Comparing the fine specificity of DNA binding by NF-kappaB p50 and p52 using principal coordinates analysis.

Principal coordinates analysis has been proposed as an efficient way of predicting the binding affinity of a transcription factor to different DNA motifs, as it can model complex interactions that are difficult to represent with standard position-weight matrices. Here we evaluate its ability to distinguish the DNA binding properties of two closely related proteins, the homodimeric forms of NF-kappaB p50 and p52. When tested experimentally against 50 different variants of the generalised NF-kappaB motif GGRRNNYYCC, the binding specificities of p50 and p52 were similar but not identical (correlation rho = 0.

Saving the photons: mapping X-rays by position-tagged spectrometry.

Since the early years of X-ray spectrometry in electron microscopes, mapping the locations of chemical elements has been important. The X-rays needed in large numbers for this are rare, owing to poor production efficiency compared with electron signals, and at risk of loss by many mechanisms such as missing the limited solid angle of the detector, absorption before reaching the detector and pulse pile-up conventional digital mapping hardware reduces the information contained in the X-ray spectrum at each pixel to the itegrated counts from a few regions of interest.The acquisition technique of position-tagged spectrometry eliminates the conflict between the desire to see full frame X-ray images quickly versus the analytical advantages of having complete spectra for each pixel.

Multiple schwannomas of the foot. Case report and strategy for treatment.

Determining the appropriate treatment of a benign tumor of a peripheral nerve in the foot and ankle region presents a clinical dilemma, as resection of the tumor will cause loss of nerve function and create the possibility of a painful neuroma. Several surgical solutions to this problem were used in the care of a patient who presented with painful bilateral Morton's neuromas and was found to have bilateral schwannomas on pathologic examination of the resected nerves. Subsequent evaluation for recurrent bilateral foot pain demonstrated multiple tumors along the tibial nerve in one foot.

Expression and purification of biologically active IGF-binding proteins using the LCR/Mel expression system.

The anabolic effects and bioavailability of insulin-like growth factors I and II (IGF-I, IGF-II) are regulated in part by a family of IGF-binding proteins (IGFBPs). There are six known members of the IGFBP family, which share distinct structural characteristics and functional activities. To study the binding properties of these proteins, we have expressed recombinant IGFBP-3 and IGFBP-4 using the LCR/Mel expression system.

Initial sequencing and comparative analysis of the mouse genome.

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences.

Quantifying the similarities within fold space.

We have used GRATH, a graph-based structure comparison algorithm, to map the similarities between the different folds observed in the CATH domain structure database. Statistical analysis of the distributions of the fold similarities has allowed us to assess the significance for any similarity. Therefore we have examined whether it is best to represent folds as discrete entities or whether, in fact, a more accurate model would be a continuum wherein folds overlap via common motifs.

Melanoma associated with pseudoepitheliomatous hyperplasia: a case series and investigation into the role of epidermal growth factor receptor.

Background: Pseudoepitheliomatous hyperplasia (PEH) is a reactive epithelial proliferation that occurs in response to underlying infectious, inflammatory, and neoplastic conditions. The histologic features of PEH may simulate squamous cell carcinoma and may obscure an underlying malignant process. The association of PEH with benign melanocytic nevi is well described in the literature.

Caring for civilians during peace keeping missions: priorities and decisions.

Humanitarian assistance is increasingly being offered by the military in operations other than war. Balancing issues of resources, priorities, and security is important but complicated. Sometimes errors are made that are costly, either in terms of public relations, morale, or lives.

Predicting protein cellular localization using a domain projection method.

We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a "small-world network", linked by no more than seven degrees of separation. Projection of the domains onto two-dimensional space reveals three clusters that correspond to cellular compartments containing secreted, cytoplasmic, and nuclear proteins.

A first-generation linkage disequilibrium map of human chromosome 22.

DNA sequence variants in specific genes or regions of the human genome are responsible for a variety of phenotypes such as disease risk or variable drug response. These variants can be investigated directly, or through their non-random associations with neighbouring markers (called linkage disequilibrium (LD)). Here we report measurement of LD along the complete sequence of human chromosome 22.

Quantitative prediction of NF-kappa B DNA-protein interactions.

We describe a general method based on principal coordinates analysis to predict the effects of single-nucleotide polymorphisms within regulatory sequences on DNA-protein interactions. We use binding data for the transcription factor NF-kappaB as a test system. The method incorporates the effects of interactions between base pair positions in the binding site, and we demonstrate that such interactions are present for NF-kappaB.

Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks.

We describe a method to simultaneously detect and fine map quantitative trait loci (QTL) that is especially suited to the mapping of modifier loci in mouse mutant models. The method exploits the high level of historical recombination present in a heterogeneous stock (HS), an outbred population of mice derived from known founder strains. The experimental design is an F(2) cross between the HS and a genetically distinct line, such as one carrying a knockout or transgene.

A quantitative trait locus influencing anxiety in the laboratory rat.

A critical test for a gene that influences susceptibility to fear in animals is that it should have a consistent pattern of effects across a broad range of conditioned and unconditioned models of anxiety. Despite many years of research, definitive evidence that genetic effects operate in this way is lacking. The limited behavioral test regimes so far used in genetic mapping experiments and the lack of suitable multivariate methodologies have made it impossible to determine whether the quantitative trait loci (QTL) detected to date specifically influence fear-related traits.

Recent improvements to the SMART domain-based sequence annotation resource.

SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains.

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.

Sequence database searching methods such as BLAST, are invaluable for predicting molecular function on the basis of sequence similarities among single regions of proteins. Searches of whole databases however, are not optimized to detect multiple homologous regions within a single polypeptide. Here we have used the prospero algorithm to perform self-comparisons of all predicted Drosophila melanogaster gene products.

Automatic analysis of agarose gel images.

Motivation: Automatic tools to speed up routine biological processes are very much sought after in bio-medical research. Much repetitive work in molecular biology, such as allele calling in genetic analysis, can be made semi-automatic or task specific automatic by using existing techniques from computer science and signal processing. Computerized analysis is reproducible and avoids various forms of human error.

Finding the molecular basis of quantitative traits: successes and pitfalls.

Understanding the molecular basis of quantitative genetic variation is a principal goal for biomedicine. Although the complex genetic architecture of quantitative traits has so far largely frustrated attempts to identify genes in humans by standard linkage methodologies, quantitative trait loci (QTL) have been mapped in plants, insects and rodents. However, identifying the molecular bases of QTL remains a challenge.

A method for fine mapping quantitative trait loci in outbred animal stocks.

High-resolution mapping of quantitative trait loci (QTL) in animals has proved to be difficult because the large effect sizes detected in crosses between inbred strains are often caused by numerous linked QTLs, each of small effect. In a study of fearfulness in mice, we have shown it is possible to fine map small-effect QTLs in a genetically heterogeneous stock (HS). This strategy is a powerful general method of fine mapping QTLs, provided QTLs detected in crosses between inbred strains that formed the HS can be reliably detected in the HS.

Accurate formula for P-values of gapped local sequence and profile alignments.

A simple general approximation for the distribution of gapped local alignment scores is presented, suitable for assessing significance of comparisons between two protein sequences or a sequence and a profile. The approximation takes account of the scoring scheme (i.e.

Drunken-cell footprints: nuclease treatment of ethanol-permeabilized bacteria reveals an initiation-like nucleoprotein complex in stationary phase replication origins.

The nucleoprotein complex formed on oriC, the Escherichia coli replication origin, is dynamic. During the cell cycle, high levels of the initiator DnaA and a bending protein, IHF, bind to oriC at the time of initiation of DNA replication, while binding of Fis, another bending protein, is reduced. In order to probe the structure of nucleoprotein complexes at oriC in more detail, we have developed an in situ footprinting method, termed drunken-cell footprinting, that allows enzymatic DNA modifying reagents access to intracellular nucleoprotein complexes in E.

Local sequence alignments with monotonic gap penalties.

Motivation: Sequence alignments obtained using affine gap penalties are not always biologically correct, because the insertion of long gaps is over-penalised. There is a need for an efficient algorithm which can find local alignments using non-linear gap penalties.

Results: A dynamic programming algorithm is described which computes optimal local sequence alignments for arbitrary, monotonically increasing gap penalties, i.

Energy-Dispersive Spectrometry from Then until Now: A Chronology of Innovation.

: As part of the Microbeam Analysis Society (MAS) symposium marking 30 years of energy-dispersive spectrometry (EDS), this article reviews many innovations in the field over those years. Innovations that added a capability previously not available to the microanalyst are chosen for further description. Included are innovations in both X-ray microanalysis and digital imaging using the EDS analyzer.

Approximate statistics of gapped alignments.

A heuristic approximation to the score distribution of gapped alignments in the logarithmic domain is presented. The method applies to comparisons between random, unrelated protein sequences, using standard score matrices and arbitrary gap penalties. It is shown that gapped alignment behavior is essentially governed by a single parameter, alpha, depending on the penalty scheme and sequence composition.

Comparative gene expression profiling by oligonucleotide fingerprinting.

The use of hybridisation of synthetic oligonucleotides to cDNAs under high stringency to characterise gene sequences has been demonstrated by a number of groups. We have used two cDNA libraries of 9 and 12 day mouse embryos (24 133 and 34 783 clones respectively) in a pilot study to characterise expressed genes by hybridisation with 110 hybridisation probes. We have identified 33 369 clusters of cDNA clones, that ranged in representation from 1 to 487 copies (0.

Sequence assembly with CAFTOOLS.

Large-scale genomic sequencing requires a software infrastructure to support and integrate applications that are not directly compatible. We describe a suite of software tools built around the Common Assembly Format (CAF), a comprehensive representation of a sequence assembly as a text file. These tools form the backbone of sequencing informatics at the Sanger Centre and the Genome Sequencing Center.