Basal ganglia neural mechanisms of natural movement sequences

Natural rodent grooming and other instinctive behavior serves as a natural model of complex movement sequences. Rodent grooming has syntactic (rule-driven) sequences and more random movement patterns. Both incorporate the same movements--only the serial structure differs. Recordings of neural activity in the dorsolateral striatum and the substantia nigra pars reticulata indicate preferential activation during syntactic sequences over more random sequences. Neurons that are responsive during syntactic grooming sequences are often unresponsive or have reverse activation profiles during kinematically similar movements that occur in flexible or random grooming sequences. Few neurons could be categorized as strictly movement related--instead they were activated only in the context of particular sequential patterns of movements. Particular sequential patterns included "syntactic chain" grooming sequences of paw, head, and body movements and also "warm-up" sequences, which consist of head and body/limb movements that precede locomotion after a period of quiet resting (Golani 1992). Activation during warm-up was less intense and less frequent than during grooming sequences, but both sequences activated neurons above baseline levels, and the same neurons sometimes responded to both sequences. The fact that striatal neurons code 2 natural sequences which are made up of different constituent movements suggests that the basal ganglia may have a generalized role in sequence control. The basal ganglia are modulated by the context of the sequence and may play an executive function in the complex natural patterns of sequenced behaviour.     

Formation, fixation and reproduction of temporary connections during adaptation to physical loading

It is shown that long-term adaptation to physical loads of various intensity and duration has an influence on formation, fixation and reproduction of temporary connections in rats. Periodicity of conditioned activity has been found in the process of protracted training. After twenty days of adaptation to submaximal physical loads, the processes of fixation and reproduction of temporary connections improve whereas with elongation of adaptation the conditioned activity somewhat deteriorates. In conditions of long-term training by maximal physical loads, both elaboration and preservation of conditional reflexes in all adaptation terms is affected.     

Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc,k-Ras and c-Kit promoter sequences

We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained by an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling and molecular dynamics simulations, to derive self-consistent structural models. The formal resolution of our approach is 18 angstroms, but in some cases structural features of only a few nucleotides can be discerned. We report here five structures of long (34–70 nt) wild-type sequences selected from three cancer-related promoters: c-Myc, c-Kit and k-Ras. Each sequence studied has a unique structure. Three sequences form structures with two contiguous, stacked, G-quadruplex units. One longer sequence from c-Myc forms a structure with three contiguous stacked quadruplexes. A longer c-Kit sequence forms a quadruplex-hairpin structure. Each structure exhibits interfacial regions between stacked quadruplexes or novel loop geometries that are possible druggable targets. We also report methodological advances in our integrated structural biology approach, which now includes quantitative CD for counting stacked G-tetrads, DNaseI cleavage for hairpin detection and SAXS model refinement. Our results suggest that higher-order quadruplex assemblies may be a common feature within the genome, rather than simple single quadruplex structures.     

A Bayesian method for finding regulatory segments in DNA

A goal of the human genome project is to determine the entire sequence of DNA (3 x 10(9) base pairs) found in chromosomes. The massive amounts of data produced by this project require interpretation. A Bayesian model is developed for locating regulatory regions in a DNA sequence. Regulatory regions are areas of DNA to which specific proteins bind and control whether or not a gene is transcribed to produce templates for protein synthesis. Each human cell contains the same DNA sequence. Thus the particular function of different cells is determined by the genes that are transcribed in that cell. A Hidden Markov chain is used to model whether a small interval of the DNA is in a regulatory region or not. This can be regarded as a changepoint problem where the changepoints are the start of a regulatory or nonregulatory region. The data consists of protein-binding elements, which are short subsequences, or "words," in the DNA sequence. Although these words can occur anywhere in the sequence, a larger number are expected in regulatory regions. Therefore, regulatory regions are detected by locating clusters of words. For a particular DNA sequence, the model automatically selects those words that best predict regions of interest. Markov chain Monte Carlo methods are used to explore the posterior distribution of the Hidden Markov chain. The model is tested by means of simulations, and applied to several DNA sequences.     

Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.     

Swapping of three-dimensional domains as a molecular mechanism of dimerization of aminoacyl-tRNA synthetases

It has been shown recently that many proteins undergo oligomerization through exchange of structural elements. That process, termed a 3D domain swapping, is the replacement of a portion of the tertiary structure of a protein with an identical piece from a second polypeptide chain. When the exchange is reciprocated, domain-swapped dimers embrace with the exchange of elements of secondary structure or domains; however, if the exchange is not reciprocated but propagated along multiple polynucleotide chains, higher-order assemblies may form. In this paper we discuss swapping as a general mechanism of aminoacyl-tRNA synthetases dimerization, specifically plant methionyl-tRNA synthetase.     

A neural network model for generating complex birdsong syntax

The singing behavior of songbirds has been investigated as a model of sequence learning and production. The song of the Bengalese finch, Lonchura striata var. domestica, is well described by a finite state automaton including a stochastic transition of the note sequence, which can be regarded as a higher-order Markov process. Focusing on the neural structure of songbirds, we propose a neural network model that generates higher-order Markov processes. The neurons in the robust nucleus of the archistriatum (RA) encode each note; they are activated by RA-projecting neurons in the HVC (used as a proper name). We hypothesize that the same note included in different chunks is encoded by distinct RA-projecting neuron groups. From this assumption, the output sequence of RA is a higher-order Markov process, even though the RA-projecting neurons in the HVC fire on first-order Markov processes. We developed a neural network model of the local circuits in the HVC that explains the mechanism by which RA-projecting neurons transit stochastically on first-order Markov processes. Numerical simulation showed that this model can generate first-order Markov process song sequences.     

Microtubules support a disk-like septin arrangement at the plasma membrane of mammalian cells

Septin family proteins oligomerize through guanosine 5'-triphosphate-binding domains into core heteromers, which in turn polymerize at the cleavage furrow of dividing fungal and animal cells. Septin assemblies during the interphase of animal cells remain poorly defined and are the topic of this report. In this study, we developed protocols for visualization of authentic higher-order assemblies using tagged septins to effectively replace the endogenous gene product within septin core heteromers in human cells. Our analysis revealed that septins assemble into microtubule-supported, disk-like structures at the plasma membrane. In the absence of cell substrate adhesion, this is the predominant higher-order arrangement in interphase cells and each of the seven to eight septin family members expressed by the two analyzed cell types appears equally represented. However, studies of myeloid and lymphoid cell model systems revealed cell type-specific alterations of higher-order septin arrangements in response to substrate adhesion. Live-cell observations suggested that all higher-order septin assemblies are mutually exclusive with plasma membrane regions undergoing remodeling. The combined data point to a mechanism by which densely arranged cortical microtubules, which are typical for nonadhered spherical cells, support plasma membrane-bound, disk-like septin assemblies.     

Molecular cloning of rabbit gamma heavy chain mRNA.

A cDNA library of rabbit spleen mRNA was screened for immunoglobulin heavy chain sequences. In this paper we report the nucleotide sequence of two cDNA clones containing part of the constant region of the rabbit gamma heavy chain mRNA. The sequence encodes part of the CH2 domain (amino acids 268 to 340), the entire CH3 domain (amino acids 341 to 447) and the 3' untranslated region. This nucleotide sequence has been compared to the corresponding sequences of mouse gamma 1, gamma 2a and gamma 2b genes. The homologies between rabbit gamma chain gene sequence and each of the mouse gamma chain gene sequences are of the same magnitude order. This comparison shows that the CH2 domains are more homologous to each other than CH3 domains or 3' untranslated sequences. The presence of species specific nucleotide positions suggests that mouse gamma chain genes could have evolved from a common ancestor shortly after the mouse-rabbit species separation. Genomic blot analysis of rabbit liver DNA with the rabbit C gamma probes shows a limited number of related sequences, with little restriction site polymorphism between individual rabbits.     

The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium

DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)₇GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45°C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium.     

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

Hierarchical shotgun sequencing remains the method of choice for assembling high‐quality reference sequences of complex plant genomes. The efficient exploitation of current high‐throughput technologies and powerful computational facilities for large‐insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole‐genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high‐quality assemblies of a large number of clones to assemble map‐based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.     

Effect of diazepam on the formation of temporal connections by means of recognizable visual stimuli

In emotionally labile persons the role of the limbic link in the structure of temporary connections formed by means of a realized emotionally significant word, was studied with the help of diazepam. The diazepam turned out to be an effective agent for studying the mechanisms underlying the formation and reproduction of temporary connections in man. Against the background of its action it is not possible to elaborate a conditioned cortical reaction on emotionally significant reinforcement. This is connected by the authors with predominant action of this tranquilizer on formations of the limbic system.     

Limitations of next-generation genome sequence assembly

High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short oligonucleotide analysis package (SOAP), generated from the genomes of a Han Chinese individual and a Yoruban individual, to experimentally validated genomic features. We found that de novo assemblies were 16.2% shorter than the reference genome and that 420.2 megabase pairs of common repeats and 99.1% of validated duplicated sequences were missing from the genome. Consequently, over 2,377 coding exons were completely missing. We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.     

Actions,Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized

Behavioral evidence suggests that instrumental conditioning is governed by two forms of action control: a goal-directed and a habit learning process. Model-based reinforcement learning (RL) has been argued to underlie the goal-directed process; however, the way in which it interacts with habits and the structure of the habitual process has remained unclear. According to a flat architecture, the habitual process corresponds to model-free RL, and its interaction with the goal-directed process is coordinated by an external arbitration mechanism. Alternatively, the interaction between these systems has recently been argued to be hierarchical, such that the formation of action sequences underlies habit learning and a goal-directed process selects between goal-directed actions and habitual sequences of actions to reach the goal. Here we used a two-stage decision-making task to test predictions from these accounts. The hierarchical account predicts that, because they are tied to each other as an action sequence, selecting a habitual action in the first stage will be followed by a habitual action in the second stage, whereas the flat account predicts that the statuses of the first and second stage actions are independent of each other. We found, based on subjects'' choices and reaction times, that human subjects combined single actions to build action sequences and that the formation of such action sequences was sufficient to explain habitual actions. Furthermore, based on Bayesian model comparison, a family of hierarchical RL models, assuming a hierarchical interaction between habit and goal-directed processes, provided a better fit of the subjects'' behavior than a family of flat models. Although these findings do not rule out all possible model-free accounts of instrumental conditioning, they do show such accounts are not necessary to explain habitual actions and provide a new basis for understanding how goal-directed and habitual action control interact.     

The effect of monoamine oxidase inhibition on formation, fixation and reproduction of temporary connections]

An administration of 100 to 300 mg/kg doses of iprazid to rats and mice leads in 24 hours to a considerably higher serotonin and noradrenaline content in the brain. Defensive conditioning against this background proceeds in the same way as in control animals but the retention of elaborated reflexes is sharply disturbed. A similar effect is produced by 5-oxytryptophane. An iprazid administration after conditioning does not disturb the retention and subsequent achievement of the reflex. Inclusion of S35-methionine in the total proteins of the mice brain does not change under the influence of iprazid. A conclusion has been drawn that inhibition of monoaminoxidase by iprazid does not prevent the formation and reproduction of temporary connections, but deeply disturbs their fixation. It is suggested that the revealed disturbances of fixation of temporary connections are due to the accumulation of serotonin in the brain, which suppresses the protein synthesis in the synaptosomes or that of specific proteins.     

Adsorption of synthetic homo- and hetero-oligodeoxynucleotides onto highly oriented pyrolytic graphite: atomic force microscopy characterization

DNA adsorption on electrode surfaces is of fundamental interest for the development of DNA-based biosensors. The free adsorption of 10-mer synthetic oligodeoxynucleotides (ODNs) onto highly oriented pyrolytic graphite (HOPG) surfaces was studied using Magnetic AC mode atomic force microscopy (MAC Mode AFM). The mechanism of interaction of nucleic acids with carbon electrode surfaces was elucidated, using 10-mer synthetic homo- and hetero-ODNs sequences of known base sequences, because they allow clear interpretation of the experimental data. AFM images in air revealed different adsorption patterns and degree of HOPG surface coverage for the ODNs, and correlation with the individual structure and base sequence of each ODN molecule will be presented. The results demonstrated that the hydrophobic interactions with the HOPG hydrophobic surface explain the main adsorption mechanism, although other effects such as electrostatic and Van der Waals interactions may contribute to the free adsorption process. The ODNs interacted differently with the HOPG surface, according to the ODN sequence hydrophobic characteristics, being directly depending on the molecular mass, the hydrophobic character of the individual bases and on the secondary structure of the molecule. The importance of the type of base existent at the ODN chain extremities on the adsorption process was investigated and different adsorption patterns were obtained with ODN sequences composed by the same group of bases aligned in a different order.     

Interaction of two structurally distinct sequence types with the clathrin terminal domain beta-propeller

The amino-terminal domain of the clathrin heavy chain, which folds into a seven-bladed beta-propeller, binds directly to several endocytic proteins via short sequences based on the consensus residues LLDLD. In addition to a single LLDLD-based, type I clathrin-binding sequence, both amphiphysin and epsin contain a second, distinct sequence that is also capable of binding to clathrin directly. Here, we analyzed these sequences, which we term type II sequences, and show that the (257)LMDLA sequence in rat epsin 1 appears to be a weak clathrin-binding variant of the sequence (417)PWDLW originally found in human amphiphysin II. The structural features of the type II sequence required for association with clathrin are distinct from the LLDLD-based sequence. In the central segment of amphiphysin, the type I and type II sequences cooperate to effect optimal clathrin binding and the formation of sedimentable assemblies. Together, the data provide evidence for two interaction surfaces upon certain endocytic accessory proteins that could cooperate with other coat components to enhance clathrin bud formation at the cell surface.     

Electrographic activity in rats during elaboration of fine distinctions]

A definite correlation has been found between the background EEG, the sensory afterdischarge (SAD) of the visual cortex and the nature of the animals' behaviour. Calmer rats with a well pronounced SAD exhibited activation of a certain type of hygienic movements, as fine differentiations were presented. As a rule, the movements were accompanied by EEG synchronization. At the same time positive conditioned reflexes persisted, in spite of an increased number of collisions. In restless animals, as the stress situation became stronger, forced movements appeared against the background of EEG desynchronization with a slightly pronounced SAD, alternating with numbness and stupor. Conditioned reflexes disappeared for several weeks. It has been assumed that relative retention of temporary connections in stress situations in animals with a well pronounced SAD is linked with the defensive-stabilizing nature of the inhibitory synchronized EEG rhythms.     

The initiation of eukaryotic and prokaryotic protein synthesis: a selective accessibility and multisubstrate enzyme reaction

An extension of our unique accessibility hypothesis for the initiation of protein synthesis is proposed following a review of the initiation of protein synthesis. The E. coli model initiation sequence generated by computer from 68 initiation sequences and the eukaryotic consensus initiation sequence derived by non-computer analysis of 211 initiation sequences do not contain a specific base in any position; they are only assigned preferred bases. The initiation site, in other words, is a varied sequence of preferred bases and its sequence is non-unique. This indicates that the ribosomal recognition of the initiation site may be the result of multiple interactions that are cooperative and cumulative and typical of multisubstrate enzymes. Because of this characteristic, the model of multisubstrate enzymes with broad substrate specificity is proposed as a paradigm for the initiation of protein synthesis. As predicted by this model, changes in the leader and downstream sequences that improve the agreement with the preferred base sequence do indeed enhance the rate of protein synthesis. The eukaryotic/prokaryotic hybrid studies show a considerable overlap in the specificities of the two groups of ribosomes. The scanning of the mRNA from the 5'-end postulated by the scanning hypothesis is not a necessary step since eukaryotic ribosomes are able to bind to internal mRNA sites and initiate synthesis. Our unique accessibility hypothesis, which is extended by coupling cooperative and cumulative specificity in ribosomal function, is referred to for brevity as the cumulative specificity hypothesis. The hypothesis actually postulates a selective accessibility and cooperative-cumulative specificity mechanism; it is able to account for the behavior of both eukaryotic and prokaryotic initiation of protein synthesis. From another perspective, the hypothesis can be regarded as providing a mechanism that enables ribosomes to recognize the IS in the absence of a unique initiation sequence.