Water quality in karstlands at Mole Creek, Tasmania

Samples from 28 sites at Mole Creek were analysed for a range of water quality indicators. Low or negligible bacterial counts were obtained for sites with mainly forested catchments; cleared catchments gave more variable and generally higher results. Higher turbidity and nitrate levels were recorded in cleared catchments, suggesting increased erosion and nutrient loading of streams. A comparison of water quality parameters at streamsinks and related springs shows that the karst aquifer is not an efficient water purifier. Rapid capture of surface run off via solutional openings, coupled with the pipe-like efficiency with which karst conduits transfer the water, constrains the potential for the karst aquifer to ameliorate water pollution problems. This connection between surface and underground environments is a key consideration for sustainable land management in karstlands. We conclude that karst aquifers have more in common with surface streams than non-karstic ground-water systems, in terms of their water purification properties. Water from two bores was found to be relatively free of microbiological pollution, despite being located in disturbed catchments. This suggests that ground-water sourced from bores is less affected by activities at the surface, although further work is required to confirm this

Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface

Experiments show that spike-triggered stimulation performed with Bidirectional Brain-Computer-Interfaces (BBCI) can artificially strengthen connections between separate neural sites in motor cortex (MC). What are the neuronal mechanisms responsible for these changes and how does targeted stimulation by a BBCI shape population-level synaptic connectivity? The present work describes a recurrent neural network model with probabilistic spiking mechanisms and plastic synapses capable of capturing both neural and synaptic activity statistics relevant to BBCI conditioning protocols. When spikes from a neuron recorded at one MC site trigger stimuli at a second target site after a fixed delay, the connections between sites are strengthened for spike-stimulus delays consistent with experimentally derived spike time dependent plasticity (STDP) rules. However, the relationship between STDP mechanisms at the level of networks, and their modification with neural implants remains poorly understood. Using our model, we successfully reproduces key experimental results and use analytical derivations, along with novel experimental data. We then derive optimal operational regimes for BBCIs, and formulate predictions concerning the efficacy of spike-triggered stimulation in different regimes of cortical activity.Comment: 35 pages, 9 figure

Parameter estimation of S-distributions with alternating regression

We propose a novel 3-way alternating regression (3-AR) method as an effective strategy for the estimation of parameter values in S-distributions from frequency data. The 3-AR algorithm is very fast and performs well for error-free distributions and artificial noisy data obtained as random samples generated from S-distributions, as well as for traditional statistical distributions and for actual observation data. In rare cases where the algorithm does not immediately converge, its enormous speed renders it feasible to select several initial guesses and search settings as an effective countermeasure.Peer Reviewe

Parameter estimation in biochemical systems models with alternating regression

BACKGROUND: The estimation of parameter values continues to be the bottleneck of the computational analysis of biological systems. It is therefore necessary to develop improved methods that are effective, fast, and scalable. RESULTS: We show here that alternating regression (AR), applied to S-system models and combined with methods for decoupling systems of differential equations, provides a fast new tool for identifying parameter values from time series data. The key feature of AR is that it dissects the nonlinear inverse problem of estimating parameter values into iterative steps of linear regression. We show with several artificial examples that the method works well in many cases. In cases of no convergence, it is feasible to dedicate some computational effort to identifying suitable start values and search settings, because the method is fast in comparison to conventional methods that the search for suitable initial values is easily recouped. Because parameter estimation and the identification of system structure are closely related in S-system modeling, the AR method is beneficial for the latter as well. Specifically, we show with an example from the literature that AR is three to five orders of magnitudes faster than direct structure identifications in systems of nonlinear differential equations. CONCLUSION: Alternating regression provides a strategy for the estimation of parameter values and the identification of structure and regulation in S-systems that is genuinely different from all existing methods. Alternating regression is usually very fast, but its convergence patterns are complex and will require further investigation. In cases where convergence is an issue, the enormous speed of the method renders it feasible to select several initial guesses and search settings as an effective countermeasure

Dip patch clamp currents suggest electrodiffusive transport of the polyelectrolyte DNA through lipid bilayers

Spassova M, Tsoneva I, Petrov AG, Petkova JI, Neumann E. Dip patch clamp currents suggest electrodiffusive transport of the polyelectrolyte DNA through lipid bilayers. Biophysical Chemistry. 1994;52(3):267-274.Planar lipid bilayers formed from monolayers of diphytanoyl lecithin (DPhL) were found to interact with plasmid DNA (5.6 kbp; M(r) = 3.7 X 10(6)) leading to an increase in the conductance of the membrane. The association of DNA with a lipid bilayer greatly facilitates the transport of the small ions of the main salt KCl. The appearance of long-lived current levels, for instance, of 27.6 pA at V-m = +60 mV membrane voltage, where the actual contact (adsorption) is electrophoretically enhanced, suggests a locally conductive DNA/lipid interaction zone where parts of the DNA strand may be transiently inserted in the bilayer, leaving other parts of the DNA probably protruding out from the outer surface of the bilayer. At V-m = -60 mV, where DNA can be electrophoretically moved away from the membrane, the membrane current is practically zero. This current asymmetry is initially also observed at higher voltages, for instance at 200 mV. However, if the voltage sign (V-m = +200 mV) is changed after a transient positive current (approximate to 15 pA) was observed, there is also now (at V-m = -200 mV) a finite negative current at the negative membrane voltage. Thus, it appears that at V-m = +200 mV the adsorbed parts of the polyelectrolyte DNA are not only transiently inserted in, but actually also electrophoretically pulled through, the porous zones onto the other membrane side leaving the bilayer structure basically intact. These data provide direct electric evidence for the electrophoretic transport of a highly charged and hydrated macromolecule, probably together with the associated gegen-ions, through the thin hydrophobic film of the lipid bilayer

Shaping Robust System through Evolution

Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness of the phenotype. Here we study how this dynamical system is robust to noise during development and to genetic change by mutation. We adopt a simplified transcription regulation network model to govern gene expression, which gives a fitness function. Through simulations of the network that undergoes mutation and selection, we show that a certain level of noise in gene expression is required for the network to acquire both types of robustness. The results reveal how the noise that cells encounter during development shapes any network's robustness, not only to noise but also to mutations. We also establish a relationship between developmental and mutational robustness through phenotypic variances caused by genetic variation and epigenetic noise. A universal relationship between the two variances is derived, akin to the fluctuation-dissipation relationship known in physics

Peculiarities of the Weyl - Wigner - Moyal formalism for scalar charged particles

A description of scalar charged particles, based on the Feshbach-Villars formalism, is proposed. Particles are described by an object that is a Wigner function in usual coordinates and momenta and a density matrix in the charge variable. It is possible to introduce the usual Wigner function for a large class of dynamical variables. Such an approach explicitly contains a measuring device frame. From our point of view it corresponds to the Copenhagen interpretation of quantum mechanics. It is shown how physical properties of such particles depend on the definition of the coordinate operator. The evolution equation for the Wigner function of a single-charge state in the classical limit coincides with the Liouville equation. Localization peculiarities manifest themselves in specific constraints on possible initial conditions.Comment: 16 pages, 2 figure

The evolution of plasticity of dauer larva developmental arrest in the nematode Caenorhabditis elegans.

Organisms can end up in unfavourable conditions and to survive this they have evolved various strategies. Some organisms, including nematodes, survive unfavourable conditions by undergoing developmental arrest. The model nematode Caenorhabditis elegans has a developmental choice between two larval forms, and it chooses to develop into the arrested dauer larva form in unfavourable conditions (specifically, a lack of food and high population density, indicated by the concentration of a pheromone). Wild C. elegans isolates vary extensively in their dauer larva arrest phenotypes, and this prompts the question of what selective pressures maintain such phenotypic diversity? To investigate this we grew C. elegans in four different environments, consisting of different combinations of cues that can induce dauer larva development: two combinations of food concentration (high and low) in the presence or absence of a dauer larva-inducing pheromone. Five generations of artificial selection of dauer larvae resulted in an overall increase in dauer larva formation in most selection regimes. The presence of pheromone in the environment selected for twice the number of dauer larvae, compared with environments not containing pheromone. Further, only a high food concentration environment containing pheromone increased the plasticity of dauer larva formation. These evolutionary responses also affected the timing of the worms' reproduction. Overall, these results give an insight into the environments that can select for different plasticities of C. elegans dauer larva arrest phenotypes, suggesting that different combinations of environmental cues can select for the diversity of phenotypically plastic responses seen in C. elegans.We would like to thank Henrique Teotonio for the gift of the G140.A population, Louise Hughes and Laura Weldon for technical help, two anonymous reviewers for their comments, and NERC for funding.This is the final published version of the article. It was originally published in Ecology and Evolution (Diaz SA, Viney M, Ecology and Evolution 2015, 5(6), 1343–1353, doi:10.1002/ece3.1436) http://dx.doi.org/10.1002/ece3.143

Selective Electrodialysis for Copper Removal from Brackish Water and Coal Seam Gas Water

This study investigates the removal rate of divalent ions during partial desalination of brackish water using electrodialysis (ED). An experiment was conducted with a benchtop PCCell electrodialysis instrument in batch mode with a non-ion selective membrane. The removal rate of total copper, a valuable plant micronutrient, was analysed. Both copper chloride and copper sulphate removal compared to sodium chloride removal were studied. The copper and the sulphate content in the diluate declined logarithmically with a removal rate of around 98 % for copper in both experiments, and 100 % for sulphate over three hours at a starting temperature of 23 °C. Copper and sulphate were removed faster than sodium chloride at 72 %. The temperature of the diluate increased by 15 % during the three-hour run. The loss of water from the diluate was approximately 10 %, limiting brine production. Modelling indicated that the Mass/Charge ratio of ions could be an indicator of the removal rate of anions, especially if they have, like sulphur, a large effective radius, whereas the Effective Ionic Radius can be an indicator for the removal of cations. The smaller the ionic radius, the faster the removal rate of the cation. This model can be used to customise nutrient concentration in the water end product. The customised water has a potential to be used for fertigation, saving the farmer money by retaining beneficial plant nutrients in the water

Morphology of Pyramidal Neurons in the Rat Prefrontal Cortex: Lateralized Dendritic Remodeling by Chronic Stress

The prefrontal cortex (PFC) plays an important role in the stress response. We filled pyramidal neurons in PFC layer III with neurobiotin and analyzed dendrites in rats submitted to chronic restraint stress and in controls. In the right prelimbic cortex (PL) of controls, apical and distal dendrites were longer than in the left PL. Stress reduced the total length of apical dendrites in right PL and abolished the hemispheric difference. In right infralimbic cortex (IL) of controls, proximal apical dendrites were longer than in left IL, and stress eliminated this hemispheric difference. No hemispheric difference was detected in anterior cingulate cortex (ACx) of controls, but stress reduced apical dendritic length in left ACx. These data demonstrate interhemispheric differences in the morphology of pyramidal neurons in PL and IL of control rats and selective effects of stress on the right hemisphere. In contrast, stress reduced dendritic length in the left ACx