Real‐time model based process monitoring of enzymatic biodiesel production

In this contribution we extend our modelling work on the enzymatic production of biodiesel where we demonstrate the application of a Continuous‐Discrete Extended Kalman Filter (a state estimator). The state estimator is used to correct for mismatch between the process data and the process model for Fed‐batch production of biodiesel. For the three process runs investigated, using a single tuning parameter, q_x = 2 × 10^?2 which represents the uncertainty in the process model, it was possible over the entire course of the reaction to reduce the overall mean and standard deviation of the error between the model and the process data for all of the five measured components (triglycerides, diglycerides, monoglycerides, fatty acid methyl esters, and free fatty acid). The most significant reduction for the three process runs, were for the monoglyceride and free fatty acid concentration. For those components, there was over a ten‐fold decrease in the overall mean error for the state estimator prediction compared with the predictions from the pure model simulations. It is also shown that the state estimator can be used as a tool for detection of outliers in the measurement data. For the enzymatic biodiesel process, given the infrequent and sometimes uncertain measurements obtained we see the use of the Continuous‐Discrete Extended Kalman Filter as a viable tool for real time process monitoring. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:585–595, 2015     

Changing modified regions in the genome in hematopoietic stem cell differentiation

In the process of hematopoietic stem cell (CD133⁺ cell) differentiation, a drastic change in gene expression occurs which must be regulated by epigenetic mechanisms. One strategy for CD133⁺ cell differentiation analysis is to identify genomic DNA regions that have been modified in the process of differentiation. However, it is difficult to obtain large amounts of genomic DNA from uniform CD133⁺ cells. Based on this situation, we screened genomic DNA regions where modifications change during the process of differentiation in human CD133⁺ cells using differential methylation site scanning (DMSS), which is a method of identifying differentially methylated regions of the genome from a small number of cells. As a result, we cloned three DNA fragments which corresponded to centrosomal protein 68 kDA (Cep68), TRIO and F-actin binding protein (TRIOBP), and AMP-activated protein kinase beta (AMPKb).     

The Subcellular Distribution of T-Type Ca2+ Channels in Interneurons of the Lateral Geniculate Nucleus

Inhibitory interneurons (INs) in the lateral geniculate nucleus (LGN) provide both axonal and dendritic GABA output to thalamocortical relay cells (TCs). Distal parts of the IN dendrites often enter into complex arrangements known as triadic synapses, where the IN dendrite plays a dual role as postsynaptic to retinal input and presynaptic to TC dendrites. Dendritic GABA release can be triggered by retinal input, in a highly localized process that is functionally isolated from the soma, but can also be triggered by somatically elicited Ca²⁺-spikes and possibly by backpropagating action potentials. Ca²⁺-spikes in INs are predominantly mediated by T-type Ca²⁺-channels (T-channels). Due to the complex nature of the dendritic signalling, the function of the IN is likely to depend critically on how T-channels are distributed over the somatodendritic membrane (T-distribution). To study the relationship between the T-distribution and several IN response properties, we here run a series of simulations where we vary the T-distribution in a multicompartmental IN model with a realistic morphology. We find that the somatic response to somatic current injection is facilitated by a high T-channel density in the soma-region. Conversely, a high T-channel density in the distal dendritic region is found to facilitate dendritic signalling in both the outward direction (increases the response in distal dendrites to somatic input) and the inward direction (the soma responds stronger to distal synaptic input). The real T-distribution is likely to reflect a compromise between several neural functions, involving somatic response patterns and dendritic signalling.     

Arsenic and fluoride removal by potato peel and rice husk (PPRH) ash in aqueous environments

Finding appropriate adsorbent may improve the quality of drinking water in those regions where arsenic (As) and fluoride (F^?) are present in geological formations. In this study, we evaluated the efficiency of potato peel and rice husk ash (PPRH-ash)-derived adsorbent for the removal of As and F from contaminated water. Evaluation was done in batch adsorption experiments, and the effect of pH, initial adsorbate concentration, contact time, and adsorbent dose were studied. Characteristics of adsorbents were analyzed using scanning electron micropcope (SEM) and Fourier transform infrared (FTIR) spectroscopy. Both the Langmuir and Freundlich isotherm models fitted well for F^? and As sorption process. The maximum adsorption capacity of adsorbent for As and F^? was 2.17 μg g^?1 and 2.91 mg g^?1, respectively. The As and Fi removal was observed between pH 7 and 9. The sorption process was well explained with pseudo-second order kinetic model. Arsenic adsorption was not decreased in the presence of carbonate and sulfate. Results from this study demonstrated potential utility of this agricultural biowaste, which could be developed into a viable filtration technology for As and F^? removal in As- and F-contaminated water streams.     

A model of cooperative effect of AMPA and NMDA receptors in glutamatergic synapses

Glutamatergic synapses play a pivotal role in brain excitation. The synaptic response is mediated by the activity of two receptor types (AMPA and NMDA). In the present paper we propose a model of glutamatergic synaptic activity where the fast current generated by the AMPA conductance produces a local depolarization which activates the voltage- and [Mg²⁺]-dependent NMDA conductance. This cooperative effect is dependent on the biophysical properties of the synaptic spine which can be considered a high input resistance specialized compartment. Herein we present results of simulations where different values of the spine resistance and of the Mg²⁺ concentrations determine different levels of cooperativeness between AMPA and NMDA receptors in shaping the post-synaptic response.     

A Cellular Automata Model of Proton Hopping Down a Channel

Proton hopping is the process where a H‐atom on a hydronium ion forms a H‐bond with the O‐atom of a neighboring H₂O molecule. There is then an exchange of bonding forces when that covalent bond of the H‐atom in the hydronium ion changes to a H‐bond, and the previous H‐bond changes to a covalent bond with the neighboring O‐atom. The neighboring molecule now becomes a hydronium (H₃O⁺) ion. This process repeats itself very rapidly among neighboring hydronium and H₂O molecules. There is a flow of protonic character through bulk H₂O, referred to as proton hopping. This process carries information through living systems where H₂O is present. A cellular automata model of proton hopping down a channel has been created and studied. Variations in the rate of proton entry into the channel and the effects of the polar character of the channel walls was studied using the model. The behavior of the models corresponds to experimental results.     

Uptake,efflux and metabolism of the polyamine putrescine in rabbit lung slices

The herbicide paraquat is a selective pulmonary toxin in many mammals, including man, and its pulmonary toxicity has been attributed to selective uptake by a polyamine transport system in lung. In the present study, we investigated the characteristics of this transport process in rabbit lung slices. [¹⁴C]Putrescine was accumulated by both saturable and non-saturable processes and the accumulated putrescine was non-effluxable over 60 min. The saturable component was inhibited by spermine and paraquat. Moreover, uptake studies in Na⁺-deficient medium indicated that the lack of Na⁺ may selectively enhance uptake via the non-saturable process. The two components also differed in the metabolic fate of accumulated substrate. At 0.6 μM putrescine, where the saturable process predominated, 98% of the ¹⁴C in the perchloric acid-soluble fraction of tissue homogenates was present as putrescine, whilst 3% of the accumulated substrate was found in the acid-insoluble fraction. With 500 μM putrescine, where the non-saturable process predominated, 82% of the ¹⁴C in the acid-soluble fraction was present as putrescine and 15% of accumulated putrescine was found in the acid-insoluble fraction. The acid-insoluble ¹⁴C was localised mainly in the 700 g and 4500 g pellets obtained after homogenising the tissue. We conclude that there are two components to putrescine uptake in rabbit lung slices, both of an apparently irreversible nature. We suggest that the components represent compartmentalisation of putrescine in selective pulmonary cell-types or separate subcellular organelles. The observed metabolism and covalent binding of putrescine appeared to be associated with the non-saturable component only.     

Fast adaptation of cooperative channels engenders Hopf bifurcations in auditory hair cells

Since the pioneering work of Thomas Gold, published in 1948, it has been known that we owe our sensitive sense of hearing to a process in the inner ear that can amplify incident sounds on a cycle-by-cycle basis. Called the active process, it uses energy to counteract the viscous dissipation associated with sound-evoked vibrations of the ear’s mechanotransduction apparatus. Despite its importance, the mechanism of the active process and the proximate source of energy that powers it have remained elusive, especially at the high frequencies characteristic of amniote hearing. This is partly due to our insufficient understanding of the mechanotransduction process in hair cells, the sensory receptors and amplifiers of the inner ear. It has been proposed previously that cyclical binding of Ca²⁺ ions to individual mechanotransduction channels could power the active process. That model, however, relied on tailored reaction rates that structurally forced the direction of the cycle. Here we ground our study on our previous model of hair-cell mechanotransduction, which relied on cooperative gating of pairs of channels, and incorporate into it the cyclical binding of Ca²⁺ ions. With a single binding site per channel and reaction rates drawn from thermodynamic principles, the current model shows that hair cells behave as nonlinear oscillators that exhibit Hopf bifurcations, dynamical instabilities long understood to be signatures of the active process. Using realistic parameter values, we find bifurcations at frequencies in the kilohertz range with physiological Ca²⁺ concentrations. The current model relies on the electrochemical gradient of Ca²⁺ as the only energy source for the active process and on the relative motion of cooperative channels within the stereociliary membrane as the sole mechanical driver. Equipped with these two mechanisms, a hair bundle proves capable of operating at frequencies in the kilohertz range, characteristic of amniote hearing.     

On control of the function of the sodium-potassium pump in malignant cells

This paper introduces a double-layer enzyme-membrane model representing the Na⁺−K⁺ pump in living cells. We present a mathematical solution to the problem of controlling the sodium flux in malignant cells, where an inhibitor exists in the outer layer of the membrane. We give an algorithm for the numerical resolution of this problem of optimal control with illustrations. Finally, we point out the biological importance of this study.     

Identifying Sites for Elk Restoration in Arkansas

Abstract: We used spatial data to identify potential areas for elk (Cervus elaphus) restoration in Arkansas. To assess habitat, we used locations of 239 elk groups collected from helicopter surveys in the Buffalo National River area of northwestern Arkansas, USA, from 1992 to 2002. We calculated the Mahalanobis distance (D²) statistic based on the relationship between those elk-group locations and a suite of 9 landscape variables to evaluate winter habitat in Arkansas. We tested model performance in the Buffalo National River area by comparing the D² values of pixels representing areas with and without elk pellets along 19 fixed-width transects surveyed in March 2002. Pixels with elk scat had lower D² values than pixels in which we found no pellets (logistic regression: Wald χ² = 24.37, P < 0.001), indicating that habitat characteristics were similar to those selected by the aerially surveyed elk. Our D² model indicated that the best elk habitat primarily occurred in northern and western Arkansas and was associated with areas of high landscape heterogeneity, heavy forest cover, gently sloping ridge tops and valleys, low human population density, and low road densities. To assess the potential for elk-human conflicts in Arkansas, we used the analytical hierarchy process to rank the importance of 8 criteria based on expert opinion from biologists involved in elk management. The biologists ranked availability of forage on public lands as having the strongest influence on the potential for elk-human conflict (33%), followed by human population growth rate (22%) and the amount of private land in row crops (18%). We then applied those rankings in a weighted linear summation to map the relative potential for elk-human conflict. Finally, we used white-tailed deer (Odocoileus virginianus) densities to identify areas where success of elk restoration may be hampered due to meningeal worm (Parelaphostrongylus tenuis) transmission. By combining results of the 3 spatial data layers (i.e., habitat model, elk-human conflict model, deer density), our model indicated that restoration sites located in west-central and north-central Arkansas were most favorable for reintroduction.     

The influence of space dimension on the large-time behavior in a reaction–diffusion system modeling diallelic selection

We study a mathematical model from population genetics, describing a single-locus diallelic (A/a) selection–migration process. The model consists of a coupled system of three reaction–diffusion equations, one for the density of each genotype, posed in the whole space \mathbb Rⁿ{\mathbb R^n}. The genotype AA is advantageous, due to a smaller death rate, and we consider the fully recessive case where the other two genotypes aa and Aa have the same (higher) death rate. In the nondiffusive (spatially homogeneous) case, the disadvantageous gene a is always eliminated in the large time limit. In the presence of diffusion, when the birth rate exceeds a certain threshold value, we prove that this conclusion is still true for dimensions n ≤ 2, whereas for n ≥ 3 there exist initial distributions for which the advantageous gene A ultimately disappears. This is the first rigorous result of this type for the full system, and it solves a problem which seems to have been open since the celebrated work of Aronson and Weinberger (Lecture notes in mathematics, vol 446, Springer, New York, pp 5–49, 1975; Adv Math 30, 33–76, 1977), where similar results had been obtained for a simplified scalar model, that they derived as an approximation of the full system. Interestingly, we moreover show that, at the threshold value of the birth rate, the cut-off dimension shifts from n = 2 to n = 6.     

The zebrafish (Danio rerio) caudal complex – a model to study vertebral body fusion

Impairment of segmentation during embryonic development leads to congenital fusion of vertebrae. Nevertheless, vertebral fusion can also occur during post‐embryonic life. Fusion can cause reduction in mobility and may be pathological, but it can also be part of normal development and mechanically required, such as in the teleost caudal skeleton, or in the tetrapod sacrum. Using a series of closely spaced ontogenetic stages of zebrafish, stained for mineralized (Alizarin red) and cartilaginous (Alcian blue) structures, we have characterized all fusions occurring during the formation of the caudal skeleton. The urostyle results from the vertebral fusion of the compound centrum preural1‐ural1 [PU1⁺+U1] and ural2 [U2⁺]. Based on developmental and morphological characters: (i) number of vestigial haemal arches, (ii) occasional presence of a haemal arch rudiment, (iii) occasional individuals with separate centra rudiments or distinct mineralization time points, and (iv) evidence for internal separation, we propose that the urostyle forms as a fusion product of five, and not three vertebral centra, as previously described. The last fusion to occur in development, between the compound centrum [PU1⁺+U1] and U2⁺, is a relatively slow process that typically occurs in Cypriniformes and Salmoniformes and is therefore considered reliable to monitor the fusion process. The vertebrae adjacent to the urostyle, preurals 2 and 3, are highly susceptible to fusion, and thus inadequate as a negative control to fusion, in contrast to trunk vertebrae, where fusion is never observed. With this we have established the basis for a new model to study vertebral fusion and to unravel cellular and molecular events underlying this process.     

Interaction between the C-terminal domains of N and P proteins of measles virus investigated by NMR

In this paper we investigate the interaction between the C-terminal domains of the measles virus phosphoprotein (XD) and nucleoprotein (N_TAIL) by using nuclear magnetic resonance chemical shift perturbation experiments. Using both N_TAIL constructs and peptides, we show that contrary to the conserved Box2 region (N^489-506), the C-terminal region of N_TAIL (N^513-525) does not directly interact with XD, and yet affects binding to XD. We tentatively propose a model where the C-terminus of N_TAIL would stabilize the N_TAIL-XD complex either via a functional coupling with N^489-506 or by reducing the entropic penalty associated to the binding-coupled-to-folding process.

Structured summary

MINT-7009780, MINT-7009793, MINT-7009808: N-tail (uniprotkb:Q89933) and P (uniprotkb:P03422) bind (MI:0407) by nuclear magnetic resonance (MI:0077)     

Carvedilol inhibition of lipid peroxidation. A new antioxidative mechanism

To define the molecular mechanism(s) of carvedilol inhibition of lipid peroxidation we have utilized model systems that allow us to study the different reactions involved in this complex process.

Carvedilol inhibits the peroxidation of sonicated phosphatidylcholine liposomes triggered by FeCl₂ addition whereas atenolol, pindolol and labetalol are ineffective. The inhibition proved not to be ascribable (a) to an effect on Fe²⁺ autoxidation and thus on the generation of oxygen derived radical initiators; (b) to the scavenging of the inorganic initiators O^·-₂ and ^·OH; (c) to an effect on the reductive cleavage of organic hydroperoxides by FeCl₂; (d) to the scavenging of organic initiators. The observations that (a) carvedilol effectiveness is inversely proportional to the concentration of FeCl₂ and lipid hydroperoxides in the assay; (b) the drug prevents the onset of lipid peroxidation stimulated by FeCl₃ addition and; (c) it can form a complex with Fe³⁺, suggest a molecular mechanism for carvedilol action. It may inhibit lipid peroxidation by binding the Fe³⁺ generated during the oxidation of Fe²⁺ by lipid hydroperoxides in the substrate. The lag time that carvedilol introduces in the peroxidative process would correspond to the time taken for carvedilol to be titrated by Fe³⁺; when the drug is consumed the Fe³⁺ accumulates to reach the critical parameter that stimulates peroxidation. According to this molecular mechanism the antioxidant potency of carvedilol can be ascribed to its ability to bind a species, Fe³⁺, that is a catalyst of the process and to its lipophilic nature that concentrates it in the membranes where Fe³⁺ is generated by a site specific mechanism.     

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm

Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals across the landscape is of primary importance in watershed management. Traditional economics methods of finding the lowest-cost solution in the watershed context (e.g.,^5,12,20) assume that off-site impacts can be accurately described as a proportion of on-site pollution generated. Such approaches are unlikely to be representative of the actual pollution process in a watershed, where the impacts of polluting sources are often determined by complex biophysical processes. The use of modern physically-based, spatially distributed hydrologic simulation models allows for a greater degree of realism in terms of process representation but requires a development of a simulation-optimization framework where the model becomes an integral part of optimization.Evolutionary algorithms appear to be a particularly useful optimization tool, able to deal with the combinatorial nature of a watershed simulation-optimization problem and allowing the use of the full water quality model. Evolutionary algorithms treat a particular spatial allocation of conservation practices in a watershed as a candidate solution and utilize sets (populations) of candidate solutions iteratively applying stochastic operators of selection, recombination, and mutation to find improvements with respect to the optimization objectives. The optimization objectives in this case are to minimize nonpoint-source pollution in the watershed, simultaneously minimizing the cost of conservation practices. A recent and expanding set of research is attempting to use similar methods and integrates water quality models with broadly defined evolutionary optimization methods^{3,4,9,10,13-15,17-19,22,23,25}. In this application, we demonstrate a program which follows Rabotyagov et al.''s approach and integrates a modern and commonly used SWAT water quality model⁷ with a multiobjective evolutionary algorithm SPEA2²⁶, and user-specified set of conservation practices and their costs to search for the complete tradeoff frontiers between costs of conservation practices and user-specified water quality objectives. The frontiers quantify the tradeoffs faced by the watershed managers by presenting the full range of costs associated with various water quality improvement goals. The program allows for a selection of watershed configurations achieving specified water quality improvement goals and a production of maps of optimized placement of conservation practices.     

Seeing the Forest through the Trees: towards a Unified View on Physiological Calcium Regulation of Voltage-Gated Sodium Channels

Voltage-gated sodium channels (Na_Vs) underlie the upstroke of the action potential in the excitable tissues of nerve and muscle. After opening, Na_Vs rapidly undergo inactivation, a crucial process through which sodium conductance is negatively regulated. Disruption of inactivation by inherited mutations is an established cause of lethal cardiac arrhythmia, epilepsy, or painful syndromes. Intracellular calcium ions (Ca²⁺) modulate sodium channel inactivation, and multiple players have been suggested in this process, including the cytoplasmic Na_V C-terminal region including two EF-hands and an IQ motif, the Na_V domain III-IV linker, and calmodulin. Calmodulin can bind to the IQ domain in both Ca²⁺-bound and Ca²⁺-free conditions, but only to the DIII-IV linker in a Ca²⁺-loaded state. The mechanism of Ca²⁺ regulation, and its composite effect(s) on channel gating, has been shrouded in much controversy owing to numerous apparent experimental inconsistencies. Herein, we attempt to summarize these disparate data and propose a novel, to our knowledge, physiological mechanism whereby calcium ions promote sodium current facilitation due to Ca²⁺ memory at high-action-potential frequencies where Ca²⁺ levels may accumulate. The available data suggest that this phenomenon may be disrupted in diseases where cytoplasmic calcium ion levels are chronically high and where targeted phosphorylation may decouple the Ca²⁺ regulatory machinery. Many Na_V disease mutations associated with electrical dysfunction are located in the Ca²⁺-sensing machinery and misregulation of Ca²⁺-dependent channel modulation is likely to contribute to disease phenotypes.     

In silico strategies to couple production of bioethanol with growth in cyanobacteria

Cyanobacteria have been considered as promising candidates for sustainable bioproduction from inexpensive raw materials, as they grow on light, carbon dioxide, and minimal inorganic nutrients. In this study, we present a genome-scale metabolic network model for Synechocystis sp. PCC 6803 and study the optimal design of the strain for ethanol production by using a mixed integer linear problem reformulation of a bilevel programming problem that identifies gene knockouts which lead to coupling between growth and product synthesis. Five mutants were found, where the in silico model predicts coupling between biomass growth and ethanol production in photoautotrophic conditions. The best mutant gives an in silico ethanol production of 1.054 mmol·gDW ⁻¹·h ⁻¹.     

Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction

Relaxation data obtained previously for the double helix coil transition of oligoriboadenylates and oligoribouridylates are compared to the results of numerical calculations according to various models. In these models the helix coil transition is described by individual rate constants for the first steps of helix formation, whereas the rate constants of the following steps of helix chain growth are assumed to be uniform. The existence of various helix intermediates containing the same number of base pairs is accounted for by statistical factors. First a quasistationary treatment of a zipper model is used for an analysis of the influence of various model parameters. Then relaxation spectra are calculated including helix coil intermediates explicitly without any assumption of quasistationarity. The relaxation spectrum calculated for any chain length N comprises N—1 fast processes with time constants in the range of 0.1 to 0.5 μs and one slow process with a time constant τ depending upon the nucleotide concentration (τ is usually in the ms time range). The fast processes are associated mainly with the unzippering at helix ends and are usually characterized by relatively small amplitudes, whereas the slow process represents the overall helix coil transition usually characterized by a very large amplitude.Consideration of staggered helix series (where the different helix scries are coupled to each other by the single stranded state) leads to a spectrum of slow relaxation processes with one separate relaxation process for each helix series. It is shown that this “non-sliding” staggering zipper model is not consistent with the experimental results. The measured relaxation curves can be represented by single exponentials for nucleotide chain lengths 8 to 11 (within experimental accuracy). This is also true for conditions where several, clearly separated time constants should be expected according to the theoretical model. The experimental data suggest the existence of a direct coupling between different series of staggered helices by a chain sliding mechanism with a time constant < 1ms. Chain sliding may be explained by diffusion of helix defects along the double helix such as diffusion of small loops. A simple model calculation for the diffusion of a bulge loop assuming quasistationarity suggests a sliding time constant around 100 μs for a helix comprising 10 base pairs.Finally some thermodynamic and kinetic parameters are evaluated according to the “sliding” staggering zipper model: The negative activation enthalpy observed for helix recombination can he described using a series of nucleation parameters indicating reduced stability constants for the first three base pairs. Nucleation may usually be achieved with the formation of the third or fourth base pair depending upon the magnitude of the chain growth parameter. The rate constant of helix chain growth is around 10⁶ s^?1 at 0.05 M [Na⁺] and increases to about 4 × 10⁶ s^?1 at 0.17 M [Na⁺].