Kinds Of Sequences Research Articles

Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects.

The relationship between the level of repetitiveness in genomic sequences and genome size has been re-investigated making use of the rapidly growing database of complete eubacterial and archaeal genome sequences combined with the fragmentary but now large amount of data from eukaryotic genomes. Relative simplicity factors (RSFs), which measure the repetitiveness of sequences, were calculated and significantly simple motifs (SSMs), which identify the kinds of sequences that are repeated, were identified. A previously reported correlation between genome size and repetitiveness was confirmed, but it was shown that the higher RSFs seen in eukaryotic genomes also reflect a generally higher level of repetitiveness independent of genome size differences. Differences in genome size are responsible for about 10% of the variance in RSF seen between species. The spectrum of SSMs seen within a genome differed markedly within the eubacteria but less so in eukaryotes and, particularly, in archaea. Species with SSM spectra that differ from the norm tend also to have high RSFs for their genome size and to be pathogens that make use of repetitive sequences to avoid host defence responses. Some of the variance in repetitiveness seen in other species may therefore also reflect the action of selection, although other forces such as variation in the effectiveness of mechanisms for regulating slippage errors of replication, may also be important.

Quantitative biostratigraphy and species evolutionary sequence

Introduction of species evolutionary sequence into the quantitative biostratigraphy is a significant work, either for studying biologic evolution or for making stratigraphic correlation and reconstructing geologic history. The quantitative biostratigraphy is to determine biostratigraphic event sequences by using probabilistic analysis. The evolutionary sequence systematics can efficiently ascertain species evolutionary sequences. Two methods have been proposed to determine the sequence of species-disappearance events: (1) species extinction events can be closed by last occurrence events using quantitative biostratigraphic analysis; (2) the duration of a species may be approximately replaced by the duration of its parent species. To combine these two methods for determining the sequence of species disappearance is the best way up to now. A consulting standard sequence that consists of the speciation sequence of Permian waagenophylloid corals and the biostratigraphic event sequence of other important fossils in Permian is used as an example. The group spearman rank-correlation test is used to test the consulting standard sequence by comparing four types of calculations and two kinds of sequences and to find abnormal events. Based on the found abnormal events in the test, the consulting standard sequence is revised to deal with different conditions. Sequences of speciation and species-disappearance, and species duration are determined. Application of species evolutionary sequence to quantitative biostratigraphy can largely improve the quality of biostratigraphic event sequence. In stratigraphic correlation, furthermore, event sequences have higher precision than range biozones.

Genomic signal processing

Genomics is a highly cross-disciplinary field that creates paradigm shifts in such diverse areas as medicine and agriculture. It is believed that many significant scientific and technological endeavors in the 21st century will be related to the processing and interpretation of the vast information that is currently revealed from sequencing the genomes of many living organisms, including humans. Genomic information is digital in a very real sense; it is represented in the form of sequences of which each element can be one out of a finite number of entities. Such sequences, like DNA and proteins, have been mathematically represented by character strings, in which each character is a letter of an alphabet. In the case of DNA, the alphabet is size 4 and consists of the letters A, T, C and G; in the case of proteins, the size of the corresponding alphabet is 20. As the list of references shows, biomolecular sequence analysis has already been a major research topic among computer scientists, physicists, and mathematicians. The main reason that the field of signal processing does not yet have significant impact in the field is because it deals with numerical sequences rather than character strings. However, if we properly map a character string into, one or more numerical sequences, then digital signal processing (DSP) provides a set of novel and useful tools for solving highly relevant problems. For example, in the form of local texture, color spectrograms visually provide significant information about biomolecular sequences which facilitates understanding of local nature, structure, and function. Furthermore, both the magnitude and the phase of properly defined Fourier transforms can be used to predict important features like the location and certain properties of protein coding regions in DNA. Even the process of mapping DNA into proteins and the interdependence of the two kinds of sequences can be analyzed using simulations based on digital filtering. These and other DSP-based approaches result in alternative mathematical formulations and may provide improved computational techniques for the solution of useful problems in genomic information science and technology.

Localization of symbiotic clostridia in the mixed segment of the termite Nasutitermes takasagoensis (Shiraki).

Phylogeny and the distribution of symbiotic bacteria in the mixed segment of the wood-eating termite Nasutitermes takasagoensis (Shiraki) were studied. Bacterial 16S rRNA genes (rDNA) were amplified from the mixed segment of the gut by PCR, and two kinds of sequences were identified. The phylogenetic tree was constructed by neighbor-joining and maximum parsimony methods to identify symbionts harbored in the mixed segment. They are classified as low-G+C-content gram-positive bacteria and are most closely related to the genus Clostridium. The distribution of these bacteria throughout the whole gut was examined by PCR using specific primers, which suggested that they are confined to the mixed segment despite the presence of bacteria throughout the gut. In situ hybridization indicated that the symbiotic bacteria were localized to the ectoperitrophic space between the midgut wall and the peritrophic membrane in the mixed segment. Electron microscopy revealed the close association between these bacteria and the mesenteric epithelium, suggesting that they have some interactions with the gut tissue of termites.

Addition of signal leader sequences to the N-termini of olfactory receptor proteins enhances their expression in Xenopus oocytet.

Several recent papers have reported the difficulties in expressing olfactory receptor proteins (ORs) in heterologous systems, and proposed that some sequences in ORs have negative effects on their efficient expression. To obtain an efficient expression system of ORs, we modified N-terminal sequences of ORs through the addition of exogenous sequences. Three kinds of sequences, designated as 5HT, V, and VL, were used. 5HT and V corresponded to the signal leader (SL) sequences of 5HT 3R and VIPR, respectively. VL corresponded to the first extracellular region of VIPR containing the SL sequence and three potential asparagine- (Asn-) linked glycosylation sites. The myc epitope was also added to the C-termini of the sequences. Several ORs including 17 of rat, GUST43 of rat, Y1 of medaka, FOR1-3 of pufferfish, 47E of carp, and ODR-10 of nematode were subjected to the modifications, and the RNAs encoding modified ORs were injected into Xenopus oocytes. The membrane fraction of the oocytes were analyzed by Western blotting to examine the expression of the proteins. In the cases of ORs modified with 5HT and V, only ODR-10 and 47E, both of which have more than two Asn-linked glycosylation sites in their extracellular regions, were detected as the bands of predicted molecular weights. On the other hand, most of the ORs modified with VL showed the bands of predicted molecular weights. These results suggest that SL sequences together with potential Asn-linked glycosylation sites have positive effects on the expression of ORs in heterologous systems.

Some polynomials associated with up-down permutations

Up-down permutations, introduced many years ago by André under the name alternating permutations, were studied by Carlitz and coauthors in a series of papers in the 1970s. We return to this class of permutations and discuss several sets of polynomials associated with them. These polynomials allow us to divide up-down permutations into various subclasses, with the aid of the exponential formula. We find explicit, albeit complicated, expressions for the coefficients, and we explain how one set of polynomials counts up-down permutations of even length when evaluated at x=1, and of odd length when evaluated at x=2. We also introduce a new kind of sequence that is equinumerous with the up-down permutations, and we give a bijection.

Intraspecific variation in Cannabis sativa L. based on intergenic spacer region of chloroplast DNA.

We analyzed the nucleotide sequences of the non-coding region of chloroplast DNA: the intergenic spacer between trnL (UAA) 3'exon and trnF (GAA). Two kinds of sequence, "type-1" and "type-2," were detected in 33 populations of Cannabis sativa. The length of the "type-1" fragment was 354 bp. In contrast, the "type-2" fragment from 3 populations was 353 bp long, with only one base deletion compared to "type-1." The fragment length from Humulus lupulus was 353 bp with a 1-bp deletion, and ten 1-bp substitutions compared to the sequences from C. sativa "type-1." Furthermore, we could clearly identify differences between C. sativa and H. lupulus using single-strand conformation polymorphism of PCR products (PCR-SSCP) analysis.

SELF-ORGANIZATION AND CHAOS IN ATMOSPHERE

The paper contains considerations concerning two main phenomena in the dynamics of the atmosphere: self-organization and deterministic chaos. Coexisting, they can form the sequence modeling of living systems: Birth → Evolution → Death. Such kind of sequences are very universal in the atmosphere (atmospheric fronts, cyclones, etc.) Since deterministic chaos is investigated in literature intensively, in this paper the main attention is on the investigation of instabilities or phase transitions of the self-organization type. To this end the thermodynamics of the processes running far from equilibrium has been discussed. Two main instabilities of zonal, westerly flow have been investigated, applying the method of the Lapunov function. Following the procedure of nonequilibrium thermodynamics, sufficient conditions for the instabilities of zonal, westerly barotropic and baroclinic flows have been formulated. Applying the linear approximation to the boundary-value problem of the atmospheric flow in a layer heated below, the sequence of phenomena, from a heat conductivity, through the Benard convection, to a deterministic chaos, induced by the growing gradient of temperature, is presented.

Molecular modeling of closed circular DNA thermodynamic ensembles

Many modeling studies of supercoiled DNA are based on equilibrium structures from theoretical calculations or energy minimization. Since closed circular DNAs are flexible, it is possible that errors are introduced by calculating properties from a single minimum energy structure, rather than from a complete thermodynamic ensemble. We have investigated this question using molecular dynamics simulations on a low resolution molecular mechanics model in which each base pair is represented by three points (a plane). This allows the inclusion of sequence-dependent variations of tip, inclination, and twist. Three kinds of sequences were tested: (1) homogeneous DNA, in which all base pairs have the helicoidal parameters of an ideal, average B-DNA; (2) random sequence DNA; and (3) curved DNA. We examined the rate of convergence of various structural parameters. Convergence for most of these is slowest for homogeneous sequences, more rapid for random sequences, and most rapid for curved sequences. The most slowly converging parameter is the antipodes profile. In a plasmid with N base pairs (bp), the antipodes distance is the distance dij from base pair i to base pair j halfway around the plasmid, j = i + N/2. The antipodes profile at time tau is a plot of dij over the range i = 1, N/2. In a homogeneous plasmid, convergence requires that the antipodes profile averaged over time must be flat. Even in the small plasmids examined here, the average properties of the ensembles were found to differ from those of static equilibrium structures. These effects will be even more dramatic for larger plasmids. Further, average and dynamic properties are affected by both plasmid size and sequence.

Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells.

To analyze genomic changes resulting from double-strand break (DSB) repair, transgenic tobacco plants were obtained that carried in their genome a restriction site of the rare cutting endonuclease I-SceI within a negative selectable marker gene. After induction of DSB repair via Agrobacterium-mediated transient expression of I-SceI, plant cells were selected that carried a loss-of-function phenotype of the marker. Surprisingly, in addition to deletions, in a number of cases repair was associated with the insertion of unique and repetitive genomic sequences into the break. Thus, DSB repair offers a mechanism for spreading different kinds of sequences into new chromosomal positions. This may have evolutionary consequences particularly for plants, as genomic alterations occurring in meristem cells can be transferred to the next generation. Moreover, transfer DNA (T-DNA), carrying the open reading frame of I-SceI, was found in several cases to be integrated into the transgenic I-SceI site. This indicates that DSB repair also represents a pathway for the integration of T-DNA into the plant genome.

In vivo selection of Rous sarcoma virus mutants with randomized sequences in the packaging signal.

Retrovirus genomes contain a sequence at the 5' end which directs their packaging into virions. In Rous sarcoma virus, previous studies have identified important segments of the packaging signal, Psi, and support elements of a secondary-structure prediction. To further characterize this sequence, we used an in vivo selection strategy to test large collections of mutants. We generated pools of full-length viral DNA molecules with short stretches of random sequence in Psi and transfected each pool into avian cells. Resulting infectious virus was allowed to spread by multiple passages, so that sequences could compete and the best could be selected. This method provides information on the kinds of sequences allowed, as well as those that are most fit. Several predicted stem-loop structures in Psi were tested. A stem at the base of element O3 was highly favored; only sequences which maintained base pairing were selected. Two other stems, at the base and in the middle of element L3, were not conserved: neither base pairing nor sequence was maintained. A single mutation, G213U, was seen upstream of the randomized region in all selected L3 stem mutants; we interpret this to mean that it compensates for the defects in L3. Randomized mutations adjacent to G213 maintained the wild-type base composition but not its sequence. The kissing-loop sequence at end of L3, postulated to function in genome dimerization, was not required for infectivity but was selected for over time. Finally, a deletion of L3 was constructed and found to be poorly infectious.

Theoretical properties of LFSRs for built-in self test

Linear Feedback Shift-Registers have been studied for a long time as interesting solutions for error detection and correction techniques in transmissions. In the test domain, and principally in Built-In Self Test applications, they are often used as generators of pseudo-random test sequences. Conversely, their potential to generate prescribed deterministic test sequences is dealt within more recent works, and nowadays, allows the investigation of efficient test with a pseudo-deterministic BIST technique. Pseudo-deterministic test sequences are composed of both deterministic and pseudo-random test patterns and offer high fault coverage with a tradeoff between test length and hardware cost. In this paper, synthesis techniques for LFSRs that embed such kind of sequences are described.

Phylogenetic identification of the symbiotic hypermastigote Trichonympha agilis in the hindgut of the termite Reticulitermes speratus based on small-subunit rRNA sequence.

The phylogeny of a symbiotic hypermastigote Trichonympha agilis (class Parabasalia; order Hypermastigida) in the hindgut of the lower termite Reticulitermes speratus was examined by a strategy that does not rely on cultivation. From mixed-population DNA obtained from the termite gut, small subunit (16S-like) ribosomal RNA sequences were directly amplified by the polymerase chain reaction method using primers specific for eukaryotes. Comparative sequence analysis of the clones revealed two kinds of sequences, one from the termite itself and the other from a symbiotic protist. A fluorescent-labeled oligonucleotide probe for the latter sequence was designed and used in whole-cell hybridization experiments to provide direct visual evidence that the sequence originated from a larger hypermastigote in the termite hindgut, Trichonympha agilis. According to the phylogenetic trees constructed, the hypermastigote represented one of the deepest branches of eukaryotes. The hypermastigote along with members of the order Trichomonadida formed a monophyletic lineage, indicating that this hypermastigote and trichomonads shared a recent common ancestry.

5611341 External trigger imaging method and apparatus in magnetic resonance inspection apparatus

An external trigger method in a magnetic resonance inspection apparatus includes the steps of inputting collectively imaging control data including an imaging portion of a subject, the kind of sequences, a time interval between the sequences and the number of times of repetition of the sequences, executing a pre-processing sequence corresponding to the imaging sequence set to be first executed, and checking whether the time interval until the start of the imaging sequence to be next executed is set to a predetermined value. The imaging sequence is started by an external trigger when the time interval is set to the indefinite value. The imaging sequence is started after the passage of the time of the predetermined value when the time interval is set to the predetermined value.

Molecular modeling of closed circular DNA thermodynamic ensembles

Many modeling studies of supercoiled DNA are based on equilibrium structures from theoretical calculations or energy minimization. Since closed circular DNAs are flexible, it is possible that errors are introduced by calculating properties from a single minimum energy structure, rather than from a complete thermodynamic ensemble. We have investigated this question using molecular dynamics simulations on a low resolution molecular mechanics model in which each base pair is represented by three points (a plane). This allows the inclusion of sequence-dependent variations of tip, inclination, and twist. Three kinds of sequences were tested: (1) homogeneous DNA, in which all base pairs have the helicoidal parameters of an ideal, average B-DNA; (2) random sequence DNA; and (3) curved DNA. We examined the rate of convergence of various structural parameters. Convergence for most of these is slowest for homogeneous sequences, more rapid for random sequences, and most rapid for curved sequences. The most slowly converging parameter is the antipodes profile. In a plasmid with N base pairs (bp), the antipodes distance is the distance dij from base pair i to base pair j halfway around the plasmid, j = i + N/2. The antipodes profile at time t is a plot of dij over the range i = 1, N/2. In a homogeneous plasmid, convergence requires that the antipodes profile averaged over time must be flat. Even in the small plasmids examined here, the average properties of the ensembles were found to differ from those of static equilibrium structures. These effects will be even more dramatic for larger plasmids. Further, average and dynamic properties are affected by both plasmid size and sequence. © 1996 John Wiley & Sons, Inc.

Zoophycos distribution and sequence stratigraphy. Examples from the Jurassic and Cretaceous deposits of southeastern France

The trace fossil Zoophycos is characteristic in certain Jurassic and Cretaceous basinal deposits of southeastern France. These deposits are cyclic marl/limestone alternations, in which depositional sequences can easily be recognized. Two kinds of sequence have been studied: the marl/limestone couplet and the third-order sequence. Detailed observations show that Zoophycos has a particular position in the sequences. In the marl/limestone couplet, the trace is concentrated towards the upper part of the calcareous beds. The burrow is also present in the lower part of the beds and at the top of the underlying marls, but is less abundant. The same kind of burrow distribution occurs in the third-order sequences: Zoophycos is concentrated in the upper part of the calcareous bundles, which are interpreted as lowstand systems tracts, while it is totally lacking in the superimposed more marly sequence, which probably corresponds to the lower part of the transgressive systems tracts. The burrow may be present throughout the highstand systems tracts, which overlie the maximum flooding surfaces, but is less abundant. The particular distribution of Zoophycos is related to the fluctuations of certain environmental factors, the most important of which are the carbonate productivity, the sedimentation rate and the substrate consistency. Zoophycos can be proposed as a useful marker of sequence boundaries and of the transgressive surfaces in distal deposits where other signals for sequence analysis are often lacking.

Transgenic models of HTLV-I mediated disease and latency.

HTLV-I infection is the etiologic agent for a form of adult T cell leukemia (ATLL) (HINUMA et al. 1981; POIESZ et al. 1980; ROBERT et al. 1982; YOSHIDA et al. 1984). A peculiarity of this virus is its long incubation period prior to the development of malignancy and the low percentage of patients who eventually develop disease. Studies in Japan and Jamaica indicate that the latency period may range up to 40 years with a lifetime incidence of ATLL of 2%–4% in seropositive individuals (MURPHY et al. 1989). In vitro, HTLV-I transforms human lymphocytes but carries no clearly identifiable cellular oncogene-like homolog. In addition, no site-specific integration pattern has been identified (SEIKI et al. 1984). Circumstantial data has implicated the HTLV-I tax gene in transformation. This gene encodes a 40 kDa protein with at least partial localization to the nucleus. It is a potent transcriptional activator of its own promoter and those of numerous other oncogenes and cytokines (reviewed Smith and Greene 1991; Yoshida 1994). Tax is always retained but usually not expressed in ATLL, whereas deletions in other portions of the viral genome are common in transformed cells. Tax alone has been shown to transform fibroblasts in vitro (Pozzatti et al. 1990; Tanaka et al. 1990). Nevertheless, most attempts to directly transform human T cells with tax alone have failed. In vitro studies have demonstrated that Tax can activate the promoters of the interleukin-2 (IL-2) receptor (IL-2R) α chain, granulocyte/macrophage colony- stimulating factor (GM-CSF), fos, Platelet-derived growth factor (PDGF), IL-6, vimentin, nerve growth factor (NGF), transforming growth factor-β (TGF-β), HIV long terminal repeat (LTR), as well as its own LTR (reviewed Gitlin et al. 1993). It thus may have pleiomorphic effects on cell growth and inflammation. Mutational analysis of the target sequences of Tax in these promoters have revealed two kinds of sequences, an ATF-like, which occurs in the HTLV-I LTR and in fos, and an NF-KB-like sequence, which occurs in the HIV LTR and in the IL-2R (reviewed in Smith and Greene 1991; Nerenberg 1992; Gitlin et al. 1993).KeywordsLong Terminal RepeatTransgenic ModelSerum Response FactorTropical Spastic ParaparesisFibroblastic TumorThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Cross-correlation of p-ary GMW sequences

The cross-correlation function of p-ary (p prime) GMW sequences is investigated. The well-known m-sequences are incorporated in these sequences. GMW sequences also have the two-level autocorrelation function, but their linear span may be much larger than those of m sequences. The calculation of the cross-correlation function of GMW sequences is reduced to the cross-correlation of the m-sequences because many results on this kind of sequence are known. In the literature, only the cross-correlation function of an m sequence with a GMW sequence has been known up to now. >

Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences

Compression and reconstruction of spatially invariant linearly additive image sequences with suppression of noise and undesired features

New results are presented for an important class of image sequences characterized as being spatially invariant and linearly additive based on their image-formation processes. In these kinds of sequences, all features are positionally invariant in each image of a given sequence but have varying gray-scale properties. Examples of appropriate image sequences include multispectral image sequences and certain temporal image sequences. Features associated with different image-formation processes generally will have unique signatures describing the manner in which they vary over the sequence that can be used to generate linear filters for isolating selected image-formation processes or for performing data compression. Starting with an explicit mathematical model, techniques are presented for generating optimal filters using simultaneous diagonalization to suppress noise and undesired image-formation processes and to provide data compression.