A note on the information content of graphs

The role played by the group of a graph in determining sets of equivalent points is exposed and illustrated by a few simple examples.     

A structural and a functional aspect of stable information processing by the brain

Brain is an expert in producing the same output from a particular set of inputs, even from a very noisy environment. In this article a model of neural circuit in the brain has been proposed which is composed of cyclic sub-circuits. A big loop has been defined to be consisting of a feed forward path from the sensory neurons to the highest processing area of the brain and feed back paths from that region back up to close to the same sensory neurons. It has been mathematically shown how some smaller cycles can amplify signal. A big loop processes information by contrast and amplify principle. How a pair of presynaptic and postsynaptic neurons can be identified by an exact synchronization detection method has also been mentioned. It has been assumed that the spike train coming out of a firing neuron encodes all the information produced by it as output. It is possible to extract this information over a period of time by Fourier transforms. The Fourier coefficients arranged in a vector form will uniquely represent the neural spike train over a period of time. The information emanating out of all the neurons in a given neural circuit over a period of time can be represented by a collection of points in a multidimensional vector space. This cluster of points represents the functional or behavioral form of the neural circuit. It has been proposed that a particular cluster of vectors as the representation of a new behavior is chosen by the brain interactively with respect to the memory stored in that circuit and the amount of emotion involved. It has been proposed that in this situation a Coulomb force like expression governs the dynamics of functioning of the circuit and stability of the system is reached at the minimum of all the minima of a potential function derived from the force like expression. The calculations have been done with respect to a pseudometric defined in a multidimensional vector space.     

A novel aspect of NADPH production in ageing Penicillium chrysogenum

NADPH is involved in many basically important anabolic processes. For a long time, pentose phosphate pathway (PPS) was regarded as the most important source of NADPH in fungi. Here we present evidence of a metabolic switch to an alternative NADPH-producing pathway in ageing Penicillium chrysogenum cultures, which involves NADP+ -specific isocitrate dehydrogenase (NADP+ -ID) rather than PPS enzymes. Considering the main biochemical functions of NADPH, we propose that NADP+ -ID could have deep impact on many physiological processes switched on glucose deprivation including proteinase production or penicillin biosynthesis. We also demonstrate that although the alternative pathway was inferior to PPS when the fungus was grown on well-utilisable carbon sources yet it could have an important role in fatty acid biosynthesis as well as in the maintenance of high intracellular NADPH/NADP+ ratios.     

Epigenomics: novel aspect of genomic regulation

An International Symposium on Epigenomics took place at Yonsei University, Korea in December, 2006. The meeting brought to light new aspects of genome regulation by DNA and protein modification.     

Conformation of viroids.

Viroids are uncoated infectious RNA molecules (MW 107 000-127 000) known as pathogens of certain higher plants. Thermodynamic and kinetic studies were carried out on highly purified viroid preparations by applying UV-absorption melting analysis and temperature jump methods. The thermal denaturation of viroids is characterized by high thermal stability, high cooperativity and a high degree of base pairing. Two relaxation processes could be resolved; a process in the sec range could be evaluated as an independent all-or-none-transition with the following properties: reaction enthalpy= 550 kcal/mol, activation enthalpy of the dissociation = 470 kcal/mol; G : C content = 72 %. These data indicate the existence of an uninterrupted double helix of 52 base pairs. A process in the msec range involves 15 - 25 base pairs which are most probably distributed over several short double helical stretches. A tentative model for the secondary structure of viroids isproposed and the possible functional implications of their physicochemical properties are discussed.     

Dynamics and interactions of viroids

Viroids are single stranded circular RNA molecules of 120,000 daltons which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but do replicate only as a part of a larger plant virus. The structure and structural transitions have been investigated by thermodynamic, kinetic and hydrodynamic methods and have been compared to results from calculations of the most favorable native structures and the denaturation process. The algorithm of Zuker et al. was modified for the application to circular nucleic acids. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids, although described in the literature as viroid-like, show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but sequences generated by a computer. The comparison of viroids, virusoids and circular RNA of random sequences underlines the uniqueness of viroid structure. The interactions of viroids with dye and oligonucleotide-ligands and with RNA-polymerase II from wheat germ, which enzyme replicates viroids in vitro, has been studied in order to correlate viroid structure and its ability for specific interactions. Specificity of the interactions may be interpreted on the basis of the neighbourhood of double stranded and single stranded regions. In the host cell viroids are localized in the cell nucleus; they may be detected as free nucleic acids and in high molecular weight complexes together with other RNA and proteins.     

A novel aspect of the inhibition by arsenicals of binding-protein-dependent galactose transport in gram-negative bacteria.

The inhibitory effects of arsenate and arsenite on binding-protein-dependent transport systems are reconsidered. It is shown that arsenate inhibits binding-protein-dependent galactose transport in proteoliposomes energized either by dihydrolipoamide and NAD+ or by a membrane potential (under conditions where ATP metabolism is not implicated); this result is in contradiction with the current interpretation of arsenate inhibition of binding-protein-dependent transport systems (which is based on ATP depletion) and can be explained by reference to the recently discovered ATP inhibition of the binding-protein-dependent galactose transport. In whole cells, the greater inhibition by arsenate of lipoamide-dependent transport than of protonmotive-force-dependent transport may be explained by a modification by arsenate of the pools of several compounds metabolized by 2-oxo-acid dehydrogenases (which have been implicated in binding-protein-dependent transport). The inhibition of binding-protein-dependent galactose transport by arsenite is probably linked to the inhibition by arsenite of the galactose-stimulated lipoamide dehydrogenase activity implicated in this transport and is reminiscent of the known arsenite inhibition of lipoamide dehydrogenases.     

On the information content of the genetic code

In living organisms 20 amino acids along with the terminator value(s) are encoded by 64 codons giving a degeneracy of the codons as described by the genetic code. A basic theoretical problem of genetic codes is to explain the particular distribution of degeneracies of partitions involved in the codes. In this work the degeneracy problem is considered in the framework of information theory. It is shown by direct numerical evaluation of a certain degeneracy information function associated with the genetic code that the degeneracy of the codes is observed to be related to the optimization of this function.     

Structure and structure formation of viroids

The structure of viroids and the mechanism of structure formation were investigated by different methods. Results from gel analysis, partial degradation pattern, electron microscopy, dye binding, hydrodynamic studies, and temperature-jump kinetics were interpreted in a common structural and mechanistic scheme. Gel analysis, electron microscopy and kinetic investigations show that viroids may assume the native as well as metastable conformations under the same conditions. The native conformation is obtained by complete renaturation, i.e. slow cooling throughout the transition range (e.g. 52 to 48 ° C for potato spindle tuber viroid (PST viroid) in 0.01 m-sodium cacodylate, pH 6.8). In contrast, metastable conformations were trapped if viroids were redissolved in the cold from their ethanol precipitate or if they were denatured and cooled quickly.The native secondary structure of the recently sequenced PST viroid (Gross et al., 1978) was optimized for the free energy of base-pairing. The scheme agrees with that proposed by Gross et al. (1978), which was derived from chemical arguments. The extended structure does not undergo tertiary structure folding under a wide range of conditions, as was concluded from electron microscopy, sedimentation measurements and binding studies of ethidium bromide and a new dye specific for A · U pairs (2-(4′-aminophenyl)-5-(4′-methylpiperazin-1″yl)-benzirnidazol).Intermediate structures during viroid denaturation were analysed on theoretical and experimental grounds. The experimental data, in combination with the model calculations, show that all of the native base-pairs of viroids are dissociated in one highly co-operative main transition, and that during the same process very stable hairpins are formed that are not present in the native structure. The formation of stable hairpins induces a new type of long range cooperativity, which is responsible in part for the high co-operativity observed experimentally. This interpretation is in good agreement with kinetic results presented elsewhere (Henco et al., 1979).In order to understand the uniqueness of viroids, the structure and the conformational transitions of circular RNA molecules of the same base composition as PST viroids but with 359 nucleotides arranged randomly, were studied theoretically. Common viroid features, such as the number of base-pairs, the high co-operativity and the formation of very stable hairpins, are found to be improbable in such random sequences. It is concluded that various viroid species, although differing in nucleotide sequence, follow common principles of structure and structure formation.     

On the information content of discrete phylogenetic characters

Journal of Mathematical Biology - Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a...     

A comparative analysis of the information content in long and short SAGE libraries

Background  

Serial Analysis of Gene Expression (SAGE) is a powerful tool to determine gene expression profiles. Two types of SAGE libraries, ShortSAGE and LongSAGE, are classified based on the length of the SAGE tag (10 vs. 17 basepairs). LongSAGE libraries are thought to be more useful than ShortSAGE libraries, but their information content has not been widely compared. To dissect the differences between these two types of libraries, we utilized four libraries (two LongSAGE and two ShortSAGE libraries) generated from the hippocampus of Alzheimer and control samples. In addition, we generated two additional short SAGE libraries, the truncated long SAGE libraries (tSAGE), from LongSAGE libraries by deleting seven 5' basepairs from each LongSAGE tag.     

A novel murine Staufen isoform modulates the RNA content of Staufen complexes

Mouse Staufen (mStau) is a double-stranded RNA-binding protein associated with polysomes and the rough endoplasmic reticulum (RER). We describe a novel endogenous isoform of mStau (termed mStau(i)) which has an insertion of six amino acids within dsRBD3, the major double-stranded RNA (dsRNA)-binding domain. With a structural change of the RNA-binding domain, this conserved and widely distributed isoform showed strongly impaired dsRNA-binding ability. In transfected cells, mStau(i) exhibited the same tubulovesicular distribution (RER) as mStau when weakly expressed; however, when overexpressed, mStau(i) was found in large cytoplasmic granules. Markers of the RER colocalized with mStau(i)-containing granules, showing that overexpressed mStau(i) could still be associated with the RER. Cotransfection of mStau(i) with mStau relocalized overexpressed mStau(i) to the reticular RER, suggesting that they can form a complex on the RER and that a balance between these isoforms is important to achieve proper localization. Coimmunoprecipitation demonstrated that the two mStau isoforms are components of the same complex in vivo. Analysis of the immunoprecipitates showed that mStau is a component of an RNA-protein complex and that the association with mStau(i) drastically reduces the RNA content of the complex. We propose that this new isoform, by forming a multiple-isoform complex, regulates the amount of RNA in mStau complexes in mammalian cells.