An efficient algorithm for the identification of structured motifs in DNA promoter sequences

We propose a new algorithm for identifying cis-regulatory modules in genomic sequences. The proposed algorithm, named RISO, uses a new data structure, called box-link, to store the information about conserved regions that occur in a well-ordered and regularly spaced manner in the data set sequences. This type of conserved regions, called structured motifs, is extremely relevant in the research of gene regulatory mechanisms since it can effectively represent promoter models. The complexity analysis shows a time and space gain over the best known exact algorithms that is exponential in the spacings between binding sites. A full implementation of the algorithm was developed and made available online. Experimental results show that the algorithm is much faster than existing ones, sometimes by more than four orders of magnitude. The application of the method to biological data sets shows its ability to extract relevant consensi.     

Computing distribution of scale independent motifs in biological sequences

The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the fractal structure of that coordinate system. Consequently, the investigation of distribution of symbolic motifs at multiple scales is hampered by an inexact association between distance and sequence dissimilarity. A solution to this problem could unleash the use of iterative maps as phase-state representation of sequences where its statistical properties can be conveniently investigated. In this study a family of kernel density functions is described that accommodates the fractal nature of iterative function representations of symbolic sequences and, consequently, enables the exact investigation of sequence motifs of arbitrary lengths in that scale-independent representation. Furthermore, the proposed kernel density includes both Markovian succession and currently used alignment-free sequence dissimilarity metrics as special solutions. Therefore, the fractal kernel described is in fact a generalization that provides a common framework for a diverse suite of sequence analysis techniques.     

On the origin of distribution patterns of motifs in biological networks

Background

Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour.

Results

We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links.

Conclusion

The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins.     

Identification and analysis of putative promoter motifs in Flavivirus genome

The genus Flavivirus comprises medically significant pathogenic virus; causing several infections in humans worldwide. Flavivirus genomes are 10-11 kb approximately and encode both structural and non structural region. The non structural region plays fundamental role in the stability, regulation and cell cycle of virus. The complete genomes of 26 Flavivirus were used for identification of promoter motifs through in silico approaches. The promoter sequences were encoded in merely 16 viruses and 10 viruses could not encode it. All these in silico identified promoter motifs was confirmed and verified with the known experimental data. This analysis suggests that presence of promoter may play a crucial role in the pattern of gene expression, regulation networks, cell specificity and development. It may also be useful for designing efficient expression vector and target specific delivery system in the gene therapy.     

An examination of some basic assumptions of DNA distribution analysis using biological data.

An examination is made of how the observed DNA distributions spread from their original biological distributions. Using distributions from testicular and hepatic tissue we find that the current assumptions for DNA distribution analysis need reexamination and suggest how this might be done.     

Identification and analysis of putative promoter motifs in bovine herpes virus

The purpose of this study is to identify and analyse the putative promoter motifs in the bovine herpes virus which causes severaldiseases in cattle worldwide including bovine mastitis with large economic impact on dairy industry. Bovine mastitis caused dueto virus is often neglected as bacterial infections are held mainly responsible for the disease. Therefore, in this in silico investigationwith all the existing experimental data a total of 147 promoter were identified along with their sequences from three genome vizbovine herpes virus 1 (BHV), bovine herpes virus 4 and bovine herpes virus 5, out of which 39 promoters were from bovine herpesvirus 4 (BHV 4), 95 from BHV1 and 13 from BHV5 and it was observed that BHV1 and BHV5 have a close evolutionary history.However, they belong to the same subfamily and size of the genome and GC% of BHV1 and BHV5 was almost equal and very highcompare to that of BHV4. This analysis may help in designing the live attenuated vaccine against BHV causing bovine mastitis thatreduces the incidence of bovine mastitis. Identification of promoters may also help in designing of expression vectors which help inbetter understanding of the regulation of gene expression. In the era of large genomics and proteomics prediction of promoters inthe whole genome is crucial for the advancement of drug discovery and gene therapy.     

Analysis of free D-serine in mammals and its biological relevance

D-Serine is a unique endogenous substance enriched in the brain at the exceptionally high concentrations as a free D-amino acid in mammals throughout their life. Peripheral tissues and blood contain low or trace levels of the D-amino acid. In the nervous systems, D-serine appears to act as an intrinsic coagonist for the N-methyl-D-aspartate type glutamate receptor (NMDA receptor) based upon the following characteristics: (i) D-serine stereoselectively binds to and stimulates the glycine-regulatory site of the NMDA receptor consisting of GRIN1/GRIN2 subunits more potently than glycine with an affinity and ED50 at high nanomolar ranges, (ii) the selective elimination of D-serine in brain tissues attenuates the NMDA receptor functions, indicating an indispensable role in physiological activation of the glutamate receptor, and (iii) the distribution of D-serine is uneven and closely correlated with that of the binding densities of the various NMDA receptor sites, and especially of the GRIN2B subunit in the brain. Moreover, d-serine exerts substantial influence on the GRIN1/GRIN3-NMDA and δ2 glutamate receptor. In the brain and retina, metabolic processes of D-serine, such as biosynthesis, extracellular release, uptake, and degradation, are observed and some candidate molecules that mediate these processes have been isolated. The fact that the mode of extracellular release of D-serine in the brain differs from that of classical neurotransmitters is likely to be related to the detection of D-serine in both glial cells and neurons, suggesting that d-serine signals could be required for the glia-synapse interaction. Moreover, the findings from the basic experiments and clinical observations support the views that the signaling system of endogenous free D-serine plays important roles, at least, through the action on the NMDA receptors in the brain wiring development and the regulation of higher brain functions, including cognitive, emotional and sensorimotor function. Based upon these data, aberrant D-serine-NMDA receptor interactions have been considered to be involved in the pathophysiology of a variety of neuropsychiatric disorders including schizophrenia and ischemic neuronal cell death. The molecular and cellular mechanisms for regulating the D-serine signals in the nervous system are, therefore, suitable targets for studies aiming to elucidate the causes of neuropsychiatric disorders and for the development of new treatments for intractable neuropsychiatric symptoms.     

Methods for homocysteine analysis and biological relevance of the results

It is now widely accepted that increased total plasma homocysteine (tHcy) is a risk factor for cardiovascular disease. Hyperhomocysteinemia can be caused by impaired enzyme function as a result of genetic mutation or vitamin B (B(2), B(6), B(9), B(12)) deficiency. A lot of methods are now available for tHcy determination. High-pressure liquid chromatography (HPLC) with fluorescence detection are at present the most widely used methods but immunoassays, easier to use, begin to supplant in-house laboratory methods. In order to help with the choice of a main relevant homocysteine analytical method, the characteristics, performances and limits of the main current methods are reviewed. One major drawback among all these available methods is the transferability which is not clearly established to date. The impact of both inter-method and inter-laboratory variations on the interpretation of the tHcy results are discussed.     

Tyrosine oxidation products: analysis and biological relevance

Summary. Dityrosine is found in several proteins as a product of UV irradiation, -irradiation, aging, exposure to oxygen free radicals, nitrogen dioxide, peroxynitrite, and lipid hydroperoxides. Interest of dityrosine in proteins is based on its potential as a specific marker for oxidatively damaged proteins and their selective proteolysis, hence it could be used as a marker for oxidative stress. Dityrosine is also the product of normal post-translational processes affecting specific structural proteins. Since post-translational modification of a given amino acid in a protein is equivalent to the substitution of that residue by an analogue, it has been proposed that the covalent modification of amino acids may serve as a marking step for protein degradation.     

Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology

Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony.     

Discriminant analysis of promoter regions in Escherichia coli sequences

We have previously developed a general method based on the statisticaltechnique of discriminant analysis to predict splice junctionsin eukaryotic mRNA sequences [Nakata, K., Kanehisa, M. and DeLisi,C. (1985) Nucleic Acids Res., 13, 5327–5340]. In orderto evaluate further applicability of this method, we now analyzethe promoter region of Escherichia coli sequences. The attributesused for discrimination include the accuracy of consensus sequencepatterns measured by the perceptron algorithm, the thermal stabilitymap, the base composition and the Calladine-Dickerson rulesfor helical twist angle, roll angle, torsion angle and propellertwist angle. When applied to selected E. coli sequences in theGenBank database, the method correctly identifies 75 % of thetrue promoter regions. Received on May 15, 1987; accepted on April 17, 1988     

D-Amino acids in aged proteins: analysis and biological relevance

Homochirality is essential for life. L-Amino acids are exclusively used as substrates for the polymerization and formation of peptides and proteins in living systems. However, d-amino acids, which are enantiomers of L-amino acids, were recently detected in various living organisms in the form of free D-amino acids and D-amino acid residues in peptides and proteins. In particular, D-aspartyl (Asp) residues have been detected in various proteins from diverse tissues of elderly individuals. Here, we describe three important aspects of our research: (i) a method for detecting D-β-Asp at specific sites in particular proteins, (ii) a likely spontaneous mechanism by which Asp residues in proteins invert and isomerize to the D-β-form with age under physiological conditions, (iii) a discussion of factors that favor such a reaction.     

RNA motifs that determine specificity between a viral replicase and its promoter

The 3' end of brome mosaic virus RNA contains a tRNA-like sequence that directs its RNA synthesis. A stem loop structure in this sequence, stem loop C (SLC), was investigated using NMR, and correlated with its ability to direct RNA synthesis by its replicase. SLC consists of two discrete domains, a flexible stem with an internal loop and a rigid stem containing a 5'-AUA-3' triloop. Efficient RNA synthesis requires the sequence on only one side of the flexible stem and a specific compact conformation of the triloop. A high resolution structure of the triloop places the 5' adenine out in solution, and the 3' adenine within the triloop, held tightly through stacking and unusual hydrogen bonds. This high resolution structure of an RNA promoter from a (+)-strand RNA virus provides new insights into how the RNA-dependent RNA polymerase binds to the RNA to initiate synthesis.