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Results for “reduced representation sequencing”

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PubMed2001

Silencing of HTR1B and reduced expression of EDN1 in human lung cancers, revealed by methylation-sensitive representational difference analysis.

Aberrantly hypermethylated genes in human lung cancers were searched for by a genome scanning technique, methylation-sensitive-representational difference analysis (MS-RDA). A total of 59 DNA fragments were isolated as those methylated more heavily in either/both of two lung squamous cell carcinoma cell lines, EBC-1 and LK-2, than in a primary culture of normal human bronchial epithelium, NHBE. Thirty-four DNA fragments, whose hypermethylation was confirmed in primary squamous cell carcinomas, were sequenced. By database searches, 17 of them were shown to be located within 2 kb of putative CpG islands, and five of the 17 DNA fragments had transcribed regions of known genes in their vicinities. By RT-PCR of the five genes in the carcinoma cell lines and NHBE, decreased expression of HTR1B (5-hydroxytryptamine receptor 1B) and EDN1 (endothelin-1) was observed. Sequencing after bisulfite modification showed that the CpG island in the promoter region of HTR1B was hypermethylated, while that of EDN1 was not. Demethylation and re-expression of HTR1B were observed after treatment of LK-2 cells with 5-aza-2'-deoxycytidine. In primary lung cancers, decreased mRNA expression of HTR1B was observed in 11 of 20 cases, and that of EDN1 was in 16 of 20 cases. Immunohistochemical analysis of endothelin-1 confirmed that its immunoreactivity was reduced in squamous cell carcinoma cells compared with that in normal bronchial epithelial cells. Considering that endothelin-1 induces apoptosis in melanoma cells and that silencing of endothelin receptor B is observed in prostate cancers, its reduced expression was speculated to confer a growth advantage to lung cancer cells. MS-RDA was shown to isolate DNA fragments that are hypermethylated and silenced, such as HTR1B, and those whose expressions are altered and the methylation statuses outside the promoter region are altered, such as EDN1.

Aged↗

PubMed1995

Protocol care for hypertension supported by an expert system.

1. PURPOSE. Hypertension if one of the major prevalent diseases that influences the prognosis of chronic diseases. Primary care should attract much attention in the management of hypertension. The management of hypertension includes not only the use of antihypertensiove drugs, but also the modification of unhealthy lifestyles. Multi-dimensional approaches are required for the management of hypertensive patients. This system supports the standard protocol care for hypertensive patients and the database for clinical epidemiology. 2. DESIGN CONSIDERATIONS. This system has several functions that support the appropriate management of hypertensive patients. The first one is clinical database management. The second is the evaluation of the clinical conditions in hypertension. The third is the decision support system for the selection of treatments for hypertension. 3. SYSTEM DESCRIPTION. This system administers the clinical database, which includes symptoms and signs, laboratory data, and prescriptions. The database deals with the temporal course of the patient's status. The system that evaluates the patient's condition and the decision support system have some knowledge bases. The knowledge bases consist of the evaluation of the patient's condition, the appropriate selection of laboratory examinations, and suggestions for treatments, which involve a life-style modification and the proper prescription of medication. 4. STATUS REPORTS. The relational database was developed for handling the patient's records. These records were displayed on the terminal according to the temporal sequence. The graphical representations of the medical data were displayed in order to understand the patient's status. 5. LESSON LEARNED. This kind of protocol care system is expected to support the proper medical care of patients. Excess medications and laboratory examinations will be excluded under the protocol care, thus reducing unnecessary medical expense. The system will enhance the randomized clinical trials that verify the effects of the treatments. Violation of the protocol care is treated according to the several levels. 6. FUTURE PLANS. This system will be introduced to the occupational health care fields. The efficacy of improving the clinical quantity, and the effect of reducing the medical budget concerning hypertension will be verified.

Clinical Protocols↗

PubMed2001

Pruned median networks: a technique for reducing the complexity of median networks.

Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not tree-like. In these cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins.

Base Sequence↗

PubMed2026

Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome.

High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared to a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.

FISH↗

PubMed2006

Symbolic dynamics of coupled map lattices.

We present a method to reduce the [FORMULA: SEE TEXT] dynamics of coupled map lattices (CMLs) of N invertibly coupled unimodal maps to a sequence of N-bit symbols. We claim that the symbolic description is complete and provides for the identification of all fixed points, periodic orbits, and dense orbits as well as an efficient representation for studying pattern formation in CMLs. We give our results for CMLs in terms of symbolic dynamical concepts well known for one-dimensional chaotic maps, including generating partitions, Gray orderings, and kneading sequences. An example utilizing coupled quadratic maps is given.

Journal Article↗

PubMed1989

Visual control of movement patterns and the grammar of action.

In this experiment adult subjects copied three types of material (letters, reversed letters and geometric shapes) with and without sight of the hand and the writing trace. Without vision the number of movement segments decreased and the sequence and direction of movements were altered. This means that subjects did not use a fixed stored representation to produce items nor did they obey the rules of Goodnow and Levine's (1973) grammar of action. When spatial location is made more difficult by the removal of vision, movement production is simplified to reduce the number of relocations required. The use of consistent directions of movement depends on the ability to use visual control of spatial location.

Form Perception↗

PubMed2005

Design considerations for array CGH to oligonucleotide arrays.

BACKGROUND: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. METHODS: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. RESULTS: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. CONCLUSION: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.

Aneuploidy↗

PubMed1994

The prevention of spinal injuries in rugby football.

The incidence of injuries to the spinal cord sustained at rugby in South Africa, New Zealand and Australia is reviewed. Ninety-seven injuries seen at Stoke Mandeville Hospital at the National Spinal Injuries Centre (NSIC) between 1956 and 1993 are analysed in detail. There were 93 accidents at rugby union, two at American football and two at rugby league. The injuries were of the cervical spine apart from four hysterics and one thoracic injury. The thoracic injury occurred after the game when the player fell downstairs. The injuries were analysed according to the mechanism of injury, the neurological condition, the causation, the standard of the player and the position in the field. The injuries caused were the result of force being applied to the skull which was transmitted to the cervical spine resulting in injury to the cervical cord. As a result of this research, representations were made to the appropriate authorities and changes in the laws were made. As a result of these law changes there has been a dramatic reduction in the overall number of injuries and the elimination of the injury from the loose scrum. This paper discusses the historical sequence of how these preventative measures came about to reduce the incidence of injuries and the legal implications whereby the authors took part in two law suits. The legal consequences are analysed in detail.

Adolescent↗

PubMed2001

LINUCS: linear notation for unique description of carbohydrate sequences.

The use of proteomics databases has become indispensable for daily work of molecular biologists, but this situation has not yet been achieved for carbohydrate applications. One obvious reason is that existing data collections are only rarely annotated and no cross-linking to other resources exists. The existence of a generally accepted linear, canonical description for carbohydrates which can be readily processed by computers will enable efficient automatic cross-linking of distributed carbohydrate data collections by serving as a unique and unambiguous database access key. Various possibilities to derive a canonical notation are discussed. They can be divided into attempts that require structure description alone and alternatives that profit from the fact that a preferred graph direction (non-reducing to reducing end) exists within the structure. To open a fruitful discussion among glycoscientists a possible solution is presented where the reducing monosaccharide unit is selected as graph root and linkage information is used to define the priority of the various branches. A Web interface (http://www.dkfz.de/spec/linucs/) has been created that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form.

Algorithms↗

PubMed1995

A kinetic model for subtractive hybridization.

Nucleic acid sequences that differ in abundance between two populations (target sequences) can be cloned by multiple rounds of subtractive hybridization and amplification by PCR. These sequences can be cDNAs representing up-regulated mRNAs, or genomic DNAs from deletion mutants. We have derived an equation that describes the recovery of such sequences, and have used this to simulate the outcome of up to 10 rounds of subtractive hybridization and PCR amplification. When the model was tested by comparing its predictions with the published results from genomic and cDNA subtractions, the predictions of the model were generally in good agreement with the published data. We have modelled the outcomes of genomic subtractions, for a variety of genomes, and have used it to compare various strategies for enriching targets. The model predicts that for genomes of less than 5 x 10(8) bp, deletions of as small as 1 kbp should represent > 99% of the DNA after three to six rounds of hybridization (depending on the enrichment procedure). As genomes increase in size, the kinetics of hybridization become an important limiting factor. However, even for genomes as large as 3 x 10(9) bp, it should be possible to isolate deletions of 5 kbp using the appropriate conditions. These simulations suggest that such methods offer a realistic alternative to chromosome walking for identifying genomic deletions for which there are known phenotypes, thereby considerably reducing time and effort. For cDNA subtractive hybridization, the model predicts that after six rounds of hybridization, sequences that do not differ in abundance between the tester and driver populations (the background) will represent < 1% of the subtracted population, and even quite modestly upregulated cDNAs should be successfully enriched. Where several up-regulated cDNAs are present, the predicted final representation is dependent on both the initial abundance and the degree of up-regulation.

Animals↗

PubMed1992

Privileged access by irrelevant speech to short-term memory: the role of changing state.

Memory for visually presented items is impaired by speech that is played as an irrelevant background. The paper presents the view that changing state of the auditory material is an important prerequisite for this disruption. Four experiments studied the effects of sounds varying in complexity in an attempt to establish which features of changing state in the auditory signal lead to diminished recall. Simple unvarying or repetitive speech sounds were not sufficient to induce the irrelevant speech effect (Experiment 1): in addition, simple analogues of speech, possessing regular or irregular envelopes and using a range of carriers, failed to imitate the action of speech (Experiment 2). Variability of between-utterance phonology in the irrelevant stream (Experiment 3) emerged as a crucial factor. Moreover, predictability of the syllable sequence did not reduce the degree of disruption (Experiment 4) suggesting that supra-syllabic characteristics of the speech are of little importance. The results broadly support the idea that disruption of short-term memory only occurs when the speech stream changes in state. It is argued that disruption occurs in memory when cues to serial order based on phonological representations of heard material interfere with the phonological codes of visual origin. It is suggested that cues to changing state of the speech input contaminate those associated with items of visual origin, which are already in a phonological store.

Adolescent↗

PubMed1993

The order and orientation of a cluster of metalloproteinase genes, stromelysin 2, collagenase, and stromelysin, together with D11S385, on chromosome 11q22-q23.

A cluster of metalloproteinase genes, stromelysin, fibroblast collagenase, and stromelysin 2 together with the anonymous DNA marker D11S385, was mapped using pulsed-field gel electrophoresis to a 135-kb region of chromosome 11q22-q23. The physical proximity of these markers was subsequently confirmed using two YAC clones, and their relative order was established as stromelysin 2-collagenase-stromelysin-D11S385. The pattern of marker representation in a panel of radiation-reduced chromosome 11 hybrids suggests that the metalloproteinase gene/D11S385 cluster is orientated with STMY2 closest to the centromere.

Animals↗

PubMed1996

Displacement correction and surface reconstruction of the retina using scanning laser ophthalmoscopic images.

A method for a three-dimensional surface reconstruction of the retina in the area of the papilla is presented. The surface reconstruction is based on a sequence of discrete gray-level images of the retina recorded by a scanning laser ophthalmoscope (SLO). The underlying assumption of the surface reconstruction algorithm developed here is that the depth information is also encoded in the brightness values of the single pixels in addition to the ordinary spatial 2D information. The brightness of an image position depends on the degree of reflection of a confocal laser beam. Only those surface structures located directly in the focus plane of the confocal laser beam produce a high response to the laser light. The displacements between the single images of a sequence are considered to be approximately linear and are corrected by applying the cepstrum technique. The depth is estimated from the volumetric representation of the image sequence by searching for the maximal value of the brightness within a computed depth profile, at every image position. In the resulting images, disturbances occurring during the recording cause incorrect local estimations of the depth. These local disturbances are corrected by applying specially developed surface improvement processes. The work is concluded with a comparison of several different approaches to reduce the noise and disturbances in SLO image data.

Algorithms↗

PubMedDate not supplied

Predicting enzyme subclass by functional domain composition and pseudo amino acid composition.

As a continuous effort to use the sequence approach to identify enzymatic function at a deeper level, investigations are extended from the main enzyme classes (Protein Sci. 2004, 13, 2857-2863) to their subclasses. This is indispensable if we wish to understand the molecular mechanism of an enzyme at a deeper level. For each of the 6 main enzyme classes (i.e., oxidoreductase, transferase, hydrolase, lyase, isomerase, and ligase), a subclass training dataset is constructed. To reduce homologous bias, a stringent cutoff was imposed that all the entries included in the datasets have less than 40% sequence identity to each other. To catch the core feature that is intimately related to the biological function, the sample of a protein is represented by hybridizing the functional domain composition and pseudo amino acid composition. On the basis of such a hybridization representation, the FunD-PseAA predictor is established. It is demonstrated by the jackknife cross-validation tests that the overall success rate in identifying the 21 subclasses of oxidoreductases is above 86%, and the corresponding rates in identifying the subclasses of the other 5 main enzyme classes are 94-97%. The high success rates imply that the FunD-PseAA predictor may become a useful tool in bioinformatics and proteomics of the post-genomic era.

Amino Acid Sequence↗

PubMed2003

Local similarity in RNA secondary structures.

We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar regions in RNA secondary structures. The time complexity of our algorithm is O(|F(1)| |F(2) deg(F(1)) deg(F(2)) (deg(F(1)) + deg(F(2))) where |F(i)| is the number of nodes in forest F(i) and deg (F(i)) is the degree of F(i). We provide carefully engineered dynamic programming implementations using dense, two-dimensional tables which considerably reduces the space requirement. We suggest a new representation of RNA secondary structures as forests that allow reasonable scoring of edit operations on RNA secondary structures. The comparison of RNA secondary structures is facilitated by a new visualization technique for RNA secondary structure alignments. Finally, we show how potential regulatory motifs can be discovered solely by their structural preservation, and independent of their sequence conservation and position.

Algorithms↗

PubMedDate not supplied

A mathematical representation of the expert panel's guidelines for high blood cholesterol case-finding and treatment.

The National Cholesterol Education Program (NCEP) for high blood cholesterol case-finding and treatment recommended discrete treatments according to the results of sequential measurements of continuous variables (total and low-density lipoprotein cholesterol [LDL-C]). These measurements are subject to intra- and interindividual variability. The authors describe a computer simulation of the NCEP that acknowledges these complexities. The simulation reduces the NCEP into steps, which are represented in a decision tree. The calculation of probabilities at chance nodes takes into account the conditional nature of sequential measurements of blood cholesterol. The simulation tracks medical resource use and estimates LDL-C reductions within 20 strata, each defining 5% of population distribution for LDL-C. This approach enables a detailed representation of the case-finding process--the sequence of blood cholesterol tests and associated cut-off values that identify individuals needing more intensive evaluation and treatment.

Cholesterol↗

PubMed1995

In vivo occupancy of histone gene proximal promoter elements reflects gene copy number-dependent titratable transactivation factors and cross-species compatibility of regulatory sequences.

To assess systematically the structural and functional aspects of histone gene transcription within a chromosomal context, we stably integrated an extensive set of human histone H4 gene constructs into mouse C127 cells. Levels of expression were determined by S1 nuclease protection assays for multiple mouse monoclonal cell lines containing these human H4 genes. For each cell line, we quantitated the number of integrated human H4 genes by Southern blot analysis. The results indicate that the expression of the human H4 gene is in part copy number dependent at low gene dosages. However, the level of expression varies among different cell lines containing similar numbers of copies of the same H4 gene construct. This result suggests that position-dependent chromosomal integration effects contribute to H4 gene transcription, consistent with the roles of long-range gene organization and nuclear architecture in gene regulation. At high copy number, the level of human H4 gene expression per copy decreased, and endogenous mouse H4 mRNA levels were also reduced. Furthermore, in vivo occupancy at the human H4 gene immediate 5' regulatory elements, as defined by genomic fingerprinting, showed copy number-dependent protein/DNA interactions. Hence, human and mouse H4 genes compete for titratable transcription factors in a cellular environment. Taken together, these results indicate cross-species compatibility and suggest limited representation in vivo of the factors involved in regulating histone H4 gene transcription.

Animals↗

PubMed1980

Fluctuation in polyadenylate size and content in exponential- and stationary-phase cells of Saccharomyces cerevisiae.

Stationary-phase cells of Saccharomyces cerevisiae were found to have a reduced polyadenylate [poly(A)] content as compared with exponential-phase cells. A sizing procedure for poly(A) was devised to distinguish between alternative hypotheses to explain this reduction. Two major size classes of poly(A) were found. The decreased representation of the larger of the two classes accounted for the majority of the poly(A) loss. The remainder of the loss was accounted for by fewer poly(A)-containing sequences. The smaller of the two poly(A) classes was apparently not of mitochondrial origin and may be added transcriptionally.

Poly A↗