Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment

*_Background:_* The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (_Leptonychotes weddellii_) genes.

*_Results:_* Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation. 

*_Conclusion:_* In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.
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Comprehensive analysis of circadian periodic pattern in plant transcriptome

Abstract Background Circadian rhythm is a crucial factor in orchestration of plant physiology, keeping it in synchrony with the daylight cycle. Previous studies have reported that up to 16% of plant transcriptome are circadially expressed. Results Our studies of mammalian gene expression revealed circadian baseline oscillation in nearly 100% of genes. Here we present a comprehensive analysis of periodicity in two independent data sets. Application of the advanced algorithms and analytic approached already tested on animal data reveals oscillation in almost every gene of Arabidopsis thaliana. Conclusion This study indicates an even more pervasive role of oscillation in molecular physiology of plants than previously believed. Earlier studies have dramatically underestimated the prevalence of circadian oscillation in plant gene expression.</p

Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway

*Background*&#xd;&#xa;It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. &#xd;&#xa;&#xd;&#xa;*Results*&#xd;&#xa;We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different regions within the 3&#x2019; end of the last exon. We demonstrate that in murine brown adipose tissue two downstream 3&#x2019; probe sets experience circadian baseline oscillation in counter-phase to the upstream probe set. Such differences in expression patterns are a telltale sign of alternative splicing within the last exon of SOCS3. In contrast, all three probe sets oscillated in a common phase in murine liver and white adipose tissue. This suggests that the regulation of SOCS3 expression in brown fat is tissue specific. Another component of the signaling pathway, Janus kinase (JAK), is directly regulated by SOCS and has alternative transcript probe sets oscillating in counter-phase in a white adipose tissue specific manner.&#xd;&#xa; &#xd;&#xa;*Conclusion*&#xd;&#xa;We hypothesize that differential oscillation of alternative transcripts may provide a mechanism to maintain steady levels of expression in spite of circadian baseline variation

Deterministic Chaos in Digital Cryptography

This thesis studies the application of deterministic chaos to digital cryptography. Cryptographic systems such as pseudo-random generators (PRNG), block ciphers and hash functions are regarded as a dynamic system (X, j), where X is a state space (Le. message space) and f : X -+ X is an iterated function. In both chaos theory and cryptography, the object of study is a dynamic system that performs an iterative nonlinear transformation of information in an apparently unpredictable but deterministic manner. In terms of chaos theory, the sensitivity to the initial conditions together with the mixing property ensures cryptographic confusion (statistical independence) and diffusion (uniform propagation of plaintext and key randomness into cihertext). This synergetic relationship between the properties of chaotic and cryptographic systems is considered at both the theoretical and practical levels: The theoretical background upon which this relationship is based, includes discussions on chaos, ergodicity, complexity, randomness, unpredictability and entropy. Two approaches to the finite-state implementation of chaotic systems (Le. pseudo-chaos) are considered: (i) floating-point approximation of continuous-state chaos; (ii) binary pseudo-chaos. An overview is given of chaotic systems underpinning cryptographic algorithms along with their strengths and weaknesses. Though all conventional cryposystems are considered binary pseudo-chaos, neither chaos, nor pseudo-chaos are sufficient to guarantee cryptographic strength and security. A dynamic system is said to have an analytical solution Xn = (xo) if any trajectory point Xn can be computed directly from the initial conditions Xo, without performing n iterations. A chaotic system with an analytical solution may have a unpredictable multi-valued map Xn+l = f(xn). Their floating-point approximation is studied in the context of pseudo-random generators. A cryptographic software system E-Larm ™ implementing a multistream pseudo-chaotic generator is described. Several pseudo-chaotic systems including the logistic map, sine map, tangent- and logarithm feedback maps, sawteeth and tent maps are evaluated by means of floating point computations. Two types of partitioning are used to extract pseudo-random from the floating-point state variable: (i) combining the last significant bits of the floating-point number (for nonlinear maps); and (ii) threshold partitioning (for piecewise linear maps). Multi-round iterations are produced to decrease the bit dependence and increase non-linearity. Relationships between pseudo-chaotic systems are introduced to avoid short cycles (each system influences periodically the states of other systems used in the encryption session). An evaluation of cryptographic properties of E-Larm is given using graphical plots such as state distributions, phase-space portraits, spectral density Fourier transform, approximated entropy (APEN), cycle length histogram, as well as a variety of statistical tests from the National Institute of Standards and Technology (NIST) suite. Though E-Larm passes all tests recommended by NIST, an approach based on the floating-point approximation of chaos is inefficient in terms of the quality/performance ratio (compared with existing PRNG algorithms). Also no solution is known to control short cycles. In conclusion, the role of chaos theory in cryptography is identified; disadvantages of floating-point pseudo-chaos are emphasized although binary pseudo-chaos is considered useful for cryptographic applications.Durand Technology Limite

Permutation test for periodicity in short time series data

Abstract Background Periodic processes, such as the circadian rhythm, are important factors modulating and coordinating transcription of genes governing key metabolic pathways. Theoretically, even small fluctuations in the orchestration of circadian gene expression patterns among different tissues may result in functional asynchrony at the organism level and may contribute to a wide range of pathologic disorders. Identification of circadian expression pattern in time series data is important, but equally challenging. Microarray technology allows estimation of relative expression of thousands of genes at each time point. However, this estimation often lacks precision and microarray experiments are prohibitively expensive, limiting the number of data points in a time series expression profile. The data produced in these experiments carries a high degree of stochastic variation, obscuring the periodic pattern and a limited number of replicates, typically covering not more than two complete periods of oscillation. Results To address this issue, we have developed a simple, but effective, computational technique for the identification of a periodic pattern in relatively short time series, typical for microarray studies of circadian expression. This test is based on a random permutation of time points in order to estimate non-randomness of a periodogram. The Permutated time, or Pt-test, is able to detect oscillations within a given period in expression profiles dominated by a high degree of stochastic fluctuations or oscillations of different irrelevant frequencies. We have conducted a comprehensive study of circadian expression on a large data set produced at PBRC, representing three different peripheral murine tissues. We have also re-analyzed a number of similar time series data sets produced and published independently by other research groups over the past few years. Conclusion The Permutated time test (Pt-test) is demonstrated to be effective for detection of periodicity in short time series typical for high-density microarray experiments. The software is a set of C++ programs available from the authors on the open source basis.</p

Proton Beam Emittance Growth in Run5 and Run6

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Formation of knowledge for agent technologies information security

It describes the content of the methodological basis of agent technologies. The problems of intelligent information agents in information security monitoring system. Obtained formalization of a system for the expansion of the methodological basis of agent technologies in information securityОписано содержание методологического базиса агентных технологий. Сформулированы задачи интеллектуальных информационных агентов в системе мониторинга информационной безопасности. Выделена система формализаций для расширения методологического базиса агентных технологий при обеспечении информационной безопасност

Creating a profile competence in information security in the research study

It formulated the main goal of the research practices in the magistracy in «Information Security». Defined profile professional competence. Submitted content requirements for knowledge and skills of students upon successful completion of practiceСформулирована основная цель научно-исследовательской практики в магистратуре по направлению «Информационная безопасность». Определены профильные профессиональные компетенции. Представлено содержание требований к знаниям и умениям студента после успешного завершения практик