Modeling of the pyruvate production with Escherichia coli: comparison of mechanistic and neural networks-based models

Three different models: the unstructured mechanistic black-box model, the input–output neural network-based model and the externally recurrent neural network model were used to describe the pyruvate production process from glucose and acetate using the genetically modified Escherichia coli YYC202 ldhA::Kan strain. The experimental data were used from the recently described batch and fed-batch experiments [ Zelić B, Study of the process development for Escherichia coli-based pyruvate production. PhD Thesis, University of Zagreb, Faculty of Chemical Engineering and Technology, Zagreb, Croatia, July 2003. (In English); Zelić et al. Bioproc Biosyst Eng 26:249–258 (2004); Zelić et al. Eng Life Sci 3:299–305 (2003); Zelić et al Biotechnol Bioeng 85:638–646 (2004)]. The neural networks were built out of the experimental data obtained in the fed-batch pyruvate production experiments with the constant glucose feed rate. The model validation was performed using the experimental results obtained from the batch and fed-batch pyruvate production experiments with the constant acetate feed rate. Dynamics of the substrate and product concentration changes was estimated using two neural network-based models for biomass and pyruvate. It was shown that neural networks could be used for the modeling of complex microbial fermentation processes, even in conditions in which mechanistic unstructured models cannot be applied.     

A computational model of rapid task-related plasticity of auditory cortical receptive fields

Receptive field properties of neurons in A1 can rapidly adapt their shapes during task performance in accord with specific task demands and salient sensory cues (Fritz et al., Hearing Research, 206:159–176, 2005a, Nature Neuroscience, 6: 1216–1223, 2003). Such modulatory changes selectively enhance overall cortical responsiveness to target (foreground) sounds and thus increase the likelihood of detection against the background of reference sounds. In this study, we develop a mathematical model to describe how enhancing discrimination between two arbitrary classes of sounds can lead to the observed receptive field changes in a variety of spectral and temporal discrimination tasks. Cortical receptive fields are modeled as filters that change their spectro-temporal tuning properties so as to respond best to the discriminatory acoustic features between foreground and background stimuli. We also illustrate how biologically plausible constraints on the spectro-temporal tuning of the receptive fields can be used to optimize the plasticity. Results of the model simulations are compared to published data from a variety of experimental paradigms.     

Evolving mechanical properties of a model of abdominal aortic aneurysm

The novel three-dimensional (3D) mathematical model for the development of abdominal aortic aneurysm (AAA) of Watton et al. Biomech Model Mechanobiol 3(2): 98–113, (2004) describes how changes in the micro-structure of the arterial wall lead to the development of AAA, during which collagen remodels to compensate for loss of elastin. In this paper, we examine the influence of several of the model’s material and remodelling parameters on growth rates of the AAA and compare with clinical data. Furthermore, we calculate the dynamic properties of the AAA at different stages in its development and examine the evolution of clinically measurable mechanical properties. The model predicts that the maximum diameter of the aneurysm increases exponentially and that the ratio of systolic to diastolic diameter decreases from 1.13 to 1.02 as the aneurysm develops; these predictions are consistent with physiological observations of Vardulaki et al. Br J Surg 85:1674–1680 (1998) and Lanne et al. Eur J Vasc Surg 6:178–184 (1992), respectively. We conclude that mathematical models of aneurysm growth have the potential to be useful, noninvasive diagnostic tools and thus merit further development.     

Use of the valine biosynthetic pathway to convert glucose into isobutanol

Microbiological synthesis of higher alcohols (1-butanol, isobutanol, 2-methyl-1-butanol, etc.) from plant biomass is critically important due to their advantages over ethanol as a motor fuel. In recent years, the use of branched-chain amino acid (BCAA) biosynthesis pathways together with heterologous Ehrlich pathway enzyme system (Hazelwood et al. in Appl Environ Microbiol 74:2259–2266, 2008) has been proposed by the Liao group as an alternative approach to aerobic production of higher alcohols as new-generation biofuels (Atsumi et al. in Nature 451:86–90, 2008; Atsumi et al. in Appl Microbiol Biotechnol 85:651–657, 2010; Cann and Liao in Appl Microbiol Biotechnol 81:89–98, 2008; Connor and Liao in Appl Environ Microbiol 74:5769–5775, 2008; Shen and Liao in Metab Eng 10:312–320, 2008; Yan and Liao in J Ind Microbiol Biotechnol 36:471–479, 2009). On the basis of these remarkable investigations, we re-engineered Escherichia coli valine-producing strain H-81, which possess overexpressed ilvGMED operon, for the aerobic conversion of sugar into isobutanol. To redirect valine biosynthesis to the production of alcohol, we also—as has been demonstrated previously (Atsumi et al. in Nature 451:86–90, 2008; Atsumi et al. in Appl Microbiol Biotechnol 85:651–657, 2010; Cann and Liao in Appl Microbiol Biotechnol 81:89–98, 2008; Connor and Liao in Appl Environ Microbiol 74:5769–5775, 2008; Shen and Liao in Metab Eng 10:312–320, 2008; Yan and Liao in J Ind Microbiol Biotechnol 36:471–479, 2009)—used enzymes of Ehrlich pathway. In particular, in our study, the following heterologous proteins were exploited: branched-chain 2-keto acid decarboxylase (BCKAD) encoded by the kdcA gene from Lactococcus lactis with rare codons substituted, and alcohol dehydrogenase (ADH) encoded by the ADH2 gene from Saccharomyces cerevisiae. We show that expression of both of these genes in the valine-producing strain H-81 results in accumulation of isobutanol instead of valine. Expression of BCKAD alone also resulted in isobutanol accumulation in the culture broth, supporting earlier obtained data (Atsumi et al. in Appl Microbiol Biotechnol 85:651–657, 2010) that native ADHs of E. coli are also capable of isobutanol production. Thus, in this work, isobutanol synthesis by E. coli was achieved using enzymes similar to but somewhat different from those previously used.     

Bone tissue,lyophilized and stored at room temperature for 15 days or more,is not capable of transmitting HIV,HCV or HBV

Over the past 57 years, 17 recipients of frozen bone have been infected with: HIV (Centers for Disease Control and Prevention in Morb Mortal Wkly Rep MMWR 37(39):597–599, 1988; Li et al. in J Formos Med Assoc 100(5):350–351, 2001; Simonds et al. in NEJM 326(11):726–732, 1992; Schratt et al. in Unfallchirurg 99(9):679–684, 1996); HCV (Eggen and Nordbo in NEJM 326(6):411, 1992; Conrad et al. in J Bone Joint Surg Am 77:214–224, 1995; Trotter in J Bone Joint Surg Am 851(11):2215–2217, 2003; Tugwell et al. in Ann of Internal Med 143(9):648–654, 2005); or HBV (Shutkin in J Bone Joint Surg Am 36:160–162, 1954). However, bone, lyophilized and stored at room temperature, has never transmitted these viral diseases. A literature review was undertaken to determine whether there is any evidence that lyophilized bone is capable of transmitting HIV, HCV and HBV.     

Leader neurons in leaky integrate and fire neural network simulations

In this paper, we highlight the topological properties of leader neurons whose existence is an experimental fact. Several experimental studies show the existence of leader neurons in population bursts of activity in 2D living neural networks (Eytan and Marom, J Neurosci 26(33):8465–8476, 2006; Eckmann et al., New J Phys 10(015011), 2008). A leader neuron is defined as a neuron which fires at the beginning of a burst (respectively network spike) more often than we expect by chance considering its mean firing rate. This means that leader neurons have some burst triggering power beyond a chance-level statistical effect. In this study, we characterize these leader neuron properties. This naturally leads us to simulate neural 2D networks. To build our simulations, we choose the leaky integrate and fire (lIF) neuron model (Gerstner and Kistler 2002; Cessac, J Math Biol 56(3):311–345, 2008), which allows fast simulations (Izhikevich, IEEE Trans Neural Netw 15(5):1063–1070, 2004; Gerstner and Naud, Science 326:379–380, 2009). The dynamics of our lIF model has got stable leader neurons in the burst population that we simulate. These leader neurons are excitatory neurons and have a low membrane potential firing threshold. Except for these two first properties, the conditions required for a neuron to be a leader neuron are difficult to identify and seem to depend on several parameters involved in the simulations themselves. However, a detailed linear analysis shows a trend of the properties required for a neuron to be a leader neuron. Our main finding is: A leader neuron sends signals to many excitatory neurons as well as to few inhibitory neurons and a leader neuron receives only signals from few other excitatory neurons. Our linear analysis exhibits five essential properties of leader neurons each with different relative importance. This means that considering a given neural network with a fixed mean number of connections per neuron, our analysis gives us a way of predicting which neuron is a good leader neuron and which is not. Our prediction formula correctly assesses leadership for at least ninety percent of neurons.     

Comments on the entropy-based transmission/disequilibrium test

It has recently been claimed in this journal (Zhao et al. in Hum Genet 121:357–367, 2007) that a so-called “entropy-based” TDT test has improved power over the standard TDT test of Spielman et al. (Am J Hum Genet 52:506–516, 1993). We show that this claim is contradicted by standard statistical theory as well as by our simulation results. We show that the incorrect claim arises because of inappropriate assumptions, and also show that the entropy-based statistic has various undesirable properties.     

Attractor models of working memory and their modulation by reward

This work reports an empirical examination of two key issues in theoretical neuroscience: distractibility in the context of working memory (WM) and its reward dependence. While these issues have been examined fruitfully in isolation (e.g. Macoveanu et al. in Biol Cybern 96(4): 407–19, 2007), we address them here in tandem, with a focus on how distractibility and reward interact. In particular, we parameterise an observation model that embodies the nonlinear form of such interactions, as described in a recent neuronal network model (Gruber et al. in J Comput Neurosci 20:153–166, 2006). We observe that memory for a target stimulus can be corrupted by distracters in the delay period. Interestingly, in contrast to our theoretical predictions, this corruption was only partial. Distracters do not simply overwrite target; rather, a compromise is reached between target and distracter. Finally, we observed a trend towards a reduced distractibility under conditions of high reward. We discuss the implications of these findings for theoretical formulations of basal and dopamine (DA)-modulated neural bump- attractor networks of working memory.     

Evolutionary tradeoff and equilibrium in an aquatic predator-prey system

Due to the conventional distinction between ecological (rapid) and evolutionary (slow) timescales, ecological and population models have typically ignored the effects of evolution. Yet the potential for rapid evolutionary change has been recently established and may be critical to understanding how populations persist in changing environments. In this paper we examine the relationship between ecological and evolutionary dynamics, focusing on a well-studied experimental aquatic predator-prey system (Fussmann et al., 2000, Science, 290, 1358–1360; Shertzer et al., 2002, J. Anim. Ecol., 71, 802–815; Yoshida et al., 2003, Nature, 424, 303–306). Major properties of predator-prey cycles in this system are determined by ongoing evolutionary dynamics in the prey population. Under some conditions, however, the populations tend to apparently stable steady-state densities. These are the subject of the present paper. We examine a previously developed model for the system, to determine how evolution shapes properties of the equilibria, in particular the number and identity of coexisting prey genotypes. We then apply these results to explore how evolutionary dynamics can shape the responses of the system to ‘management’: externally imposed alterations in conditions. Specifically, we compare the behavior of the system including evolutionary dynamics, with predictions that would be made if the potential for rapid evolutionary change is neglected. Finally, we posit some simple experiments to verify our prediction that evolution can have significant qualitative effects on observed population-level responses to changing conditions.     

Genome-wide meta-analysis for rheumatoid arthritis

Meta-analysis is being increasingly used as a tool for integrating data from different studies of complex phenotypes, because the power of any one study to identify causal loci is limited. We applied a novel meta-analytical approach (Loesgen et al. in Genet Epidemiol 21(Suppl 1):S142–S147, 2001) in compiling results from four studies of rheumatoid arthritis in Caucasians including two studies from NARAC (Jawaheer et al. in Am J Hum Genet 68:927–936, 2001; Jawaheer et al. in Arthritis Rheum 48:906–916, 2003), one study from the UK (MacKay et al. in Arthritis Rheum 46:632–639, 2001) and one from France (Cornelis et al. in Proc Natl Acad Sci USA 95:10746–10750, 1998). For each study, we obtained NPL scores by performing interval mapping (2 cM intervals) using GeneHunter2 (Kruglyak et al. in Am J Hum Genet 58:1347–1363, 1996; Markianos et al. in Am J Hum Genet 68:963–977, 2001). The marker maps differed among the three consortium groups, therefore, the marker maps were aligned after the interval mapping was completed and the NPL scores that were within 1 cM of each other were combined using the method of Loesgen et al. (Genet Epidemiol 21(Suppl 1):S142–S147, 2001) by calculating the weighted average of the NPL score. This approach avoids some problems in analysis encountered by using GeneHunter2 when some markers in the sample are not genotyped. This procedure provided marginal evidence (P<0.05) of linkage on chromosome 1, 2, 5 and 18, strong evidence (P<0.01) on chromosomes 8 and 16, and overwhelming evidence in the HLA region of chromosome 6.     

Chaperone receptors: guiding proteins to intracellular compartments

Despite mitochondria and chloroplasts having their own genome, 99% of mitochondrial proteins (Rehling et al., Nat Rev Mol Cell Biol 5:519–530, 2004) and more than 95% of chloroplast proteins (Soll, Curr Opin Plant Biol 5:529–535, 2002) are encoded by nuclear DNA, synthesised in the cytosol and imported post-translationally. Protein targeting to these organelles depends on cytosolic targeting factors, which bind to the precursor, and then interact with membrane receptors to deliver the precursor into a translocase. The molecular chaperones Hsp70 and Hsp90 have been widely implicated in protein targeting to mitochondria and chloroplasts, and receptors capable of recognising these chaperones have been identified at the surface of both these organelles (Schlegel et al., Mol Biol Evol 24:2763–2774, 2007). The role of these chaperone receptors is not fully understood, but they have been shown to increase the efficiency of protein targeting (Young et al., Cell 112:41–50, 2003; Qbadou et al., EMBO J 25:1836–1847, 2006). Whether these receptors contribute to the specificity of targeting is less clear. A class of chaperone receptors bearing tetratricopeptide repeat domains is able to specifically bind the highly conserved C terminus of Hsp70 and/or Hsp90. Interestingly, at least of one these chaperone receptors can be found on each organelle (Schlegel et al., Mol Biol Evol 24:2763–2774, 2007), which suggests a universal role in protein targeting for these chaperone receptors. This review will investigate the role that chaperone receptors play in targeting efficiency and specificity, as well as examining recent in silico approaches to find novel chaperone receptors.     

The Repair Response to Osteochondral Implant Types in a Rabbit Model

Current treatments for damaged articular cartilage (i.e., shaving the articular surface, perforation or abrasion of the subchondral bone, and resurfacing with periosteal and perichondrial resurfacing) often produce fibrocartilage, or hyaline-appearing repair that is not sustained over time (Henche 1967, Ligament and Articular Cartilage Injuries. Springer-Verlag, New York, NY, pp. 157–164; Insall 1974, Clin. Orthop. 101: 61–67; Mitchell and Shepard 1976, J. Bone Joint Surg. [Am.] 58: 230–233; O’Driscoll et al. 1986, J. Bone Joint Surg. [Am.] 68: 1017–1035; 1989, Trans. Orthop. Res. Soc. 14: 145; Kim et al. 1991, J. Bone Joint Surg. [Am.] 73: 1301–1315). Autologous chondrocyte transplantation, although promising, requires two surgeries, has site-dependent and patient age limitations, and has unknown long-term donor site morbidity (Brittberg et al. 1994, N Engl. J. Med. 331: 889–895; Minas 2003, Orthopedics 26: 945–947; Peterson et al. 2003, J. Bone Joint Surg. Am. 85-A(Suppl. 2): S17–S24). Osteochondral allografts remain a widely used method of articular resurfacing to delay arthritic progression. The present study compared the histological response to four types of osteochondral implants in a rabbit model: autograft, frozen, freeze-dried, and fresh implants. Specimens implanted in the femoral groove were harvested at 6 and 12 weeks. Results showed similar restoration of the joint surface regardless of implant type, with a trend toward better repair at the later timepoint. As has been observed in other studies (Frenkel et al. 1997, J. Bone Joint Surg. 79B: 281–286; Toolan et al. 1998, J. Biomed. Mater. Res. 41: 244–250), each group in this study had at least one specimen in which a healthy-appearing surface on the implant was not well-integrated with host tissues. Although the differences were not statistically significant, freeze-dried implants at both timepoints had the best histological scores. The osteochondral grafts tested successfully restored the gross joint surface and congruity. At 12 weeks, no significant differences were observed between the various allografts and autologous osteochondral grafts.     

Comments on ‘Is Partial Coherence a Viable Technique for Identifying Generators of Neural Oscillations?’

To aid prospective neural connectivity inference analysts and hoping to preclude misconception spread, we exploit the didatic value of some of the issues raised by Albo et al. (Biol Cybern 90: 318–326, 2004) who claim that signal-to-noise ratio (SNR) values can lead to mistakes in structural inference when using partial coherence in connection to Gersch’s 1970 method for spotting signal sources (Gersch in Math Biosci 14: 177– 196, 1972). We show theoretically that Gersch’s method is able only to spot which measurement of some common underlying factor has the least amount of additive noise and that this has nothing to do with any reasonable notion of ‘causality’ as suggested by Albo et al. (Biol Cybern 90: 318–326, 2004). We also show that despite the inherent structural ambiguity of the model used by Albo et al. (Biol Cybern 90: 318–326, 2004) to back their claim, its data can nonetheless furnish the correct time precedence hierarchy between the activities in its measured structures, both when simple (correlation) and more sophisticated methods are used (partial directed coherence) (Baccala and Sameshima in Biol Cybern 84:463–474, 2001a) in a true depiction of time series causality.     

S100β Protein Expression: Gender- and Age-Related Daily Changes

S100β is a soluble protein released by glial cells mainly under the activation of the 5-HT1A receptor. It has been reported as a neuro-trophic and -tropic factor that promotes neurite maturation and outgrowth during development. This protein also plays a role in axonal stability and the plasticity underlying long-term potentiation in adult brains. The ability of S100β to rapidly regulate neuronal morphology raises the interesting point of whether there are daily rhythm or gender differences in S100β level in the brain. To answer this question, the S100β expression in adult female and male rats, as well as in adult female CD-21 and S100β −/− female mice, were investigated. Scintillation counting and morphometric analysis of the immunoreactivity of S100β, showed rhythmic daily expression. The female and male rats showed opposite cycles. Females presented the highest value at the beginning of the rest phase (5:00 h), while in males the maximum value appeared in the beginning of the motor activity period (21:00 h). These results confirm previous S100β evaluations in human serum and cerebrospinal fluid reporting the protein’s function as a biomarker for brain damage (Gazzolo et al. in Clin Chem 49:967–970, 2003; Clin Chim Acta 330:131–133, 2003; Pediatr Res 58:1170–1174, 2005), similar behavior was also observed for GFAP in relation to Alzheimer Disease (Fukuyama et al. in Eur Neurol 46:35–38, 2001). The data should be taken into account when considering S100β as a biomarker of health condition. In addition, the results raise questions on which structure or condition imposes these rhythms as well as on the physiological meaning of the observed gender differences.     

Serum Zinc Concentrations in Cystic Fibrosis Patients Aged Above 4 Years: A Cross-sectional Evaluation

Aim Assess the risk of zinc (Zn) deficiency in the older cystic fibrosis (CF) population. Method Cross-sectional investigation of all CF patients above the age of 4 followed at the Ghent University center between 2002 and 2003. Data on age, weight, height z-score, pancreatic and pulmonary functions, chronic Pseudomonas infection, and CF transmembrane conductance regulator (CFTR) mutations were collected. Serum Zn, vitamins (vit) A and E, retinol-binding protein (RBP), albumin, sedimentation rate, total IgG, and cholesterol were determined. Serum Zn was compared with a local healthy control group (Van Biervliet et al., Biol Trace Elem Res 94:33–40, 2003) and with literature data (Hotz C, et al. Am J Clin Nutr 78:756–764, 2003). Results 101 patients (median age 16 years) were included. There was no difference in serum Zn concentration between CF patients and controls. In CF patients no difference in serum Zn concentration between pancreatic-sufficient or pancreatic-insufficient patients was seen. Serum Zn was not associated to nutritional status or height z-score. A significant association serum Zn to serum albumin (p < 0.0005) and to vit A (p < 0.01) was seen. No associations of serum Zn to serum vit E, RBP, cholesterol, or CFTR were present, but there is a significant association serum Zn to forced vital capacity (p < 0.01). Serum Zn was not associated to inflammatory parameters or chronic Pseudomonas infection. Conclusion Comparison of CF patients with local controls revealed no significant differences. However, because persisting steatorrhea increases Zn loss (Easley et al., J Pediatr Gastroenterol Nutr 26:136–139, 1998) and 12.6% of our population has a serum Zn below the p value of 2.5 of the NHANES II study (Hotz C, et al. Am J Clin Nutr 78:756–764, 2003), there could remain an increased risk of Zn deficiency in some CF patients. Furthermore, the association with pulmonary function needs more investigation.     

mGluR7 Genetics and Alcohol: Intersection Yields Clues for Addiction

Development of addiction to alcohol or other substances can be attributed in part to exposure-dependent modifications at synaptic efficacy leading to an organism which functions at an altered homeostatic setpoint. Genetic factors may also influence setpoints and the stability of the homeostatic system of an organism. Quantitative genetic analysis of voluntary alcohol drinking, and mapping of the involved genes in the quasi-congenic Recombinant QTL Introgression strain system, identified Eac2 as a Quantitative Trait Locus (QTL) on mouse chromosome 6 which explained 18% of the variance with an effect size of 2.09 g/kg/day alcohol consumption, and Grm7 as a quantitative trait gene underlying Eac2 [Vadasz et al. in Neurochem Res 32:1099–1112, 100, Genomics 90:690–702, 102]. In earlier studies, the product of Grm7 mGluR7, a G protein-coupled receptor, has been implicated in stress systems [Mitsukawa et al. in Proc Natl Acad Sci USA 102:18712–18717, 63], anxiety-like behaviors [Cryan et al. in Eur J Neurosci 17:2409–2417, 14], memory [Holscher et al. in Learn Mem 12:450–455, 26], and psychiatric disorders (e.g., [Mick et al. in Am J Med Genet B Neuropsychiatr Genet 147B:1412–1418, 61; Ohtsuki et al. in Schizophr Res 101:9–16, 72; Pergadia et al. in Paper presented at the 38th Annual Meeting of the Behavior Genetics Association, Louisville, Kentucky, USA, 76]. Here, in experiments with mice, we show that (1) Grm7 knockout mice express increased alcohol consumption, (2) sub-congenic, and congenic mice carrying a Grm7 variant characterized by higher Grm7 mRNA drink less alcohol, and show a tendency for higher circadian dark phase motor activity in a wheel running paradigm, respectively, and (3) there are significant genetic differences in Grm7 mRNA abundance in the mouse brain between congenic and background mice identifying brain areas whose function is implicated in addiction related processes. We hypothesize that metabotropic glutamate receptors may function as regulators of homeostasis, and Grm7 (mGluR7) is involved in multiple processes (including stress, circadian activity, reward control, memory, etc.) which interact with substance use and the development of addiction. In conclusion, we suggest that mGluR7 is a significant new therapeutic target in addiction and related neurobehavioral disorders.     

The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography

The ¹H NMR chemical shifts of the heme methyl groups of the ferriheme complex of metneuroglobin (Du et al. in J. Am. Chem. Soc. 125:8080–8081, 2003) predict orientations of the axial histidine ligands (Shokhirev and Walker in J. Biol. Inorg. Chem. 3:581–594, 1998) that are not consistent with the X-ray data (Vallone et al. in Proteins Struct. Funct. Bioinf. 56:85–94, 2004), and the EPR spectrum (Vinck et al. in J. Am. Chem. Soc. 126:4516–4517, 2004) is only marginally consistent with these data. The reasons for these inconsistencies appear to be rooted in the high degree of aqueous solution exposure of the heme group and the fact that there are no strong hydrogen-bond acceptors for the histidine imidazole N–H protons provided by the protein. Similar inconsistencies may exist for other water-soluble heme proteins, and ¹H NMR spectroscopy provides a simple means to verify whether the solution structure of the heme center is the same as or different from that in the crystalline state.     

A Model for Multi-site Pacing of Fibrillation Using Nonlinear Dynamics Feedback

Traditionally, cardiac defibrillation requires a strong electric shock. Many unwanted side effects of this shock could be eliminated if defibrillation were performed using weak stimuli applied to several locations throughout the heart. Such multi-site pacing algorithms have been shown to defibrillate both experimentally (Pak et al., Am J Physiol 285:H2704–H2711, 2003) and theoretically (Puwal and Roth, J Biol Systems 14:101–112, 2006). Gauthier et al. (Chaos, 12:952–961, 2002) proposed a method to pace the heart using an algorithm based on nonlinear dynamics feedback applied through a single electrode. Our study applies a related but simpler algorithm, which essentially configures each electrode as a demand pacemaker, to simulate the multi-site pacing of fibrillating cardiac tissue. We use the numerical model developed by Fenton et al. (Chaos, 12:852–892, 2002) as the reaction term in a reaction–diffusion equation that we solve over a two-dimensional sheet of tissue. The defibrillation rate after pacing for 3 s is about 30%, which is significantly higher than the spontaneous defibrillation rate and is higher than observed in previous experimental and theoretical studies. Tuning the algorithm period can increase this rate to 45%. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.