ventral tergite action.Spiracle opening was accompanied by two types of body movements. Higher frequency telescoping body movements at the beginning of opening resulted in high amplitude SEC and TS pressure peaks. High frequency tergite movements caused subelytral pressure peaks and led to a saw tooth like CO₂ release pattern in a burst. We propose that during the burst open mesothoracic spiracles increase the compliance of the subelytral cavity allowing big volumes of tracheal air being pulled out by convection.     

A comparative study on the anatomy and development of different shapes of domatia in Cinnamomum camphora (Lauraceae)

BACKGROUND AND AIMS: Domatia are small organs usually found in the axils of major veins on the underside of leaves and, although they have received wide attention from ecologists, few detailed reports exist on their anatomy or development. This study is focused on the domatia of Cinnamomum camphora (Lauraceae) and is the first comparative study on the anatomy and development of the different shapes of domatia within a single plant. METHODS: Four types of domatia in C. camphora leaves were observed on paraffin sections under a microscope. KEY RESULTS: The domatia consisted of six histological parts: the upper epidermis, the upper mesophyll tissue, spongy tissue, the lower mesophyll tissue, the tissue filling the rim opening, and the lower epidermis. They differed from the non-domatial lamina mainly in the cell structure of the upper and lower mesophyll tissue and the rim tissue. Differences in domatium shapes were mainly associated with differences in the structure of the upper mesophyll and in the number and size of the rim tissue cells. Differences in the development of domatium types were observed in terms of initiation timing, differentiation of the upper mesophyll cells and degree of rim tissue development. CONCLUSIONS: In domatia, active anticlinal division in the lower mesophyll cells, as compared with the upper mesophyll cells, was coordinated with dynamic growth of rim tissue cells and resulted in cavity formation. The anatomical or developmental differences among the four types of domatia were related to the positions of the domatia within a leaf. In terms of the ecological implications, the major anatomical difference between the domatia used by herbivorous and carnivorous mites was in the development of the rim tissue.     

Cofactor‐binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle,cavity, and fold space

Small molecules are recognized in protein‐binding pockets through surface‐exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein–ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise tounexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein–cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein‐binding pockets, and the local folding patterns next to the cofactor‐binding site. State‐of‐the‐art clustering techniques have been applied to group the different protein–cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Proteins 2012. © 2011 Wiley Periodicals, Inc.