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Biomedical subjects

M Steel

Publications and source records attributed to M Steel.

At least 19 recordsLinked to original sources

Distributions of cherries for two models of trees.

Null models for generating binary phylogenetic trees are useful for testing evolutionary hypotheses and reconstructing phylogenies. We consider two such null models - the Yule and uniform models - and in particular the induced distribution they generate on the number C(n) of cherries in the tree, where a cherry is a pair of leaves each of which is adjacent to a common ancestor. By realizing the process of cherry formation in these two models by extended Polya urn models we show that C(n) is asymptotically normal. We also give exact formulas for the mean and standard deviation of the C(n) in these two models. This allows simple statistical tests for the Yule and uniform null hypotheses.

Models, Biological↗

Parsimony, likelihood, and the role of models in molecular phylogenetics.

Methods such as maximum parsimony (MP) are frequently criticized as being statistically unsound and not being based on any "model." On the other hand, advocates of MP claim that maximum likelihood (ML) has some fundamental problems. Here, we explore the connection between the different versions of MP and ML methods, particularly in light of recent theoretical results. We describe links between the two methods--for example, we describe how MP can be regarded as an ML method when there is no common mechanism between sites (such as might occur with morphological data and certain forms of molecular data). In the process, we clarify certain historical points of disagreement between proponents of the two methodologies, including a discussion of several forms of the ML optimality criterion. We also describe some additional results that shed light on how much needs to be assumed about underlying models of sequence evolution in order to successfully reconstruct evolutionary trees.

Evolution, Molecular↗

Slimming on the Internet.

The first 50 websites identified on searching the Internet for 'weight loss diets' were assessed systematically and their content compared with published clinical guidelines for management of obesity. The relevance and quality of the sites varied enormously. Only 3 confined themselves to sound dietary advice. Most promoted dietary supplements or other 'slimming aids', often of uncertain composition and based on dubious physiological principles. Potential hazards--for example, those of very low calorie diets--were rarely highlighted and certain regimens on offer were potentially dangerous.

Clinical Protocols↗

Normal induction of oral tolerance in the absence of a functional IL-12-dependent IFN-gamma signaling pathway.

There is considerable evidence that regulatory cytokines play an important role in mediating the systemic tolerance found after oral administration of protein Ags. Although most existing work has focused on cytokines such as IL-4, IL-10, and TGF-beta, recent evidence from TCR transgenic systems suggests that the induction of oral tolerance is accompanied by priming of Ag-specific IFN-gamma production. IFN-gamma has also been implicated as a mediator of T cell tolerance in other models in vivo and in vitro, including that induced by aerosol administration of protein. We show here that feeding tolerogenic doses of OVA primes for IFN-gamma production in the spleen of mice with a normal T cell repertoire. However, depleting IFN-gamma at the time of feeding OVA had no effect on the induction of tolerance. In addition, tolerance was induced normally in both IFN-gamma receptor knockout (IFN-gammaR-/-) and IL-12 p40 knockout (IL-12-/-) mice. This was the case for all components of the systemic immune response and also with a variety of feeding protocols, including those believed to induce distinct regulatory mechanisms. We conclude that IL-12-dependent IFN-gamma-mediated regulation does not play an essential role in oral tolerance.

Administration, Oral↗

The impact of genetic counselling about breast cancer risk on women's risk perceptions and levels of distress.

Women referred to a familial breast cancer clinic completed questionnaires before and after counselling and at annual follow-up to assess their risk estimate and psychological characteristics. The aims were to determine whether those who attended the clinic overestimated their risk or were highly anxious and whether counselling influenced risk estimates and levels of distress. Women (n = 450) at this clinic were more likely to underestimate (39%) than overestimate (14%) their risk. Mean trait anxiety scores were higher than general population data (t = 4.9, n = 1059, P<0.001) but not significantly different from published data from other screening samples. Overestimators (z = 5.69, P<0.0001) and underestimators (z = -8.01, P<0.0001) reported significantly different risk estimates (i.e. increased accuracy) after counselling, but significant inaccuracies persisted. Over- (n = 12) and underestimators (n = 60) were still inaccurate in their risk estimates by a factor of 2 after counselling. Thirty per cent of the sample scored above the cut-off (5/6) for case identification on a screening measure for psychological distress, the General Health Questionnaire (GHQ). GHQ scores were significantly lower after counselling (t = 3.6, d.f. = 384, P = 0.0004) with no evidence of increasing risk estimate causing increased distress. The risk of distress after counselling was greater for younger women and those who were more distressed at first presentation. The counselling offered was effective in increasing the accuracy of risk perceptions without causing distress to those who initially underestimated their risk. It is worrying that inaccuracies persisted, particularly as the demand for service has since reduced the consultation time offered in this clinic. Further work is needed to evaluate alternative models of service delivery using more sophisticated methods of assessing understanding of risk.

Adult↗

Ethical, social and economic issues in familial breast cancer: a compilation of views from the E.C. Biomed II Demonstration Project.

Demand for clinical services for familial breast cancer is continuing to rise across Europe. Service provision is far from uniform and, in most centres, its evolution has been determined by local conditions, specifically by local research interests, rather than by central planning. However, in a number of countries there is evidence of progress towards co-ordinated development and audit of clinics providing risk assessment, counselling, screening and, in some cases, prophylactic intervention. Much important information should emerge from continued observation and comparative assessment of these developments. In most countries for which relevant data are available, there is a distinct bias towards higher social class among those who avail themselves of clinic facilities (in line with findings from many other health-promotion initiatives). This should be addressed when considering future organisation of clinical services. Molecular genetic studies designed to identify the underlying mutations responsible for familial breast cancer are not generally regarded as part of the clinical service and are funded through research grants (if at all). Economic considerations suggest that there is a case for keeping this policy under review. Familial cancers throw into sharp relief certain ethical and legal issues that have received much recent attention from government advisory bodies, patients' representatives, professional commentators and the popular media. Two are of particular importance; first, the right to gain access to medical records of relatives, in order to provide accurate risk assessment for a given family member, versus the right to privacy in respect of personal medical information and, second, the obligation (or otherwise) to inform family members of their risk status if they have not actively sought that knowledge. The legal position seems to vary from country to country and, in many cases, is unclear. In view of pressures to establish uniform approaches to medical confidentiality across the EC, it is important to evaluate the experience of participants in this Demonstration Programme and to apply the principle of "non-malfeasance" in formulating regulations that should govern future practice in this field. Data on economic aspects of familial breast cancer are remarkably sparse and outdated. As evidence accrues on the influence of screening and intervention programmes on morbidity and mortality, there is a strong case for evaluating the cost-effectiveness of different models of service provision.

Breast Neoplasms↗

Utilisation of prophylactic mastectomy in 10 European centres.

Increasingly women at high risk of breast cancer are opting for prophylactic surgery to reduce their risks. Data from 10 European centres that offer a risk counselling and screening service to women at risk show different approaches to the option of preventive surgery, although most centres adhere to a protocol including at least two risk counselling sessions and a psychological assessment. Thus far the combined centres have data on 174 women who have undergone prophylactic mastectomy with in excess of 400 women years of follow up. Operations were carried out on women with lifetime risks of 25-80%, with an average annual expected incidence rate of 1% per women. No breast cancers have occurred in this cohort. Long term follow up on an extended group of women will be necessary to truly address the risk of subsequent breast cancer and the psychological sequelae.

Adult↗

Serine proteases in rodent hippocampus.

Brain serine proteases are implicated in developmental processes, synaptic plasticity, and in disorders including Alzheimer's disease. The spectrum of the major enzymes expressed in brain has not been established previously. We now present a systematic study of the serine proteases expressed in adult rat and mouse hippocampus. Using a combination of techniques including polymerase chain reaction amplification and Northern blotting we show that tissue-type plasminogen activator (t-PA) is the major species represented. Unexpectedly, the next most abundant species were RNK-Met-1, a lymphocyte protease not reported previously in brain, and two new family members, BSP1 (brain serine protease 1) and BSP2. We report full-length sequences of the two new proteases; homologies indicate that these are of tryptic specificity. Although BSP2 is expressed in several brain regions, BSP1 expression is strikingly restricted to hippocampus. Other enzymes represented, but at lower levels, included elastase IV, proteinase 3, complement C2, chymotrypsin B, chymotrypsin-like protein, and Hageman factor. Although thrombin and urokinase-type plasminogen activator were not detected in the primary screen, low level expression was confirmed using specific polymerase chain reaction primers. In contrast, and despite robust expression of t-PA, the usual t-PA substrate plasminogen was not expressed at detectable levels.

Amino Acid Sequence↗

Modeling the covarion hypothesis of nucleotide substitution.

A "covarion" model for nucleotide substitution that allows sites to turn "on" and "off" with time was proposed in 1970 by Fitch and Markowitz. It has been argued recently that evidence supports such models over later, alternative models that postulate a static distribution of rates across sites. However, in contrast with these latter well-studied models, little is known about the analytic properties of the former model. Here we analyze a covarion-style model and show (i) how to obtain the evolutionary distance between two species from the expected proportion of sites where two species differ, (ii) that the covarion model gives identical results to a suitably chosen rates-across-sites model if several sequences are compared in pairs by using only the expected proportion of sites at which they differ, (iii) conditions under which the two models will give identical results if the full joint probability matrix is examined, and (iv) that the two models can, in principle, be distinguished when there are at least four monophyletic groups of species. This last result is based on a distance measure that is tree additive under certain versions of the covarion model but, in general, will not be additive under a rates-across-sites model. The measure constructed does not require knowledge of the parameters of the model and so shows that sequences generated by the covarion model do in fact contain information about the underlying tree.

Analysis of Variance↗

Gene-trapping to identify and analyze genes expressed in the mouse hippocampus.

Mice harboring random gene-trap insertions of a lacZ (beta-galactosidase)-neomycin resistance fusion cassette (beta-geo) were analyzed for expression in the hippocampus. In 4 of 15 lines reporter gene activity was observed in the hippocampal formation. In the obn line, enzyme activity was detected in the CA1-3 hippocampal subfields, in hpk expression was restricted to CA1, but in both lines reporter activity was also present in other brain regions. In the third line, kin, reporter activity was robustly expressed throughout the stratum pyrimidale of CA1-3, with only low-level expression elsewhere. The final line (glnC) displayed ubiquitous expression of the reporter and was not analyzed further. Fusion transcripts for the first three lines were characterized; all encode polypeptides with features of membrane-associated signalling proteins. The obn fusion identified a human cDNA (B2-1) encoding a pleckstrin homology (PH) domain, while hpk sequences matched the Epstein-Barr Virus (EBV) inducible G-protein coupled receptor, EBI-1. kin identified an alternative form of the abl-related nonreceptor tyrosine kinase c-arg. Electrophysiological studies on mice homozygous for the insertions revealed normal synaptic transmission, paired pulse facilitation and paired-pulse depression at Schaffer collateral-commissural CA1 synapses, and normal long-term potentiation (LTP) in obn and kin. hpk mice displayed an increase in hippocampal CA1 long-term potentiation (LTP), suggesting a role for this receptor in synaptic plasticity.

Amino Acid Sequence↗

Better methods for solving parsimony and compatibility.

Evolutionary tree reconstruction is a challenging problem with important applications in biology and linguistics. In biology, one of the most promising approaches to tree reconstruction is to find the "maximum parsimony" tree, while in linguistics, the use of the "maximum compatibility" method has been very useful. However, these problems are NP-hard, and current approaches to solving these problems amount to heuristic searches through the space of possible tree topologies (a search which can, on large trees, take months to complete). In this paper, we present a new technique, Optimal Tree Refinement, for reconstructing very large trees. Our technique is motivated by recent experimental studies which have shown that certain polynomial time methods often return contractions of the true tree. We study the use of this technique in solving maximum parsimony and maximum compatibility, and present both hardness results and polynomial time algorithms.

Algorithms↗

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

Competing hypotheses seek to explain the evolution of oxygenic and anoxygenic processes of photosynthesis. Since chlorophyll is less reduced and precedes bacteriochlorophyll on the modern biosynthetic pathway, it has been proposed that chlorophyll preceded bacteriochlorophyll in its evolution. However, recent analyses of nucleotide sequences that encode chlorophyll and bacteriochlorophyll biosynthetic enzymes appear to provide support for an alternative hypothesis. This is that the evolution of bacteriochlorophyll occurred earlier than the evolution of chlorophyll. Here we demonstrate that the presence of invariant sites in sequence datasets leads to inconsistency in tree building (including maximum-likelihood methods). Homologous sequences with different biological functions often share invariant sites at the same nucleotide positions. However, different constraints can also result in additional invariant sites unique to the genes, which have specific and different biological functions. Consequently, the distribution of these sites can be uneven between the different types of homologous genes. The presence of invariant sites, shared by related biosynthetic genes as well as those unique to only some of these genes, has misled the recent evolutionary analysis of oxygenic and anoxygenic photosynthetic pigments. We evaluate an alternative scheme for the evolution of chlorophyll and bacteriochlorophyll.

Bacteriochlorophylls↗

Inactivation of Th1 and Th2 cells by feeding ovalbumin.

Several different mechanisms have been implicated in oral tolerance to protein antigens, depending on the nature and dose of antigen used and the species under study. Here, we have investigated the basis of unresponsiveness in a well-established model of oral tolerance in mice fed 25 mg ovalbumin (OVA). Our results show that CD8+ T-cell activity is suppressed by feeding OVA and that these cells are not required for the induction of tolerance. CD4+ T cells are essential for tolerance to occur, but both Th1 and Th2 cell-dependent functions are tolerized equally in OVA-fed mice. Peripheral lymph node cells from tolerized mice rapidly undergo apoptosis when cultured in vitro but produce substantial amounts of transforming growth factor beta (TGFbeta) in response to OVA. The appearance of tolerance in vivo is preceded by a transient phase of T-cell priming, and we propose that this model of oral tolerance reflects partial activation of T cells by fed antigen, leading to selective production of TGFbeta and consequent inactivation of all effector T cells. These findings indicate that the active suppression and clonal anergy identified previously in mice with oral tolerance may not be mutually exclusive phenomena.

Administration, Oral↗

Lymphocytes from orally tolerized mice display enhanced susceptibility to death by apoptosis when cultured in the absence of antigen in vitro.

The mechanism responsible for the induction of immunological tolerance by oral administration of soluble antigen remains unclear. Here we show that, when cultured in vitro in the absence of antigen, lymphocytes from mice tolerized with a single feed of 25 mg of ovalbumin display an enhanced mortality in comparison with cells from immunized control animals. This increased cell death affects both CD4+ and CD8+ T-lymphocyte subsets, and morphological and flow cytometric analyses suggest that it occurs via apoptosis. All of the changes associated with the propensity of tolerant cells to die by apoptosis in vitro are reduced by the inclusion of the tolerizing antigen in the cultures. These results suggest that tolerance to dietary proteins is accompanied by functional changes in T lymphocytes that render them susceptible to apoptosis. This mechanism may underlie the profound and permanent tolerance to food antigens found under physiological conditions and may provide a useful basis for immunotherapy.

Administration, Oral↗

A novel cytochrome P450 expressed primarily in brain.

hct-1 (hippocampal transcript) was detected in a differential screen of a rat hippocampal cDNA library. Expression of hct-1 was enriched in the formation but was also detected in rat liver and kidney, though at much lower levels; expression was barely detectable in testis, ovary, and adrenal. In liver, unlike brain, expression was sexually dimorphic; hepatic expression was greatly reduced in female rats. In mouse, brain expression was widespread, with the highest levels being detected in corpus callosum; only low levels were detected in liver. Sequence analysis of rat and mouse hct-1 cDNAs revealed extensive homologies with cytochrome P450s (CYPs), a diverse family of heme-binding monooxygenases that metabolize a range of substrates including steroids, fatty acids, and xenobiotics. Among the CYPs, hct-1 is most similar (39% at the amino acid sequence) to cholesterol 7 alpha-hydroxylase (CYP7) and contains a postulated steroidogenic domain present in other steroid-metabolizing CYPs but clearly represents a type of CYP not previously reported. Genomic Southern analysis suggests that a single gene corresponding to hct-1 is present in mouse, rat, and human. hct-1 is unusual in that, unlike all other CYPs described, the primary site of expression is in the brain. Similarity to CYP7 and other steroid-metabolizing CYPs may argue that hct-1 (CYP7B) plays a role in steroid metabolism in brain, notable because of the documented ability of brain-derived steroids (neurosteroids) to modulate cognitive function in vivo.

Amino Acid Sequence↗

T helper 2 cells are subject to high dose oral tolerance and are not essential for its induction.

Oral administration of aqueous protein Ag results in profound immunologic tolerance, and it has been suggested previously that this reflects selective activation of Th subsets. Here we show that the induction of oral tolerance by feeding a single high dose of OVA to mice significantly reduces the production of both Th1- and Th2-dependent cytokines and is accompanied by a marked reduction of specific Abs of both the IgG2a and IgG1 isotypes in vivo. Oral tolerance was also induced normally in IL-4-deficient mice. These results indicate that both subsets of the Th cell are equally susceptible to the induction of tolerance with a single high dose of Ag delivered via the oral route and that this phenomenon does not require Th2 cells.

Administration, Oral↗