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Biomedical subjects

R Frederick

Publications and source records attributed to R Frederick.

At least 19 recordsLinked to original sources
PubMed2004

Genomic changes arising in long-term stab cultures of Escherichia coli.

Genomic scans of clones isolated from long-term stab cultures of Escherichia coli K-12 showed the loss of two large segments of the genome, with each lost segment being approximately 20 kb long. A detailed analysis of one of the deletions, located between 5.4 and 5.9 min, revealed that similar deletions had arisen in several other stab cultures. All deletions of this type exhibited a right terminus ending precisely at an IS5A element and a left terminus that varied over an approximately 5-kb range but was bordered in all but two cases by sequences belonging to the preferred consensus target sequence for IS5, YTAR. The ubiquity of such deletions in independent stab cultures and the increase in their frequency over time argue that they have a selective advantage. It is speculated that the loss of the crl locus is responsible for the selective advantage of the deletions.

DNA Transposable Elements↗
PubMed2001

Peptide-triggered conformational switch in HIV-1 RRE RNA complexes.

We have used NMR spectroscopy to determine the solution structure of a complex between an oligonucleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-1 mRNA and an in vivo selected, high affinity binding Arg-rich peptide. The peptide binds in a partially alpha-helical conformation into a pocket within the RNA deep groove. Comparison with the structure of a complex between an alpha-helical Rev peptide and RRE-IIB reveals that the sequence of the bound peptide determines the local conformation of the RRE peptide binding site. A conformational switch of an unpaired uridine base was revealed; this points out into the solvent in the Rev peptide complex, but it is stabilized inside the RNA deep groove by stacking with an Arg side chain in the selected peptide complex. The conformational switch has been visualized by NMR chemical shift mapping of the uridine H5/H6 atoms during a competition experiment in which Rev peptide was displaced from RRE-IIB by the higher affinity binding selected peptide.

Amino Acid Sequence↗
PubMed2000

Unusual cause of chest pain in a 60-year-old woman.

Chest pain is a common emergency department complaint. Many patients presenting with this complaint are discharged with the nonspecific diagnosis of musculoskeletal chest pain. That was the diagnosis given to the patient in this case at the time of her initial presentation to the ED, a diagnosis that was correct but incomplete. This case illustrates the importance of taking a complete history, including a thorough review of systems in every patient, even when the diagnosis seems obvious.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1999

RNA architecture dictates the conformations of a bound peptide.

BACKGROUND: The biological function of several viral and bacteriophage proteins, and their arginine-rich subdomains, involves RNA-mediated interactions. It has been shown recently that bound peptides adopt either beta-hairpin or alpha-helical conformations in viral and phage peptide-RNA complexes. We have compared the structures of the arginine-rich peptide domain of HIV-1 Rev bound to two RNA aptamers to determine whether RNA architecture can dictate the conformations of a bound peptide. RESULTS: The core-binding segment of the HIV-1 Rev peptide class II RNA aptamer complex spans the two-base bulge and hairpin loop of the bound RNA and the carboxy-terminal segment of the bound peptide. The bound peptide is anchored in place by backbone and sidechain intermolecular hydrogen bonding and van der Waals stacking interactions. One of the bulge bases participates in U*(A*U) base triple formation, whereas the other is looped out and flaps over the bound peptide in the complex. The seven-residue hairpin loop is closed by a sheared G*A mismatch pair with several pyrimidines looped out of the hairpin fold. CONCLUSIONS: Our structural studies establish that RNA architecture dictates whether the same HIV-1 Rev peptide folds into an extended or alpha-helical conformation on complex formation. Arginine-rich peptides can therefore adapt distinct secondary folds to complement the tertiary folds of their RNA targets. This contrasts with protein-RNA complexes in which elements of RNA secondary structure adapt to fit within the tertiary folds of their protein targets.

Arginine↗
PubMed1998

Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex.

We have determined the solution structure of a 15-mer boxB RNA hairpin complexed with a 20-mer basic peptide of the N protein involved in bacteriophage P22 transcriptional antitermination. Complex formation involves adaptive binding with the N peptide adopting a bent alpha-helical conformation that packs tightly through hydrophobic and electrostatic interactions against the major groove face of the boxB RNA hairpin, orienting the open opposite face for potential interactions with host factors and/or RNA polymerase. Four nucleotides in the boxB RNA hairpin pentaloop form a stable GNRA like tetraloop structural scaffold on complex formation, allowing the looped out fifth nucleotide to make extensive hydrophobic contacts with the bound peptide. The guanidinium group of a key arginine is hydrogen-bonded to the guanine in a loop-closing sheared G.A mismatch and to adjacent backbone phosphates. The identified intermolecular contacts account for the consequences of N peptide and boxB RNA mutations on bacteriophage transcriptional antitermination.

Amino Acid Sequence↗
PubMed1996

Identification of three new microsatellite markers in the spinocerebellar ataxia type 2 (SCA2) region and 1.2 Mb physical map.

Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disease recently mapped to chromosome 12q close to the locus D12S84 by genetic linkage analysis. To generate additional genetic markers in the SCA2 region, we constructed a physical map of the region using yeast artificial chomosome (YAC), P1 artificial chromosome (PAC) and cosmid clones. The physical map was found to agree well with the genetic map. Three novel microsatellite markers were isolated and physically mapped. A novel approach to isolate CAG repeats directly from YAC DNAs is described.

Alleles↗
PubMed1996

Heme oxygenase: a novel target for the modulation of the inflammatory response.

Chronic inflammatory diseases place a heavy social and economic burden on the resources of many nations, but the number of safe and effective treatments is limited. To date, the major research effort has concentrated on those mediators responsible for the initiation and maintenance of the pathological process. In contrast, little attention has been focused on endogenous factors responsible for the resolution of the inflammation. Heme oxygenase ((HO); EC 1.14.99.3) is the rate-limiting enzyme in the catabolism of heme to biliverdin (which is converted to bilirubin by biliverdin reductase), free iron and carbon monoxide (CO). Two isoforms of HO have been characterized, the constitutive isoform, HO-2, which is the major isoform present under physiological conditions, and the stress-induced isoform, HO-1, which has also been classified as heat-shock protein 32K (ref. 1). Increases in HO activity have been implicated in tissue protection against oxidative stress. In this communication, we describe the effects of modulating HO during an acute complement-dependent inflammatory response. Elevation of this enzyme resulted in a striking suppression, whereas inhibition of the enzyme led to a potentiation of the inflammatory response. Such novel enzyme modulation has application on the one hand to the treatment of inflammatory diseases and on the other hand to immnosuppressed states in which the impaired ability to mount an adequate inflammatory response may result in death from opportunistic infections.

Animals↗
PubMed1995

Modulation of heme oxygenase activity in rat brain and spleen by inhibitors and donors of nitric oxide.

The capacity of nitric oxide to activate or inhibit metalloprotein-containing enzymes underlies many of its biological actions. Heme oxygenase, involved in a variety of biological processes, does not contain heme but utilises it as a substrate. The substrate for nitric oxide, L-arginine (0.1-10mM), but not D-arginine, decreased heme oxygenase activity in rat brain homogenates. The arginine analogue L-NAME (0.1-10mM) increased activity in the same tissue. In spleen homogenates where endogenous nitric oxide activity is lower than in brain, these compounds had no effect. The nitric oxide donor sodium nitroprusside (0.001mM-10mM) reduced heme oxygenase activity in both brain and spleen. These results suggest that biological effects attributed to modulation of nitric oxide synthase may act via heme oxygenase.

Animals↗
PubMed1992

Ketorolac versus meperidine and hydroxyzine in the treatment of acute migraine headache: a randomized, prospective, double-blind trial.

STUDY OBJECTIVE: To compare the effectiveness of IM ketorolac with that of meperidine and hydroxyzine in the treatment of acute migraine headache. DESIGN: Prospective, randomized, double-blind trial. SETTING: Urban emergency department with an annual census of 42,000 patients. PARTICIPANTS: Forty-seven adult patients with migraines enrolled on 50 visits. INTERVENTIONS: Patients were randomly assigned to receive a single injection of either 60 mg ketorolac (group 1) or 100 mg meperidine and 50 mg hydroxyzine (group 2). Pain assessment was made using both visual-analog and verbal descriptor scales. RESULTS: At 60 minutes, 15 patients (60%) from group 1 (25) and 14 patients (56%) from group 2 (25) reported a great deal of complete relief (P = .77) Sixty-minute mean pain relief scores (3.35 versus 3.37) were different (P = .76). Nine patients (36%) from group 1 and seven patients (28%) from group 2 required additional analgesia (P = .76). CONCLUSION: Ketorolac is as effective as meperidine and hydroxyzine for the treatment of acute migraine headache.

Acute Disease↗
PubMed1991

NMR studies of the activation of the Escherichia coli trp repressor.

The Escherichia coli trp repressor binds to the trp operator in the presence of tryptophan, thereby inhibiting tryptophan biosynthesis. Tryptophan analogues lacking the alpha-amino group act as inducers of trp operon expression. We have used one- and two-dimensional 1H-NMR spectroscopy to compare the binding to the repressor of the corepressors L-tryptophan, D-tryptophan and 5-methyl-DL-tryptophan with that of the inducer indole-3-propionic acid. We have determined the chemical shifts of the indole ring protons of the ligands when bound to the protein, principally by magnetization-transfer experiments. The chemical shifts of the indole NH and C4 protons differ between corepressors and inducer. At the same time, the pattern of intermolecular NOE between protons of the protein and those of the ligand also differ between the two classes of ligand. These two lines of evidence indicate that corepressors and inducers bind differently in the binding site, and the evidence suggests that the orientation of the indole ring in the binding site differs by approximately 180 degrees between the two kinds of ligand. This is in contrast to a previous solution study [Lane, A.N. (1986) Eur. J. Biochem. 157, 405-413], but consistent with recent X-ray crystallographic work [Lawson, C.L. & Sigler, P.B. (1988) Nature 333, 869-871]. D-Tryptophan and 5-methyltryptophan, which are more effective corepressors than L-tryptophan, bind similarly to L-tryptophan. The indole ring of D-tryptophan appears to bind in essentially the same orientation as that of the L isomer. There are, however, some differences in chemical shifts and NOE for 5-methyltryptophan, which indicate that there are significant differences between the two corepressors L-tryptophan and 5-methyltryptophan in the orientation of the indole ring within the binding site.

Bacterial Proteins↗
PubMed1989

An ice nucleation reporter gene system: identification of inducible pathogenicity genes in Pseudomonas syringae pv. phaseolicola.

We have constructed derivatives of the transposon Tn3 that allow an ice nucleation gene (inaZ) to be used as 'reporter' of the transcriptional activity of genes into which it is inserted. In these derivatives (Tn3-Ice and Tn3-Spice), the lacZYA sequences of transposon Tn3-HoHo1 were replaced with inaZ lacking its native promoter. The ice nucleation activity of virB::inaZ fusions in the correct transcriptional orientation was inducible by acetosyringone, a plant metabolite which activates the vir operon of Agrobacterium tumefaciens Ti plasmids, while fusions in the opposite orientation were unresponsive to the inducer. Tn3-Spice was also used to investigate the expression of a cluster of genes (hrp) which control pathogenicity and hypersensitivity elicited by Pseudomonas syringae pv. phaseolicola. An inducible region was identified which is expressed at low levels in vitro but becomes activated when the bacteria come into contact with the susceptible host, bean. Activation of this region occurred within 2 h post-inoculation and was nearly complete by the time the bacteria began to multiply in the leaf tissue. The inaZ reporter appears to be at least 10(5)-fold more sensitive than lacZ in P.s.phaseolicola. Thus, the inaZ fusion system provides a sensitive, convenient and inexpensive tool for the study of bacterial gene expression, particularly during plant pathogenesis, and should be generally useful as a reporter gene system in Gram-negative bacteria.

Amino Acid Sequence↗
PubMed1989

Expert systems survey on biodegradation of xenobiotic chemicals.

To determine the feasibility of developing an expert system for biodegradability assessment, a survey was conducted in which biodegradation experts were asked to estimate rates and products of degradation for 50 chemicals. These chemicals, which varied widely in structure, were considered representative of the spectrum of premanufacture notice chemicals subject to EPA review under the Toxic Substances Control Act. There was substantial agreement among the 22 experts on both sites of initial attack and rates of degradation. The approximate order in which various groups were viewed as contributing to aerobic biodegradability is as follows: ester, amide, anhydride greater than hydroxyl greater than carboxyl, epoxide, site of unsaturation greater than benzene ring, methyl, methylene. Hydrolyzable groups, azo bonds, halogens, and nitro groups were preferred sites of anaerobic attack. Among the negative influences on aerobic biodegradability were molecular mass, branching, halogenation, and nitrogen heterocycles. Results also indicate that estimates of removal by biodegradation in aerobic wastewater treatment and time for aerobic ultimate and primary degradation were well correlated, and that the predictive value of such correlations could be improved using correction factors for certain classes of chemicals. The results lend support to existing rules of thumb, but also offer additional insight that will prove useful in designing a prototype system.

Biodegradation, Environmental↗
PubMed1985

Effects of dexamethasone, progesterone, and testosterone on IOP and GAGs in the rabbit eye.

The effects of steroids on intraocular pressure and on aqueous outflow pathway (AOP) and adjacent anterior segment tissue glycosaminoglycans (GAGs) were studied in New Zealand Red rabbits treated for 4 wk with dexamethasone, hydroxymethyl-progesterone and methyl-testosterone. Only topical administration of dexamethasone resulted in a significant increase in intraocular pressure. The eyes were labeled in vitro for 1 hr with GAG precursors, [3H]-glucosamine and [35S]-sulfate, and maintained as whole organ cultures. The GAGs were biochemically isolated, fractionated by gel filtration chromatography and subjected to selective GAG degradative procedures. The total content of hyaluronic acid and chondroitin sulfate was analyzed by high performance liquid chromatography. In dexamethasone-treated eyes, the total content of hyaluronic acid was decreased in the AOP, although the specific activity of [3H]-glucosamine did not change. The total content of chondroitin sulfate was increased in the AOP and iris-ciliary body, while the specific activity of the [35S]-label was decreased in the AOP, iris-ciliary body, and sclera. The changes in the AOP GAGs in dexamethasone-treated eyes may be important factors for the development of dexamethasone-induced ocular hypertension in the rabbit.

Animals↗
PubMed1977

Differences in cardiac function with prolonged physical training for cardiac rehabilitation.

Ten men aged 40 to 68 years with clinical manifestations of cardiovascular disease and who had participated for 2 to 59 months in a physical training program for cardiac rehabilitation were studied. All 10 underwent measurements of maximal oxygen uptake and invasive studies of cardiac output, using the direct Fick method, at rest and at graded levels of exercise in the upright posture. Of four men who left the training program, three continued activities individually. Physiologic measurements were repeated after a lapse of 13 to 38 months (average 23 months). The rate of change in maximal oxygen uptake relative to normal changes with aging was decelerated in four men over an average of 21.8 months and was accelerated in six men over an average of 23.2 months. At comparable oxygen requirements of exercise, stroke volume and cardiac output were unchanged in the former group but significantly decreased in the latter. Arterial oxygen content and arteriovenous oxygen difference increased in both groups. These results show that prolonged physical training results in physiologic adaptations of cardiac rehabilitation even though deterioration of cardiac function with advancing disease is probable in some patients.

Adult↗
PubMed1976

Comparison of active participants and dropouts in CAPRI cardiopulmonary rehabilitation programs.

Of 547 men and 56 women enrolled up to April 1974 in Cardiopulmonary Research Institute (CAPRI) community programs for cardiopulmonary rehabilitatation, 84.5 percent had clinical manifestations of coronary heart disease. These medically supervised programs of physical training involved 30 to 60 minutes of graded levels of working, calisthenics and, if indicated, jogging for 3 mornings/week. Altogether 352 (58.4 percent) dropped out after an average of 8.6 months for men and 5.7 months for women. The remaining 230 men and 21 women remained active for 22 and 20 months, respectively. In retrospect, there were few minor differences between active participants and dropouts in physical characteristics, clinical diagnoses and responses to exercise testing on enrollment. Elapsed time to morbidity tended to be longer in active persons than in dropouts. Over one half of active men and about one third of dropouts were working. Of six early deaths, one occurred before training was instituted, and five within the first 2 weeks of training. Among men, the respective total mortality rates were 2.7 and 4.7/100 person-years for active participants and dropouts; among women, the rates were 0 and 3.8 respectively. Whereas 24 episodes of cardiac arrest occurred in 13 men, with three fatalities outside the training program, in 11 instances of exertional arrest during class training all defibrillations were successful. Without this benefit of medical supervision there would have been little difference in mortality experience.

Animals↗