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PubMed1984

The 5'-terminal sequence of U1 RNA complementary to the consensus 5' splice site of hnRNA is single-stranded in intact U1 snRNP particles.

The 5'-terminal region of U1 snRNA is highly complementary to the consensus exon-intron regions of hnRNA and it has been suggested that U1 snRNP might play a role in the splicing of the pre-mRNA by intermolecular base-pairing between these regions. Here the secondary structure of the 5' terminus of U1 RNA in the isolated native U1 snRNP particle has been investigated by site-directed enzymatic cleavage of the RNA. Individual oligodeoxynucleotides complementary to various sequences within the first 15 nucleotides of the 5' terminus of U1 RNA have been tested for their ability to form stable DNA X RNA hybrids, with subsequent cleavage of the U1 RNA by RNase H. Our results show unequivocally that the 9 nucleotides at the 5' terminus which are complementary to a consensus 5' splice site are indeed single-stranded in the intact U1 snRNP particle, and are not protected by snRNP proteins. However, they also indicate that the U1 sequence complementary to an intron's consensus 3' end is not readily available for intermolecular base-pairing, either in the intact U1 snRNP particle or in the deproteinized U1 RNA molecule. Therefore our data favour the possibility that U1 snRNP plays a role only in the recognition of a 5' splice site of hnRNA, rather than being involved in the alignment of both ends of an intron for splicing.

Autoantibodies↗

PubMed1985

The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini.

Our previous DNA sequence comparisons of 3' terminal portions from equivalent herpes simplex virus type 1 (HSV-1) and HSV-2 genes identified a conserved sequence (consensus YGTGTTYY; Y = pyrimidine) located approximately 30bp downstream from the AATAAA signal. We report here that this signal is located downstream from 67% of the mammalian mRNA 3' termini examined. Using constructions with the bacterial chloramphenicol acetyl transferase (CAT) gene linked to an HSV 'terminator' fragment, we show that deletions in the 'terminator' reduce CAT activities and the levels of CAT mRNA 3' termini. Specifically: (1) deletions of downstream sequences which extend up to the consensus YGTGTTYY signal reduce CAT levels to values 35% of those obtained with undeleted plasmids, (2) a deletion of a further 14bp, which removes the YGTGTTYY consensus but not the poly A site, reduces CAT activities to 1%-4%. The levels of CAT mRNA 3' termini reflect the reductions in CAT activities however, levels of mRNA 5' termini are unaffected by these deletions. The RNA produced in the absence of the YGTGTTYY signal is present in the cytoplasm although no CAT activity is detectable.

Acetyltransferases↗

PubMed1986

Splice site consensus sequences are preferentially accessible to nucleases in isolated adenovirus RNA.

The conformation of RNA sequences spanning five 3' splice sites and two 5' splice sites in adenovirus mRNA was probed by partial digestion with single-strand specific nucleases. Although cleavage of nucleotides near both 3' and 5' splice sites was observed, most striking was the preferential digestion of sequences near the 3' splice site. At each 3' splice site a region of very strong cleavage is observed at low concentrations of enzyme near the splice site consensus sequence or the upstream branch point consensus sequence. Additional sites of moderately strong cutting near the branch point consensus sequence were observed in those sequences where the splice site was the preferred target. Since recognition of the 3' splice site and branch site appear to be early events in mRNA splicing these observations may indicate that the local conformation of the splice site sequences may play a direct or indirect role in enhancing the accessibility of sequences important for splicing.

Adenovirus Early Proteins↗

PubMed1988

Defining the consensus sequences of E.coli promoter elements by random selection.

The consensus sequence of E.coli promoter elements was determined by the method of random selection. A large collection of hybrid molecules was produced in which random-sequence oligonucleotides were cloned in place of a wild-type promoter element, and functional -10 and -35 E.coli promoter elements were obtained by a genetic selection involving the expression of a structural gene. The DNA sequences and relative levels of function for -10 and -35 elements were determined. The consensus sequences determined by this approach are very similar to those determined by comparing DNA sequences of naturally occurring E.coli promoters. However, no strong correlation is observed between similarity to the consensus and relative level of function. The results are considered in terms of E.coli promoter function and of the general applicability of the random selection method.

Base Sequence↗

PubMed1989

The effect of E. coli host strain on the consensus sequence of regions of the human L1 transposon.

We have used highly methylation tolerant host strains to clone hyper- and hypo-methylated genomic elements from different regions of the same family of long interspersed repetitive elements from human DNA, specifically the 1.8 kilobase (kb) and 1.2kb KpnI fragments from members of the L1 family of transposable elements in which respectively some 18% and 2.7% of cytosines are methylated in vivo in human spleen DNA. The consensus of the DNA sequences of the ends of 13 clones from the hypomethylated region of human L1 agreed exactly with the consensus derived previously from clones made using conventional host strains. However the sequences of 18 of our clones from the 5' end of the hypermethylated region differed significantly from the sequences of clones made using conventional hosts (P less than 0.0001). The 5' region of the 1.8kb L1 region is a CpG island which, in human somatic tissue, appears to be maintained in a highly methylated state, including methylation at sites other than CpG dinucleotides. The consensus sequence of this region also has features suggestive of a previously unrecognized open reading frame.

Base Sequence↗

PubMed1990

Transcription in vivo directed by consensus sequences of E.coli promoters: their context heavily affects efficiencies and start sites.

We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer linking them is AT or GC rich, or is as short as 14 bp or as large as 26 bp (standard size 17 bp). However, we find that the context influences transcription efficiency by as much as an order of magnitude, and is able to scatter transcription start sites over a region of as much as 30 bp, including start sites within a CH or even between the two sequences of the CH pair. The results demonstrate that, although the CH pair can be sufficient for directing transcription by E.coli RNAP, important determinants for promoter activity are at least in part contained in the context of the consensus sequences; they advocate a synergic interplay of signals borne by the CH pair and its context, extending over all parts of the promoter sequence. A two-step model is proposed, in which properly located consensus sequences provide RNAP with facilities required for stereospecific docking along the promoter sequence; the result would be a sharp change in the local environment of the double helix inducing local isothermal unwinding. The size of the loop (related to the AT constraint in the promoter) and the extend of the environmental change required for unwinding would determine the rate of transcriptionally competent complex formation, positioning and grouping of start sites.

Base Sequence↗

PubMed1991

Nucleotides within both proximal and distal parts of the consensus sequence are important for specific DNA recognition by the herpes simplex virus regulatory protein ICP4.

The herpes simplex virus type 1 regulatory protein ICP4 is a sequence specific DNA binding protein which associates with a number of different sites, some of which include the consensus ATCGTCnnnnYCGRC. In order to investigate the involvement in DNA binding of conserved bases within the consensus, we have synthesised a family of mutant oligonucleotides and tested their ability to form a complex with ICP4. We have also compared the binding specificities of bacterially expressed fragments of ICP4 which include the DNA binding domain. Mutation of most (but not all) bases in the proximal part of the consensus greatly reduced binding by ICP4, as did a mutation affecting the distal part. Most (but not all) G residues identified in methylation interference assays were required for efficient binding. While a bacterially expressed ICP4 peptide encompassing amino acid residues 252-523 bound to DNA with a specificity similar to that of the whole protein, a shorter protein (residues 275-523) had a slightly relaxed DNA binding specificity.

Base Sequence↗

PubMed2004

Consensus alignment server for reliable comparative modeling with distant templates.

Consensus is a server developed to produce high-quality alignments for comparative modeling, and to identify the alignment regions reliable for copying from a given template. This is accomplished even when target-template sequence identity is as low as 5%. Combining the output from five different alignment methods, the server produces a consensus alignment, with a reliability measure indicated for each position and a prediction of the regions suitable for modeling. Models built using the server predictions are typically within 3 A rms deviations from the crystal structure. Users can upload a target protein sequence and specify a template (PDB code); if no template is given, the server will search for one. The method has been validated on a large set of homologous protein structure pairs. The Consensus server should prove useful for modelers for whom the structural reliability of the model is critical in their applications. It is currently available at http://structure.bu.edu/cgi-bin/consensus/consensus.cgi.

Algorithms↗

PubMed2006

Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure.

Aberrant activation of the translation initiation machinery is a common property of malignant cells, and is essential for breast carcinoma cells to manifest a malignant phenotype. How does sustained activation of the rate limiting step in protein synthesis so fundamentally alter a cell? In this report, we test the post transcriptional operon theory as a possible mechanism, employing a model system in which apoptosis resistance is conferred on NIH 3T3 cells by ectopic expression of eIF4E. We show (i) there is a set of 255 transcripts that manifest an increase in translational efficiency during eIF4E-mediated escape from apoptosis; (ii) there is a novel prototype 55 nt RNA consensus hairpin structure that is overrepresented in the 5'-untranslated region of translationally activated transcripts; (iii) the identified consensus hairpin structure is sufficient to target a reporter mRNA for translational activation under pro-apoptotic stress, but only when eIF4E is deregulated; and (iv) that osteopontin, one of the translationally activated transcripts harboring the identified consensus hairpin structure functions as one mediator of the apoptosis resistance seen in our model. Our findings offer genome-wide insights into the mechanism of eIF4E-mediated apoptosis resistance and provide a paradigm for the systematic study of posttranscriptional control in normal biology and disease.

5' Untranslated Regions↗

PubMed2000

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.

A consensus approach has been developed for identifying distant structural homologues. This is based on the CATH Dictionary of Homologous Superfamilies (DHS), a database of validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies (URL: http://www. biochem.ucl.ac.uk/bsm/dhs). Multiple structural alignments have been generated for 362 well-populated superfamilies in the CATH structural domain database and annotated with secondary structure, physicochemical properties, functional sequence patterns and protein-ligand interaction data. Consensus functional information for each superfamily includes descriptions and keywords extracted from SWISS-PROT and the ENZYME database. The Dictionary provides a powerful resource to validate, examine and visualize key structural and functional features of each homologous superfamily. The value of the DHS, for assessing functional variability and identifying distant evolutionary relationships, is illustrated using the pyridoxal-5'-phosphate (PLP) binding aspartate aminotransferase superfamily. The DHS also provides a tool for examining sequence-structure relationships for proteins within each fold group.

Amino Acid Sequence↗

PubMed2005

Leflunomide in rheumatoid arthritis: recommendations through a process of consensus.

OBJECTIVES: To determine, by consensus, the optimal use of leflunomide in rheumatoid arthritis (RA), using a multidisciplinary panel of experts and performing meta-analyses of available data. METHODS: A multidisciplinary panel of experts in RA was convened. Important questions, pertinent to the use of leflunomide in the treatment of RA, were defined by consensus at an initial meeting. Each question was allocated to subgroups of two or three members, who worked separately to prepare a balanced opinion, based on published literature, data from individual patients taking part in phase II and phase III clinical trials provided by Aventis, and data from a USA-based medical claims database (AETNA). The full group then reconvened to agree on an overall consensus statement. Recommendations concerning efficacy and tolerability versus comparator drugs and placebo were derived from two new meta-analyses. RESULTS: Leflunomide was at least as effective as sulphasalazine and methotrexate, and equally well tolerated on meta-analysis of trial data. Overall withdrawal rates for all adverse events were similar for all three drugs. Avoidance of the loading dose reduces 'nuisance' side-effects (e.g. nausea), but probably delays the onset of action. Adverse events could usually be managed by dose reduction and/or symptomatic therapy. CONCLUSIONS: On the basis of efficacy, safety and cost, leflunomide should be considered in patients with RA who have failed first-line DMARD drug therapy. In refractory cases, leflunomide may be used in combination with, for example, methotrexate before biological agents. Therapy should be initiated by a specialist, but repeat prescribing in general practice on a shared care basis is acceptable using agreed protocols. Clear mechanisms are required to monitor toxicity, with good communication between the patient and rheumatologist to manage nuisance side-effects and avoid unnecessary discontinuation of leflunomide.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed2002

Carboxy-terminal proteolytic processing at a consensus furin cleavage site is a prerequisite event for quail ZPC secretion.

In avian species, a glycoprotein homologous to mammalian ZPC is synthesized in the granulosa cells of developing follicles. We have previously reported that the newly synthesized ZPC (proZPC) in granulosa cells is cleaved at a consensus furin cleavage site to generate mature ZPC prior to secretion. In the present study, we examined the effect of the proteolytic cleavage of proZPC on ZPC secretion by using a specific inhibitor of furin endoprotease and site-directed mutagenesis of the furin cleavage site. Western blot analysis demonstrated that the furin inhibitor efficiently blocked both the proteolytic cleavage of proZPC and the subsequent ZPC secretion. A site-directed mutant that possessed a mutated sequence for furin cleavage was not secreted from the cells. The immunocytochemical observations indicated that proZPC produced in the presence of a furin inhibitor or those produced by the site-directed mutant of the furin cleavage site had accumulated in the endoplasmic reticulum. These results indicate that proZPC is proteolytically cleaved at the consensus furin cleavage site with furin-like protease, and the failure of this cleavage results in its accumulation in the endoplasmic reticulum. Therefore, the C-terminal proteolytic processing of proZPC at the consensus furin cleavage site is a prerequisite event for quail ZPC secretion.

Animals↗

PubMed1994

Changes in blood transfusion practices after the introduction of consensus guidelines in Mwanza region, Tanzania.

OBJECTIVE: To assess the effect of introducing consensus guidelines on avoidable blood transfusions in Mwanza region, Tanzania. METHODS: Avoidable blood transfusions were determined among 842 blood transfusion recipients in eight hospitals in 1991. In a workshop with senior health workers from the region, consensus guidelines for the prescription of blood transfusions were developed and introduced in the hospitals and after 7 months intervention data were collected on 1042 blood transfusion recipients. The 1991 and 1992 data were compared to estimate the change in the proportion of avoidable blood transfusions. RESULTS: In blood transfusion recipients aged < 5 years there was a significant reduction in the proportion of avoidable blood transfusions from 257 (52%) out of 498 to 197 (33%) out of 595 (P < 0.001), especially at the peripheral hospitals. For children the proportion decreased from 25 to 17% (P < 0.05) and for operated patients the percentage remained at 24%. In pregnant women there was a significant increase in the proportion of avoidable blood transfusions from 10 to 27% and in adults from 37 (25%) out of 146 to 121 (50%) out of 242. The improvement in peripheral hospitals was offset by a similar deterioration in the referral hospital, thus no overall reduction was achieved in the proportion of avoidable blood transfusions. CONCLUSION: The development and introduction of consensus guidelines was not sufficient to change prescribing practice. The proportion of avoidable blood transfusions decreased only in hospitals where compliance was maintained through regular clinic meetings and strict supervision by senior medical staff.

Blood Transfusion↗

PubMed1997

Dementia and driving: an attempt at consensus.

The number of older drivers in Sweden will be rapidly increasing during the next decades. A possible relationship exists between the increased relative crash risk of older drivers and the prevalence of age-related diseases such as dementia. However, a clear-cut policy for evaluating driving competence in demented persons is still lacking. In recognition of this fact, the Swedish National Road Administration invited a group of researchers to formulate a consensus on the issue of driving and dementia. This consensus document is aimed at providing primary care physicians with practical advice concerning the assessment of cognitive status in relation to driving. Suggestions are based on a review of existing research and discuss the use of general and driving-specific sources of information available to the physician. Consensus was reached on the statement that a diagnosis of moderate to severe dementia precludes driving and that certain individuals with mild dementia should be considered for a specialized assessment of their driving competence.

Aged↗

PubMed1994

Management of moderate head injury in childhood: degree of consensus among Canadian pediatric emergency physicians.

The purpose of this study was to assess the degree of consensus among Canadian pediatric emergency physicians regarding the management of moderate head injury in children. A questionnaire regarding the management of moderate head injury in a child was developed, and it concentrated on indications for admission and policies regarding skull radiograph. The questionnaire was given to all pediatricians who are members of the Emergency Section of the Canadian Pediatric Society (n = 33) and who represent 15 Canadian pediatric emergency departments. The outcome was measured by the degree of consensus regarding management of children with moderate head injury. Twenty-three of 33 (70%) questionnaires, representing 14 of 15 (93%) emergency departments, were returned. Only five of 23 (22%) questionnaires report routinely admitting otherwise well children with short (three minutes or less) loss of consciousness; five (22%) routinely order a skull radiograph - three (13%) routinely do both. Certain clinical indicators led to 70 to 80% agreement regarding admission: severe headache, seizures, depressed skull fracture, and persistent vomiting. Agreement of more than 70% regarding indications for ordering a skull radiograph was achieved only for clinical suspicion of a depressed skull fracture. In conclusion, for the average child who is well after a loss of consciousness after a head injury lasting three minutes or less, the majority of respondents do not routinely admit the child or order a routine skull radiograph. A reasonable degree of consensus (70-80%) regarding ordering of skull radiographs and admission is based on clinical criteria.

Canada↗

PubMed2001

Treatment of depression in women: a summary of the expert consensus guidelines.

Women constitute two-thirds of patients suffering from common depressive disorders, making the treatment of depression in women a substantial public health concern. However, high-quality, empirical data on depressive disorders specific to women are limited, and there are no comprehensive evidence-based practice guidelines on the best treatments for these illnesses. To bridge the gap between research evidence and key clinical decisions, the authors developed a survey of expert opinion concerning treatment of four depressive conditions specific to women: premenstrual dysphoric disorder, depression in pregnancy, postpartum depression in a mother choosing to breast-feed, and depression related to perimenopause/menopause. The survey asked about 858 treatment options in 117 clinical situations and included a broad range of pharmacological, psychosocial, and alternative medicine approaches. The survey was sent to 40 national experts on women's mental health issues, 36 (90%) of whom completed it. The options, scored using a modified version of the RAND Corporation's 9-point scale for rating appropriateness of medical decisions, were assigned one of three categorical rankings-first line/preferred choice, second line/alternate choice, third line/usually inappropriate-based on the 95% confidence interval of each item's mean rating. The expert panel reached consensus (defined as a non-random distribution of scores by chi-square "goodness-of-fit" test) on 76% of the options, with greater consensus in situations involving severe symptoms. Guideline tables indicating preferred treatment strategies were then developed for key clinical situations. The authors summarize the expert consensus methodology they used and then, for each of the four key areas, review the treatment literature and summarize the experts' recommendations and how they relate to the research findings. For women with severe symptoms in each area we asked about, the first-line recommendation was antidepressant medication combined with other modalities (generally psychotherapy). These recommendations parallel existing guidelines for severe depression in general populations. For initial treatment of milder symptoms in each situation, the panel was less uniform in recommending antidepressants, and either gave equal endorsement to other treatment modalities (e.g., nutritional or psychobehavioral approaches in PMDD; hormone replacement in perimenopause) or preferred psychotherapy over medication (during conception, pregnancy, or lactation). In all milder cases, however, antidepressants were recommended as at least second-line options. Among antidepressants, selective serotonin reuptake inhibitors (SSRIs) were recommended as first-line treatment in all situations. The specific SSRIs that were preferred depended on the particular clinical situation. Tricyclic antidepressants were highly rated alternatives to SSRIs in pregnancy and lactation. In evaluating many of the treatment options, the experts had to extrapolate beyond controlled data in comparing treatment options with each other or in combination. Within the limits of expert opinion and with the expectation that future research data will take precedence, these guidelines provide some direction for addressing common clinical dilemmas in women, and can be used to inform clinicians and educate patients regarding the relative merits of a variety of interventions.

Journal Article↗

PubMed2003

The "Gent" consensus on perforator flap terminology: preliminary definitions.

Due to its increasing popularity, more and more articles on the use of perforator flaps have been reported in the literature during the past few years. Because the area of perforator flaps is new and rapidly evolving, there are no definitions and standard rules on terminology and nomenclature, which creates confusion when surgeons try to communicate and compare surgical techniques. This article attempts to represent the opinion of a group of pioneers in the field of perforator flap surgery. This consensus was reached after a terminology consensus meeting held during the Fifth International Course on Perforator Flaps in Gent, Belgium, on September 29, 2001. It stipulates not only the definitions of perforator vessels and perforator flaps but also the correct nomenclature for different perforator flaps. The authors believe that this consensus is a foundation that will stimulate further discussion and encourage further refinements in the future.

Humans↗

PubMed2006

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.

Journal Article↗