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D Baker

Publications and source records attributed to D Baker.

At least 37 records · Page 2Linked to original sources
PubMed1997

A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding.

To gain insight into the free energy changes accompanying protein hydrophobic core formation, we have used computer simulations to study the formation of small clusters of nonpolar solutes in water. A barrier to association is observed at the largest solute separation that does not allow substantial solvent penetration. The barrier reflects an effective increase in the size of the cavity occupied by the expanded but water-excluding cluster relative to both the close-packed cluster and the fully solvated separated solutes; a similar effect may contribute to the barrier to protein folding/unfolding. Importantly for the simulation of protein folding without explicit solvent, we find that the interactions between nonpolar solutes of varying size and number can be approximated by a linear function of the molecular surface, but not the solvent-accessible surface of the solutes. Comparison of the free energy of cluster formation to that of dimer formation suggests that the assumption of pair additivity implicit in current protein database derived potentials may be in error.

Kinetics↗
PubMed1997

Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns.

We have used cluster analysis to identify recurring sequence patterns that transcend protein family boundaries. A subset of these patterns occur predominantly in a single type of local structure in proteins. Here we characterize the three-dimensional structures and contexts in which these sequence patterns occur, with particular attention to the interactions responsible for their structural selectivity.

Algorithms↗
PubMed1997

Polygenic control of experimental allergic encephalomyelitis in Biozzi ABH and BALB/c mice.

Experimental allergic encephalomyelitis (EAE) is a chronic inflammatory disease of the central nervous system (CNS), with many similarities to multiple sclerosis (MS). Susceptibility to EAE is under genetic control of both the major histocompatibility complex (MHC) and unknown non-MHC gene products. This study uses a selective cross between EAE-susceptible ABH and low responder BALB/c mice, where disease is dominant and affects female mice significantly more than males. In a genome screen using microsatellite markers, linkage analysis suggests that genes encoded on chromosomes 4, 8, 10, 11, 12 and 17 contribute to the development of EAE (p < 0.05), although none of these putative EAE loci fulfilled the criteria for significant linkage. Interestingly, genotype frequency showed significant deviation from the expected random distribution of alleles on chromosomes 4, 8 and 17, (p < 0.001), with 32% of mice developing disease, exhibiting all 3 alleles (p < 0.001). This may indicate complex interactions amongst gene products in the EAE phenotype. This and other recent studies in different mouse strains underlies that EAE is a complex polygenic trait and may provide clues to the genetic mechanisms involved in autoimmune diseases such as multiple sclerosis.

Animals↗
PubMed1997

Characterization of the cellular and cytokine response in the central nervous system following Semliki Forest virus infection.

Cytokines are important mediators in the pathogenesis of central nervous system (CNS) inflammatory diseases including multiple sclerosis (MS), experimental allergic encephalomyelitis (EAE), viral encephalitis and virus induced demyelinating diseases. We have used immunohistochemical techniques to characterize the mononuclear cell infiltrate and cytokine profiles in the CNS following infection of mice with the demyelinating A7(74) strain of Semliki Forest virus (SFV), an important viral model of MS. Mononuclear cell infiltrates in the CNS, first observed at 3 days and maximal during clearance of infectious virus, were comprised predominantly of CD8+ lymphocytes. F4/80+ macrophage/microglia and CD45/B220+ B lymphocytes were most numerous during the subsequent phase of demyelination. CD4+ T-lymphocytes were observed at low levels throughout infection. By immunostaining MHC class I, IL-1beta , IL-3 and TGF beta1 were constitutively expressed in normal mice and were upregulated following infection. MHC class II, IL-1alpha, IL-2, IL-2R, TNF-alpha and IL-6 were strongly upregulated in the CNS of SFV-infected mice and mice with chronic relapsing EAE. The spatial and temporal distribution of these cytokines during the course of disease was analysed. Whereas IL-1alpha, IL-1beta, IL-10, and TGF beta1 were observed on day 3 following infection GMCSF, IL-2 and TNF alpha were first apparent at day 7 when the cellular infiltration in the CNS was most intense. In contrast IFN gamma and IL-6 were first observed on day 10 prior to the demyelination phase of disease. Cytokines in the lesions of demyelination suggest a role in the pathogeneisis of myelin damage. Based on cytokine profiles no clear bias of either a Th1 or Th2 response was observed in the CNS during infection.

Alphavirus Infections↗
PubMed1997

The relationship between condition-specific morbidity, social support and material deprivation in pregnancy and early motherhood. ALSPAC Survey Team. Avon Longitudinal Study of Pregnancy and Childhood.

Poorer health has been consistently associated with both low levels of social support and material deprivation. It has been proposed that social support constitutes a causal link between health and deprivation such that those with lower socio-economic status have poorer health because their lack of social support makes them more vulnerable to disease. This assumption was tested in this study for women moving from pregnancy to early motherhood. The sample of 9208 women was drawn from the Avon Longitudinal Study of Pregnancy and Childhood (ALSPAC). Health status was measured by self-report of morbidity for three contrasting conditions: backache, depression and urinary infection. Data were collected by self-completion questionnaire at eight weeks prepartum and at eight weeks postpartum. The sample was divided into four groups for each condition on the basis of identification of the condition (1) on both occasions, (2) on neither occasion, (3) at eight weeks prepartum only, and (4) at eight weeks postpartum only. Chi-square tests were used to measure the association between presence or absence of a condition as defined above, material deprivation and low social support. Responses on an eight item social support questionnaire tapping emotional, instrumental and communal aspects of perceived social support were compared between these groups for each condition. Results showed significant associations, in late pregnancy and early motherhood, between poorer health and both material deprivation and low social support for two of the three conditions, depression and urinary infection. Changes in levels of perceived social support occurred as a consequence of motherhood; the percentage of women perceiving their partner to be supportive decreased as did the percentage of those who felt that their family or friends would help with financial difficulties; in contrast, the percentage of those perceiving that other mothers/neighbours offered support increased from late pregnancy to early motherhood. The extent and direction of such change was consistently associated with the presence or absence of depression, but not with backache or urinary infection. When mental health "improved", in that depression was present pre- but not postpartum, the percentage feeling supported increased and vice versa. This pattern was in evidence across all items of social support. It was concluded that perceived social support was unlikely in itself to constitute a causal link between poorer health and lower socio-economic status. In this context the relationship between social support and depression requires further consideration, particularly the extent to which they constitute component parts of a more general feeling of emotional well-being, a construct which is, in its turn, in need of further articulation in relation to health outcomes.

Adult↗
PubMed1997

Characterization of the free energy spectrum of peptostreptococcal protein L.

BACKGROUND: Native state hydrogen/deuterium exchange studies on cytochrome c and RNase H revealed the presence of excited states with partially formed native structure. We set out to determine whether such excited states are populated for a very small and simple protein, the IgG-binding domain of peptostreptococcal protein L. RESULTS: Hydrogen/deuterium exchange data on protein L in 0-1.2 M guanidine fit well to a simple model in which the only contributions to exchange are denaturant-independent local fluctuations and global unfolding. A substantial discrepancy emerged between unfolding free energy estimates from hydrogen/deuterium exchange and linear extrapolation of earlier guanidine denaturation experiments. A better determined estimate of the free energy of unfolding obtained by global analysis of a series of thermal denaturation experiments in the presence of 0-3 M guanidine was in good agreement with the estimate from hydrogen/deuterium exchange. CONCLUSIONS: For protein L under native conditions, there do not appear to be partially folded states with free energies intermediate between that of the folded and unfolded states. The linear extrapolation method significantly underestimates the free energy of folding of protein L due to deviations from linearity in the dependence of the free energy on the denaturant concentration.

Bacterial Proteins↗
PubMed1997

Functional rapidly folding proteins from simplified amino acid sequences.

Early protein synthesis is thought to have involved a reduced amino acid alphabet. What is the minimum number of amino acids that would have been needed to encode complex protein folds similar to those found in nature today? Here we show that a small beta-sheet protein, the SH3 domain, can be largely encoded by a five letter amino acid alphabet but not by a three letter alphabet. Furthermore, despite the dramatic changes in sequence, the folding rates of the reduced alphabet proteins are very close to that of the naturally occurring SH3 domain. This finding suggests that despite the vast size of the search space, the rapid folding of biological sequences to their native states is not the result of extensive evolutionary optimization. Instead, the results support the idea that the interactions which stabilize the native state induce a funnel shape to the free energy landscape sufficient to guide the folding polypeptide chain to the proper structure.

Amino Acid Sequence↗
PubMed1997

Inequality in health and health service use for mothers of young children in south west England. Survey Team of the Avon Longitudinal Study of Pregnancy and Childhood Team.

OBJECTIVE: To establish the degree of association between relative deprivation and any variation in condition specific morbidity and in consultations with general practitioners for mothers of young children. STUDY DESIGN: Condition specific morbidity and general practitioner consultation (GP) rates were recorded by means of self reports on a postal questionnaire. Subjects were asked to record whether they had suffered from any of 16 common conditions and, if so, whether they had consulted the GP. Relative deprivation was measured using indicators such as home ownership, overcrowded living conditions, car ownership, and partners' employment status. Information was also collected about the women's own employment status, their ages, and parity. SETTING: The three district health authorities of Bristol. All women expecting a baby between April 1991 and December 1992 were invited to participate. SUBJECTS: Altogether 11040 mothers who completed questionnaires about their own health and well being at 8 months postpartum as part of the Avon longitudinal study of pregnancy and childhood. OUTCOME MEASURES: The percentage of mothers reporting any of 16 common conditions since the birth of their child and the proportion of them who consulted the GP if a condition was reported. chi 2 tests of independence were used to examine the association between condition specific morbidity and social, demographic, and maternal characteristics. Latent class analysis was used to "cluster" mothers according to the particular configuration of social, demographic, and maternal characteristics associated with levels of morbidity for each of the six most commonly reported conditions. The probability of consulting a GP was then compared between clusters. RESULTS: Relative deprivation had a greater impact on morbidity and GP consultation for stress related conditions such as depression, anxiety, and headache/migraine. For all these conditions, higher levels of self reported morbidity and a greater probability of consulting the doctor were associated with a cluster of social disadvantage-living in rented accommodation, non-employment, younger age, and lower educational status. For other conditions such as backache, haemorrhoids, and cough/cold, however, higher morbidity was associated with a cluster of advantage-home ownership, uncrowded living conditions, use of car, and partner in employment. Where there was variation in the probability of consulting the GP for these conditions, it was linked to parity rather than socioeconomic factors. Higher levels of morbidity for all but one condition (backache) were also associated with having more than one child, but this cross-cut socioeconomic and demographic cluster characteristics; both more affluent, older mothers and younger, more deprived mothers were likely to be multiparous. CONCLUSIONS: Relative deprivation was associated with poorer mental but not physical health for this population of mothers of young children. These findings have implications for a more targeted approach to reducing inequality in health. The importance of examining inequality in health for women in relation to their own material circumstances, their employment status, and parity, is emphasised.

Adult↗
PubMed1997

Regulation of chronic relapsing experimental allergic encephalomyelitis by endogenous and exogenous glucocorticoids.

Expression, development and resolution of the acute form of experimental allergic encephalomyelitis (EAE), typically induced in the highly susceptible Lewis rat, are closely regulated by endogenous corticosteroids. Administration of synthetic glucocorticoids also efficiently controls the manifestation of disease. The pivotal role played by the corticosteroids in modifying the induction and progression of EAE is further emphasised by a reversal of corticoid-mediated effects through adrenalectomy or treatment with the steroid receptor antagonist RU486 (mifepristone). Chronic relapsing EAE (CREAE) is characterised by acute symptoms, periods of remission and re-emergence of disease. The mechanisms governing the development of CREAE are unclear, but may require the regulatory influence of endogenous glucocorticoids. The current study has monitored circulating corticosteroids throughout the course of CREAE in the Biozzi ABH mouse and found that major fluctuations in systemic levels coincide with the relapsing-remitting phases of the disease. Furthermore, increasing circulating adrenocorticoids through administration of the steroidal compound dexamethasone markedly suppresses the occurrence of acute signs. The importance of the glucocorticoids in controlling CREAE is again highlighted by the intensification of symptoms and reduction in the survival rate of inoculated mice receiving RU486 prior to and during the acute phase of disease. The data reinforce the amelioratory actions of exogenous and naturally occurring glucocorticoids in the pathogenesis of EAE and extend earlier observations in the monophasic disease by demonstrating corticosteroid-dependent effects in a relapsing-remitting mouse model.

Animals↗
PubMed1997

The anatomy of an OPTI: Part 2. The CORE system. Ohio Osteopathic Hospital Association. Ohio Association of Osteopathic Medical Directors. Ohio Osteopathic Association.

In July 1995, the American Osteopathic Association (AOA) Board of Trustees passed new regulations regarding the accreditation of osteopathic graduate medical education (GME) by establishing the Osteopathic Postdoctoral Training Institutions (OPTI) system. This system must be phased in by July 1999. The principal changes resulting from the OPTI system include establishing requirements for college cosponsorship of GME programs and for the number of residency programs, interns, and residents to be trained by the OPTI. In essence, OPTI is an osteopathic acronym for consortium. Each OPTI must include at least one college of osteopathic medicine (COM) and one AOA-accredited hospital. The OPTIs will be subject to interval AOA inspections and will be required to demonstrate a governing system, mission statement, organizational structure, and the presence of faculty development programs. The first article in this two-part series, published in the October JAOA, provided a general blueprint for OPTI building and presented both positive and negative issues germane to the formation of OPTIs. Part 2 reinforces the considerations outlined in Part 1 by describing the formation of a large OPTI--the Ohio University College of Osteopathic Medicine (OU-COM) Centers of Osteopathic Regional Education (CORE) system. Key features are described, including the mission statement, organizational structure, committee system, governance, GME programs, operations, and budget.

Accreditation↗
PubMed1997

Use of DNA polymorphisms to monitor engraftment after allogeneic bone marrow transplantation.

Bone marrow transplantation (BMT) has been established as a life-saving procedure in hematologic malignancies and bone marrow failure syndromes, and it may be valuable in other types of neoplastic disease. DNA polymorphisms are used to monitor engraftment after transplantation from a related or unrelated donor. DNA polymorphisms are not useful after autologous BMT or if the donor is an identical twin. The most valuable polymorphism for this purpose is caused by variation in certain repeated sequences that are known as variable number of tandem repeats (VNTR). The VNTRs are valuable because they each have several alleles increasing the probability of finding one that is useful in a given case. This method can be used to sensitively detect small amounts of residual recipient hematopoiesis. To accomplish this the laboratory must first find a polymorphic allele that is unique in the recipient. Detection of the unique allele in peripheral blood or bone marrow after BMT is tantamount to finding recipient hematopoiesis. The presence of both donor and recipient hematopoiesis can result in a state of stable mixed chimerism and not necessarily presage a relapse after BMT for leukemia; however, the presence of residual recipient cells in some cases may indicate an increased probability of relapse, particularly in chronic myelogenous leukemia.

Bone Marrow Transplantation↗
PubMed1997

Biochemistry and pharmacology of 7alpha-substituted androstenediones as aromatase inhibitors.

The inhibition of aromatase, the enzyme responsible for converting androgens to estrogens, is therapeutically useful for the endocrine treatment of hormone-dependent breast cancer. Research by our laboratory has focused on developing competitive and irreversible steroidal aromatase inhibitors, with an emphasis on synthesis and biochemistry of 7alpha-substituted androstenediones. Numerous 7alpha-thiosubstituted androst-4-ene-3,17-diones are potent competitive inhibitors, and several 1,4-diene analogs, such as 7alpha-(4'-aminophenylthio)-androsta-1,4-diene-3,17-di one (7alpha-APTADD), have demonstrated effective enzyme-activated irreversible inhibition of aromatase in microsomal enzyme assays. One focus of current research is to examine the effectiveness and biochemical pharmacology of 7alpha-APTADD in vivo. In the hormone-dependent 7,12-dimethylbenz(a)anthracene (DMBA)-induced rat mammary carcinoma model system, 7alpha-APTADD at a 50 mg/kg/day dose caused an initial decrease in mean tumor volume during the first week, and tumor volume remained unchanged throughout the remaining 5-week treatment period. This agent lowers serum estradiol levels and inhibits ovarian aromatase activity. A second research area has focused on the synthesis of more metabolically stable inhibitors by replacing the thioether linkage at the 7alpha position with a carbon-carbon linkage. Several 7alpha-arylaliphatic androst-4-ene-3,17-diones were synthesized by 1,6-conjugate additions of appropriate organocuprates to a protected androst-4,6-diene or by 1,4-conjugate additions to a seco-A-ring steroid intermediate. These compounds were all potent inhibitors of aromatase with apparent Kis ranging between 13 and 19 nM. Extension of the research on these 7alpha-arylaliphatic androgens includes the introduction of a C1-C2 double bond in the A-ring to provide enzyme-activated irreversible inhibitors. The desired 7alpha-arylaliphatic androsta-1,4-diene-3,17-diones were obtained from their corresponding 7alpha-arylaliphatic androst-4-ene-3,17-diones by oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). These inhibitors demonstrated enzyme-mediated inactivation of aromatase with apparent k(inact)s ranging from 4.4 x 10(-4) to 1.90 x 10(-3) s(-1). The best inactivator of the series was 7alpha-phenpropylandrosta-1,4-diene-3,17-dione, which exhibited a T(1/2) of 6.08 min. Aromatase inhibition was also observed in MCF-7 human mammary carcinoma cell cultures and in JAr human choriocarcinoma cell cultures, exhibiting IC50 values of 64-328 nM. The 7alpha-arylaliphatic androgens thus demonstrate potent inhibition of aromatase in both microsomal incubations and in choriocarcinoma cell lines expressing aromatase enzymatic activity. Additionally, the results from these studies provide further evidence for the presence of a hydrophobic binding pocket existing near the 7alpha-position of the steroid in the active site of aromatase. The size of the 7alpha-substituent influences optimal binding of steroidal inhibitors to the active site and affects the extent of enzyme-mediated inactivation observed with androsta-1,4-diene-3,17-dione analogs.

Androstenedione↗