Measurement of Slow Spontaneous Release of 11-cis-Retinal from Rhodopsin

The vertebrate visual photoreceptor rhodopsin (Rho) is a unique G protein-coupled receptor as it utilizes a covalently tethered inverse agonist (11-cis-retinal) as the native ligand. Previously, electrophysiological studies showed that ligand binding of 11-cis-retinal in dark-adapted Rho was essentially irreversible with a half-life estimated to be 420 years, until after thermal isomerization to all-trans-retinal, which then slowly dissociates. This long lifetime of 11-cis-retinal binding was considered to be physiologically important for minimizing background signal (dark noise) of the visual system. However, in vitro biochemical studies on the thermal stability of Rho showed that Rho decays with a half-life on the order of days. In this study, we resolve the discrepancy by measuring the chromophore exchange rate of the bound 11-cis-retinal chromophore with free 9-cis-retinal from Rho in an in vitro phospholipid/detergent bicelle system. We conclude that the thermal decay of Rho primarily proceeds through spontaneous breaking of the covalent linkage between opsin and 11-cis-retinal, which was overlooked in the electrophysiological recording. We estimate that this slow spontaneous release of 11-cis-retinal from Rho should result in 10⁴ to 10⁵ free opsin molecules in a dark-adapted rod cell—a number that is three orders of magnitude higher than previously expected. We also discuss the physiological implications of these findings on the basal activity of opsins and the associated dark noise in the visual system.     

Retention of phytosiderophores by the soil solid phase – adsorption and desorption

Plant and Soil - Graminaceous plants exude phytosiderophores (PS) for acquiring Fe. Adsorption of PS and its metal complexes to the soil solid phase reduces the FePS solution concentration and...     

The performance of dogs in detecting α-ionone in the vapor phase

Summary Concentration-response functions for-ionone were established for four German shepherds (Figs. 3 and 4). The dogs were tested in a three choice behavioral apparatus (Fig. 2), and trained, by a restricted operant procedure, to establish an approach-avoidance discrimination between odor and air. Odorant concentrations were presented from an olfactometer calibrated by gas chromatography. Minimum detectable concentrations fell within the range 4.0×10^4.5–4.0×10^6.5 molecules/cm³. Concentration-response curves for three of the dogs show a clear double reversal in slope which is statistically significant and which divides the curve into a slowly descending upper limb, best fitted by a parabolic function, and a rapidly descending lower limb, best fitted by a cubic function (Figs. 5 and 6). There is evidence that this division might reflect a dual receptor mechanism. When performance during testing stabilized for a given concentration and the concentration was then lowered by a certain magnitude, the new performance level depended markedly on that magnitude. No evidence was found to suggest that adaptation to the test odor influenced performance. As defined by a differential threshold fraction (Flow/Flow) one dog's ability to discriminate between differences in flow rate fell in the range 0.12–0.08.We thank the U.S. Air Force, Air Force Office of Scientific Research for their generous support of this work (Grant No. 73-2425 to D.G.Moulton).-ionone was donated by Givaudan Inc. (Dr. J. Dorsky). We also thank Mr. Paul Phillips for able technical assistance and Dr. T. Burlingame for gas chromatographic measurements.     

Estimation of effective cleanup radius for soil‐vapor extraction systems

Soil‐vapor extraction (SVE) is a standard and effective in situ treatment for the removal of volatile contaminants from vadose‐zone soil. The duration of SVE operation required to reach site closure is quite variable, however, ranging up to several years or more. An understanding of the contaminant recovery rate as a function of distance from each vapor‐extraction well allows SVE systems to be designed so that cleanup goals can be achieved within a specified time frame.

A simple one‐dimensional model has been developed that provides a rough estimate of the effective cleanup radius (defined as “the maximum distance from a vapor extraction point through which sufficient air is drawn to remove the required fraction of contamination in the desired time") for SVE systems. Because the model uses analytical rather than numerical methods, it has advantages over more sophisticated, multidimensional models, including simplicity, speed, versatility, and robustness.

The contaminant removal rate at a given distance from the vapor‐extraction point is assumed to be a function of the local rate of soil‐gas flow, the contaminant soil concentration, and the contaminant volatility. Soil‐gas flow rate as a function of distance from the vapor‐extraction point is estimated from pilot test data by assuming that the infiltration of atmospheric air through the soil surface is related to the vacuum in the soil. Although widely applicable, the model should be used with some caution when the vadose zone is highly stratified or when venting contaminated soil greater than 30 ft below grade. Since 1992, Groundwater Technology, Inc. has been using this model routinely as a design tool for SVE systems.     

Molecular basis of ion permeability in a voltage‐gated sodium channel

Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na⁺ ≈ Li⁺ ≫ K⁺, Ca²⁺, Mg²⁺) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.     

Is the signal from the mesophyll to the guard cells a vapour‐phase ion?

Previous studies have suggested that the red light and CO₂ responses of stomata are caused by a signal from the mesophyll to the guard cells. Experiments were conducted to test the idea that this signal is a vapour‐phase ion. Stomata in isolated epidermes of Tradescantia pallida were found to respond to air ions created by an electrode that was positioned under the epidermes. Anthocyanins in the epidermes of this species were observed to change colour in response to these air ions, and this change in colour was attributed to changes in pH. A similar change in lower epidermal colour was observed in intact leaves upon illumination and with changes in CO₂ concentration. Based on the change in epidermal colour, the pH of the epidermis was estimated to be approximately 7.0 in darkness and 6.5 in the light. Stomata in isolated epidermes responded to pH when suspended over (but not in contact with) solutions of different pH. We speculate that stomatal responses to CO₂ and light are caused by vapour‐phase ions, possibly hydronium ions that change the pH of the epidermis.     

Phylogenetic positions of several amitochondriate protozoa——Evidence from phylogenetic analysis of DNA topoisomerase II

In the 1980s some special protozoa were gradually recognized: being eukaryotes, they possess some characteristics between prokaryotes and eukaryotes, for example, lack of eukaryotic organelle such as mi-tochondria, and even 70S ribosomes in some species, containing 16S, 23S rRNA like those of prokaryotes. These protozoa contain diplomonads (e.g. intestinal parasite Giardia), parabasalids (e.g. venereal disease pathogen Trichomonas), microsporidia (e.g. the human pathogen Encephalitozoon), a…     

Characterization of calcium ion sensitive region for β-mannanase from Streptomyces thermolilacinus

Despite the widespread industrial applications of β-mannanase, the relations between the enzymatic properties and metal ions remain poorly understood. To elucidate the effects of metal ions on β-mannanase, thermal stability and hydrolysis activity were characterized. The stman and tfman genes encoding β-mannanase (EC.3.2.1.78) from Streptomyces thermolilacinus NBRC14274 and Thermobifida fusca NBRC14071 were cloned and expressed in Escherichia coli. The thermal stability of each enzyme shifted to the 7-9°C high temperature in the presence of Ca(2+) compared with that in the absence of Ca(2+). These results show that the thermal stability of StMan and TfMan was enhanced by the presence of Ca(2+). StMan, but not TfMan, required Ca(2+) for the hydrolysis activity. To identify the Ca(2+) sensitive region of StMan, we prepared eight chimeric enzymes. Based on the results of the relationship between Ca(2+) and hydrolysis activity, the region of amino-acid residues 244-349 of StMan was responsible for a Ca(2+) sensitive site.     

Lipid and phase specificity of α-toxin from S. aureus

The pore forming toxin Hla (α-toxin) from Staphylococcus aureus is an important pathogenic factor of the bacterium S. aureus and also a model system for the process of membrane-induced protein oligomerisation and pore formation. It has been shown that binding to lipid membranes at neutral or basic pH requires the presence of a phosphocholine-headgroup. Thus, sphingomyelin and phosphatidylcholine may serve as interaction partners in cellular membranes. Based on earlier studies it has been suggested that rafts of sphingomyelin are particularly efficient in toxin binding. In this study we compared the oligomerisation of Hla on liposomes of various lipid compositions in order to identify the preferred interaction partners and conditions. Hla seems to have an intrinsic preference for sphingomyelin compared to phosphatidylcholine due to a higher probability of oligomerisation of membrane bound monomer. We also can show that increasing the surface density of Hla-binding sites enhances the oligomerisation efficiency. Thus, preferential binding to lipid rafts can be expected in the cellular context. On the other hand, sphingomyelin in the liquid disordered phase is a more favourable binding partner for Hla than sphingomyelin in the liquid ordered phase, which makes the membrane outside of lipid rafts the more preferred region of interaction. Thus, the partitioning of Hla is expected to strongly depend on the exact composition of raft and non-raft domains in the membrane.     

Role of ubiquitin‐proteasome‐dependent proteolytic process in degradation of muscle protein from diabetic rabbits

The activity of ATP, ubiquitin (Ub)dependent proteases partially purified from skeletal muscle (psoas) from alloxan diabetic rabbits was determined at different periods of insulin deficiency. Two days after alloxan injection, no change was observed in the activity of ATP, Ubdependent proteases, but this activity increased 3 and 5 days after diabetes induction, attaining 181% of control values on the 5th day. However, after this early rise, the activity of muscle ATP, Ubdependent proteases decreased, returning to values that did not differ significantly from controls 7 and 10 days after alloxan injection. After 15 days, the activity of these proteases was 57% lower than in muscle from control rabbits. Both the initial increase and the subsequent fall in the activity of the enzymes were prevented by insulin treatment of alloxan diabetic rabbits. The data suggest that Ubproteasomedependent proteolysis have an important role in the control of muscle protein degradation and may be regulated by insulin.     

Correction to: Environmental life cycle implications of upscaling lithium‐ion battery production

The International Journal of Life Cycle Assessment -     

New microbial fossils from ∼1.3 billion‐year‐old rocks of Eastern California

New types of microbial fossils and new occurrences of fossils previously reported only from the Beck Spring Dolomite of the Pahrump Group are now recognized from each of the three formations of the Pahrump Group (Crystal Spring Formation, Beck Spring Dolomite, and Kingston Peak Formation) approximately 1.3 X 10° years old. Comprising perhaps eight or nine distinctive forms, these fossils are characteristically preserved as faint ghostlike structures whose low‐contrast outlines are clearly revealed only when illuminated by a xenon lamp and recorded on high‐contrast film. They represent a distinctive, previously overlooked or neglected type of preservation that has significantly extended the known distribution of microbial fossils in the Pahrump. They include the oldest occurrence known to us of filaments designatable as Girvanella and apparently the first from rocks of pre‐Phanerozoic age. Similar fossils were also found, using the same techniques, in the Chuar Group of the Grand Canyon and in the Uluntui Suite of middle Riphean age in eastern Siberia. Although time correlation of pre‐Phanerozoic rocks based on similar microbial assemblages would be premature, similarity between such assemblages in all formations of the Pahrump Group and with that of the Uluntui Suite is consistent with the inferred unity and middle Riphean age of the Pahrump Group. In addition to the Girvanella we find two smaller types of filaments, two kinds of simple spheroids, and three composite forms (two spheroids and one stalked cluster) that attain diameters up to 80 μm and are probably eucaryotic.     

Toxicological screening of chemical emissions from municipal solid waste landfills. application of a predictive framework to a state‐of‐the‐art facility

A screening‐level risk assessment was used to identify chemicals of potential health concern emitted during the normal operation of an hypothetical state‐of‐the‐art municipal solid waste landfill. Data on the amount of contaminants (carcinogens, non‐carcinogenic systemic toxicants, odorous compounds, and particulate‐bound metals) were obtained from existing facilities and used to estimate ground‐level air concentrations of airborne chemicals at the point of maximum impact (property line) and at year 20 (year of maximum emissions from the landfill). Concentrations of leachate components present in the corresponding underlying aquifer were also estimated. Intakes of chemicals experienced by a series of human receptors were then computed using either single‐media or multi‐media algorithms. Carcinogens of concern were selected as those contributing to a lifetime excess cancer risk (LECR) greater than 10^‐6; for non‐carcinogenic systemic toxicants and odorous volatiles an Exposure Ratio (ER=intake or concentration/RfD, RfC, odor threshold) greater than 0.1 was used as cut‐off. The results obtained identified a final set of air emission components (n = 25) constituted mainly of carcinogenic and odorous substances whereas 2 leachate components were retained. Additional analysis using more refined risk‐based approaches are necessary to verify the relevance of these projections.     

Comparative genome‐wide analysis of small RNAs of major Gram‐positive pathogens: from identification to application

In the recent years, the number of drug- and multi-drug-resistant microbial strains has increased rapidly. Therefore, the need to identify innovative approaches for development of novel anti-infectives and new therapeutic targets is of high priority in global health care. The detection of small RNAs (sRNAs) in bacteria has attracted considerable attention as an emerging class of new gene expression regulators. Several experimental technologies to predict sRNA have been established for the Gram-negative model organism Escherichia coli. In many respects, sRNA screens in this model system have set a blueprint for the global and functional identification of sRNAs for Gram-positive microbes, but the functional role of sRNAs in colonization and pathogenicity for Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis and Clostridium difficile is almost completely unknown. Here, we report the current knowledge about the sRNAs of these socioeconomically relevant Gram-positive pathogens, overview the state-of-the-art high-throughput sRNA screening methods and summarize bioinformatics approaches for genome-wide sRNA identification and target prediction. Finally, we discuss the use of modified peptide nucleic acids (PNAs) as a novel tool to inactivate potential sRNA and their applications in rapid and specific detection of pathogenic bacteria.     

Microbial leaching of arsenic from low‐sulfide gold mine material

Drainages from high‐sulfide tailings near abandoned lode deposits in Alaska, U.S.A., and Yukon, Canada, were found to be acidic, to contain large numbers of Thiobacillus ferrooxidans, and to have high concentrations of dissolved arsenic. Drainages from active placer gold mines are not acidic, but T. ferrooxidans and concentrations of dissolved arsenic exceeding 10 μg/L are found in some streams affected by placer mine drainage. Placer mine material containing low amounts of sulfides (326 (μg/g) and moderately high amounts of arsenic (700 μg/g) was leached with growing cultures of T. ferrooxidans, T. ferrooxidans‐spent filtrate, and acid ferric sulfate. The results showed that while more arsenic was released from this material by growing cultures of T. ferrooxidans than by abiotic controls, acid ferric sulfate released much more arsenic than did either growing cultures of T. ferrooxidans or spent culture filtrate containing oxidized iron. Cation exchange chromatography showed that oxidized iron from T. ferrooxidans culture filtrate is chemically less reactive than the iron in aqueous solutions of ferric sulfate salt. These results indicate that arsenic release from both high‐ and low‐sulfide mine wastes is enhanced biologically, but that rates and amounts of arsenic release are primarily controlled by iron species.     

Engineering aspects of biological ion channels—from biosensors to computational models for permeation

Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate “superkingdom” clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum “Pseudofungi”, which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main “saprolegnian” and “peronosporalean” lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host–pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic “saprolegnian line” is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.     

Extraction of nuclear DNA from bone of skeletonized and fluid‐preserved museum specimens

Obtaining DNA sequences, particularly nuclear DNA, from museum specimens is challenging. We sequenced nuclear DNA from small bone fragments of skeletonized and fluid‐fixed museum specimens of squamate reptiles by using a forensic protocol developed for isolating DNA from human bones. The method yielded high quality nuclear DNA sequences from bones taken from 11 of 21 (52.4%) skeletonized or desiccated specimens, the oldest of which dated back to 1938, and 1 of 9 (11.1%) fluid‐preserved specimens, which was collected in 1957.     

Reassessment of the cold‐labile nature of phosphofructokinase from a hibernating ground squirrel

This study reassesses the proposal that cellular conditions of low temperature and relative acidosis during hibernation contribute to a suppression of phosphofructokinase (PFK) activity which, in turn, contributes to glycolytic rate suppression during torpor. To test the proposal that a dilution effect during in vitro assay of PFK was the main reason for activity loss (tetramer dissociation) at lower pH values, the influence of the macromolecular crowding agent, polyethylene glycol 8000 (PEG), on purified skeletal muscle PFK from Spermophilus lateralis was evaluated at different pH values (6.5, 7.2 and 7.5) and assay temperatures (5, 25 and 37°C). A 78 ± 2.5% loss of PFK activity during 1 h incubation at 5°C and pH 6.5 was virtually eliminated when 10% PEG was present (only 7.0 ± 1.5% activity lost). The presence of PEG also largely reversed PFK inactivation at pH 6.5 at warmer assay temperatures and reversed inhibitory effects by high urea (50 or 400 mM). Analysis of pH curves at 5°C also indicated that ~ 70% of activity would remain at intracellular pH values in hibernator muscle. The data suggest that under high protein concentrations in intact cells that the conditions of relative acidosis, low temperature or elevated urea during hibernation would not have substantial regulatory effects on PFK.