Classification of triplet periodicity in the DNA sequences of genes from KEGG databank

Totally, 472 288 regions of triplet periodicity were found in 578 868 genes from KEGG databank version 29 and classified. A new concept of triplet periodicity class and a measure of similarity between periodicity classes were introduced. Overall, 2520 classes were created and contained 94% of the triplet periodicity cases found. A similar correlation between the triplet periodicity and reading frame was observed for 92% of triplet periodicity regions contained in different classes. The remaining triplet periodicity regions displayed a shift of the reading frame relative to that common for the majority of genes belonging to the same triplet periodicity class. The hypothetical amino acid sequences were deduced from the periodicity regions according to the reading frame characteristic of the given triplet periodicity class. BLAST analysis demonstrated that 2660 hypothetical amino acid sequences display a statistically significant similarity to proteins from the Uni-Prot databank. It was supposed that 8% of the triplet periodicity regions contained in the classes have frameshift mutations. The triplet periodicity classes can be used to identify the coding regions in genes and to searching for frameshift mutations.     

Classification of triplet periodicity in DNA sequences of genes taken from KEGG databank

We conducted classification for 472,288 regions of triplet periodicity found in 578,868 genes from release 29 of KEGG databank. A new concept of triplet periodicity class and a measure of similarity between them are introduced. Totally 2520 classes were created that contain 94% of found triplet periodicity. For 92% of triplet periodicity regions contained in classes an identical linkage of triplet periodicity to reading frame is observed. For the rest triplet periodicity cases a shift between reading frame of a gene and reading frame common for majority of genes contained in a class of triplet periodicity was observed. These periodicity regions were encoded into hypothetical amino acid sequences in accordance with reading frame built by triplet periodicity class. By BLAST program it was shown that 2660 hypothetical amino acid sequences have statistically significant similarity with proteins from UniProt databank. We suppose that 8% of triplet periodicity regions that joined classes mutated by means of reading frame shift. Created classes of triplet periodicity can be used for identification of coding regions of genes as well as for searching for mutations arisen from reading frame shift.     

Latent Periodicity of Protein Sequences

This article is in the area of protein sequence investigation. It studies protein sequence periodicity. The notion of latent periodicity is introduced. A mathematical method for searching for latent periodicity in protein sequences is developed. Implementation of the method developed for known cases of perfect and imperfect periodicity is demonstrated. Latent periodicity of many protein sequences from the SWISS-PROT data bank is revealed by the method and examples of latent periodicity of amino acid sequences are demonstrated for: the translation initiation factor EIF-2B (epsilon subunit) of Saccharomyces cerevisiae from the E2BE_YEAST sequence; the E.coli ferrienterochelin receptor from the FEPA_ECOLI sequence; the lysozyme of Bacteriophage SF6 from the LY_BPSF6 sequence; lipoamide dehydrogenase of Azotobacter vinelandii from the DLDH_AZOVI sequence. These protein sequences have latent periods equal to six, two, seven and 19 amino acids, respectively. We propose that a possible purpose of the amino acid sequence latent periodicity is to determine certain protein structures.     

Method revealing latent periodicity of the nucleotide sequences modified for a case of small samples.

An earlier reported method for revealing latent periodicity of the nucleotide sequences has been considerably modified in a case of small samples, by applying a Monte Carlo method. This improved method has been used to search for the latent periodicity of some nucleotide sequences of the EMBL data bank. The existence of the nucleotide sequences' latent periodicity has been shown for some genes. The results obtained have implied that periodicity of gene structure is projected onto the periodicity of primary amino acid sequences and, further, onto spatial protein conformation. Even though the periodic structure of gene sequences has been eroded, it is still retained in primary and/or spatial structures of corresponding proteins. Furthermore, in a few cases the study of genes' periodicity has suggested their possible evolutionary origin by multifold duplications of some gene's fragments.     

Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences

A model of perfect tandem repeat with random pattern has been considered. It expands a notion of approximate tandem repeat and describes new kind of latent periodicity in biological sequences, which has been named profile periodicity. Based on this model, an original spectral-statistical approach has been proposed for the estimation of size of the periodicity pattern in sequences of approximate tandem repeats. In contrast to existing approaches, this is applicable in practical conditions of unrepresentative samples (for standard criteria). This approach is suitable and effective for preliminary automated revelation of latent periodicity. The advantages of the spectral-statistical approach to estimation of the periodicity pattern for approximate tandem repeats have been demonstrated in comparison with the other methods.     

Identification of latent periodicity in amino acid sequences of protein families

For detection of the latent periodicity of the protein families responsible for various biological functions, methods of information decomposition, cyclic profile alignment, and the method of noise decomposition have been used. The latent periodicity, being specific to a particular family, is recognized in 94 of 110 analyzed protein families. Family specific periodicity was found for more than 70% of amino acid sequences in each of these families. Based on such sequences the characteristic profile of the latent periodicity has been deduced for each family. Possible relationship between the recognized latent periodicity, evolution of proteins, and their structural organization is discussed.     

Latent sequence periodicity of some oncogenes and DNA-binding protein genes

A method of latent periodicity search is developed. We use mutualinformation to reveal the latent periodicity of mRNA sequences.The latent periodicity of an mRNA sequence is a periodicitywith a low level of similarity between any two periods insidethe mRNA sequence. The mutual information between an artificialnumerical sequence and an mRNA sequence is calculated. The lengthof the artificial sequence period is varied from 2 to 150. Thehigh level of the mutual information between artificial andmRNA sequences allows us to find any type of latent periodicityof mRNA sequence. The latent periodicity of many mRNA codingregions has been found. For example, the retinoblastoma geneof HSRBS clone contains a region with a latent period equalto 45 bases. The A-RAF oncogene of HSARAFIR clone contains aregion with a latent period equal to 84 bases. Integrated sequencesfor the regions with latent periodicity are determined. Thepotential significance of latent periodicity is discussed.     

Periodicity in spatial data and geostatistical models: autocorrelation between patches

Several recent studies in landscape ecology have found periodicity in correlograms or semi-variograms calculated, for instance, from spatial data of soils, forests, or animal populations. Some of the studies interpreted this as an indication of regular or periodic landscape patterns. This interpretation is in disagreement with other studies that doubt whether such analysis is valid. The objective of our study was to explore the relationship between periodicity in landscape patterns and geostatistical models. We were especially interested in the validity of the assumption that periodicity in geostatistical models indicates periodicity in landscape pattern, and whether the former can characterize frequency and magnitude of the latter. We created maps containing various periodic spatial patterns, derived correlograms from these, and examined periodicity in the correlograms. We also created non-regular maps that we suspected would cause periodicity in correlograms. Our results demonstrate that a) various periodic spatial patterns produce periodicity in correlograms derived from them, b) the distance-lags at which correlograms peak correspond to the average distances between patch centers, c) periodicity is strongest when the diameter of patches is equal to the distance between patch edges, d) periodicity in omni-directional correlograms of complex spatial patterns (such as checkerboards) are combinations of several waves because inter-patch distances differ with direction; multiple directional correlograms can decompose such complexity, and e) periodicity in correlograms can also be caused when the number of patches in a study site is small. These results highlight that correlograms can be used to detect and describe regular spatial patterns. However, it is crucial to ensure that the assumption of stationarity is not violated, i.e., that the study area contains a sufficiently large number of patches to avoid incorrect conclusions.     

Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis

We used a power spectrum method to identify periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to prokaryotic and eukaryotic genomes and genomes. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in eubacteria. The 10-bp periodicity was also prevalent in the eukaryotes such as the worm Caenorhabditis elegans. Additionally, in the worm genome, a 68-bp periodicity in chromosome I, a 59-bp periodicity in chromosome II, and a 94-bp periodicity in chromosome III were found. In human chromosomes 21 and 22, approximately 167- or 84-bp periodicity was detected along the entire length of these chromosomes. Because the 167-bp is identical to the length of DNA that forms two complete helical turns in nucleosome organization, we speculated that the respective sequences may correspond to arrays of a special compact form of nucleosomes clustered in specific regions of the human chromosomes. This periodic element contained a high frequency of TGG. TGG-rich sequences are known to form a specific subset of folded DNA structures, and therefore, the sequences might have potential to form specific higher order structures related to the clustered occurrence of a specific form of the speculated nucleosomes.     

Relationship between the axial periodicity and staining of collagen by the Masson trichrome procedure

Synopsis Although wide variations in the axial periodicity of collagen fibrils in tissue sections have been reported previously, the comparative study presented in this paper of the axial periodicity and the Masson trichrome staining of collagen fibres from different tensional situations demonstrates that marked variations in collagen axial periodicity can be directly correlated with the tensional state of the tissues before fixation and with their Masson trichrome staining reaction.Collagen fibres from tensional situations consistently exhibit a longer periodicity and retain the Acid Fuchsin component of the Masson trichrome procedure, whilst collagen fibres from non-tensional situations have a shorter periodicity, fail to retain the Acid Fuchsin component, and are coloured by the Light Green counterstain.     

Latent periodicity of protein families, identified with the indel-aware algorithm

Latent amino acid repeats seem to be widespread in genetic sequences and to reflect their structure, function, and evolution. We have recently identified latent periodicity in more than 150 protein families including protein kinases and various nucleotide-binding proteins. The latent repeats in these families were correlated to their structure and evolution. However, a majority of known protein families were not identified with our latent periodicity search algorithm. The main presumable reason for this was the inability of our techniques to identify periodicities interspersed with insertions and deletions. We designed the new latent periodicity search algorithm, which is capable of taking into account insertions and deletions. As a result, we identified many novel cases of latent periodicity peculiar to protein families. Possible origins of the periodic structure of these families are discussed. Summarizing, we presume that latent periodicity is present in a substantial portion of known protein families. The latent periodicity matrices and the results of Swiss-Prot scans are available from http://bioinf.narod.ru/del/.     

Latent periodicity of serine-threonine and tyrosine protein kinases and another protein families

We identified latent periodicity in catalytic domains of approximately 85% of serine/threonine and tyrosine protein kinases. Similar results were obtained for other 22 protein domains. We also designed the method of noise decomposition, which is aimed to distinguish between different periodicity types of the same period length. The method is to be used in conjunction with the cyclic profile alignment, and this combination is able to reveal structure-related or function-related patterns of latent periodicity. Possible origins of the periodic structure of protein kinase active sites are discussed. Summarizing, we presume that latent periodicity is the common property of many catalytic protein domains.     

Periodicity exhibited by Dirofilaria immitis microfilariae identified in dogs of Korea

Microfilarial periodicity of Dirofilaria immitis (the dog heartworm) was determined at two hr intervals for 72 consecutive hrs in 10 naturally infected war dogs, 3-9 years old, in Korea to facilitate harvest of the microfilariae for possible use in laboratory works and to elucidate further the periodicity of the microfilaria depending on geographic location. Although the periodicity had been observed as being low-grade nocturnal, maximal microfilarial counts were found at 21:00 hr and minimal at 11:00 hr, giving rise to an evident peak in fluctuation of the larval counts. This is the first record of the periodicity of the microfilariae identified as D. immitis in Korea.     

LEPSCAN--a web server for searching latent periodicity in DNA sequences

A web server for searching latent periodicity based on the method of modified profile analysis has been developed. This method allows searching latent periodicity in presence of insertions and deletions. During searching process, the periodicity classes are used which were found by us earlier for various groups of organisms. Period length belongs to the range 2-20 nt, not including the triplet periodicity. The results obtained are subjected to various filtration steps to ensure their statistical significance. Availability: The use of web server is free for non-commercial users. No registration is required. URL of the server is http://victoria.biengi.ac.ru/lepscan. Current software version is 1.06.     

Temperature change of the ripple structure in fully hydrated dimyristoylphosphatidylcholine/cholesterol multibilayers.

The ripple structure was studied as a function of temperature in fully hydrated dimyristoylphosphatidylcholine (DMPC)/cholesterol multibilayers using synchrotron x-ray small-angle diffraction and freeze-fracture electron microscopy. In the presence of cholesterol, the ripple structure appears below the pretransition temperature of pure DMPC multibilayers. In this temperature range the ripple periodicity is relatively large (25-30 nm) and rapidly decreases with increasing temperature. In this region, defined as region I, we observed coexistence of the P beta' phase and the L beta' phase. The large ripple periodicity is caused by the formation of the P beta' phase region in which cholesterol is concentrated and the L beta' phase region from which cholesterol is excluded. An increase in ripple periodicity also takes place in the narrow temperature range just below the main transition temperature. We define this temperature region as region III, where the ripple periodicity increases dramatically toward the main transition temperature. In region II, between regions I and III, the ripple periodicity decreases gradually with temperature. This behavior is quite similar to that of pure DMPC. Temperature-versus-ripple periodicity curves are parallel among pure DMPC and DMPCs with various cholesterol contents. We explain this behavior in terms of a model proposed by other workers.     

Classification analysis of a latent dinucleotide periodicity of plant genomes

The information decomposition (ID) method has been used for searching dinucleotide periodicities, including latent ones, in plant genomes. In nucleotide sequences of genomes of various plants from the GenBank database, 14766 sequences with a periodicity of two nucleotides have been found. Classification of the periodicity matrices of the detected DNA sequences has yielded 141 classes of dinucleotide periodicity. Since ID does not detect periodicities with nucleotide deletions or insertions, modified profile analysis (MPA) has been applied to the obtained classes to reveal DNA sequences with dinucleotide periodicities containing nucleotide deletions and insertions. Combined use of ID and MPA has permitted the detection of 80 396 DNA sequences with dinucleotide periodicities in the genomes of various plants. The biological role of dinucleotide periodicity in the detected sequences is discussed.     

ISOLATION AND PROPERTIES OF SECRETORY GRANULES FROM RAT ISLETS OF LANGERHANS : II. Ultrastructure of the Beta Granule

Beta granules isolated from rat islets of Langerhans and subjected only to phosphotungstic acid had, in negatively stained images, a 50-A periodicity. This periodicity was also observed in thin-section profiles of beta granules in intact cells. In shadowed preparations, the granules were spherical in shape and had irregular edges and surface structure. The presence of such a periodicity in the beta granule indicates that its matrix may be composed of a crystalline material.