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Results for “reduced representation sequencing”

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PubMed2005

Modified representational difference analysis: isolation of differentially expressed mRNAs from rare cell populations.

Representational difference analysis of cDNAs (cDNA-RDA) is a sensitive subtractive hybridization technique capable of isolating rare mRNAs differentially expressed in two cell populations. cDNA-RDA can detect sequences represented at 0.0001% in the starting mRNA. By using reverse transcriptase polymerase chain reaction (PCR), cDNA-RDA also lends itself to studies in which samples are derived from limited numbers of cells. Standard cDNA-RDA protocols depend upon the presence of specific restriction enzyme sites in each cDNA, typically enzymes with four base recognition sequences. These sites are used to reduce the cDNA size range and provide primer sites for subsequent PCR amplification. Consequently, transcripts containing fewer than two of the chosen restriction sites are undetectable by cDNA-RDA. We have developed a restriction enzyme site-independent cDNA-RDA protocol called modified RDA (MRDA). We constructed MRDA test sequences from random hexamer-primed cDNA, thereby increasing the representation of mRNAs which are excluded by cDNA-RDA protocols. MRDA is also more efficient than cDNA-RDA at removing highly expressed housekeeping genes during the subtractive hybridization process, thereby allowing more efficient isolation of preferentially expressed mRNAs. Using MRDA, we isolated cDNAs differentially expressed between limited numbers of human CD4(+) naive and memory T lymphocyte subsets and skin- and gut-homing memory T cell subsets.

Cells↗

PubMed2002

Schema-based processing in auditory scene analysis.

What is the involvement of what we know in what we perceive? In this article, the contribution of melodic schema-based processes to the perceptual organization of tone sequences is examined. Two unfamiliar six-tone melodies, one of which was interleaved with distractor tones, were presented successively to listeners who were required to decide whether the melodies were identical or different. In one condition, the comparison melody was presented after the mixed sequence: a target melody interleaved with distractor tones. In another condition, it was presented beforehand, so that the listeners had precise knowledge about the melody to be extracted from the mixture. In the latter condition, recognition performance was better and a bias toward same responses was reduced, as compared with the former condition. A third condition, in which the comparison melody presented beforehand was transposed up in frequency, revealed that whereas the performance improvement was explained in part by absolute pitch or frequency priming, relative pitch representation (interval and/or contour structure) may also have played a role. Differences in performance as a function of mean frequency separation between target and distractor sequences, when listeners did or did not have prior knowledge about the target melody, argue for a functional distinction between primitive and schema-based processes in auditory scene analysis.

Adult↗

PubMed2006

Effects of L1 retrotransposon insertion on transcript processing, localization and accumulation: lessons from the retinal degeneration 7 mouse and implications for the genomic ecology of L1 elements.

The retinal degeneration 7 (rd7) mouse is a naturally occurring model of enhanced S-cone syndrome, Goldman-Favre syndrome and clumped pigmentary retinopathy in humans, allelic disorders caused by inactivation of a photoreceptor-specific nuclear hormone receptor, NR2E3. We show here that the rd7 mutation arose from the antisense insertion of a long interspersed nuclear element (LINE-1) (or L1) into exon 5 of the mouse Nr2e3 gene. L1 insertion blocks splicing of Nr2e3 intron 5 by separating an inefficient splice donor from essential splicing enhancers within exon 5, with the result that incompletely spliced transcripts accumulate to high levels at the mutant Nr2e3 locus in photoreceptor nuclei. The high efficiency of transcription through the 7 kb L1 was unexpected and led us to compare the effect on transcript abundance of sense or antisense L1 insertions in transfected cells. In a variety of sequence contexts antisense L1 insertions had little or no effect on transcript levels or the production of full-length transcripts, whereas sense L1 insertions reduced transcript levels from several-fold to more than 10-fold. A bioinformatic analysis of all mouse L1s shows a approximately 2-fold under-representation of L1s in introns when compared with bulk genomic DNA, and, within introns, a further approximately 2-fold under-representation of sense when compared with antisense L1s. Interestingly, there is no evidence for orientation-specific positive or negative selection within any subregions of the L1 element. These data suggest that L1s have evolved to present the host transcriptional machinery with a minimally disruptive profile in the antisense orientation such that antisense intronic L1s often escape purifying negative selection.

Animals↗

PubMed2003

Description of protein-DNA complexes in terms of electron-density topological features.

This paper presents a computer-modelling approach for the generation of low-resolution representations of two protein-DNA complexes, NF-kappaB and HIF-1. The representation is obtained by topological analysis of electron-density maps at 2.85 A crystallographic resolution, which leads to a set containing a limited number of critical points (CP). Analyses of the structure and properties of the CP graphs (density at peak position, volume and ellipticity), as well as comparisons with other reduced representations, are performed in order to assess the usefulness of such representations in molecular-docking applications at medium resolution.

Amino Acid Sequence↗

PubMed1982

[Changes in the representation of repeating DNA sequences in nuclear RNAs of early loach embryos].

The hybridization kinetics of nuclear RNAs of loach embryos labelled with [3H]uridine for 1 hour with DNA excess shows that during embryogenesis (from the blastula to the gastrula stage) the number of newly formed RNA molecules transcribed from repeating DNA sequences in considerably reduced. This occurs both in the RNA fraction extracted from the nuclei with phenol pH 7.7 and having a low sedimentation coefficient and a low degree of polyadenylation, and in the RNA fraction extracted with phenol pH 9.0 having a higher sedimentation coefficient and a higher degree of polyadenylation.

Animals↗

PubMed1997

Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment.

Statistical potentials based on pairwise interactions between C alpha atoms are commonly used in protein threading/fold-recognition attempts. Inclusion of higher order interaction is a possible means of improving the specificity of these potentials. Delaunay tessellation of the C alpha-atom representation of protein structure has been suggested as a means of defining multi-body interactions. A large number of parameters are required to define all four-body interactions of 20 amino acid types (20(4) = 160,000). Assuming that residue order within a four-body contact is irrelevant reduces this to a manageable 8,855 parameters, using a nonredundant dataset of 608 protein structures. Three lines of evidence support the significance and utility of the four-body potential for sequence-structure matching. First, compared to the four-body model, all lower-order interaction models (three-body, two-body, one-body) are found statistically inadequate to explain the frequency distribution of residue contacts. Second, coherent patterns of interaction are seen in a graphic presentation of the four-body potential. Many patterns have plausible biophysical explanations and are consistent across sets of residues sharing certain properties (e.g., size, hydrophobicity, or charge). Third, the utility of the multi-body potential is tested on a test set of 12 same-length pairs of proteins of known structure for two protocols: Sequence-recognizes-structure, where a query sequence is threaded (without gap) through the native and a non-native structure; and structure-recognizes-sequence, where a query structure is threaded by its native and another non-native sequence. Using cross-validated training, protein sequences correctly recognized their native structure in all 24 cases. Conversely, structures recognized the native sequence in 23 of 24 cases. Further, the score differences between correct and decoy structures increased significantly using the three- or four-body potential compared to potentials of lower order.

Models, Chemical↗

PubMed2025

Efficient storage and regression computation for population-scale genome sequencing studies.

MOTIVATION: The growing availability of large-scale population biobanks has the potential to significantly advance our understanding of human health and disease. However, the massive computational and storage demands of whole genome sequencing (WGS) data pose serious challenges, particularly for underfunded institutions or researchers in developing countries. This disparity in resources can limit equitable access to cutting-edge genetic research. RESULTS: We present novel algorithms and regression methods that dramatically reduce both computation time and storage requirements for WGS studies, with particular attention to rare variant representation. By integrating these approaches into PLINK 2.0, we demonstrate substantial gains in efficiency without compromising analytical accuracy. In an exome-wide association analysis of 19.4 million variants for the body mass index phenotype in 125 077 individuals (AllofUs project data), we reduced runtime from 695.35 min (11.5 h) on a single machine to 1.57 min with 30 GB of memory and 50 threads (or 8.67 min with 4 threads). Additionally, the framework supports multi-phenotype analyses, further enhancing its flexibility. AVAILABILITY AND IMPLEMENTATION: Our optimized methods are fully integrated into PLINK 2.0 and can be accessed at: https://www.cog-genomics.org/plink/2.0/.

Humans↗

PubMed2001

SNP analysis to dissect human traits.

The analysis of complex human diseases has been spurred by the number of published genomic sequence variants - many identified in the course of sequencing the human genome. But, to be useful for genetic analysis, variants have to be mapped accurately, their frequencies in various populations determined, and automated high-throughput assay techniques developed. Recently proposed methods address these issues: the use of 'reduced representation shotgun' methods for more efficient detection of single nucleotide polymorphisms (SNPs), the employment of high-throughput genotyping techniques, the development of SNP maps that incorporate information about linkage disequilibrium, and the use of SNPs in identifying susceptibility genes for common illnesses.

Chromosome Mapping↗

PubMed1993

Constitutive transcription of the osteocalcin gene in osteosarcoma cells is reflected by altered protein-DNA interactions at promoter regulatory elements.

The bone-specific osteocalcin (OC) gene is transcribed only after completion of proliferation in normal diploid calvarial-derived osteoblasts during extracellular matrix mineralization. In contrast, the OC gene is expressed constitutively in both proliferating and nonproliferating ROS 17/2.8 osteosarcoma cells. To address molecular mechanisms associated with these tumor-related modifications in transcriptional control, we examined sequence-specific interactions of transactivation factors at key basal and hormone-responsive elements in the OC gene promoter. In ROS 17/2.8 cells compared to normal diploid osteoblasts, the absence of a stringent requirement for cessation of proliferation to support both induction of OC transcription and steroid hormone-mediated transcriptional modulation is reflected by modifications in transcription factor binding at (i) the two primary basal regulatory elements, the OC box (which contains a CCAAT motif as a central core) and the TATA/glucocorticoid-responsive element domain, and (ii) the vitamin D-responsive element. Particularly striking are two forms of the vitamin D receptor complex that are present in proliferating osteoblasts and osteosarcoma cells. Both forms of the complex are sensitive to vitamin D receptor antibody and retinoic X receptor antibody. After the down-regulation of proliferation, only the lower molecular weight complex is found in normal diploid osteoblasts. Both forms of the complex are present in nonproliferating ROS 17/2.8 cells with increased representation of the complex exhibiting reduced electrophoretic mobility that is phosphorylation-dependent.

Animals↗

PubMedDate not supplied

Alignment with context dependent scoring function.

In the paper by Gambin et al. (2002) we introduced the model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which the cost of a substitution depends on the surrounding symbols. Consequently, in this model the cost of transforming one sequence into another depends on the order of editing operations. In this paper, we strengthen some of our results which concern reconstructing (the representation of) all the orders of operations which yield this optimal cost. We also present a procedure to construct context-dependent substitution tables and discuss the distribution of scores of local contextual alignment, which is shown to follow the extreme value distribution in the gap-free, reduced context case. We also demonstrate a linear time algorithm to compute the optimal local and global alignment without gaps.

Algorithms↗

PubMed1980

Influence of chlorambucil, a bifunctional alkylating agent, on DNA replication and histone gene expression in HeLa S3 cells.

We have examined the influence of chlorambucil, a bifunctional alkylating agent that inhibits cell proliferation, on DNA replication and histone gene expression in exponentially growing HeLa S3 cells. During the period of treatment with chlorambucil (up to 3 days), neither transcription nor translation in general appeared to be affected, but the incorporation of [14C]thymidine into DNA was reduced to 15% of control values by the third day. The appearance of newly synthesized histones and non-histone proteins on chromatin was inhibited with a time course similar to that for inhibition of DNA synthesis. However, the representation of histone messenger RNA sequences in various cellular compartments did not appear to be affected by chlorambucil treatment, in contrast to the loss of histone messenger RNA sequences from polyribosomes following the more rapid inhibition of DNA and histone synthesis by 1-beta-D-arabinofuranosylcytosine or hydroxyurea. The possibility is considered that chlorambucil interferes with histone gene expression at posttranscriptional or posttranslational levels. We also conclude that the inhibition of DNA synthesis by chlorambucil is most probably an indirect effect, a result of the inhibition of cells in the G2 phase of the cell cycle.

Cell Division↗

PubMed2002

Spatio-temporal dynamics of odor representations in the mammalian olfactory bulb.

We explored the spatio-temporal dynamics of odor-evoked activity in the rat and mouse main olfactory bulb (MOB) using voltage-sensitive dye imaging (VSDI) with a new probe. The high temporal resolution of VSDI revealed odor-specific sequences of glomerular activation. Increasing odor concentrations reduced response latencies, increased response amplitudes, and recruited new glomerular units. However, the sequence of glomerular activation was maintained. Furthermore, we found distributed MOB activity locked to the nasal respiration cycle. The spatial distribution of its amplitude and phase was heterogeneous and changed by sensory input in an odor-specific manner. Our data show that in the mammalian olfactory bulb, odor identity and concentration are represented by spatio-temporal patterns, rather than spatial patterns alone.

Animals↗

PubMed2005

Subspecies composition and founder contribution of the captive U.S. chimpanzee (Pan troglodytes) population.

Chimpanzees are presently classified into three subspecies: Pan troglodytes verus from west Africa, P.t. troglodytes from central Africa, and P.t. schweinfurthii from east Africa. A fourth subspecies (P.t. vellerosus), from Cameroon and northern Nigeria, has been proposed. These taxonomic designations are based on geographical origins and are reflected in sequence variation in the first hypervariable region (HVR-I) of the mtDNA D-loop. Although advances have been made in our understanding of chimpanzee phylogenetics, little has been known regarding the subspecies composition of captive chimpanzees. We sequenced part of the mtDNA HVR-I region in 218 African-born population founders and performed a phylogenetic analysis with previously characterized African sequences of known provenance to infer subspecies affiliations. Most founders were P.t. verus (95.0%), distantly followed by the troglodytes schweinfurthii clade (4.6%), and a single P.t. vellerosus (0.4%). Pedigree-based estimates of genomic representation in the descendant population revealed that troglodytes schweinfurthii founder representation was reduced in captivity, vellerosus representation increased due to prolific breeding by a single male, and reproductive variance resulted in uneven representation among male P.t.verus founders. No increase in mortality was evident from between-subspecies interbreeding, indicating a lack of outbreeding depression. Knowledge of subspecies and their genomic representation can form the basis for phylogenetically informed genetic management of extant chimpanzees to preserve rare genetic variation for research, conservation, or possible future breeding.

Africa↗

PubMed2003

Rheumatoid arthritis susceptibility and interleukin 10: a study of two ethnically diverse populations.

INTRODUCTION: IL-10 is an immunoregulatory cytokine which may modulate disease expression in rheumatoid arthritis (RA). The IL-10 gene is highly polymorphic with a number of single nucleotide polymorphisms in the promoter region and two microsatellite loci, IL10.R and IL10.G, 4 kb and 1.1 kb 5' of the transcription initiation site. It has been reported that allele 2 of the IL10.R microsatellite (IL10.R2) is associated with increased IL-10 secretion and IL10.R3 with reduced secretion. Subsequently, over-representation of IL10.R2 and under-representation of IL10.R3 in three independent RA groups has been reported. The aim of the current study is to determine whether there is an association between the IL10.R2 allele and RA in two ethnically distinct populations. METHODS: IL10.R genotypes were determined by semi-automated DNA sequencing technology in 186 UK Caucasians and 138 South Africans of Zulu or Sotho origin, fulfilling the 1987 American College of Rheumatology (ACR) criteria for RA. The Caucasian patients had relatively severe disease and comprised 75 patients with RA vasculitis, 22 with Felty's syndrome and 89 who had undergone a joint replacement (hip or knee) within 15 years of the onset of disease. Allele frequencies were compared with 296 Caucasians and/or 73 South Africans. RESULTS: The frequency of the IL10.R2 allele was significantly greater in the South Africans (RA and controls) than in the Caucasians (0.78 vs 0.66, P=1 x 10(-6)), while the frequency of IL10.R3 was less common (0.16 vs 0.3, P=1 x 10(-8)). No differences were observed in either IL10.R2 or IL10.R3 frequencies between patients and controls in either population. CONCLUSIONS: We were unable to confirm any association between IL10.R alleles and RA in this study. However, significant differences were demonstrated in the frequency of IL10.R2 and IL10.R3 between the two ethnic groups. The relatively high frequency of IL10.R2 in the South African population (0.78) would have reduced the power to detect an association with RA.

Adult↗

PubMed2001

Automatic segmentation algorithm for the extraction of lumen region and boundary from endoscopic images.

A new segmentation algorithm for lumen region detection and boundary extraction from gastro-intestinal (GI) images is presented. The proposed algorithm consists of two steps. First, a preliminary region of interest (ROI) representing the GI lumen is segmented by an adaptive progressive thresholding (APT) technique. Then, an adaptive filter, the Iris filter, is applied to the ROI to determine the actual region. It has been observed that the combined APT-Iris filter technique can enhance and detect the unclear boundaries in the lumen region of GI images and thus produces a more accurate lumen region, compared with the existing techniques. Experiments are carried out to determine the maximum error on the extracted boundary with respect to an expert-annotated boundary technique. Investigations show that, based on the experimental results obtained from 50 endoscopic images, the maximum error is reduced by up to 72 pixels for a 256 x 256 image representation compared with other existing techniques. In addition, a new boundary extraction algorithm, based on a heuristic search on the neighbourhood pixels, is employed to obtain a connected single pixel width outer boundary using two preferential sequence windows. Experimental results are also presented to justify the effectiveness of the proposed algorithm.

Algorithms↗

PubMed2006

Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores.

Identifying protein-protein interfaces is crucial for structural biology. Because of the constraints in wet experiments, many computational methods have been proposed. Without knowing any information about the partner chains, a new method of predicting protein-protein interaction interface residues purely based on evolutionary information in heterocomplexes is proposed here. Unlike traditional approaches using multiple sequence alignment profiles to represent the conservation level for each residue, we make predictions based on the concept of residue conservation scores so that the dimension of the feature vector for each residue can be drastically reduced, at least 20 times less than conventional methods. Based on the representation approach, a simple linear discriminant function is used to make predictions, so the computational complexity of the whole prediction procedure can also be greatly decreased. By testing our approach on 69 heterocomplex chains, experimental results demonstrate the performance of our approach is indeed superior to current existing methods.

Computational Biology↗

PubMed1996

Physical mapping of the bloom syndrome region by the identification of YAC and P1 clones from human chromosome 15 band q26.1.

The gene for Bloom syndrome (BLM) has been mapped to human chromosome 15 band q26.1 by homozygosity mapping. Further refinement of the location of BLM has relied upon linkage-disequilibrium mapping and somatic intragenic recombination. In combination with these mapping approaches and to identify novel DNA markers and probes for the BLM candidate region, a contiguous representation of the 2-Mb region that contains the BLM gene was generated and is presented here. YAC and P1 clones from the region have been identified and ordered by using previously available genetic markers in the region along with newly developed sequence-tagged sites from radiation-reduced hybrids, polymorphic dinucleotide repeat loci, and end sequences of YACs and P1s. A long-range restriction map of the 2-Mb region that allowed estimation of the distance between polymorphic microsatellite loci is also reported. This map and the DNA markers derived from it were instrumental in the recent identification of the BLM gene.

Adenosine Triphosphatases↗

PubMed1991

Contextual dependencies in motor skills.

The development of contextual dependencies during motor skill acquisition was examined. Environmental context was varied along intentional and incidental dimensions. Intentional stimuli were defined as essential for achieving skilled performance, whereas incidental stimuli were defined as those that have the potential to become associated with specific tasks due to their selective presence in the learning environment. Experiment 1 demonstrated the occurrence of contextual dependencies for the learning of four-key typing sequences. Contextual dependencies were diminished in Experiment 2 when the number of keys used in the sequences was reduced. In Experiment 3, a retention condition was incorporated, in which both the intentional and the incidental stimuli were not available; this confirmed that task difficulty mediated the development of contextual dependencies. These findings are discussed with respect to the incorporation of environmental contextual stimuli with memorial representations of movement information.

Adult↗