Identification of two-neuron FitzHugh-Nagumo model based on the speed-gradient and filtering.

The paper is devoted to the parameter identification problem for two-neuron FitzHugh-Nagumo models under condition when only one variable, namely, the membrane potential, is measured. Another practical assumption is that both variable derivatives cannot be measured. Finally, it is assumed that the sensor measuring the membrane potential is imprecise, and all measurements have some unknown scaling factor. These circumstances bring additional difficulties to the parameters' estimation problem, and therefore, such case was not studied before. To solve the problem first, the model is transformed to a more simple form without unmeasurable variables. Variables obtained from applying a second-order real filter-differentiator are used instead of unmeasurable derivatives. Then, an adaptive system, parameters of which are estimates of original system parameters, is designed. The estimation (identification) goal is to properly adjust parameter estimates. To this end, the speed-gradient method is employed. The correctness of the obtained solution is proved theoretically and illustrated by computer simulation in the Simulink environment. The sufficient conditions of asymptotically correct identification for the speed-gradient method with integral objective function are formulated and proved. The novelty of the paper is that in contrast to existing solutions to the FitzHugh-Nagumo identification problem, we take into account a systematic error of the membrane potential measurement. Furthermore, the parameters are estimated for a system composed of two FitzHugh-Nagumo models, which open perspectives for using the proposed results for modeling and estimation of parameters for neuron population.

Complex partial synchronization patterns in networks of delay-coupled neurons.

We study the spatio-temporal dynamics of a multiplex network of delay-coupled FitzHugh-Nagumo oscillators with non-local and fractal connectivities. Apart from chimera states, a new regime of coexistence of slow and fast oscillations is found. An analytical explanation for the emergence of such coexisting partial synchronization patterns is given. Furthermore, we propose a control scheme for the number of fast and slow neurons in each layer. This article is part of the theme issue 'Nonlinear dynamics of delay systems'.

Control of oscillations in vibration machines: Start up and passage through resonance.

Control of oscillations in mechanical systems in the start-up and passage through resonance modes is studied. In both cases, the control algorithm is based on the speed-gradient method with energy-based goal functions. It is shown that for Hamiltonian 1-degree of freedom (DOF) systems, it is generically possible to move the system from any initial state to any final state by means of a controlling force of arbitrarily small intensity. Controlled passage through resonance is studied for a 5-DOF vibration machine taking friction into account. It is shown by simulation that applying feedback control makes passage through lower resonance feasible with smaller control intensity compared with passage through resonance under constant control torque. The specific feature of this paper is consideration of the case when constant control torques do not allow the rotors even to start rotation. Applying feedback control allows rotors to overcome gravity and to start rotation. Another key novelty of this paper is comparison of the results obtained from the simulation with the experimental results obtained from the two-rotor laboratory mechatronic stand. It appears that most results are qualitatively the same, which confirms the adequacy of the model.

Synchronization in heterogeneous FitzHugh-Nagumo networks with hierarchical architecture.

We study synchronization in heterogeneous FitzHugh-Nagumo networks. It is well known that heterogeneities in the nodes hinder synchronization when becoming too large. Here we develop a controller to counteract the impact of these heterogeneities. We first analyze the stability of the equilibrium point in a ring network of heterogeneous nodes. We then derive a sufficient condition for synchronization in the absence of control. Based on these results we derive the controller providing synchronization for parameter values where synchronization without control is absent. We demonstrate our results in networks with different topologies. Particular attention is given to hierarchical (fractal) topologies, which are relevant for the architecture of the brain.

[Coding region of far-red fluorescent protein katushka contains a strong donor splice site].

Computer analysis predicted a strong donor splice site within the 3'-part of the far-red fluorescent protein Katushka coding region. To test the functional activity of this site a model vector has been constructed. This vector encoded Katushka and green fluorescent protein TagGFP2 with a gene fragment of tafazzin in between. Normal splicing of this pre-mRNA should result in a frameshift between Katushka and TagGFP2. Alternatively, after splicing at internal katushka donor splice site appearance of Katushka-TagGFP2 fusion protein was expected. Expression of this construct in a mammalian cell culture led to bright red and green fluorescence. Therefore, katushka-specific donor splice site is functional. Disruption of this splice site by several silent substitutions resulted in red-only fluorescent cells that corresponded to normal splicing. The mutant katushka can be used for visualization of pre-mRNA splicing at single cell level by fluorescence microscopy and flow cytometry.

Adaptive tuning of feedback gain in time-delayed feedback control.

We demonstrate that time-delayed feedback control can be improved by adaptively tuning the feedback gain. This adaptive controller is applied to the stabilization of an unstable fixed point and an unstable periodic orbit embedded in a chaotic attractor. The adaptation algorithm is constructed using the speed-gradient method of control theory. Our computer simulations show that the adaptation algorithm can find an appropriate value of the feedback gain for single and multiple delays. Furthermore, we show that our method is robust to noise and different initial conditions.

Control of a noise-induced transition in a nonlinear dynamical system.

Feedback control is applied to change conditions of a noise-induced transition in a nonlinear second order dynamic system. The mathematical model used in the analysis is a system of two-component equations describing operation of a semiconductor-gas-discharge image converter. The control algorithm is proposed using the speed-gradient method for a linearized model system. It is found by computer simulations that, under conditions when the noise is effective in determining the destructive dynamics of the system without control, the role of noise can be essentially suppressed by a proper feedback control. The control efficiency depends on the amplitude of control signal in a nonmonotonic way, thus demonstrating a resonancelike regularity. Application of the proposed control method can be useful in solving other problems, such as providing survival of endangered species in ecology, improving stability of lasers, etc.

[Spectral diversity among the members of the family of Green Fluorescent Protein in hydroid jellyfish (Cnidaria, Hydrozoa)].

The cDNAs encoding the genes of new proteins homologous to the well-known Green Fluorescent Protein (GFP) from the hydroid jellyfish Aequorea victoria were cloned. Two green fluorescent proteins from one un-identified anthojellyfish, a yellow fluorescent protein from Phialidium sp., and a nonfluorescent chromoprotein from another unidentified anthojellyfish were characterized. Thus, a broad diversity of GFP-like proteins among the organisms of the class Hydrozoa in both spectral properties and primary structure was shown.

Diversity and evolution of the green fluorescent protein family.

The family of proteins homologous to the green fluorescent protein (GFP) from Aequorea victoria exhibits striking diversity of features, including several different types of autocatalytically synthesized chromophores. Here we report 11 new members of the family, among which there are 3 red-emitters possessing unusual features, and discuss the similarity relationships within the family in structural, spectroscopic, and evolutionary terms. Phylogenetic analysis has shown that GFP-like proteins from representatives of subclass Zoantharia fall into at least four distinct clades, each clade containing proteins of more than one emission color. This topology suggests multiple recent events of color conversion. Combining this result with previous mutagenesis and structural data, we propose that (i) different chromophore structures are alternative products synthesized within a similar autocatalytic environment, and (ii) the phylogenetic pattern and color diversity in reef Anthozoa is a result of a balance between selection for GFP-like proteins of particular colors and mutation pressure driving the color conversions.

GFP-like chromoproteins as a source of far-red fluorescent proteins.

We have employed a new approach to generate novel fluorescent proteins (FPs) from red absorbing chromoproteins. An identical single amino acid substitution converted novel chromoproteins from the species Anthozoa (Heteractis crispa, Condylactis gigantea, and Goniopora tenuidens) into far-red FPs (emission lambda(max)=615-640 nm). Moreover, coupled site-directed and random mutagenesis of the chromoprotein from H. crispa resulted in a unique far-red FP (HcRed) that exhibited bright emission at 645 nm. A clear red shift in fluorescence of HcRed, compared to drFP583 (by more than 60 nm), makes it an ideal additional color for multi-color labeling. Importantly, HcRed is excitable by 600 nm dye laser, thus promoting new detection channels for multi-color flow cytometry applications. In addition, we generated a dimeric mutant with similar maturation and spectral properties to tetrameric HcRed.

"Fluorescent timer": protein that changes color with time.

We generated a mutant of the red fluorescent protein drFP583. The mutant (E5) changes its fluorescence from green to red over time. The rate of color conversion is independent of protein concentration and therefore can be used to trace time-dependent expression. We used in vivo labeling with E5 to measure expression from the heat shock-dependent promoter in Caenorhabditis elegans and from the Otx-2 promoter in developing Xenopus embryos. Thus, E5 is a "fluorescent timer" that can be used to monitor both activation and down-regulation of target promoters on the whole-organism scale.

Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence.

A novel gene for advanced red-shifted protein with an emission maximum at 593 nm was cloned from Discosoma coral. The protein, named dsFP593, is highly homologous to the recently described GFP-like protein drFP583 with an emission maximum at 583 nm. Using the remarkable similarity of the drFP583 and dsFP593 genes, we performed a 'shuffling' procedure to generate a pool of mutants consisting of various combinations of parts of both genes. One 'hybrid gene' was chosen for subsequent random mutagenesis, which resulted in a mutant variant with a uniquely red-shifted emission maximum at 616 nm.

Natural animal coloration can Be determined by a nonfluorescent green fluorescent protein homolog.

It is generally accepted that the colors displayed by living organisms are determined by low molecular weight pigments or chromoproteins that require a prosthetic group. The exception to this rule is green fluorescent protein (GFP) from Aequorea victoria that forms a fluorophore by self-catalyzed protein backbone modification. Here we found a naturally nonfluorescent homolog of GFP to determine strong purple coloration of tentacles in the sea anemone Anemonia sulcata. Under certain conditions, this novel chromoprotein produces a trace amount of red fluorescence (emission lambda(max) = 595 nm). The fluorescence demonstrates unique behavior: its intensity increases in the presence of green light but is inhibited by blue light. The quantum yield of fluorescence can be enhanced dramatically by single amino acid replacement, which probably restores the ancestral fluorescent state of the protein. Other fluorescent variants of the novel protein have emission peaks that are red-shifted up to 610 nm. They demonstrate that long wavelength fluorescence is attainable in GFP-like fluorescent proteins.

Expression of PTTG and prc1 genes during telencephalic neurogenesis.

We present the first time/space analysis using in situ hybridization for PTTG and prc1 genes during development of the mouse telencephalon. During the stages E11.5-E13.5 PTTG and prc1 are expressed in most tissues of the embryo. Within the telencephalon, PTTG and prc1 are found exclusively inside of the ventricular zone (VZ). The intensity of the expression of both genes in the ventricular zone reaches its peak by E15.5. Expression starts to decrease by E18.5, it is still visible at least up to P2 and not detectable in the adult brains. Expression of the prc1 gene, but not that of the PTTG, is also found in the mitoticaly active cells outside of the VZ within the telencephalon. Most of the cells expressing the PTTG gene were found in the lower part of the ventricular zone suggesting that the level of PTTG mRNA is regulated during different phases of the mitotic cycle.

Fluorescent proteins from nonbioluminescent Anthozoa species.

We have cloned six fluorescent proteins homologous to the green fluorescent protein (GFP) from Aequorea victoria. Two of these have spectral characteristics dramatically different from GFP, emitting at yellow and red wavelengths. All the proteins were isolated from nonbioluminescent reef corals, demonstrating that GFP-like proteins are not always functionally linked to bioluminescence. The new proteins share the same beta-can fold first observed in GFP, and this provided a basis for the comparative analysis of structural features important for fluorescence. The usefulness of the new proteins for in vivo labeling was demonstrated by expressing them in mammalian cell culture and in mRNA microinjection assays in Xenopus embryos.

Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization.

The availability of bacterial genome sequences raises an important new problem - how can one move from completely sequenced microorganisms as a reference to the hundreds and thousands of other strains or isolates of the same or related species that will not be sequenced in the near future? An efficient way to approach this task is the comparison of genomes by subtractive hybridization. Recently we developed a sensitive and reproducible subtraction procedure for comparison of bacterial genomes, based on the method of suppression subtractive hybridization (SSH). In this work we demonstrate the applicability of subtractive hybridization to the comparison of the related but markedly divergent bacterial species Escherichia coli and Salmonella typhimurium. Clone libraries representing sequence differences were obtained and, in the case of completely sequenced E. coli genome, the differences were directly placed in the genome map. About 60% of the differential clones identified by SSH were present in one of the genomes under comparison and absent from the other. Additional differences in most cases represent sequences that have diverged considerably in the course of evolution. Such an approach to comparative bacterial genomics can be applied both to studies of interspecies evolution - to elucidate the "strategies" that enable different genomes to fit their ecological niches - and to development of diagnostic probes for the rapid identification of pathogenic bacterial species.

PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.

Genes that are characteristic of only certain strains of a bacterial species can be of great biologic interest. Here we describe a PCR-based subtractive hybridization method for efficiently detecting such DNAs and apply it to the gastric pathogen Helicobacter pylori. Eighteen DNAs specific to a monkey-colonizing strain (J166) were obtained by subtractive hybridization against an unrelated strain whose genome has been fully sequenced (26695). Seven J166-specific clones had no DNA sequence match to the 26695 genome, and 11 other clones were mixed, with adjacent patches that did and did not match any sequences in 26695. At the protein level, seven clones had homology to putative DNA restriction-modification enzymes, and two had homology to putative metabolic enzymes. Nine others had no database match with proteins of assigned function. PCR tests of 13 unrelated H. pylori strains by using primers specific for 12 subtracted clones and complementary Southern blot hybridizations indicated that these DNAs are highly polymorphic in the H. pylori population, with each strain yielding a different pattern of gene-specific PCR amplification. The search for polymorphic DNAs, as described here, should help identify previously unknown virulence genes in pathogens and provide new insights into microbial genetic diversity and evolution.

[Cloning of region-specific genetic markers of planaria using a new method--ordered differential display]. / Klonirovanie region-spetsifichnykh geneticheskikh markerov planarii s pomoshch'iu novogo metoda--uporiadochennogo differentsional'nogo displeiia.

A new method for finding differentially expressed genes, termed ordered differential display of mRNAs (ODD), was used in the search for region-specific molecular markers of freshwater planarian Dugesia tigrina. In this method, the effect of selective suppression of a polymerase chain reaction (PCR) is used for the differential amplification of a pool of 3'-terminal cDNA fragments generated by digestion of cDNAs with a restriction endonuclease. In the resulting amplified cDNAs, every mRNA is represented by a cDNA fragment whose length is determined by the position of the restriction site nearest to the 3'-terminus. Subsequent PCR with primers 3'-extended by two random nucleotides allowed the amplification of 1/192 part of all cDNA molecules present in the sample. The comparison of the generated pools of cDNA molecules separated by PAGE leads to the identification of differentially expressed sequences. The systematic study of the total mRNA pool is achieved by the successive use of all possible combinations of extended primers. Some sequences preferentially expressed along the anterior-posterior axis of planarian were identified using ODD.

[Biosynthesis of human calcitonin and mini-proinsulin in bacterial cells in the form of hybrid proteins with corresponding antisense peptides and a metal-binding peptide]. / Biosintez v bakterial'nykh kletkakh kal'tsitonina i mini-proinsulina cheloveka v vide gibridnykh belkov s sootvetstvuiushchimi antismyslovymi peptidami i metallsviazyvaiushchim peptidom.

To verify experimentally the molecular recognition theory, plasmids were constructed that provided the efficient synthesis of hybrid proteins composed of human calcitonin or miniproinsulin, the corresponding antisense peptides, and a histidine-rich metal-binding peptide. A method for isolation of the hybrid proteins by metal-chelating chromatography, cleavage, and renaturation was developed.