Effect of detection heterogeneity in occupancy‐detection models: an experimental test of time‐to‐first‐detection methods

Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time‐to‐first‐detection (TTD) occupancy models have been proposed as a cost–effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validated the performance of occupancy‐detection models by creating a situation where occupancy is known, and model outputs can be compared with the truth. We tested the performance of TTD occupancy models in the face of detection heterogeneity using an experiment based on standard survey methods to monitor koala Phascolarctos cinereus populations in Australia. Known numbers of koala faecal pellets were placed under trees, and observers, uninformed as to which trees had pellets under them, carried out a TTD survey. We fitted five TTD occupancy models to the survey data, each making different assumptions about detectability, to evaluate how well each estimated the true occupancy status. Relative to the truth, all five models produced strongly biased estimates, overestimating detection probability and underestimating the number of occupied trees. Despite this, goodness‐of‐fit tests indicated that some models fitted the data well, with no evidence of model misfit. Hence, TTD occupancy models that appear to perform well with respect to the available data may be performing poorly. The reason for poor model performance was unaccounted for heterogeneity in detection probability, which is known to bias occupancy‐detection models. This poses a problem because unaccounted for heterogeneity could not be detected using goodness‐of‐fit tests and was only revealed because we knew the experimentally determined outcome. A challenge for occupancy‐detection models is to find ways to identify and mitigate the impacts of unobserved heterogeneity, which could unknowingly bias many models.     

Mechanotransduction by Membrane Proteins: C. elegans PEZO-1 is a mechanosensitive ion channel involved in food sensation

PIEZO channels are force sensors essential for physiological processes, including baroreception and proprioception. The Caenorhabditis elegans genome encodes an orthologue gene of the Piezo family, pezo-1, which is expressed in several tissues, including the pharynx. This myogenic pump is an essential component of the C. elegans alimentary canal, whose contraction and relaxation are modulated by mechanical stimulation elicited by food content. Whether pezo-1 encodes a mechanosensitive ion channel and contributes to pharyngeal function remains unknown. Here, we leverage genome editing, genetics, microfluidics, and electropharyngeogram recording to establish that pezo-1 is expressed in the pharynx, including in a proprioceptive-like neuron, and regulates pharyngeal function. Knockout (KO) and gain-of-function (GOF) mutants reveal that pezo-1 is involved in fine-tuning pharyngeal pumping frequency, as well as sensing osmolarity and food mechanical properties. Using pressure-clamp experiments in primary C. elegans embryo cultures, we determine that pezo-1 KO cells do not display mechanosensitive currents, whereas cells expressing wild-type or GOF PEZO-1 exhibit mechanosensitivity. Moreover, infecting the Spodoptera frugiperda cell line with a baculovirus containing the G-isoform of pezo-1 (among the longest isoforms) demonstrates that pezo-1 encodes a mechanosensitive channel. Our findings reveal that pezo-1 is a mechanosensitive ion channel that regulates food sensation in worms.     

Kinetics improvement of high-grade sulphides bioleaching by effects separation

Abstract: The kinetics of bioleaching of sulphide concentrates by Thiobacillus ferrooxidans can be improved by performing separately the two operations relating the two effects involved in the indirect contact mechanism, (1) chemical leaching and (2) biological oxidation of the Fe2+ produced in the chemical stage (IBES: Indirect Bioleaching with Effects Separation). This scheme permits the separate enhancement of each stage. On the one hand, the chemical attack of the ferric iron to sulphides can be performed at a higher temperature. On the other hand, the biological oxidation stage is more effective when biofilm models are applied. At the same time, inhibitory phenomena produced as a result of the bacterial breaking caused by the abrasion of the solid particles on microorganisms are prevented. In this work the 1BES process has been applied to a Spanish copper-zinc and a copper sulphide concentrate. The objective has been to selectively dissolve zinc, which may be recovered by solvent exraction, the remaining residue being a copper concentrate suitable for pyrometallurgical treatment. The attributes of moderate temperature, atmospheric pressure, low cost of the leaching agent, flexibility and effectiveness make the process very attractive from an economic point of view.     

Agonist-dependent traffic of raft-associated Ras and Raf-1 is required for activation of the mitogen-activated protein kinase cascade

Stimulation of HIRcB fibroblasts with insulin leads to accumulation of active components of the mitogen-activated protein kinase cascade in endocytic compartments. However, the factors that regulate the mobilization of these components through the endocytic pathway and the relevance of this event to cellular signaling remain unclear. Here we report that Ras proteins are associated with lipid rafts in resting HIRcB fibroblasts. Ras is rapidly internalized into the endocytic compartment following stimulation with insulin. The redistribution of Ras is independent of its activation. Attachment of the C-terminal 20 amino acids of Ha-Ras to green fluorescent protein was sufficient to target this construct to the same loci as the endogenous Ras protein, indicating that Ras distribution is a consequence of the association of its lipid modified C terminus with membranes. Depletion of plasma membrane cholesterol delocalized Ras and blocked insulin-dependent Ras traffic. Cholesterol depletion also blocked insulin-dependent phosphorylation of MEK and mitogen-activated protein kinase (MAPK) but had no effects on the translocation and activation of Raf-1. A second inhibitor of endocytosis, cytochalasin D, also blocked insulin-dependent MAPK phosphorylation. Taken together, these results suggest that mobilization of active Raf-1 through the endocytic compartment is required for completion of the MAPK cascade.     

Chromatin reorganization during spermiogenesis of the mollusc Thais hemostoma (Muricidae): implications for sperm nuclear morphogenesis in cenogastropods

Thais is a cenogastropod mollusc belonging to the Muricidae family. The sperm nuclear morphogenesis of Thais develops in two well-defined and peculiar steps. In the first one, the round early spermatidyl nucleus is penetrated by an endonuclear channel, which arranges as a helix at the inner nuclear surface and organizes the condensing chromatin all around. In the second step, the spiral channel stretches, dragging along the associated chromatin and leading to a definitive cylinder-shaped sperm nucleus. Simultaneously with these changes in nuclear shape, the chromatin is sequentially organized in granules, fibres, lamellae, and, finally, in a very condensed structure, whereas the spermiogenic DNA-associated proteins become more basic and simple. The sperm nucleus contains a small group of protamines consisting of only four types of amino acid (lysine, arginine, glycine, and serine). The most remarkable fact on nuclear spermiogenesis in Thais is that, whereas the chromatin condensation process, the nuclear proteins, and the final shape of sperm nucleus are very similar to those in other muricidae studied, the pathway of nuclear morphogenesis is completely different. We propose an independent genetic control for those two spermiogenic events (chromatin condensation and nucleomorphogenesis). Finally we discuss briefly the main traits of nucleomorphogenesis of muricid molluscs.     

Ethanol effect on the chick embryo ossification: a macroscopic and microscopic study

This study attempts to analyze anomalies in avian embryos induced macroscopically and microscopically when exposed to ethanol (EtOH) during the first stages of development. Fertilized chicken eggs were employed in this study. The eggs were incubated at 37.8 degrees C. Some of the eggs were treated on day 0 with EtOH (20%, 40% and 60%) by instillation in the air sac. The control group was instilled with 0.1 ml of NaCl at 0.9%. Other eggs were treated on the 4th post-incubation day, employing the same methodology. The embryos in both groups were removed from the eggs on the 11th incubation day and examined using a dissecting binocular microscope. After macroscopic analysis, the samples obtained were fixed in 10% formol, photographed and processed according to common histological techniques and the Picrosirius method. Embryos treated with EtOH demonstrated a significant weight decrease. Microscopic analysis by means of the Picrosirius method revealed that the intra-membranous ossification process presents less development, and therefore there was less type I collagen in trabecular bone in the embryos post-exposure to EtOH with respect to the control.     

The 2.15 A crystal structure of CG-16, the developmentally regulated homodimeric chicken galectin

Differential developmental regulation of expression, fine-specificity differences in ligand recognition and disparate capacity for homodimerization are characteristics of the two currently known proto-type chicken galectins. The X-ray crystal structure of the first avian galectin, the homodimeric agglutinin from chicken liver (CG-16), has been solved in the absence of ligand in two crystal forms. Although the arrangement of lectin dimers in the two crystals is different, the structure of the monomers and their association into the extended beta-sandwich that characterises the dimer are virtually identical. The fold establishes a beta-sandwich motif composed of a five-stranded and a six-stranded beta-sheet evocative of proto-type mammalian galectins. The carbohydrate-binding site is occupied by six water molecules that take the place of the sugar in the complex. They help to stabilise in the absence of the ligand the spatial arrangement of the amino acid side-chains involved in sugar recognition. Docking of N-acetyllactosamine into the binding site reveals that three of these water molecules, which are in direct contact with the protein, occupy positions equivalent to the key sugar hydroxyl groups, namely the hydroxyls at positions 4 and 6 of the galactose unit and at position 3 of the N-acetylglucosamine unit. Crystallographic data are fully consistent with the binding features in solution previously derived from chemical mapping with deoxy, fluoro and O-methyl derivatives and laser photo-CIDNP (chemically induced dynamic nuclear polarisation) studies. The possible molecular basis for the monomeric character of the chicken intestinal galectin as well as potential mechanisms of oxidative inactivation by disulphide bridging are evaluated on the basis of the given structural information concerning the CG-16 dimer interface and the cysteine residues, respectively.     

Effect of cell ageing on Ca2+ influx into human red cells

The effect of cell ageing on Ca2+ entry was studied in this work, using sub-populations of young and old human red cells, separated by stringent percoll density gradients. Additionally, the influence of an osmotic gradient was investigated as a model for shear stress. Ca2+ entry was assessed at 37 degrees C, under conditions where the Ca2+ pump was either inhibited by NaVO3 (0.5-10 mM) or inactivated by ATP depletion. The entry was linear with time up to 1 h. No differences in Ca2+ influx between the two sub-populations were detected in isotonic Na(+)-medium. In contrast, after incubation in anisosmotic media, Ca2+ entry into old cells was significantly higher than into younger cells. In hypotonic Na(+)-medium, the entry into old cells was not affected by La3+ (10 microM) whilst it was partially blocked by Gd3+ at a similar level (half-maximal effect attained with about 1 microM Gd3+). The entry into young cells was only slightly stimulated by these lanthanides at low concentrations (10 microM), regardless of the tonicity of incubation medium. Further increasing Gd3+ levels above 10 microM markedly enhanced Ca2+ entry into both cell types. The selective blockade of Ca2+ influx by low Gd3+ concentrations suggests presence of mechano-sensitive channels, that become preferentially activated in old cells. Activation of these channels during in-vivo microcirculation may help to explain the increased Ca2+ content of senescent cells.     

Formin is a processive motor that requires profilin to accelerate actin assembly and associated ATP hydrolysis

Motile and morphogenetic cellular processes are driven by site-directed assembly of actin filaments. Formins, proteins characterized by formin homology domains FH1 and FH2, are initiators of actin assembly. How formins simply bind to filament barbed ends in rapid equilibrium or find free energy to become a processive motor of filament assembly remains enigmatic. Here we demonstrate that the FH1-FH2 domain accelerates hydrolysis of ATP coupled to profilin-actin polymerization and uses the derived free energy for processive polymerization, increasing 15-fold the rate constant for profilin-actin association to barbed ends. Profilin is required for and takes part in the processive function. Single filaments grow at least 10 microm long from formin bound beads without detaching. Transitory formin-associated processes are generated by poisoning of the processive cycle by barbed-end capping proteins. We successfully reconstitute formin-induced motility in vitro, demonstrating that this mechanism accounts for the puzzlingly rapid formin-induced actin processes observed in vivo.     

Physiological stress in ecology: lessons from biomedical research

Increasingly, levels of the 'stress hormones' cortisol and corticosterone are being used by ecologists as indicators of physiological stress in wild vertebrates. The amplitude of hormonal response is assumed to correlate with the overall health of an animal and, by extension, the health of the population. However, much of what is known about the physiology of stress has been elucidated by the biomedical research community. I summarize five physiological mechanisms that regulate hormone release during stress that should be useful to ecologists and conservationists. Incorporating these physiological mechanisms into the design and interpretation of ecological studies will make these increasingly popular studies of stress in ecological settings more rigorous.