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sequence complexity OF POLY(A) RNA FROM PHYSARUM-POLYCEPHALUM

WILHELM ROUXS ARCHIVES OF DEVELOPMENTAL BIOLOGY 1982年第6期191卷 341-347页

作者： BAECKMANN, A SAUER, HW UNIV WURZBURG INST ZOOL D-8700 WURZBURG FED REP GER

Poly(A) RNA from S phase, G2 phase and starved macroplasmodia of Physarum contain mRNA sequences which translated in vitro, yield similar patterns of polypeptides after fluorography. Reassociation of nick-translated DNA (Cot) allows the isolation of highly labeled single copy DNA which, after saturation hybridization with poly(A) RNA, gives values of 23% for growth and 17% for starvation. Homologous cDNA/poly(A) RNA hybridization reactions (Rot) indicate that 22-28% of the genome is transcribed during growth and 12% during starvation and that .apprx. 1/2 of the cDNA reacts with 0.1% of the genome and could represent 50-80 RNA species, each present in .apprx. 1000 copies per nucleus. Up to 25,000 different RNA species, 1-5 copies each per nucleus, are estimated to be present during growth and .apprx. 15,000 during starvation. Heterologous cDNA/poly(A) RNA hybridization reactions (Rot) indicate that the RNA sequences in S and G2 phase of the cell cycle are similar, with RNA sequences being more abundant in G2 phase. During starvation .apprx. 25% of the sequences present during growth cannot be detected and those sequences present during growth have become diluted during starvation.

关键词： Physarum Development RNA sequence complexity

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sequence complexity of disordered protein

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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2001年第1期42卷 38-48页

作者： Romero, P Obradovic, Z Li, XH Garner, EC Brown, CJ Dunker, AK Washington State Univ Dept Biochem & Biophys Sch Mol Biosci Pullman WA 99164 USA Washington State Univ Sch Elect Engn & Comp Sci Pullman WA 99164 USA

Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins. Compared to sequences from ordered proteins, these variously characterized intrinsically disordered segments and proteins, and also a collection of low-complexity sequences, typically have obviously higher levels of protein-specific subsets of the following amino acids: R, K, E, P, and S, and lower levels of subsets of the following: C, W, Y, I, and V. The Swiss Protein database of sequences exhibits significantly higher amounts of both low-complexity and predicted-to-be-disordered segments as compared to a non-redundant set of sequences from the Protein Data Bank, providing additional data that nature is richer in disordered and low-complexity segments compared to the commonness of these features in the set of structurally characterized proteins. Proteins 2001;42:38-48, (C) 2000 Wiley-Liss, Inc.

关键词： protein disorder sequence complexity neural network predictors

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Estimating the sequence complexity of a random oligonucleotide population by using in vitro thermal melting and C_ot analyses

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NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2005年第3期1卷 220-230页

作者： Kim, Jin-Woo Carpenter, Dylan P. Deaton, Russell Univ Arkansas Dept Biol & Agr Engn Fayetteville AR 72701 USA Univ Arkansas Dept Comp Sci & Comp Engn Fayetteville AR 72701 USA Univ Arkansas Cell & Mol Biol Grad Program Fayetteville AR 72701 USA

Randomly generated oligonucleotide populations have a high potential to serve as pools for selecting non-cross-hybridizing sequences, which are useful for nanoscale self-assembly and biological and biomedical applications, as well as for DNA computing applications. In this study a nonlinear kinetic model was developed for the complexity estimation of large unknown polynucleotide populations and was experimentally verified. The model was implemented to estimate the sequence complexity of the random 20 base-pair population after in vitro renaturation experiments. The kinetic behaviors of the random 20mers were also evaluated with in vitro thermal melting experiments. This study represents a step in realizing the potential of random oligonucleotides for DNA computing and nanoscale self-assembly applications for biology and medicine. (C) 2005 Elsevier Inc. All rights reserved.

关键词： Random oligonucleotides sequence complexity Thermal melting and C(o)t analysis Nano/biotechnology

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A look at the effect of sequence complexity on pressure destabilisation of DNA polymers

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BIOPHYSICAL CHEMISTRY 2015年 199卷 34-38页

作者： Rayan, Gamal Macgregor, Robert B., Jr. Univ Toronto Leslie Dan Fac Pharm Dept Pharmaceut Sci Toronto ON M5S 3M2 Canada

Our previous studies on the helix-coil transition of double-stranded DNA polymers have demonstrated that molar volume change (Delta V) accompanying the thermally-induced transition can be positive or negative depending on the experimental conditions, that the pressure-induced transition is more cooperative than the heat-induced transition [Rayan and Macgregor, J Phys Chem B 2005, 109, 15558-15565], and that the pressure-induced transition does not occur in the absence of water [Rayan and Macgregor, Biophys Chem, 2009, 144, 62-66]. Additionally, we have shown that Delta V values obtained by pressure-dependent techniques differ from those obtained by ambient pressure techniques such as PPC [Rayan et al. J Phys Chem B 2009, 113, 1738-1742] thus shedding light on the effects of pressure on DNA polymers. Herein, we examine the effect of sequence complexity, and hence cooperativity on pressure destabilisation of DNA polymers. Working with Clostridium perfringes DNA under conditions such that the estimated Delta V of the helix-coil transition corresponds to -1.78 mL/mol (base pair) at atmospheric pressure, we do not observe the pressure-induced helix-coil transition of this DNA polymer, whereas synthetic copolymers poly[d(A-T)] and poly[d(I-C)] undergo cooperative pressure-induced transitions at similar Delta V values. We hypothesise that the reason for the Jack of pressure-induced helix-coil transition of C perfringens DNA under these experimental conditions lies in its sequence complexity. (C) 2015 Elsevier B.V. All rights reserved.

关键词： DNA physical chemistry Helix-coil transition Pressure-denaturation Volume change sequence complexity

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sequence complexity of Polyadenylate Ribonucleic Acid in El Mouse Brain

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Psychiatry and Clinical Neurosciences 1986年第3期40卷 361-365页

作者： Hirayama, Eiichi Yamagami, Sakae Onishi, Hiroshi Chikami, Takashi Mori, Koichi Kawakita, Yukio Department of Neuropsychiatry Osaka City University Medical School Osaka Japan

Abstract: To elucidate the sequence complexity of polyadenylate messenger RNA [poly(A+)mRNA] regarding the seizure‐susceptible E1 mouse brain, the proportion of complexity was measured by saturation hybridization using a single‐copy DNA (scDNA) with excess RNA. At saturation, 3.81, 3.85 and 4.00% of scDNA hybridized with polysomal poly (A)mRNAs of El(+), EI(O) which had not been convulsed, and ddY (nonsusceptible) mice, respectively. The additive hybridization of a mixture of El(+) and ddY mouse mRNAs was 4.04%. The results suggest that there are considerable overlapping sets within the poly(A)mRNA sequences between the ddY and El mice, but the complexity of ddY mice mRNA is slightly larger than that of the El mice, whereas poly(A) heterogeneous nuclear RNA (hnRNA) hybridized with about 18% of scDNA in three strains of mice. Copyright © 1986, Wiley Blackwell. All rights reserved

关键词： El mouse brain heterogeneous nuclear RNA polyadenylate messenger RNA sequence complexity single‐copy DNA

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Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity

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PROTEIN SCIENCE 2024年第4期33卷 e4951-e4951页

作者： Mahapatra, Anindita Newberry, Robert W. Univ Texas Austin Dept Chem 105 E 24th St Austin TX 78712 USA

The Parkinson's-associated protein alpha-synuclein (alpha-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of alpha-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to alpha-syn LLPS, independent of fibrillation. Herein, using a combination of subtle missense mutations, we show that LLPS of alpha-syn is highly sensitive to its sequence complexity. In fact, we find that even a highly conservative mutation (V16I) that increases sequence complexity without perturbing physicochemical and structural properties, is sufficient to reduce LLPS by 75%;this effect can be reversed by an adjacent V-to-I mutation (V15I) that restores the original sequence complexity. A18T, a complexity-enhancing PD-associated mutation, was likewise found to reduce LLPS, implicating sequence complexity in alpha-syn pathogenicity. Furthermore, leveraging the differences in LLPS propensities among different alpha-syn variants, we demonstrate that fibrillation of alpha-syn does not necessarily correlate with its LLPS. In fact, we identify mutations that selectively perturb LLPS or fibrillation of alpha-syn, unlike previously studied mutations. The variants and design principles reported herein should therefore empower future studies to disentangle these two phenomena and distinguish their (patho)biological roles.

关键词： aggregation alpha-synuclein phase separation sequence complexity

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Rapid sequence Homology Assessment by Subsampling the Genome Space Using Difference Sets

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IEEE TRANSACTIONS ON INFORMATION THEORY 2010年第2期56卷 756-770页

作者： Brodzik, Andrzej K. Mitre Corp Bedford MA 01730 USA

Availability of DNA data is growing roughly at the rate specified by Moore's law. In many molecular biology applications this data must be compared with a reference sequence, either to establish similarity of genomes or to identify functionally homologous subsequences. Current approaches based on pair-wise sequence alignments are computationally expensive and often data dependent. To ameliorate this problem, alternative, less complex sequence comparison schemes, designed to capture the essential features of genomes, must be explored. In this work a new sequence comparison approach, based on difference set models, is proposed. These models are conceptually appropriate, as they quantify, in a certain sense, two key genome attributes: sequence complexity and symbol repetition. Moreover, it is shown that difference sets are abundant in bacterial genomes and that they coincide with homologous sequence segments. These findings motivate the construction of compact representations of DNA sequences in the difference set space. An alignment of these representations permits computationally efficient identification of differences between the DNA sequences. To illustrate the efficacy of the difference set approach, characterization of indels in closely related bacillus anthracis strains is performed, resulting in the discovery of two previously unreported collections of polymorphisms. In addition to these results, an open problem of extending the difference set approach to difference set and almost difference set families, for the analysis of more distant DNA sequences, is discussed.

关键词： Almost difference sets bacillus anthracis correlation cyclic difference sets DNA sequence alignment DNA sequence homology assessment DNA sequence markers phase-only matched filter random sequence repetition sequence complexity

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Guessing Individual sequences: Generating Randomized Guesses Using Finite-State Machines

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IEEE TRANSACTIONS ON INFORMATION THEORY 2020年第5期66卷 2912-2920页

作者： Merhav, Neri Technion IIT Andrew & Erna Viterbi Fac Elect Engn IL-32000 Haifa Israel

Motivated by earlier results on universal randomized guessing, we consider an individual-sequence approach to the guessing problem: in this setting, the goal is to guess a secret, individual (deterministic) vector x(n) = (x(1),..., x(n)), by using a finite-state machine that sequentially generates randomized guesses from a stream of purely random bits. We define the finite-state guessing exponent as the asymptotic normalized logarithm of the minimum achievable moment of the number of randomized guesses, generated by any finite-state machine, until x(n) is guessed successfully. We show that the finite-state guessing exponent of any sequence is intimately related to its finite-state compressibility (due to Lempel and Ziv), and it is asymptotically achieved by the decoder of (a certain modified version of) the 1978 Lempel-Ziv data compression algorithm (a.k.a. the LZ78 algorithm), fed by purely random bits. The results are also extended to the case where the guessing machine has access to a side information sequence, y(n) = ( y(1),..., y(n)), which is also an individual sequence.

关键词： Guessing exponent individual sequences sequence complexity finite-state machine Lempel-Ziv algorithm incremental parsing side information randomized guessing

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Pseudo-randomness and complexity of binary sequences generated by the chaotic system

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COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION 2011年第2期16卷 761-768页

作者： Nian-Sheng, Liu Jimei Univ Sch Comp Engn Xiamen 361021 Fujian Peoples R China

The pseudo-randomness and complexity of binary sequences generated by chaotic systems are investigated in this paper. These chaotic binary sequences can have the same pseudo-randomness and complexity as the chaotic real sequences that are transformed into them by the use of Kohda's quantification algorithm. The statistical test, correlation function, spectral analysis, Lempel-Ziv complexity and approximate entropy are regarded as quantitative measures to characterize the pseudo-randomness and complexity of these binary sequences. The experimental results show the finite binary sequences generated by the chaotic systems have good properties with the pseudo-randomness and complexity of sequences. However, the pseudo-randomness and complexity of sequence are not added with the increase of sequence length. On the contrary, they steadily decrease with the increase of sequence length in the criterion of approximate entropy and statistical test. The constraint of computational precision is a fundamental reason resulting in the problem. So only the shorter binary sequences generated by the chaotic systems are suitable for modern cryptography without other way of adding sequence complexity in the existing computer system. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Chaos sequence complexity Pseudo-randomness Chaotic binary sequence

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2007年第2期28卷 508-512页

作者： Li, Chun Wang, Aj-Hua Xing, Lili Bohai Univ Dept Math Jinzhou 121000 Peoples R China

In this article, we propose a relatively similar measure to compare RNA secondary structures. We first transform an RNA secondary structure into a special sequence representation. Then, on the basis of symbolic sequence complexity. we obtain the relative distance of RNA secondary structures. The examination of similarities/dissimilarities of a set of RNA secondary structures at the 3'-terminus of different viruses illustrates the utility of the approach. (C) 2006 Wiley Periodicals, Inc.

关键词： RNA secondary structure sequence complexity similarity virus

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