High olfactory sensitivity for dimethyl sulphide in harbour seals

Productive areas are patchily distributed at sea and represent important feeding grounds for many marine organisms. Although pinnipeds are known to travel on direct routes and return regularly to particular feeding sites, the environmental information seals use to perform this navigation is as yet unknown. As atmospheric dimethyl sulphide (DMS) has been demonstrated to be a reliable indicator for profitable foraging areas, we tested seals for their ability to smell DMS at concentrations typical for the marine environment. Using a go/no-go response paradigm we determined the DMS detection threshold in two harbour seals (Phoca vitulina vitulina). DMS stimuli from 8.05 x 108 to 8 pmol (DMS)m(-3)(air) were tested against a control stimulus using a custom-made olfactometer. DMS-thresholds determined for both seals (20 and 13 pmol m(-3)) indicate that seals can detect ambient concentrations associated with high primary productivity, e.g. in the North Atlantic. Thus, seals possess an extraordinarily high olfactory sensitivity for DMS, which could provide a sensory basis for identifying or orienting to profitable foraging grounds.     

Long-term stability of a biofilter treating dimethyl sulphide

 The biofiltration of dimethyl sulphide (Me₂S) and other volatile sulphur compounds results in the accumulation of the metabolite sulphuric acid in the carrier material. Regeneration of an acidified (pH 4.7), Hyphomicrobium-MS3-inoculated compost biofilter degrading Me₂S was not possible by trickling tap water (days 0–28) or a KH₂PO₄/K₂HPO₄ buffer solution (1.26 g PO^3- ₄ l^-1, pH 7) (days 29–47) over the bioreactor at a superficial liquid flow rate of 34 lm^-2 day^-1. Since the protons produced displaced nutrient cations (Na⁺, K⁺, Ca²⁺, Mg²⁺, NH⁺ ₄) from the cation-exchange sites on the compost material, 95% of the SO^2- ₄ was leached as the corresponding sulphate salts and not as sulphuric acid. Concomitantly, the pH of the compost material decreased from 4.7 to 3.9 over the 47 days rinsing period. Moreover, the rinsing procedure resulted in the leaching of essential microbial nutrients from the compost material, such as NH⁺ ₄ (22.3% wash-out over the 47-day rinsing period) and PO^3- ₄ (39.3% washout over the 28-day tap-water rinsing period). However, mixing limestone powder into the Me₂S-degrading compost biofilter was a successful approach to controlling the pH in the optimal range for the inoculum Hyphomicrobium MS3 (pH 6–7). A stoichiometric neutralisation reaction (molar ratio CaCO₃/H₂SO₄=1.1) was observed between the CaCO₃ added and the metabolite of the Me₂S degradation, while high elimination capacities (above 100 g Me₂S m^-3 day^-1) were obtained over a prolonged (more than 100 days) period. Received: 1 December 1995/Received revision: 26 April 1995 Accepted: 29 April 1996     

Dolomite limits acidification of a biofilter degrading dimethyl sulphide

The applicability of dolomite particlesto control acidificationin a Hyphomicrobium MS3inoculated biofilter removingdimethyl sulphide (Me₂S) wasstudied. While direct inoculationof the dolomite particles with theliquid microbial culture was notsuccessful, start-up ofMe₂S-degradation in thebiofilter was observed when thedolomite particles were mixed with33% (wt/wt) of Hyphomicrobium MS3-inoculatedcompost or wood bark material.Under optimal conditions, anelimination capacity (EC) of 1680~g Me₂S m^-3 d^-1 wasobtained for the compost/dolomitebiofilter. Contrary to a wood barkor compost biofilter, no reductionin activity due to acidificationwas observed in these biofiltersover a 235 day period because ofthe micro environmentneutralisation of the microbialmetabolite H₂SO₄ with thecarbonate in the dolomite material.However, performance of thebiofilter decreased when themoisture content of the mixedcompost/dolomite material droppedbelow 15%. Next to this, nutrientlimitation resulted in a gradualdecrease of the EC andsupplementation of a nitrogensource was a prerequisite to obtaina long-term high EC (> 250 gMe₂S m^-3 d^-1) forMe₂S. In relation to thisnitrogen supplementation, it wasobserved that stable ECs forMe₂S were obtained when thisnutrient was dosed to the biofilterat a Me₂S-C/NH₄Cl-Nratio of about 10.Abbreviations:DW – dry weight,EC – elimination capacity,Me₂S – dimethyl sulphide,OL – organic loading rate,VS - volatile solids     

Plk1 docking to GRASP65 phosphorylated by Cdk1 suggests a mechanism for Golgi checkpoint signalling

GRASP65, a structural protein of the Golgi apparatus, has been linked to the sensing of Golgi structure and the integration of this information with the control of mitotic entry in the form of a Golgi checkpoint. We show that Cdk1-cyclin B is the major kinase phosphorylating GRASP65 in mitosis, and that phosphorylated GRASP65 interacts with the polo box domain of the polo-like kinase Plk1. GRASP65 is phosphorylated in its C-terminal domain at four consensus sites by Cdk1-cyclin B, and mutation of these residues to alanine essentially abolishes both mitotic phosphorylation and Plk1 binding. Expression of the wild-type GRASP65 C-terminus but not the phosphorylation defective mutant in normal rat kidney cells causes a delay but not the block in mitotic entry expected if this were a true cell cycle checkpoint. These findings identify a Plk1-dependent signalling mechanism potentially linking Golgi structure and cell cycle control, but suggest that this may not be a cell cycle checkpoint in the classical sense.     

Processive capping by formin suggests a force-driven mechanism of actin polymerization

Regulation of actin polymerization is essential for cell functioning. Here, we predict a novel phenomenon-the force-driven polymerization of actin filaments mediated by proteins of the formin family. Formins localize to the barbed ends of actin filaments, but, in contrast to the standard capping proteins, allow for actin polymerization in the barbed direction. First, we show that the mechanism of such "leaky capping" can be understood in terms of the elasticity of the formin molecules. Second, we demonstrate that if a pulling force acts on the filament end via the leaky cap, the elastic stresses can drive actin polymerization. We estimate that a moderate pulling force of approximately 3.4 pN is sufficient to reduce the critical actin concentration required for barbed end polymerization by an order of magnitude. Furthermore, the pulling force increases the polymerization rate. The suggested mechanism of force-driven polymerization could be a key element in a variety of cellular mechanosensing devices.     

Mutational analysis of a signaling aptamer suggests a mechanism for ligand-triggered structure-switching

Structure-switching signaling aptamers are nucleic acids that change shape upon binding to a specific ligand. Previously, we applied a new in vitro selection strategy to isolate structure-switching RNA aptamers responsive to the aminoglycoside antibiotic tobramycin. Here, we report the results of mutational analysis, secondary structure modeling, and ligand-specificity studies that suggest a mechanism for tobramycin-triggered structure switching.     

Comparative sequence analysis suggests a conserved gating mechanism for TRP channels

The transient receptor potential (TRP) channel superfamily plays a central role in transducing diverse sensory stimuli in eukaryotes. Although dissimilar in sequence and domain organization, all known TRP channels act as polymodal cellular sensors and form tetrameric assemblies similar to those of their distant relatives, the voltage-gated potassium (Kv) channels. Here, we investigated the related questions of whether the allosteric mechanism underlying polymodal gating is common to all TRP channels, and how this mechanism differs from that underpinning Kv channel voltage sensitivity. To provide insight into these questions, we performed comparative sequence analysis on large, comprehensive ensembles of TRP and Kv channel sequences, contextualizing the patterns of conservation and correlation observed in the TRP channel sequences in light of the well-studied Kv channels. We report sequence features that are specific to TRP channels and, based on insight from recent TRPV1 structures, we suggest a model of TRP channel gating that differs substantially from the one mediating voltage sensitivity in Kv channels. The common mechanism underlying polymodal gating involves the displacement of a defect in the H-bond network of S6 that changes the orientation of the pore-lining residues at the hydrophobic gate.     

A systematic approach to pair secretory cargo receptors with their cargo suggests a mechanism for cargo selection by Erv14

The endoplasmic reticulum (ER) is the site of synthesis of secreted and membrane proteins. To exit the ER, proteins are packaged into COPII vesicles through direct interaction with the COPII coat or aided by specific cargo receptors. Despite the fundamental role of such cargo receptors in protein traffic, only a few have been identified; their cargo spectrum is unknown and the signals they recognize remain poorly understood. We present here an approach we term "PAIRS" (pairing analysis of cargo receptors), which combines systematic genetic manipulations of yeast with automated microscopy screening, to map the spectrum of cargo for a known receptor or to uncover a novel receptor for a particular cargo. Using PAIRS we followed the fate of ～150 cargos on the background of mutations in nine putative cargo receptors and identified novel cargo for most of these receptors. Deletion of the Erv14 cargo receptor affected the widest range of cargo. Erv14 substrates have a wide array of functions and structures; however, they are all membrane-spanning proteins of the late secretory pathway or plasma membrane. Proteins residing in these organelles have longer transmembrane domains (TMDs). Detailed examination of one cargo supported the hypothesis that Erv14 dependency reflects the length rather than the sequence of the TMD. The PAIRS approach allowed us to uncover new cargo for known cargo receptors and to obtain an unbiased look at specificity in cargo selection. Obtaining the spectrum of cargo for a cargo receptor allows a novel perspective on its mode of action. The rules that appear to guide Erv14 substrate recognition suggest that sorting of membrane proteins at multiple points in the secretory pathway could depend on the physical properties of TMDs. Such a mechanism would allow diverse proteins to utilize a few receptors without the constraints of evolving location-specific sorting motifs.     

Bivalent binding of IgA1 to FcalphaRI suggests a mechanism for cytokine activation of IgA phagocytosis

FcalphaRI, the receptor specific for the Fc region of immunoglobulin A (IgA), is responsible for IgA-mediated phagocytosis, oxidative burst, and antibody-dependent cellular cytotoxicity. Using the techniques of analytical ultracentrifugation and equilibrium gel-filtration, we show that two FcalphaRI molecules bind to a single Fcalpha homodimer. Surface plasmon resonance studies confirm the 2:1 stoichiometry of binding, with equilibrium dissociation constants of 176 nM and 431 nM for the first and second binding events, respectively. The binding affinity decreases at acidic pH in a manner consistent with protonation of a single histidine residue in the binding site. A thermodynamic analysis indicates that the histidine residue does not participate in a salt-bridge in the complex; in fact, less than 10% of the free energy of binding was contributed by electrostatic interactions. The bivalent, pH-dependent interaction between FcalphaRI and IgA has important implications for cytokine-dependent phagocytosis of IgA and the FcalphaRI-mediated degradation or recycling of IgA.     

Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly

HP1 proteins are central to the assembly and spread of heterochromatin containing histone H3K9 methylation. The chromodomain (CD) of HP1 proteins specifically recognizes the methyl mark on H3 peptides, but the same extent of specificity is not observed within chromatin. The chromoshadow domain of HP1 proteins promotes homodimerization, but this alone cannot explain heterochromatin spread. Using the S. pombe HP1 protein, Swi6, we show that recognition of H3K9-methylated chromatin in vitro relies on an interface between two CDs. This interaction causes Swi6 to tetramerize on a nucleosome, generating two vacant CD sticky ends. On nucleosomal arrays, methyl mark recognition is highly sensitive to internucleosomal distance, suggesting that the CD sticky ends bridge nearby methylated nucleosomes. Strengthening the CD-CD interaction enhances silencing and heterochromatin spread in vivo. Our findings suggest that recognition of methylated nucleosomes and HP1 spread on chromatin are structurally coupled and imply that methylation and nucleosome arrangement synergistically regulate HP1 function.     

Distribution pattern of Notch3 mutations suggests a gain-of-function mechanism for CADASIL

Mutations in Notch3 cause the syndrome CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy). The mechanism by which these mutations result in a CADASIL phenotype has been widely speculated upon. A first step toward understanding a disease mechanism is to learn whether the mutations result in the loss of Notch3 function, in particular, its role in signaling or in the gain of a novel function. Notch3 genomic sequences were analyzed for sites of conservation across species. We present here a bioinformatic analysis of the Notch paralogs and orthologs that suggest that CADASIL mutations result in a gain of function. This finding diminishes the likelihood that a Notch3 signaling deficit is responsible for the phenotype and increases the likelihood that CADASIL joins the growing list of neurological diseases with protein deposits due to misfolding and aggregation.     

A Melanesian alpha-thalassemia mutation suggests a novel mechanism for regulating gene expression

A Melanesian variant of the genetic disease alpha-thalassemia has recently been shown to be due to a single-nucleotide polymorphism located between the adult alpha-globin genes and their enhancers. The finding that this mutation creates a novel promoter provides support for a mechanism of gene regulation by facilitated chromatin looping.     

Pelagic seabird flight patterns are consistent with a reliance on olfactory maps for oceanic navigation

Homing studies have provided tantalizing evidence that the remarkable ability of shearwaters (Procellariiformes) to pinpoint their breeding colony after crossing vast expanses of featureless open ocean can be attributed to their assembling cognitive maps of wind-borne odours but crucially, it has not been tested whether olfactory cues are actually used as a system for navigation. Obtaining statistically important samples of wild birds for use in experimental approaches is, however, impossible because of invasive sensory manipulation. Using an innovative non-invasive approach, we provide strong evidence that shearwaters rely on olfactory cues for oceanic navigation. We tested for compliance with olfactory-cued navigation in the flight patterns of 210 shearwaters of three species (Cory''s shearwaters, Calonectris borealis, North Atlantic Ocean, Scopoli''s shearwaters, C. diomedea Mediterranean Sea, and Cape Verde shearwaters, C. edwardsii, Central Atlantic Ocean) tagged with high-resolution GPS loggers during both incubation and chick rearing. We found that most (69%) birds displayed exponentially truncated scale-free (Lévy-flight like) displacements, which we show are consistent with olfactory-cued navigation in the presence of atmospheric turbulence. Our analysis provides the strongest evidence yet for cognitive odour map navigation in wild birds. Thus, we may reconcile two highly disputed questions in movement ecology, by mechanistically connecting Lévy displacements and olfactory navigation. Our approach can be applied to any species which can be tracked at sufficient spatial resolution, using a GPS logger.     

Structure of a calcium-dependent 11R-lipoxygenase suggests a mechanism for Ca2+ regulation

Lipoxygenases (LOXs) are a key part of several signaling pathways that lead to inflammation and cancer. Yet, the mechanisms of substrate binding and allosteric regulation by the various LOX isoforms remain speculative. Here we report the 2.47-Å resolution crystal structure of the arachidonate 11R-LOX from Gersemia fruticosa, which sheds new light on the mechanism of LOX catalysis. Our crystallographic and mutational studies suggest that the aliphatic tail of the fatty acid is bound in a hydrophobic pocket with two potential entrances. We speculate that LOXs share a common T-shaped substrate channel architecture that gives rise to the varying positional specificities. A general allosteric mechanism is proposed for transmitting the activity-inducing effect of calcium binding from the membrane-targeting PLAT (polycystin-1/lipoxygenase/α-toxin) domain to the active site via a conserved π-cation bridge.     

The sensitivity of synthesis of human cartilage matrix to inhibition by IL-1 suggests a mechanism for the development of osteoarthritis

The damage to articular cartilage, characteristic of arthritic disease, is usually ascribed to increased degradative activity by enzymes or free radicals from locally activated cells. We propose that inhibition of matrix synthesis, and consequential impairment of the natural repair process, may be at least as important in chronic joint disease.     

Modification of calcium fluxes by dimethyl sulfoxide and 2-butoxyethanol in sarcoplasmic reticulum vesicles: a possible mechanism for skeletal muscle relaxation induced by dimethyl sulfoxide

In order to investigate the mechanism of skeletal muscle relaxation induced by dimethyl sulfoxide, 2-butoxyethanol and dimethyl sulfoxide were examined for their effects on 1) Ca2+ uptake into and efflux from sarcoplasmic reticulum vesicles prepared from rabbit fast skeletal muscle and crayfish tail muscle by the murexide method, 2) ATPase activities of rabbit reticulum vesicles, 3) the isolated phrenic nerve-diaphragm preparation of the rat and 4) crayfish opener muscle preparation. Ca2+ efflux rate from rabbit reticulum vesicles was markedly decreased with increasing concentrations (5-20% v/v) of dimethyl sulfoxide without affecting the maximum Ca2+ uptake by the reticulum. 2-Butoxyethanol showed quite contrary effects. Dimethyl sulfoxide strongly inhibited the activity of basal ATPase rather than of Ca2+-dependent ATPase. 2-Butoxyethanol did not significantly inhibit the activity of basal ATPase, but markedly increased Ca2+-dependent ATPase activity. Antagonisms between dimethyl sulfoxide and caffeine were demonstrated either in contractions of crayfish opener muscles or in the Ca2+ release from crayfish sarcoplasmic reticulum vesicles. These results indicate a possibility that dimethyl sulfoxide reversibly induces skeletal muscle relaxation mainly in the sarcoplasmic reticulum by means of decreasing the rate and the amount of Ca2+ release from the reticulum.     

Linking performance to microbiology in biofilters treating dimethyl sulphide in the presence and absence of methanol

The performance and microbiology of two inorganic biofilters treating dimethyl sulphide (DMS) in the presence and absence of methanol was investigated. Addition of methanol was shown to result in an increase in DMS removal for methanol loadings below 90 g MeOH per cubic metre per hour with the optimal methanol loading around 10–15 g MeOH per cubic metre per hour for a DMS loading of 3.4 g DMS per cubic metre per hour, a fivefold increase in the DMS removal rate compared to the biofilter treating DMS alone. Microbial community analysis revealed that the addition of methanol led to a significant increase of up to an order of magnitude in the abundance of Hyphomicrobium spp. in the biofilter co-treating DMS and methanol compared to the biofilter treating DMS alone, whilst there was no significant difference in the abundance of Thiobacillus spp. between the two biofilters. Given the behaviour of the biofilter co-treating DMS and methanol, the magnitude of the increase in Hyphomicrobium spp. in the biofilter co-treating DMS and methanol and the ability of Hyphomicrobium spp. to use both methanol and DMS as growth substrates, it was concluded that Hyphomicrobium spp. were the microorganisms responsible for the bulk of the DMS degradation in the biofilter co-treating DMS and methanol.