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PubMed1994

IS231A insertion specificity: consensus sequence and DNA bending at the target site.

In its natural host, Bacillus thuringiensis, the insertion sequence IS231A is preferentially inserted into the terminal inverted repeats of the transposon Tn4430. Using a novel transposition assay, we demonstrate that the Tn4430 ends behave as insertion hot spots for IS231A in Escherichia coli. Sequence analysis reveals that IS231A insertion sites match the 5'-GGG(N)5CCC-3' consensus. However, this consensus is not the only determinant of IS231A insertion specificity. Although both Tn4430 ends have identical sequences, one is strongly preferred to the other and the orientation of insertion into this end is not random. We demonstrate that this preference is determined by the flanking regions of the site. These regions display a conserved periodic organization of their sequence which, by conferring anisotropic flexibility, would induce the DNA to bend in a roughly 'S'-shaped structure centered on the target consensus. DNA conformation analysis by polyacrylamide gel electrophoresis indeed shows that the preferred target site of IS231A is flanked by DNA segments curved in opposite directions. We present a model in which DNA bendability and curvature would contribute to the positioning of IS231A transposase on the target DNA.

Bacillus thuringiensis↗

PubMed2006

Metabolic syndrome--a new world-wide definition. A Consensus Statement from the International Diabetes Federation.

AIMS: To establish a unified working diagnostic tool for the metabolic syndrome (MetS) that is convenient to use in clinical practice and that can be used world-wide so that data from different countries can be compared. An additional aim was to highlight areas where more research into the MetS is needed. PARTICIPANTS: The International Diabetes Federation (IDF) convened a workshop held 12-14 May 2004 in London, UK. The 21 participants included experts in the fields of diabetes, public health, epidemiology, lipidology, genetics, metabolism, nutrition and cardiology. There were participants from each of the five continents as well as from the World Health Organization (WHO) and the National Cholesterol Education Program-Third Adult Treatment Panel (ATP III). The workshop was sponsored by an educational grant from AstraZeneca Pharmaceuticals. CONSENSUS PROCESS: The consensus statement emerged following detailed discussions at the IDF workshop. After the workshop, a writing group produced a consensus statement which was reviewed and approved by all participants. CONCLUSIONS: The IDF has produced a new set of criteria for use both epidemiologically and in clinical practice world-wide with the aim of identifying people with the MetS to clarify the nature of the syndrome and to focus therapeutic strategies to reduce the long-term risk of cardiovascular disease. Guidance is included on how to compensate for differences in waist circumference and in regional adipose tissue distribution between different populations. The IDF has also produced recommendations for additional criteria that should be included when studying the MetS for research purposes. Finally, the IDF has identified areas where more studies are currently needed; these include research into the aetiology of the syndrome.

Adipose Tissue↗

PubMed2006

Liver involvement in hereditary hemorrhagic telangiectasia: consensus recommendations.

STUDY PURPOSE: To formulate recommendations about clinical management of liver involvement in hereditary hemorrhagic telangiectasia (HHT), using a formal consensus development process. CONSENSUS PROCESS: A nominal group technique was used. A list of main clinical, diagnostic and therapeutic issues about liver involvement in HHT was generated by the organizing committee. Panel members then scored their agreement with each statement; the median score, and standard deviation for each statement were determined for each of the three successive panel rounds. These consensus statements formed the basis for recommendations graded with the strength and quality of supporting evidence. RECOMMENDATION STATEMENTS: Doppler US is sufficiently accurate and suitable for first-line imaging of the liver in the general HHT population. Liver biopsy in any patient with proven or suspected HHT should be avoided. Liver involvement in HHT is generally asymptomatic; in the minority of patients where it is symptomatic, morbidity and mortality can be substantial. The prevalence of focal nodular hyperplasia is much higher in patients with liver involvement by HHT than in the general population. Invasive therapies for liver involvement by HHT (namely liver transplantation) should be considered only in patients who have failed to respond to intensive medical therapy.

Cholestasis↗

PubMed2004

European Consensus Meeting on Foam Sclerotherapy, April, 4-6, 2003, Tegernsee, Germany.

BACKGROUND: The introduction of sclerotherapy using foam sclerosants has revitalized interest in this method of treating varicose veins. Foam is made from detergent-type sclerosants already established as safe and effective in conventional liquid sclerotherapy. OBJECTIVE: European experts in foam sclerotherapy were invited to exchange their opinions and to work on consensus statements and recommendations. METHODS: A questionnaire covering different areas of foam sclerotherapy was sent to experts who have published or presented data, participated in clinical trials, or otherwise contributed to sclerotherapy with extemporary (self-made) foam. Based on the answers, several consensus statements and recommendations were approved during the consensus meeting. RESULTS: The use of sclerosing foam is an appropriate procedure in the treatment of varicose veins. It is a powerful tool in the hands of an expert who has sufficient experience in sclerotherapy. Sclerosing foam is more powerful than liquid. Most recommendations for conventional liquid sclerotherapy also apply to foam sclerotherapy. Some differences between these two treatments were highlighted. CONCLUSION: Foam sclerotherapy is a variation of a well-established treatment that improves varicose vein management. European experts came together to harmonize their opinions about sclerosing foam. The final document reflects the experts' opinion with the aim of defining principles for a safe and effective use of sclerosing foam and for its practical application. Foam sclerotherapy allows a skilled practitioner to treat larger veins including saphenous trunks.

Dosage Forms↗

PubMed2004

Consensus statement: cardiovascular safety profile of triptans (5-HT agonists) in the acute treatment of migraine.

BACKGROUND: Health care providers frequently cite concerns about cardiovascular safety of the triptans as a barrier to their use. In 2002, the American Headache Society convened the Triptan Cardiovascular Safety Expert Panel to evaluate the evidence on triptan-associated cardiovascular risk and to formulate consensus recommendations for making informed decisions for their use in patients with migraine. OBJECTIVE: To summarize the evidence reviewed by the Triptan Cardiovascular Safety Expert Panel and their recommendations for the use of triptans in clinical practice. PARTICIPANTS: The Triptan Cardiovascular Safety Expert Panel was composed of a multidisciplinary group of experts in neurology, primary care, cardiology, pharmacology, women's health, and epidemiology. EVIDENCE AND CONSENSUS PROCESS: An exhaustive search of the relevant published literature was reviewed by each panel member in preparation for an open roundtable meeting. Pertinent issues (eg, cardiovascular pharmacology of triptans, epidemiology of cardiovascular disease, cardiovascular risk assessment, migraine) were presented as a prelude to group discussion and formulation of consensus conclusions and recommendations. Follow-up meetings were held by telephone. CONCLUSIONS: (1) Most of the data on triptans are derived from patients without known coronary artery disease. (2) Chest symptoms occurring during use of triptans are generally nonserious and are not explained by ischemia. (3) The incidence of serious cardiovascular events with triptans in both clinical trials and clinical practice appears to be extremely low. (4) The cardiovascular risk-benefit profile of triptans favors their use in the absence of contraindications.

Acute Disease↗

PubMed2005

Photic- and pattern-induced seizures: expert consensus of the Epilepsy Foundation of America Working Group.

PURPOSE: In August, 2004, the Epilepsy Foundation of America convened a workshop to begin to develop an expert consensus on photosensitive seizures. METHODS: Literature and data were reviewed, and consensus was derived from discussion. RESULTS: A flash is a potential hazard if it has luminance >or=20 cd/m2, occurs at a frequency of >or=3 Hz, and occupies a solid visual angle of >or=0.006 steradians (approximately 10% of the central visual field or 25% of screen area at typical viewing distances). A transition to or from saturated red also is considered a risk. A pattern with the potential for provoking seizures contains clearly discernible stripes, numbering more than five light-dark pairs of stripes in any orientation. When the light-dark stripes of any pattern collectively subtend at the eye from the minimal-expected viewing distance a solid angle of >0.006 steradians, the luminance of the lightest stripe is >50 cd/m2, and the pattern is presented for >or=0.5 s, then the pattern should display no more than five light-dark pairs of stripes, if the stripes change direction, oscillate, flash, or reverse in contrast; if the pattern is unchanging or smoothly drifting in one direction, no more than eight stripes. These principles are easier to apply in the case of fixed media, for example, a prerecorded TV show, which can be analyzed frame-by-frame, as compared with interactive media. CONCLUSIONS: A consensus view of stimuli likely to provoke visually evoked seizures can be developed.

Computer Terminals↗

PubMed2002

Expert consensus in the development of a European health-related quality of life measure for children and adolescents: a Delphi study.

AIM: To determine the level of consensus among experts regarding content, structure and sources of content for a new European measure of health-related quality of life in children and adolescents. METHODS: A three-round Delphi questionnaire was sent by e-mail to 24 experts in quality of life measurement in 9 European countries. Consensus was considered reached when > 90% of experts either agreed or disagreed with a given statement, or where median scores were over 6 on a scale of 1-10, and score dispersion was within predefined limits. RESULTS: Completed questionnaires were received from 20 panellists in each round. It was agreed that the new instrument should be a multidimensional, profile measure with 30-49 items covering 5-8 dimensions, which should take no more than 10-15 min to complete. Agreement was also reached on 8 specific dimensions to include in the questionnaire (psychological well-being, self-esteem, body image, cognitive functioning, mobility, energy/vitality, social relations, family/home function). Consensus was against the use of individualized questionnaires. Focus groups with children, parents and workers in the field, literature and instrument reviews were considered appropriate sources for content. CONCLUSION: Using a Delphi method in this way for the first time showed it to be a feasible and useful method for establishing a conceptual and operational framework for the Kidscreen questionnaire.

Adolescent↗

PubMed2003

Consensus-degenerate hybrid oligonucleotide primers for amplification of priming glycosyltransferase genes of the exopolysaccharide locus in strains of the Lactobacillus casei group.

A primer design strategy named CODEHOP (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (GT) gene in strains of the Lactobacillus casei group. Each hybrid primer consisted of a short 3' degenerate core based on four highly conserved amino acids and a longer 5' consensus clamp region based on six sequences of the priming GT gene products from exopolysaccharide (EPS)-producing bacteria. The hybrid primers were used to detect the priming GT gene of 44 commercial isolates and reference strains of Lactobacillus rhamnosus, L. casei, Lactobacillus zeae, and Streptococcus thermophilus. The priming GT gene was detected in the genome of both non-EPS-producing (EPS(-)) and EPS-producing (EPS(+)) strains of L. rhamnosus. The sequences of the cloned PCR products were similar to those of the priming GT gene of various gram-negative and gram-positive EPS(+) bacteria. Specific primers designed from the L. rhamnosus RW-9595M GT gene were used to sequence the end of the priming GT gene in selected EPS(+) strains of L. rhamnosus. Phylogenetic analysis revealed that Lactobacillus spp. form a distinctive group apart from other lactic acid bacteria for which GT genes have been characterized to date. Moreover, the sequences show a divergence existing among strains of L. rhamnosus with respect to the terminal region of the priming GT gene. Thus, the PCR approach with consensus-degenerate hybrid primers designed with CODEHOP is a practical approach for the detection of similar genes containing conserved motifs in different bacterial genomes.

Amino Acid Sequence↗

PubMed2005

Analysis of translational initiation in coxsackievirus B3 suggests an alternative explanation for the high frequency of R+4 in the eukaryotic consensus motif.

Translational initiation of most eukaryotic mRNAs occurs when a preinitiation complex binds to the 5' cap, scans the mRNA, and selects a particular AUG codon as the initiation site. Selection of the correct initiation codon relies, in part, on its flanking residues; in mammalian cells, the core of the "Kozak" consensus is R-3CCAUGG+4 (R=purine; the A residue is designated position +1). The R-3 is considered the most important flanking residue, followed by G+4. Picornaviral mRNAs differ from most cellular mRNAs in several ways; they are uncapped, and they contain an internal ribosome entry site that allows the ribosome to bind near the initiation codon. The initiation codon of coxsackievirus B3 (CVB3) is flanked by both R-3 and G+4 (AAAATGG). Here, we report the construction of full-length CVB3 genomes that vary at these two positions, and we evaluate the effects of these variant sequences in vitro, in tissue culture cells, and in vivo. A virus with an A-->C transversion at position -3 replicates as well as wild-type CVB3, both in tissue culture and in vivo. This virus is highly pathogenic, and its sequence is stable throughout the course of an in vivo infection. Furthermore, the in vitro translation products from this RNA are very similar to the wild type. Thus, R-3-thought to be the most functionally important component of the Kozak consensus-appears to be dispensable in CVB3. In contrast, a G-to-C transversion at G+4 is lethal; RNAs carrying this mutation fail to generate infectious virus either in tissue culture or in vivo. However, in vitro analysis indicates that G+4 has only a marginal effect on translational initiation, especially if R-3 is present; instead, the G+4 is required mainly because the second triplet of the polyprotein open reading frame must encode glycine, without which infectious virus production cannot proceed. In summary, our data indicate that CVB3 remains viable, even in vivo, in the absence of R-3, and we propose that the most important factor contributing to the high frequency of G+4-not only in CVB but also in other eukaryotic mRNAs, and thus in the consensus motif itself-may be the constraint upon the second amino acid rather than the requirements for translational initiation.

Animals↗

PubMed2006

Identification of yin-yang regulators and a phosphorylation consensus for male germ cell-associated kinase (MAK)-related kinase.

MAK (male germ cell-associated protein kinase) and MRK/ICK (MAK-related kinase/intestinal cell kinase) are human homologs of Ime2p in Saccharomyces cerevisiae and of Mde3 and Pit1 in Schizosaccharomyces pombe and are similar to human cyclin-dependent kinase 2 (CDK2) and extracellular signal-regulated kinase 2 (ERK2). MAK and MRK require dual phosphorylation in a TDY motif catalyzed by an unidentified human threonine kinase and tyrosine autophosphorylation. Herein, we establish that human CDK-related kinase CCRK (cell cycle-related kinase) is an activating T157 kinase for MRK, whereas active CDK7/cyclin H/MAT1 complexes phosphorylate CDK2 but not MRK. Protein phosphatase 5 (PP5) interacts with MRK in a complex and dephosphorylates MRK at T157 in vitro and in situ. Thus, CCRK and PP5 are yin-yang regulators of T157 phosphorylation. To determine a substrate consensus, we screened a combinatorial peptide library with active MRK. MRK preferentially phosphorylates R-P-X-S/T-P sites, with the preference for arginine at position -3 (P-3) being more stringent than for prolines at P-2 and P+1. Using the consensus, we identified a putative phosphorylation site (RPLT(1080)S) for MRK in human Scythe, an antiapoptotic protein that interacts with MRK. MRK phosphorylates Scythe at T1080 in vitro as determined by site-directed mutagenesis and mass spectrometry, supporting the consensus and suggesting Scythe as a physiological substrate for MRK.

Amino Acid Motifs↗

PubMed1994

Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core.

The myeloid zinc finger gene 1, MZF1, encodes a transcription factor which is expressed in hematopoietic progenitor cells that are committed to myeloid lineage differentiation. MZF1 contains 13 C2H2 zinc fingers arranged in two domains which are separated by a short glycine- and proline-rich sequence. The first domain consists of zinc fingers 1 to 4, and the second domain is formed by zinc fingers 5 to 13. We have determined that both sets of zinc finger domains bind DNA. Purified, recombinant MZF1 proteins containing either the first set of zinc fingers or the second set were prepared and used to affinity select DNA sequences from a library of degenerate oligonucleotides by using successive rounds of gel shift followed by PCR amplification. Surprisingly, both DNA-binding domains of MZF1 selected similar DNA-binding consensus sequences containing a core of four or five guanine residues, reminiscent of an NF-kappa B half-site: 1-4, 5'-AGTGGGGA-3'; 5-13, 5'-CGGGnGAGGGGGAA-3'. The full-length MZF1 protein containing both sets of zinc finger DNA-binding domains recognizes synthetic oligonucleotides containing either the 1-4 or 5-13 consensus binding sites in gel shift assays. Thus, we have identified the core DNA consensus binding sites for each of the two DNA-binding domains of a myeloid-specific zinc finger transcription factor. Identification of these DNA-binding sites will allow us to identify target genes regulated by MZF1 and to assess the role of MZF1 as a transcriptional regulator of hematopoiesis.

Amino Acid Sequence↗

PubMed1996

A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity.

The RFX DNA binding domain is a novel motif that has been conserved in a growing number of dimeric DNA-binding proteins, having diverse regulatory functions, in eukaryotic organisms ranging from yeasts to humans. To characterize this novel motif, we have performed a detailed dissection of the site-specific DNA binding activity of RFX1, a prototypical member of the RFX family. First, we have performed a site selection procedure to define the consensus binding site of RFX1. Second, we have developed a new mutagenesis-selection procedure to derive a precise consensus motif, and to test the accuracy of a secondary structure prediction, for the RFX domain. Third, a modification of this procedure has allowed us to isolate altered-specificity RFX1 mutants. These results should facilitate the identification both of additional candidate genes controlled by RFX1 and of new members of the RFX family. Moreover, the altered-specificity RFX1 mutants represent valuable tools that will permit the function of RFX1 to be analyzed in vivo without interference from the ubiquitously expressed endogenous protein. Finally, the simplicity, efficiency, and versatility of the selection procedure we have developed make it of general value for the determination of consensus motifs, and for the isolation of mutants exhibiting altered functional properties, for large protein domains involved in protein-DNA as well as protein-protein interactions.

Amino Acid Sequence↗

PubMed2005

First update of the international ASAS consensus statement for the use of anti-TNF agents in patients with ankylosing spondylitis.

OBJECTIVE: To update the international recommendations for use of anti-tumour necrosis factor (TNF) agents in the treatment of ankylosing spondylitis. METHODS: The published recommendations on anti-TNF treatment in ankylosing spondylitis formed the basis of the update. A questionnaire was sent to the ASAS (assessment in ankylosing spondylitis) members before the final decisions were agreed upon at an international meeting of the ASAS working group. RESULTS: Only minor changes to the original consensus statement were required. For the initiation of anti-TNF treatment, there should be: a diagnosis of definitive ankylosing spondylitis (normally based on modified New York criteria); active disease for at least four weeks, as defined by a sustained Bath ankylosing spondylitis disease activity index (BASDAI) of > or =4 on a 0-10 scale and expert opinion based on clinical findings; refractory disease, defined by failure of at least two non-steroidal anti-inflammatory drugs during a three month period, failure of intra-articular steroids (if indicated), and failure of sulfasalazine in patients with predominantly peripheral arthritis; and application of the usual precautions and contraindications for biological treatment. For monitoring anti-TNF treatment: both the ASAS core set for clinical practice and the BASDAI should be followed after the initiation of treatment. Discontinuation of anti-TNF treatment in non-responders should be considered after 6-12 weeks. Response is defined by improvement of at least 50% or 2 units (on a 0-10 scale) of the BASDAI. CONCLUSIONS: This updated consensus statement is recommended in guiding clinical practice and as a basis for developing national guidelines. Evaluation and regular update of this consensus statement is subject to further research by the ASAS group.

Antirheumatic Agents↗

PubMed2006

Consensus statement on injury definitions and data collection procedures in studies of football (soccer) injuries.

Variations in definitions and methodologies have created differences in the results and conclusions obtained from studies of football (soccer) injuries, making interstudy comparisons difficult. Therefore an Injury Consensus Group was established under the auspices of Fédération Internationale de Football Association Medical Assessment and Research Centre. A nominal group consensus model approach was used. A working document on definitions, methodology, and implementation was discussed by the group. Iterative draft statements were prepared and circulated to members of the group for comment before the final consensus statement was produced. Definitions of injury, recurrent injury, severity, and training and match exposures in football together with criteria for classifying injuries in terms of location, type, diagnosis, and causation are proposed. Proforma for recording players' baseline information, injuries, and training and match exposures are presented. Recommendations are made on how the incidence of match and training injuries should be reported and a checklist of issues and information that should be included in published reports of studies of football injuries is presented.

Athletic Injuries↗

PubMed1995

Consensus methods for medical and health services research.

Health providers face the problem of trying to make decisions in situations where there is insufficient information and also where there is an overload of (often contradictory) information. Statistical methods such as meta-analysis have been developed to summarise and to resolve inconsistencies in study findings--where information is available in an appropriate form. Consensus methods provide another means of synthesising information, but are liable to use a wider range of information than is common in statistical methods, and where published information is inadequate or non-existent these methods provide a means of harnessing the insights of appropriate experts to enable decisions to be made. Two consensus methods commonly adopted in medical, nursing, and health services research--the Delphi process and the nominal group technique (also known as the expert panel)--are described, together with the most appropriate situations for using them; an outline of the process involved in undertaking a study using each method is supplemented by illustrations of the authors' work. Key methodological issues in using the methods are discussed, along with the distinct contribution of consensus methods as aids to decision making, both in clinical practice and in health service development.

Consensus Statements as Topic↗

PubMed1999

A probabilistic approach to consensus multiple alignment.

We consider the problem of obtaining the maximum a posteriori probability (MAP) estimate of a consensus ancestral sequence for a set of DNA sequences. Our maximization method, called ASA (dnA Sequence Alignment), can be applied to the refinement of noisy regions of a DNA assembly, to the alignment of genomic functional sites, or to the alignment of any set of DNA sequences related by a star-like phylogeny. Along with the optimal consensus, ASA finds suboptimal solutions together with their relative probabilities. The probabilistic approach makes it possible to establish the limits to which an ancestor can in principle be recovered from diverged sequences. In simulations on rather short synthetic sequences (of length up to 80) with different coverage and error rates ranging from 5% to 30%, ASA restored the consensus from noisy observations essentially as best as is theoretically possible for the given error rates. We also illustrate the performance of ASA on the alignment of E.Coli promoters and the Alu-Sb subfamily of human repeat sequences. Since our model is a special case of a profile HMM, we give a comparison between these two approaches, as well as with other DNA alignment methods.

Base Sequence↗

PubMed2004

Enhancing research in academic radiology departments: recommendations of the 2003 Consensus Conference.

Opportunities for funded radiologic research are greater than ever, and the amount of federal funding coming to academic radiology departments is increasing. Even so, many medical school-based radiology departments have little or no research funding. Accordingly, a consensus panel was convened to discuss ways to enhance research productivity and broaden the base of research strength in as many academic radiology departments as possible. The consensus panel included radiologists who have leadership roles in some of the best-funded research departments, radiologists who direct other funded research programs, and radiologists with related expertise. The goals of the consensus panel were to identify the attributes associated with successful research programs and to develop an action plan for radiology research based on these characteristics.

Academic Medical Centers↗

PubMed2005

Management of thyroid nodules detected at US: Society of Radiologists in Ultrasound consensus conference statement.

The Society of Radiologists in Ultrasound convened a panel of specialists from a variety of medical disciplines to come to a consensus on the management of thyroid nodules identified with thyroid ultrasonography (US), with particular focus on which nodules should be subjected to US-guided fine needle aspiration and which thyroid nodules need not be subjected to fine-needle aspiration. The panel met in Washington, DC, October 26-27, 2004, and created this consensus statement. The recommendations in this consensus statement, which are based on analysis of the current literature and common practice strategies, are thought to represent a reasonable approach to thyroid nodular disease.

Humans↗