Cyclic morbidity of certain natural foci infections in the Russian Federation

A special search program for finding out hidden periodicity was used; such program made it possible to put in order the apparently chaotic sequence of numerical data that are summed up to form the resulting curve, the latter reflecting the actual dynamics of the epidemic process. The cyclic character of morbidity in tick-borne encephalitis, hemorrhagic fever with the renal syndrome (HFRS), tularemia and leptospirosis among the population of Russia for the last 45-54 years was revealed. In tick-borne encephalitis cycles lasting 17-18 years with secondary wave having the period of 3-4 years were found out. In HFRS the main cycle lasts for 16 years and has secondary rises every 3-4 years. In tularemia the main cycles last for 17 years; secondary rises and drops in morbidity were also found to occur every 3-4 years. In leptospirosis regular rises and drops in morbidity were found to occur every 4-5 years.     

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.     

Dynamics of typhoid-paratyphoid infection morbidity in Chimkent Province

The study of the time course of typhoid-paratyphoid infections in the Chimkent region for the period of 1944-1979 has revealed the periodicity of their rises (falls) repeating every 2-4 years. Since 1964 the tendency towards the decrease of morbidity has been observed. The annual rate of this decrease is 4.9%. Periodic changes in the annual level of typhoid-paratyphoid infections do not depend on the temperature of the air and the seasonal number of winged flies. There is a pronounced direct correlation between the annual morbidity level and the frequency of summer precipitations, this correlation being more pronounced during the first 2 summer months.     

周期性羽化昆虫形成机制

当昆虫类群表现为长生命周期k(k > 1)年时,成虫的羽化表现为非周期性、周期性和过渡周期性3种形式。非周期性即为成虫每年均羽化,周期性即为成虫每k年才羽化1次,过渡周期性为非周期昆虫逐渐进化为羽化周期性的必经阶段,不同年份羽化的同生群在密度上产生了显著差异,形成了小同生群和优势同生群。自然界中表现出完全羽化周期性的昆虫种类是较少的,但由于其高种群密度的成虫同步性羽化现象,对比非周期性昆虫更易暴发成灾。为明确周期性昆虫演化进程并为林区虫害防控提供理论指导,总结了周期性昆虫的种类和生活特性,不同年间的气候异质性、自然灾害、扩散到未分布区域、天敌、种间和种内竞争等因素均有可能成为过渡周期现象形成的最初驱动力,生活史延长、寄主-天敌互作、低温驱动效应、天敌不敏感-捕食者饱足效应、种间和种内竞争等是促使昆虫羽化周期性形成的可能机制。在林区管理实践中,应提前评估害虫羽化周期性产生的趋势和程度。当成虫表现出完全羽化周期性,应在集中羽化年份内采取见效快的综合防控策略,降低唯一同生群密度至经济阈值以下。当成虫表现出过渡周期性,应加大优势同生群防治力度、降低小同生群防治频率,以及采取天敌林间释放和保育技术以平衡天敌对目标害虫的不同发育阶段种群的控制作用大小,遏制或减缓天敌-寄主互作驱动下的周期性演化进程,逐渐实现由过渡周期阶段向非周期性的逆转。当成虫表现出非周期性,应减少专化性天敌的释放和针对害虫特定阶段的防治措施使用频率,优先选择作用于所有发育阶段且致死率不存在显著差异的防治手段,避免因人为干扰产生的周期性演化和进一步的成灾。     

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.     

The Informational Concept of Searching for Periodicity in Symbol Sequences

A method of informational decomposition has been developed, allowing one to reveal hidden periodicity in any symbol sequence. The informational decomposition is calculated without conversion of a symbol sequence into a numerical one, which facilitates finding periodicities in a symbol sequence. The method permits introducing an analog of the autocorrelation function of a symbol sequence. The method developed by us has been applied to reveal hidden periodicities in nucleotide and amino acid sequences, as well as in different poetical texts. Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed.     

Periodicity of exonuclease III digestion of chromatin and the pitch of deoxyribonucleic acid on the nucleosome

Exonuclease III has previously been shown to pause about every 10 nucleotides along the 3' strands while it invades the nucleosome core. Here, the exact periodicity of this digestion, i.e., the spacing of the pauses, was determined. Results showed that the exonuclease digests the first 20 nucleotides at the edge of the nucleosome core with a periodicity of approximately 11 nucleotides; in contrast, DNA closer to the center of the particle is digested with a smaller periodicity of about 10 nucleotides. These figures differ from the known periodicity of DNase I digestion, approximately 10 and 10.5 nucleotides at the edge and in the center of the nucleosome, respectively. Moreover, as shown by sedimentations in sucrose gradients, the structure of the nucleosome does not appear to be significantly altered by the gradual destruction of its DNA moiety by the exonuclease. Such stability of the nucleosome, along with other complementary observations, indicates that the transition in the digestion periodicity of the exonuclease may not be the consequence of a structural rearrangement of the particle upon trimming. This transition may rather be ascribed to the properties of the native nucleosome and to the intrinsic mechanism of action of the enzyme. Finally, evidence is presented which suggests that the exonuclease 10-nucleotide periodicity of digestion of the inner region of the nucleosome reflects a 10 base pair/turn pitch of the DNA in that region.     

Latent Periodicity of Serine/Threonine and Tyrosine Protein Kinases and Other Protein Families

A method of noise decomposition has been developed. This method allows for the identification of a latent periodicity with symbol insertions and deletions that is specific for all or most amino acid sequences belonging to the same protein family or protein domain. The latent periodicity has been identified in catalytic domains of 85% of serine/threonine and tyrosine protein kinases. Similar results have been obtained for 22 other protein families. The possible role of latent periodicity in protein families is discussed.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 420–436.Original Russian Text Copyright © 2005 by Laskin, Kudryashov, Skryabin, Korotkov.     

First maturity and spawning periodicity of hatchery‐origin pallid sturgeon in the upper Missouri River above Fort Peck Reservoir,Montana

The pallid sturgeon Scaphirhynchus albus conservation propagation program has augmented declining wild populations since the 1990s and the older age classes of hatchery‐origin fish are beginning to reach sexual maturity in the wild. Currently, the majority of the information available on the age and size at first maturity and spawning periodicity for pallid sturgeon in the upper basin is from captive hatchery‐origin pallid sturgeon (i.e. age and size at first maturity and spawning periodicity) or from wild pallid sturgeon artificially spawned in the propagation program (i.e. spawning periodicity). The purpose of this study was to document age and size at first maturity and spawning periodicity of known age hatchery‐origin pallid sturgeon that have reached maturity in the wild. Radio‐tagged pallid sturgeon in the upper Missouri River upstream of Fort Peck Reservoir were serially sampled in the early‐spring over multiple years and assigned to reproductive classifications each year based on sex‐steroid concentrations. The youngest reproductively‐active male hatchery‐origin pallid sturgeon sampled was 14.5 years old and the youngest female was 18. Hatchery‐origin males were observed having annual (N = 3) and biennial (N = 2) reproductive cycles. The observed spawning periodicity was similar to what has been reported elsewhere for the species. The youngest mature fish in this study are older and larger than what has been reported for those retained in captivity, indicating that body size alone is not a reliable predictor of maturity for pallid sturgeon.     

Developing a mathematical method to search for latent periodicity in protein amino-acid sequences with deletions and insertions

A mathematical method has been developed in order to search for latent periodicity in protein amino-acid and other symbolical sequences using dynamic programming and random matrices. The method allows the detection of the latent periodicity with insertions and deletions at positions that are unknown beforehand. The developed method has been applied to search for the periodicity in the amino-acid sequences of several proteins and in the euro/dollar exchange rate since 2001. The presence of a long period with insertions and deletions in amino-acid sequences is shown. The period length of seven amino acids is observed in the proteins that contain supercoiled regions (a coiled-coil structure) as well as of six, five, or more amino acids. The existence of the period length of 6 and 7 days, as well as 24 and 25 h in the analyzed financial time series is observed; note that this periodicity is detectable only for insertions and deletions. The causes that underlie the occurrence of the latent periodicity with insertions and deletions in amino-acid sequences and financial time series are discussed.     

Timing of mutation in hemagglutinins from influenza A virus by means of unpredictable portion of amino-acid pair and fast Fourier transform

In this study, we calculate the unpredictable portion of amino-acid pairs, which has been developed by us over the last several years, of 1201 hemagglutinins from influenza A viruses dated from 1918 to 2004 in order to compare them with respect to subtypes, species, and years. After noticing the fluctuations of unpredictable portion along the time course, we use the fast Fourier transform to find the mutation periodicity of hemagglutinins. Then we estimate our position at the current cycle of hemagglutinin evolutionary process to determine how many years remain before the next outbreak of influenza and bird flu. Finally, we use the trend line and channel to outlook the hemagglutinins for the next half a century. As our study covers almost all the full-length amino-acid sequences of hemagglutinins from various influenza A viruses, the conclusion will be valid for years until the number of hemagglutinins in protein databank will be significantly increased.     

DEAMINATION OF DEOXYCYTIDINE AND 5-METHYLDEOXYCYTIDINE IN DEVELOPING ANTHERS OF LILIUM LONGIFLORUM (VAR. CROFT)

A study has been made of developmental variations in anthers of Lilium longiflorum with respect to the deamination of deoxycytidine and 5-methyldeoxycytidine. Although a periodicity of enzymatic activities surrounding the mitotic cycle has been found, the over-all evidence is against the significance of such periodicity to chromosome duplication. On the basis of evidence obtained a distinction has been drawn between enzyme systems functioning in a broad supporting role and those immediately tied to morphogenetic events.     

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.     

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 Gen-Bank database, 14 766 sequences with a periodicity of two nucleotides have been found at a high level of statistical significance. 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.     

The Locally Optimal Method of Cyclic Alignment to Reveal Latent Periodicities in Genetic Texts: the NAD-binding Protein Sites

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying apparent regularity in their secondary structures, not being obvious at the primary structure level.     

The locally optimal method of cyclic alignment to reveal latent periodicities in genetic texts. The NAD-binding protein sites

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying the apparent regularity in their secondary structures, not being obvious at the primary structure level.     

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.     

Multi-Annual Fluctuations in Reconstructed Historical Time-Series of a European Lobster (Homarus gammarus) Population Disappear at Increased Exploitation Levels

Through the history of ecology, fluctuations of populations have been a dominating topic, and endogenous causes of fluctuations and oscillations have been recognized and studied for more than 80 years. Here we analyzed an historical dataset, covering more than 130 years, of European lobster (Homarus gammarus) catches. The data shows periodic fluctuations, which are first dampened and then disappear over time. The disappearance of the periodicity coincided with a substantial increase in fishing effort and the oscillations have not reappeared in the time series. The shifting baseline syndrome has changed our perception of not only the status of the stock, but also the regulating pressures. We describe the transition of a naturally regulated lobster population into a heavily exploited fisheries controlled stock. This is shown by the incorporation of environmental and endogenous processes in generalized additive models, autocorrelation functions and periodicity analyses of time-series.     

TSH circadian secretions in aged men and effect of phosphatidylserine treatment

In 20 euthyroid aged men (from 65 to 85 years of age) no significant circadian periodicity of thyrotropin (TSH) secretion has been shown by the population mean cosinor method. At the end of a period of 30 days of hospitalization the cosinor evaluation of TSH secretion showed a restored highly significant (p less than 0.001) circadian rhythmicity in phosphatidylserine (PS) (400 mg/daily) treated group (10 aged subjects). By contrast, hospitalization seems to further deteriorate the periodicity of the hormone secretion in 10 placebo-treated subjects.