SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

MOTIVATION

The coiled coil is a ubiquitous α-helical protein structure domain that directs and facilitates protein-protein interactions in a wide variety of biological processes. At the protein-sequence level, coiled coils are quite straightforward and readily recognized via the conspicuous heptad repeats of hydrophobic and polar residues. However, structurally they are more complicated, existing in a range of oligomer states and topologies. Here, we address the issue of predicting coiled-coil oligomeric state from protein sequence.

RESULTS

The predominant coiled-coil oligomer states in Nature are parallel dimers and trimers. Here, we improve and retrain the first-published algorithm, SCORER, that distinguishes these states, and test it against the current standard, MultiCoil. The SCORER algorithm has been revised in two key respects: first, the statistical basis for SCORER is improved markedly. Second, the training set for SCORER has been expanded and updated to include only structurally validated coiled coils. The result is a much-improved oligomer state predictor that outperforms MultiCoil, particularly in assigning oligomer state to short coiled coils, and those that are diverse from the training set.

AVAILABILITY

SCORER 2.0 is available via a web interface at http://coiledcoils.chm.bris.ac.uk/Scorer. Source code, training sets and Supporting Information can be downloaded from the same site.

Cocaine-related retiform purpura: evidence to incriminate the adulterant, levamisole

The term 'cocaine-induced pseudovasculitis' was coined to encompass a constellation of clinical and laboratory findings which mimics a systemic vasculitis but lacks confirmatory evidence of vasculitis on biopsy. Antineutrophil cytoplasmic antibodies reacting with human neutrophil elastase (HNE) have been reported to distinguish the cocaine-related syndrome from a true autoimmune vasculitis. Published cases of retiform purpura related to cocaine use are rare and an etiologic role for levamisole, a common adulterant of cocaine, has been postulated. We describe two female patients aged 39 and 49 years with cocaine-related retiform purpura, mainly affecting the legs. The initial clinical and serological profile in case 1 led to a suspicion of anti-phospholipid syndrome and in case 2 to Wegener's granulomatosis with an unexplained associated neutropenia. Skin biopsies revealed a mixed pattern of leukocytoclastic vasculitis and microvascular thrombosis in case 1 and pure microvascular thrombosis in case 2. Identification of anti-HNE antibodies in both patients linked their disease to cocaine. The mixed vasculopathic pattern in case 1 and the associated neutropenia in case 2, both known adverse effects of levamisole, point to this as the true etiologic agent. Urine toxicology shortly after a binge of cocaine use in each case was positive for levamisole.

Novel Case of Generalized Multinucleate Cell Angiohistiocytoma

Background:

Multinucleate cell angiohistiocytoma is a rare benign fibrohistiocytic and vascular proliferation, typically characterized by the development of solitary papules, in an acral distribution in otherwise healthy late middle-aged to elderly women.

Objective:

Our objectives are to present a novel case of generalized multinucleate cell angiohistiocytoma and to review the current literature regarding the clinical and histologic findings in this condition, as well as its potential causes and treatments.

Observations:

We describe a 35-year-old man who presented with generalized asymptomatic firm violaceous papules. Histopathology revealed dermal vascular proliferation; a perivascular infiltrate of lymphocytes, histiocytes, neutrophils, and plasma cells; thickened surrounding collagen bundles; and characteristic multinucleate cells with scalloped borders.

Conclusion:

Our patient is one of three patients reported to date with generalized lesions of multinucleate cell angiohistiocytoma who were all in a younger age group (20–40 years old) than previously reported for solitary lesions.

Granulomatous vasculitis in Crohn's disease: a clinicopathologic correlate of two unusual cases

Cutaneous complications occur not uncommonly in patients with Crohn's disease (CD). Gastrointestinal CD often shows non-caseating granulomas and a rare cutaneous finding in CD is a sterile granulomatous infiltrate not contiguous with the GI tract, termed extraintestinal CD (ECD). The clinical presentation of ECD is diverse. The most common histopathological presentation is a superficial and deep granulomatous infiltrate that often accompanies a mixed perivascular infiltrate. Here we report two patients with CD and skin lesions characterized on microscopy by granulomatous vasculitis. A 29-year-old female presented with papules and ulcerated nodules above the ankle. The biopsy showed dermal and superficial subcutaneous involvement by a vasocentric infiltrate of mononuclear and multinucleated histiocytes as well as mural fibrin deposition. A 35-year-old male presented with two tender indurated erythematous plaques with punched-out centers on the lower leg. Histopathologically, a granulomatous vasculitis of small and medium-sized vessels in the dermis and subcutis was evident. These two cases represent the rarely described phenomenon of cutaneous granulomatous vasculitis in CD. Previously reported examples of this entity are reviewed.

Enumerating the decomposable neighbours of a decomposable graph under a simple perturbation scheme

Given a decomposable graph, we characterize and enumerate the set of pairs of vertices whose connection or disconnection results in a new graph that is also decomposable. We discuss the relevance of this results to Markov chain Monte Carlo methods that sample or optimize over the space of decomposable graphical models according to probabilities determined by a posterior distribution given observed multivariate data.

Enumerating the junction trees of a decomposable graph

We derive methods for enumerating the distinct junction tree representations for any given decomposable graph. We discuss the relevance of the method to estimating conditional independence graphs of graphical models and give an algorithm that, given a junction tree, will generate uniformly at random a tree from the set of those that represent the same graph. Programs implementing these methods are included as supplemental material.

Inference from genome-wide association studies using a novel Markov model

In this paper we propose a Bayesian modeling approach to the analysis of genome-wide association studies based on single nucleotide polymorphism (SNP) data. Our latent seed model combines various aspects of k-means clustering, hidden Markov models (HMMs) and logistic regression into a fully Bayesian model. It is fitted using the Markov chain Monte Carlo stochastic simulation method, with Metropolis-Hastings update steps. The approach is flexible, both in allowing different types of genetic models, and because it can be easily extended while remaining computationally feasible due to the use of fast algorithms for HMMs. It allows for inference primarily on the location of the causal locus and also on other parameters of interest. The latent seed model is used here to analyze three data sets, using both synthetic and real disease phenotypes with real SNP data, and shows promising results. Our method is able to correctly identify the causal locus in examples where single SNP analysis is both successful and unsuccessful at identifying the causal SNP.

Sub-optimal doses of human recombinant erythropoietin markedly lower serum ferritin

Human recombinant erythropoietin in full dose substantially raises the haemoglobin in patients with end stage renal disease on dialysis. In lower doses no or little rise in haemoglobin is achieved but the ferritin, often very high before treatment, is disproportionately lowered. The hormone therefore may be useful in reducing iron overload in other situations.

Which tests are most useful in distinguishing between reactive thrombocytosis and the thrombocytosis of myeloproliferative disease?

In an attempt to distinguish between thrombocytosis in myeloproliferative disease (MPD) and reactive thrombocytosis (RT) the following aspects of platelet structure and function were evaluated: platelet size, platelet aggregation and adhesion, dense granule and alpha granule components. In addition plasma fibrinogen and von Willebrand factor antigen (vWFag) were measured. In all parameters measured there was a significant difference between normals and both categories of thrombocytosis, however there was considerable overlap between MPD and RT. Plasma fibrinogen emerged as the best single test to discriminate between MPD and RT, levels of less than 5.0 g/l indicating MPD and greater than 5.0 g/l indicating RT.

miRNAs in the Plant Genome: All Things Great and Small

Plants produce two major types of small RNAs that are 21 to 24 nucleotides in size. Small interfering RNAs (siRNAs) are typically involved in transcriptional gene silencing that results from the targeting of genomic DNA and triggering of histone modifications or DNA methylation. Deep sequencing experiments have demonstrated that thousands of loci, usually repetitive sequences, generate these siRNAs. In contrast, microRNAs (miRNAs) are encoded by perhaps just several hundred loci per genome that generate Pol II-derived single stranded precursors which are processed into specific miRNAs. miRNAs act in a post-transcriptional manner to regulate gene function. Recent work has focused on the identification and classification of small RNA-producing loci, as well as understanding small RNA targeting and function, and the evolution of this relatively recently discovered class of regulatory molecules.

Von Willebrand's disease and angiodysplasia treated with thalidomide

A 54-year-old man with type IIB VWD and severe angiodysplasia had such a large blood loss from the bowel that it was difficult to keep up with transfusion requirements. Treatment with factor eight concentrate barely slowed the loss. D.D.A.V.P., Octreotide, and recombinant activated Factor VII, tried separately, were ineffective. The use of Thalidomide at a dose of 150 mg daily has rendered him free from blood loss for the last six months and we suggest would be worth a trial in similar cases.

Audit of correction of high INR in an anticoagulation clinic

Examination of the ways in which staff in the anticoagulation clinic dealt with high International Normalized Ratio (INR) results, not dosed by the computer programme, revealed an unacceptable variation in dosage change. Our aim has been to produce a protocol for either manual use and/or transfer to the computer, which would safely correct INR above the upper limit of the therapeutic range, 4.5 to a maximum of 8.0 within 7 days. We collected a large number of results (4.095) and arranged them in four INR groups (4.6-5.0, 5.1-6.0, 6.1-7.0 and 7.1-8.0) and three dosage classes (<3, 3-8 and >8 mg) in order to analyse the effects of the regimens used. This has enabled us to construct a protocol partly empirically and partly by use of a graph correlating dosage change with reduction in the INR, which will now be tested in the clinic. This protocol will deal with all INR up to a maximum of 7.0 as we have decided to contact patients with higher results. Putting this protocol onto the computer should reduce manual dosing by 15%.

BGX: a fully Bayesian integrated approach to the analysis of Affymetrix GeneChip data

We present Bayesian hierarchical models for the analysis of Affymetrix GeneChip data. The approach we take differs from other available approaches in two fundamental aspects. Firstly, we aim to integrate all processing steps of the raw data in a common statistically coherent framework, allowing all components and thus associated errors to be considered simultaneously. Secondly, inference is based on the full posterior distribution of gene expression indices and derived quantities, such as fold changes or ranks, rather than on single point estimates. Measures of uncertainty on these quantities are thus available. The models presented represent the first building block for integrated Bayesian Analysis of Affymetrix GeneChip data: the models take into account additive as well as multiplicative error, gene expression levels are estimated using perfect match and a fraction of mismatch probes and are modeled on the log scale. Background correction is incorporated by modeling true signal and cross-hybridization explicitly, and a need for further normalization is considerably reduced by allowing for array-specific distributions of nonspecific hybridization. When replicate arrays are available for a condition, posterior distributions of condition-specific gene expression indices are estimated directly, by a simultaneous consideration of replicate probe sets, avoiding averaging over estimates obtained from individual replicate arrays. The performance of the Bayesian model is compared to that of standard available point estimate methods on subsets of the well known GeneLogic and Affymetrix spike-in data. The Bayesian model is found to perform well and the integrated procedure presented appears to hold considerable promise for further development.

Genetics of the DST-mediated mRNA decay pathway using a transgene-based selection

mRNA sequences that control abundance, localization and translation initiation have been identified, yet the factors that recognize these sequences are largely unknown. In this report, a transgene-based strategy designed to isolate mutants of Arabidopsis thaliana that fail to recognize these sequences is described. In this strategy, a selectable gene and a screenable marker gene are put under the control of the sequence element being analysed and mutants are selected with altered abundance of the corresponding marker RNAs. The selection of mutants deficient in recognition of the DST (downstream) mRNA degradation signal is used as a test-case to illustrate some of the technical aspects that have facilitated success. Using this strategy, we report the isolation of a new mutant, dst3, deficient in the DST-mediated mRNA decay pathway. The targeted genetic strategy described circumvents certain technical limitations of biochemical approaches. Hence, it provides a means to investigate a variety of other mechanisms responsible for post-transcriptional regulation.