A neurodynamic account of spontaneous behaviour

The current article suggests that deterministic chaos self-organized in cortical dynamics could be responsible for the generation of spontaneous action sequences. Recently, various psychological observations have suggested that humans and primates can learn to extract statistical structures hidden in perceptual sequences experienced during active environmental interactions. Although it has been suggested that such statistical structures involve chunking or compositional primitives, their neuronal implementations in brains have not yet been clarified. Therefore, to reconstruct the phenomena, synthetic neuro-robotics experiments were conducted by using a neural network model, which is characterized by a generative model with intentional states and its multiple timescales dynamics. The experimental results showed that the robot successfully learned to imitate tutored behavioral sequence patterns by extracting the underlying transition probability among primitive actions. An analysis revealed that a set of primitive action patterns was embedded in the fast dynamics part, and the chaotic dynamics of spontaneously sequencing these action primitive patterns was structured in the slow dynamics part, provided that the timescale was adequately set for each part. It was also shown that self-organization of this type of functional hierarchy ensured robust action generation by the robot in its interactions with a noisy environment. This article discusses the correspondence of the synthetic experiments with the known hierarchy of the prefrontal cortex, the supplementary motor area, and the primary motor cortex for action generation. We speculate that deterministic dynamical structures organized in the prefrontal cortex could be essential because they can account for the generation of both intentional behaviors of fixed action sequences and spontaneous behaviors of pseudo-stochastic action sequences by the same mechanism.     

Bioinformatics database infrastructure for biotechnology research

Many databases are available that provide valuable data resources for the biotechnological researcher. According to their core data, they can be divided into different types. Some databases provide primary data, like all published nucleotide sequences, others deal with protein sequences. In addition to these two basic types of databases, a huge number of more specialized resources are available, like databases about protein structures, protein identification, special features of genes and/or proteins, or certain organisms. Furthermore, some resources offer integrated views on different types of data, allowing the user to do easy customized queries over large datasets and to compare different types of data.     

A common structural feature in promoter sequences of E. coli.

We have searched promoter regions of E. coli, structural genes of the same organism, and computer-generated random sequence DNA for the occurrence of common structural features. This is done by converting the base sequence to a series of numbers representing the sequence of helix twist angles and examining these numerical sequences statistically. Common structural features are shared by the promoter regions with a much higher frequency than are found in structural genes or in random sequences. These structures appear to be scattered randomly throughout the promoters, both in terms of the number of such structures per promoter and in terms of location within each promoter. One particular structure consisting of five successive helix twist angles is reported, along with a list of 60 different hexanucleotide sequences that share this structure. The locations of these structural elements in 61 E. coli promoters are also tabulated.     

人SATB1基因5′上游序列的转录激活功能分析

在对人SATB1基因进行生物信息学分析的基础上 ,采用PCR技术 ,扩增人基因组DNA中SATB1基因 5′上游序列的 - 2 95 5～ - 9片段 ,构建了 3个分别由SATB1基因 5′上游 - 2 95 5～ - 9,- 172 7～ - 9和 - 76 0～ - 9序列片段驱动的报告载体 -pGL3 SP2 94 6 luc ,pGL3 SP1718 luc和pGL3 SP75 1 luc ,分别瞬时转染JurkatT ,K5 6 2 ,U937和HeLa细胞 ,通过测定荧光素酶的表达活性 ,观察SATB1基因 5′上游序列片段 3个删除突变体在不同细胞内活性的差异 .结果显示 ,SATB1上游序列- 2 95 5 - 9在 4种细胞中的转录激活能力为U937>JurkatT >K5 6 2 ,在HeLa细胞中基本无激活 ,提示SATB1的转录激活可能具有一定的细胞类型特异性 .3种 5′删除突变体转录激活性由大至小顺序为 - 76 0 - 9>- 2 95 5 - 9>- 172 7 - 9,提示SATB1的核心启动子可能存在于其 5′上游序列的- 76 0至 - 9bp区域中 .     

不同转录频率的酵母基因启动子序列结构差异性分析

不同基因的转录效率一般会有差异,启动子序列的组织结构可能是造成差异的原因之一。本文分别基于出现频率、Markov模型以及加权Markov模型计算出所有6碱基片段(6-mer)在不同转录频率的酵母基因启动子序列中的分布,然后利用最大最小贴近度方法分析这些基因启动子序列结构的差异情况。结果表明,酵母基因的转录频率与启动子序列结构的确有关联,转录频率相差较大的基因,它们的启动子序列结构差异一般也较大。统计分析还表明,高阶(3阶和4阶)加权Markov模型可以更有效地反映基因启动子序列的结构特征。     

Evolution of alpha-amylases: architectural features and key residues in the stabilization of the (beta/alpha)(8) scaffold

We provide a comprehensive analysis of the current enzymes with alpha-amylase activity (AAMYs) that belong to family 13 glycoside hydrolase (GH-13; 144 Archaea, Bacteria, and Eukaryota sequences from 87 different species). This study aims to further knowledge of the evolutionary molecular relationships among the sequences of their A and B domains with special emphasis on the correlation between what is observed in the structures and protein evolution. Multialignments for the A domain distinguish two clusters for sequences from Archaea organisms, eight for sequences from Bacteria organisms, and three for sequences from Eukaryota organisms. The clusters for Bacteria do not follow any strict taxonomic pathway; in fact, they are rather scattered. When we compared the A domains of sequences belonging to different kingdoms, we found that various pairs of clusters were significantly similar. Using either sequence similarity with crystallized structures or secondary-structure prediction methods, we identified in all AAMYs the eight putative beta-strands that constitute the beta-sheet in the TIM barrel of the A domain and studied the packing in its interior. We also discovered a "hidden homology" in the TIM barrel, an invariant Gly located upstream in the sequence before the conserved Asp in beta-strand 3. This Gly precedes an alpha-helix and is actively involved in capping its N-terminal end with a capping box. In all cases, a Schellman motif caps the C-terminal end of this helix.     

Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process.

After binding to a promoter Escherichia coli RNA polymerase is in contact with a region of about 70 bp. Around 20 bp of this sequence are transcribed. Information encoded within this transcribed region is involved in late steps of the functional program of a promoter. By changing such 'down-stream' sequences promoter strength in vivo can be varied more than 10-fold. By contrast, information for early steps of the promoter program such as recognition by the enzyme and formation of a stable complex resides in a central core region of about 35 bp. Our data show that the strength of a promoter can be limited at different levels of the overall process. Consequently promoters of identical strength can exhibit different structures due to an alternate optimization of their program.     

Sequence effects in single-base loops for quadruplexes

Intramolecular G-quadruplexes formed by a single DNA strand have attracted much interest due to the possibility that they may form in telomeres, oncogene promoter sequences and other biologically relevant regions of the genome. Therefore, it is important to understand the rules that govern the formation of these intramolecular structures and to determine their stabilities. We compared here 27 different sequences containing four tracts of three guanines with a medium (3) or relatively long (6-9 bases) central loop and two loops composed of a single nucleotide H (A, T or C) corresponding to the GGGHGGGN3-9GGGHGGG motif. These sequences are similar to sequence motifs that can be found in repeated and promoter sequences. Several conclusions were reached: (i) all sequences are prone to form very stable quadruplexes in potassium (Tm between 55 degrees C and 83 degrees C); (ii) these quadruplexes also form in sodium but with a strongly decreased Tm, with a 21 to 36 degrees C difference in melting temperature between Na+ and K+; (iii) a long (9 bases) central loop had a minimal deleterious impact on the stability of the quadruplex; (iv) pyrimidines are preferred over adenine in both single-base loops; (v) the folding topology is relatively robust in potassium: the CD spectra of all oligonucleotides matched the one of all-parallel stranded reference quadruplexes; (vi) conversely, in sodium the folding is diverse and sequence-dependent, as judged from CD and electrophoresis results.     

Structure, occurrence and functional significance of nonlinear phenomena in sounds of terrestrial mammals

Subharmonics, deterministic chaos, biphonations, sidebands and frequency jumps, known under joining name nonlinear phenomena, represent acoustical appearances that occur in calls of various mammals, from insectivorous to humans. Although the physical basis for appearances of the nonlinear phenomen is known in principle, such aspects as occurrence and functional significance of nonlinear phenomena, are poorly understood. We described here the structural peculiarities of these appearances based on domestic dogs' whines demonstrating all kinds of the nonlinear phenomena. The nonlinear phenomena result directly from the work of mammalian vocal apparatus--lunges, vocal folds, and vocal tract, which are responsible for its inherent functional characteristics. The mammalian vocal folds represent a system of two coupled oscillators functioning in different vibratory regimes depending on degree of synchronization in their vibrations and occurrence of coupling between the vocal folds. This functioning does not need in direct neural control for turning on the complex regimes of vocal folds' vibration and switching from one regime to another. Besides, many mammals possess anatomical structures, such as vocal membranes, pads on vocal folds, or laryngeal air sacs, that are to participate in sound production as additional oscillators extend the range of possibilities for arising of nonlinear phenomena in vocalization. On the basis of published and own data, we provide and overview of the occurrence of nonlinear phenomena in sounds of humans, nonhuman primates, canids, and rodents, and discuss the supposed functional significance of these acoustical appearances in mammalian vocal communication systems. From one side, nonlinear phenomena may be related to various physiological disorders in humans and animals. In such cases, their appearance in calls may be nonadaptive, because they permit conspecifics' to avoid owners of such "ill" voices, and points easy prey to predators. From another side, in some cases the nonlinear phenomena may arise especially for performing of some signal functions in species communication system: to enhance reliability of individual recognition, to transmit information about size of a caller over the large distance, to permit individuals of not great size mimicry acoustically under more larger animal, to introduce variety into monotonous vocal sequences in order to force other group members to pay attention to a caller, and to facilitate distance estimation to a caller and direction of its movement.     

Promoter recognition by Escherichia coli RNA polymerase. Effects of substitutions in the spacer DNA separating the -10 and -35 regions

A family of variants of the PRM promoter of lambda phage was constructed, bearing nine base pair substitutions in a stretch of the spacer DNA separating the contacted -10 and -35 regions. The substituted sequences were chosen for their potential to adopt structures different from those of average B-form DNA and thus to affect the interaction of RNA polymerase with the two contacted regions. Characterization of the promoters in vitro and in vivo provides additional support for the lack of specific contacts in the substituted spacer region and shows that a small change in the relative rotational orientation of the -10 and -35 regions is inconsequential to promoter function. However, a 2-3-fold reduction in promoter activity is observed with promoters bearing substitutions of nonalternating dG-dC base pairs in either orientation. This corroborates other studies indicating the anomalous behavior of such sequences and suggests that the structure of the spacer DNA can modulate promoter recognition.     

Discrimination of promoters by <Emphasis Type="Italic">Bacillus subtilis</Emphasis> RNA polymerase σ<Superscript>A</Superscript> and σ<Superscript>H</Superscript> holoenzymes is associated with periodic patterns in promoter nucleotide sequences

Bacillus subtilis promoters recognized by σ^A and σ^H RNA polymerases were found to have different periodic patterns of nucleotide disposition. Using a special version of Fourier analysis for symbolic sequences, Fourier spectra were obtained for the primary structure of promoters used by the two holoenzymes. Stepwise discriminant analysis with jackknife testing was performed for two promoter data sets (small and large). Based on the spectral patterns of the nucleotide sequences, the data sets could be sorted with 100% accuracy into two classes: promoters recognized by Eσ^A and by Eσ^H. Correlations were obtained between the promoter strength and the characteristics of their Fourier spectra. Moreover, perfect separation was achieved even when the “consensus” ?35 and ?10 sites were replaced by sequences of “blank symbols.” Thus, the periodicity in nucleotide distribution along the DNA chain is itself an attribute sufficient for selective recognition of the cognate promoter by RNA polymerase.     

Mathematical modeling and parameters estimation of anaerobic fermentation processes

In the paper some problems of the mathematical modeling of anaerobic (methane) fermentation of animal waste in stirred tank bioreactors are considered. Laboratory experiments are carried out with highly concentrated organic pollutants and transient step responses of the control output for continuous methane fermentation are obtained. The dynamic behavior of this process is described by sets of deterministic nonlinear differential equations from 2nd order with different structures. Static characteristics are obtained with these models analytically. Investigations by computer simulation of the methane fermentation are performed with the aim to chose appropriate models for automatic control system design of this process.