Search PubMed⌕ Search

Biomedical subjects

D M Ferguson

Publications and source records attributed to D M Ferguson.

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

Molecular simulation of dynorphin A-(1-10) binding to extracellular loop 2 of the kappa-opioid receptor. A model for receptor activation.

The structure of the second extracellular loop region (EL2) of the kappa-opioid receptor has been explored in an effort to understand the structural basis for dynorphin A binding and selectivity. Application of secondary structure prediction methods and homology modeling resulted in a turn-helix motif for the N-terminal region of kappa-EL2. A similar motif was not predicted for EL2 of either delta or mu opioid receptors. The EL2 helix was further shown to be amphiphilic and complementary to the helical component of dynorphin A. Using a model of the kappa-receptor (Metzger et al. Neurochem. Res. 1996, 21, 1287-1294), including the newly predicted EL2 turn-helix domain, a binding mode is proposed based on helix--helix interactions between hydrophobic residues of EL2 and the helical component of dynorphin A-(1-10). Molecular simulations of the receptor--ligand complex yielded structures in which the tyramine moiety or opioid "message" of dynorphin is bound within a conserved aromatic pocket in the transmembrane domain while the helical portion contacted residues in EL2 and in the extracellular end of transmembrane helices 6 and 7. The model is in general agreement with site-directed mutagenesis data and chimera studies that have identified binding domains in both the EL2 and transmembrane regions of dynorphin A. The results confirm the importance of the opioid "message" displayed by many opioid ligands but also suggest a potential mechanism of receptor activation that may be mediated by EL2 through interactions with the "address" component of dynorphin A.

Amino Acid Sequence↗
PubMed1997

Knowledge-based modeling of a bacterial dichloromethane dehalogenase.

A three-dimensional structural model of the dichloromethane dehalogenase (DCMD) from Methylophilus sp. DM11 is constructed based on sequence similarities to the glutathione S-transferases (GSTs). To maximize sequence identity and minimize gaps in the alignment, a hybrid approach is used that takes advantage of the increased homology found between DM11 and domain I of the sheep blowfly theta class GST (residues 1-79) and domain II of the human alpha class GST (residues 81-222). The resulting structure has C alpha root mean square deviations of 1.16 A in domain I and 1.83 A in domain II from the template GSTs, which compare well to those seen in other GST inter-class comparisons. The model is further applied to explore the structural basis for substrate binding and catalysis. A conserved network of hydrogen bonds is described that binds glutathione to the G site, placing the thiol group in a suitable location for nucleophilic attack of dichloromethane. A mechanism is proposed that involves activation through a hydrogen bond interaction between Ser12 and glutathione, similar to that found in the theta-GSTs. The model also demonstrates how aromatic residues in the hydrophobic site (H site) could play a role in promoting catalysis: His116 and Trp117 are ideally situated to accept a growing negative charge on a chlorine of dichloromethane, stabilizing displacement. This scheme is consistent with experimental results of single-point mutations and comparisons with other GST structures and mechanisms.

Amino Acid Sequence↗
PubMed1997

Analysis of the malondialdehyde-2'-deoxyguanosine adduct pyrimidopurinone in human leukocyte DNA by gas chromatography/electron capture/negative chemical ionization/mass spectrometry.

A method is described for the assay of the major malondialdehyde-deoxyguanosine adduct (M1G) based on immunoaffinity purification and gas chromatography/electron capture/negative chemical ionization/mass spectrometry. A stable isotope of M1G-deoxyribose ([2H2]M1G-dR) was used as an internal standard. Recovery of internal standard throughout the entire assay procedure was approximately 40%. The assay showed a linear response over a range of 10-1000 pg of M1G-dR and was verified by analysis of a synthetic. M1G-containing oligomer. The limit of detection in biological samples was 100 fmol/sample, corresponding to 3 adducts/10(8) bases for 1 mg of DNA. DNA was isolated from the blood of 10 healthy human donors, and M1G levels were measured. A mean value of 6.2 +/- 1.2 adducts/10(8) bases was obtained, with no obvious differences bases on age or cigarette smoking. A small, but statistically significant difference was observed between the levels in females (5.1 +/- 0.4 adducts/10(8) bases) and males 6.7 +/- 1.1 adducts/10(8) bases). The presence of M1G in leukocyte DNA was further verified by analysis using liquid chromatography/electrospray ionization mass spectrometry.

Adult↗
PubMed1997

An assay combining cell culture with reverse transcriptase PCR to detect and determine the infectivity of waterborne Cryptosporidium parvum.

The presence of Cryptosporidium in drinking water supplies is a significant problem faced by the water industry. Although a variety of methods exist for the detection of waterborne oocysts, water utilities currently have no way of assessing the infectivity of detected oocysts and consequently are unable to accurately determine the risks posed to public health by waterborne Cryptosporidium. In this paper, the development of an infectivity assay for waterborne Cryptosporidium parvum is described. Oocysts were inoculated onto monolayers of Caco-2 cells and grown on microscope slides, and infections were detected by C. parvum specific reverse transcriptase PCR of extracted mRNA, targeting the heat shock protein 70 (hsp70) gene. A single infectious oocyst was detected by this experimental procedure. The use of concentrated samples obtained from 250 liters of finished water had no observable effect on the integrity of cell monolayers or on the infectivity of oocysts seeded into the concentrate. Intracellular developmental stages of the parasite were also detected by using fluorescently labeled antibodies. One pair of PCR primers targeting the hsp70 gene was specific for C. parvum, while a second pair recognized all species of Cryptosporidium tested. The C. parvum-specific primers amplified DNA from 1 to 10 oocysts used to seed 65 to 100 liters of concentrated environmental water samples and were compatible with multiplex PCR for the simultaneous detection of C. parvum and Giardia lambia. This paper confirms the utility of PCR for the detection of waterborne C. parvum and, most importantly, demonstrates the potential of an in vitro infectivity assay.

Animals↗
PubMed1996

Liver allograft rejection in rats depleted of CD8+ cells.

The mechanism(s) of rejection or tolerance induction is a competitive, complex process that presumably involves interactions between multiple subpopulations of T lymphocytes. We investigated the roles of CD8+ cytolytic and CD4+ helper T cells in rat strains that tolerate liver allografts and that differ at both the major histocompatibility complex (MHC) (RT1) and minor histocompatibility genes. Orthotopic liver transplantation (OLT) with arterial reconstruction was performed with Brown Norway (BN) (RT1n) donors and Lewis (RT1(1)) recipients, some of which were untreated, others treated with anti-CD8 antibody, and still others treated with anti-CD4 antibody. Liver graft rejection was monitored for 28 days on the basis of two criteria: (1) serum levels of AST enzyme at 3-day intervals and (2) liver biopsies at weekly intervals and at the time of sacrifice at the end of the study period. In the untreated control group, an elevation of AST was found to peak at day 6 after grafting, and it remained elevated until day 28 (AST 542 +/- 72 U/l). Histologically, signs of severe rejection were first observed on day 9; these changed to moderate rejection about day 21 and to mild rejection by day 28, when the animals were sacrificed. Recipients pre-treated with anti-CD8 demonstrated a significant elevation of AST within 6 days that, unlike in the control recipients, continued to rise sharply through the observation period (AST 1127 +/- 181 U/l, P = 0.009 vs control group). Liver biopsies showed mild rejection at day 9 and moderate rejection at days 21 through 28. Recipients pretreated with anti-CD4 showed a time course of enzyme elevation and severity of rejection that was not significantly different from that observed in the control group. However, anti-CD4 treatment resulted in only 75% depletion of CD4+ cells in peripheral blood as compared to complete elimination of CD8+ cells following anti-CD8 treatment. Functional studies of spleen and liver-infiltrating lymphocytes obtained after 28 days showed low proliferative response in mixed lymphocyte culture with both BN and PVG stimulator spleen and lymph node cells. These results suggest that in this donor/recipient combination, removal of CD8+ cells increases the severity of rejection as demonstrated by a progressive rise in AST and histology. Moreover, OLT in this combination results in a profound, nonspecific inhibition of proliferative T-cell responses to MHC alloantigens.

Animals↗
PubMed1996

Application of the message-address concept to the docking of naltrexone and selective naltrexone-derived opioid antagonists into opioid receptor models.

A binding site model for the opioid family of G-protein coupled receptors (GPCRs) is proposed based on the message-address concept of ligand recognition. Using ligand docking studies of the universal opioid antagonist, naltrexone, the structural basis for "message' recognition is explored across all three receptor types, mu, delta, and kappa. The binding mode proposed and basis for selectivity are also rationalized using the naltrexone-derived ligands, naltrindole (NTI) and norbinaltorphimine (nor BNI). These ligands are docked to the receptor according to the common naltrexone core or message. The resulting orientation places key "address' elements in close proximity to amino acid residues critical to selectivity among receptors types. Selectivity is explained by sequence differences in the mu, delta, and kappa receptors at these recognition points. Support for the model is derived from site directed mutagenesis studies and ligand binding data for the opioid receptors and other related GPCRs.

Amino Acid Sequence↗
PubMed1996

Perinuclear antineutrophil cytoplasmic antibodies in patients with Crohn's disease define a clinical subgroup.

BACKGROUND & AIMS: Antineutrophil cytoplasmic antibodies (ANCA) have been consistently detected in a subgroup of patients with Crohn's disease (CD). This study was designed to determine whether serum ANCA expression in patients with CD characterizes an identifiable clinical subgroup. METHODS: The study population consisted of 69 consecutive patients with an established diagnosis of CD as determined by a combination of characteristic clinical, radiographic, endoscopic, and histopathologic criteria. Sera from the patients were analyzed for the presence of ANCAs using the fixed neutrophil enzyme-linked immunosorbent assay (ELISA) assay. Perinuclear ANCA (pANCA)-positive and cytoplasmic ANCA (cANCA)-positive results by ELISA were confirmed by indirect immunofluorescence staining. Clinical profiles of the ANCA-positive patients with CD were compared with those of patients with CD not expressing ANCA (ANCA-negative). RESULTS: pANCA-positive patients with CD have endoscopically and/or histopathologically documented left-sided colitis and symptoms of left-sided colonic inflammation, clinically reflected by rectal bleeding and mucus discharge, urgency, and treatment with topical agents. One hundred percent of patients with CD expressing pANCA had "UC-like" features. CONCLUSIONS: In patients with CD, serum pANCA expression characterizes a UC-like clinical phenotype. Stratification of CD by serum pANCA provides evidence of heterogeneity within CD and suggests a common intestinal mucosal inflammatory process among a definable subgroup of patients with CD and UC expressing this marker.

Adult↗
PubMed1995

On the role of extracellular loops of opioid receptors in conferring ligand selectivity.

Based on an analysis of results taken from site-directed mutagenesis studies performed on opioid receptors, a role for the extracellular loops in conferring opioid subtype selectivity is proposed. It is suggested that the extracellular loop regions (which represent the region of highest sequence variability among opioid subtypes) interact with opioid ligands in a primarily non-specific fashion. Although these interactions are non-specific, they appear to play a discriminatory role in ligand binding and, in certain cases, prevent particular ligands from binding among receptor subtypes. We propose that selectivity may be imparted through a mechanism of exclusion, rather than specific pharmacophore recognition within the extracellular loops and N-terminal domain. This hypothesis is supported by a careful analysis of the binding profiles of several selective and non-selective ligands to a variety of chimeric mutants. These results, when combined with results taken from single-point mutation experiments point to the existence of a high affinity binding pocket within the transmembrane region which may be common among the opioid subtypes.

Analgesics↗
PubMed1993

An increase in cytosolic protease activity during liver preservation. Inhibition by glutathione and glycine.

Degradative cytosolic proteolysis contributes to cell injury following ATP depletion. Although ATP depletion is a salient feature of ischemic liver storage for transplantation, information regarding cytosolic protease activity during liver storage is lacking. Thus our aim was to measure liver cytosolic protease activity following ischemic storage. A progressive increase in total cytosolic protease activity was observed over time at both 37 degrees C and 4 degrees C, but the increase was greater at 37 degrees C. Total cellular proteolysis was also temperature-dependent during anoxia (37 degrees C > 4 degrees C), demonstrating a physiologic correlation between cellular proteolysis and measurements of cytosolic protease activity. The stimulation of total cytosolic protease activity was due to an increase in metallo- and aspartate protease activity. Of particular interest, glutathione (GSH) inhibited both metalloprotease and aspartate protease activity from cytosol of stored livers. Glycine, the carboxyl-terminal amino acid of GSH, also inhibited both metalloprotease and aspartate protease activity. In addition to being an antioxidant, GSH may exert its protective effects during organ preservation by inhibiting cytosolic proteases--perhaps via its glycine moiety. These experiments support the hypothesis that degradative proteolysis contributes to liver injury during organ preservation.

Animals↗
PubMed1992

General anaesthesia in the dental surgery: a comparison of propofol and methohexitone.

General anaesthesia was assessed in 100 dental patients in general dental practice using either propofol or methohexitone. Mean induction doses were 1.7 mg/kg and 1.5 mg/kg for propofol and methohexitone, respectively. Anaesthesia was maintained with nitrous oxide and oxygen, supplemented in the majority of cases with halothane. Both groups were comparable in relation to satisfactory surgical conditions and recovery. The maximum heart rate following induction of anaesthesia was significantly greater in the group given methohexitone. Despite the satisfactory results obtained in this study the need for full resuscitation facilities will encourage the trend towards most dental general anaesthesia taking place in a hospital environment.

Adult↗
PubMed1992

Ratio of hepatic arterial-to-portal venous blood flow--validation of radionuclide techniques in an animal model.

The ratio of hepatic arterial-to-portal venous blood flow can be determined from the analysis of a first-pass bolus through the liver by a number of techniques. This study examines the validity of four radiotracer techniques in an animal model. Thirty-four flow studies (3 mCi 99mTc-DTPA/study) were performed in seven anesthetized pigs. Images were acquired for 200 sec and time-activity curves were generated from lung, liver and kidney ROIs. These curves were analyzed using a slope-based (HPI), a height-based (mHAR) and two deconvolution-based methods employing exponential or gamma variate fits. There was an excellent correlation (r greater than 0.9) between results obtained with flow probes and the radiotracer techniques, with the exception of the HPI technique (r = 0.75). The mHAR and deconvolution techniques were inaccurate at very low and high arterial flows, due respectively to noise limitations and hemodynamic instability in the animal. Nevertheless, these techniques appear to be the most promising for routine clinical use.

Animals↗
PubMed1991

Application of free-energy decomposition to determine the relative stability of R and S oligodeoxyribonucleotide methylphosphonates.

The stereoselective stability of oligodeoxyribonucleotide methylphosphonates is examined using free-energy computer simulations. These modified phosphate linkages have the potential to be important antisense therapeutics that can be targeted on specific sequences of single- and double-stranded DNA, as well as crucial RNA messages. The stability of hybrid duplexes that contain these modified linkages is known experimentally to depend on the configuration of the chiral phosphonate center. Free-energy decomposition calculations were performed on three DNA oligomers to determine the origin of the structural interactions and physical properties that influence the relative stability of R and S methylphosphonate diastereomers. The strategy applied used free-energy decomposition methods to evaluate the free-energy contributions from selected groups. The results indicated that only three groups have a steric effect on the stability: the C2' and C3' substituents on the S diastereomer (5' side) and the C5' substituents on the R diastereomer (3' side). The balance considerably favors the R configuration in all the isomers studied and is not sequence dependent. The electrostatic effects were much more variable and were shown to be dependent on the conformation of duplex. The solvent interactions, however, were consistent and contributed favorably to the stability of the R over the S diastereomer. This favorable solvation energy for the R diastereomer was surprising (since the methyl group is more solvent exposed in this configuration) and was further supported by ab initio and associated free-energy calculations. This study concludes that oligonucleotides containing R-methylphosphonate linkages will normally form more stable duplexes than the corresponding S diastereomer irrespective of sequence, but also points that conformational changes may allow for a reversal in stability.

Base Sequence↗
PubMed1984

Prepubertal periodontitis affecting the deciduous and permanent dentition in a patient with cyclic neutropenia. A case report and discussion.

Neutropenia is a transient or chronic blood disorder characterized by a decrease in the number of circulating polymorphonuclear leukocytes (PMNs). Neutrophils are a major cellular defense against infection, and depletion of these cells is potentially fatal. Stomatitis and gingivitis frequently are seen in patients with neutropenia. Therefore, the diagnosis of severe oral pathoses of obscure origin must include a differential white blood cell count. The importance of the dentist's role is dramatically illustrated in the rare case reported here, since the oral condition was the reason for this patient's definitive blood work-up. The report illustrates the importance of the laboratory assessment in dental patients with unusual periodontal destruction or other inexplicable oral changes.

Aggressive Periodontitis↗