A Brownian ratchet for protein translocation including dissociation of ratcheting sites

We study a model for the translocation of proteins across membranes through a nanopore using a ratcheting mechanism. When the protein enters the nanopore it diffuses in and out of the pore according to a Brownian motion. Moreover, it is bound by ratcheting molecules which hinder the diffusion of the protein out of the nanopore, i.e. the Brownian motion is reflected such that no ratcheting molecule exits the pore. New ratcheting molecules bind at rate γ. Extending our previous approach (Depperschmidt and Pfaffelhuber in Stoch Processes Appl 120:901–925, 2010) we allow the ratcheting molecules to dissociate (at rate δ) from the protein (Model I). We also provide an approximate model (Model II) which assumes a Poisson equilibrium of ratcheting molecules on one side of the current reflection boundary. Using analytical methods and simulations we show that the speeds of both models are approximately the same. Our analytical results on Model II give the speed of translocation by means of a solution of an ordinary differential equation. This speed gives an approximation for the time it takes to translocate a protein of given length.     

Scent‐Mark Identification and Scent‐Marking Behaviour in African Wild Dogs (Lycaon pictus)

Scent‐marking is common in mammals, but where signals are carried by urine and faeces, distinguishing between scent‐marking and mere elimination is problematic. To do so, we documented behaviours and context variables associated with urination and defecation in free‐ranging endangered African wild dogs (Lycaon pictus) and tested whether these were related to the responses of other dogs to deposits. We found that distinct postures were almost uniquely associated with deposits by dominant wild dogs, were more common during urination than defecation, and increased the likelihood that these deposits would be investigated by other wild dogs. The likelihood of investigation depended on the sex and dominance status of the depositor, the type of deposit and the substrate. Urine from dominant females was more likely to be investigated by other wild dogs than any other deposits, and deposits placed on vegetation were more likely to be investigated than those on bare ground. The likelihood that a deposit would be overmarked was affected by the deposit type and the sex and dominance status of the last depositor. Collectively, these results suggest that dominant wild dog urine is of greatest interest to other dogs. Our results show that some deposits by African wild dogs are not scent‐marks and that detailed observations of behaviours and context variables during elimination events can be used to distinguish deposits that are likely to be of communication value.     

Selenium Species and Their Distribution in Freshwater Fish from Argentina

The distribution and speciation of selenium (Se) in freshwater fish (muscle and liver tissue) from lakes in Argentina was investigated. Three introduced species, brown trout (Salmo trutta), rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis), and one native species, creole perch (Percichthys trucha), were investigated. Values for total selenium in muscle ranged from 0.66 to 1.61 μg/g, while in the liver, concentrations were much higher, from 4.46 to 73.71 μg/g on a dry matter basis. Separation of soluble Se species (SeCys₂, selenomethionine (SeMet), SeMeSeCys, selenite and selenate) was achieved by ion exchange chromatography and detection was performed by inductively coupled plasma–mass spectrometry. The results showed that in fish muscle, from 47 to 55 % of selenium was soluble and the only Se species identified was SeMet, which represented around 80 % of soluble Se, while in the liver, the amount of soluble Se ranged from 61 to 76 % and the percentage of species identified (SeMet and SeCys₂) was much lower and ranged from 8 to 17 % of soluble Se.     

Conservation Assessments of Arboreal Mammals in Difficult Terrain: Occupancy Modeling of Pileated Gibbons (Hylobates pileatus)

Long-term monitoring programs, wildlife surveys, and other research involving species population assessment require reliable data on population status. Given the logistically challenging nature of some species’ habitats and cryptic behaviors, collecting these data can prove to be a considerable barrier. We used detection/nondetection data from pileated gibbons (Hylobates pileatus) in the Cardamom Mountains of southwest Cambodia to estimate their population occupancy and detectability. We modeled occupancy using elevation, tree height, tree density, tree diversity, and disturbance covariates. Modeling demonstrated that 83% of the sites are occupied by Hylobates pileatus and that the detectability of the species varies positively with elevation. No clear relationship between habitat quality covariates and occupancy of Hylobates pileatus emerged. Effort analysis based on model estimates demonstrated that at high elevations, less than half the number of site visits is needed to attain the same detectability estimate precision as across all elevations. We suggest that human activities at low elevations, which affect forest composition, are the central factors impacting the detectability and occupancy of Hylobates pileatus. Longer sampling durations and/or a higher number of site visits, especially at lower elevations, increase precision of the occupancy estimator for the least effort. For effective future monitoring and research for this and similar species, using this relatively simple method, applied with repeat site visits, would allow a longitudinal comparison of detection at sites in difficult terrain.     

Effect of Microorganisms and Microbial Metabolites on Apatite Dissolution

The dissolution rate of apatite was determined in batch reactors in organic acid solutions and in microbial cultures. Inoculum for the cultures was from biotite plus apatite crystals from a granite weathering profile in South Eastern Australia. In both the biotic and the abiotic experiments, etching of the apatite surface leads to the formation of elongated spires parallel to the c axis. Apatite dissolution rates in the inorganic, acetate, and oxalate solutions increase as pH decreases from approximately 10 -11 mol/m -2 · s -1 at initial pH 5.5 to 10 -7 mol/m -2 · s -1 at initial pH 2. Under mildly acidic to near neutral pH conditions, both oxalate and acetate increased apatite dissolution by up to an order of magnitude compared to the inorganic conditions. Acetate catalyzed the reaction by forming complexes with Ca, either in solution or at the mineral surfaces. Oxalate forms complexes with Ca as well, and can also affect reaction rates and stoichiometry by forming Ca-oxalate precipitates, thus affecting solution saturation states. In all abiotic experiments, net phosphate release to solution approaches zero even when solutions are apparently undersaturated by several orders of magnitude with respect to the solubility of an ideal fluoroapatite mineral. In the microbial experiments, two enrichment cultures increased both apatite and biotite dissolution by producing organic acids, primarily pyruvate, fermentation products, and oxalate, and by lowering bulk solution pH to between 3 and 5. However, the microorganisms were also able to increase phosphate release from apatite (by two orders of magnitude) without lowering bulk solution pH by producing pyruvate and other compounds.     

Determination of Trace Element Stability in Sediments Using Redox Gel Probes: Probe Construction and Theoretical Performance

A simple and inexpensive technique is described that can be used to assess the stability of redox-sensitive compounds in the sediments of wetlands and other shallow water environments. In this method, solid redox-sensitive compounds, such as manganese dioxide (MnO 2 ), are incorporated into agar gels held in rigid plastic holders. One surface of the gel remains exposed along the length of the resulting probe. The probes are pushed vertically into sediments and are left in situ for a period of time (days to weeks), after which they are visually inspected and chemically analyzed. The diffusion of nonreactive solutes (e.g., sulfate) in 2% (wt/vol) agar was unaffected by the presence of immobilized MnO 2 particles. The rate of dissolution of particulate MnO 2 in agar gels in the presence of an external diffusing reductant (L-ascorbic acid) could be quantified by digital analysis of pixel density on gel images. Redox gel probes incubated in the sediment of a wetland built to remove manganese from circumneutral pH coal mine drainage demonstrated different patterns of depth-dependent MnO 2 stability along a 15-m transect. MnO 2 gel probe results were consistent with data obtained using sediment cores and porewater diffusion samplers.     

Noninvasive diffusive optical imaging of the auditory response to birdsong in the zebra finch

Songbirds communicate by learned vocalizations with concomitant changes in neurophysiological and genomic activities in discrete parts of the brain. Here, we tested a novel implementation of diffusive optical imaging (also known as diffuse optical imaging, DOI) for monitoring brain physiology associated with vocal signal perception. DOI noninvasively measures brain activity using red and near-infrared light delivered through optic fibers (optodes) resting on the scalp. DOI does not harm subjects, so it raises the possibility of repeatedly measuring brain activity and the effects of accumulated experience in the same subject over an entire life span, all while leaving tissue intact for further study. We developed a custom-made apparatus for interfacing optodes to the zebra finch (Taeniopygia guttata) head using 3D modeling software and rapid prototyping technology, and applied it to record responses to presentations of birdsong in isoflurane-anesthetized zebra finches. We discovered a subtle but significant difference between the hemoglobin spectra of zebra finches and mammals which has a major impact in how hemodynamic responses are interpreted in the zebra finch. Our measured responses to birdsong playback were robust, highly repeatable, and readily observed in single trials. Responses were complex in shape and closely paralleled responses described in mammals. They were localized to the caudal medial portion of the brain, consistent with response localization from prior gene expression, electrophysiological, and functional magnetic resonance imaging studies. These results define an approach for collecting neurophysiological data from songbirds that should be applicable to diverse species and adaptable for studies in awake behaving animals.