Biomedical subjects

J S Taylor

Publications and source records attributed to J S Taylor.

At least 37 records · Page 2Linked to original sources

PubMed2001

Fragmentation of electrospray-produced oligodeoxynucleotide ions adducted to metal ions.

In this article, we describe the unique fragmentations of oligodeoxynucleotides (ODNs) whose phosphate groups are completely depleted of protons and replaced with metal ions. The production of the ubiquitous [a(n) - base] ions still occurs, but no longer by transfer of an acidic phosphate proton to an adjoining 3' base. Nor is the extent of the reaction determined by the proton affinity of that base. Rather, the reaction now occurs via a cleavage 3' to both pyrimidines and purines; cleavage 3' to pyrimidine is more favorable than that 3' to purine. We also demonstrate that an ODN is more stable in the gas phase when its phosphate groups are bound to metal ions than when its phosphate groups are attached to hydrogens. This study also provides further evidence for the ODN fragmentation mechanism that involves H transfer to a nucleobase. To establish the structural utility of this new fragmentation, we applied it to distinguishing small ODNs containing a photomodified cis,syn-cyclobutane pyrimidine dimer from the parent ODNs, a system that cannot be distinguished by collisional activation of precursor species that do not contain metal ions.

Ions↗

PubMed2001

Determination of photomodified oligodeoxynucleotides by exonuclease digestion, matrix-assisted laser desorption/ionization and post-source decay mass spectrometry.

A fast method to detect and sequence photomodified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is reported. Upon treatment of modified ODNs with both phosphodiesterase I and phosphodiesterase II, the digestion stops at the sites of photomodification. Post-source decay (PSD) of MALDI-produced ions from two enzymatic digestion end products distinguishes isomers such as 5'-d(T[cis-syn]TAAGC) and 5'-d(CGAAT[cis-syn]T), which have symmetrical or identical compositions at the 3' and 5' ends, respectively. Studies have also been done to follow the kinetics for enzyme degradation of photomodified ODNs. The calculated rate constants from a mathematical treatment of the time-dependent MALDI data clearly show that the enzymatic digestion rate slows as the enzyme approaches the modified site.

Exonucleases↗

PubMed2001

Fragmentation of photomodified oligodeoxynucleotides adducted with metal ions in an electrospray-ionization ion-trap mass spectrometer.

We report the effect of metal-ion adduction on the fragmentation of oligodeoxynucleotides (ODNs) bearing DNA photoproducts. When protons on backbone phosphates of ODNs are completely replaced with metal ions, cleavages occur readily within the photoproduct moiety, whereas those cleavages do not occur in photomodified ODNs in which the phosphates are associated with protons. For example, thymine/adenine (TA*) photoproducts revert to their undamaged precursors upon collisional activation, the pyrimidine(6-4)pyrimidone product and its Dewar valence isomer show a characteristic neutral loss of C4H3NO3, and dimeric adenine photoproducts show a distinctive loss of NH2CN from the adenine six-membered ring. The product-ion mass spectra of photodamaged ODNs that are adducted to metal ions are complementary in terms of structure information to those spectra of ODNs in which the phosphates are associated with protons. The results also demonstrate that the energy required for strand cleavages is higher for ODNs adducted with metal ions than that for ODNs bound with protons. Furthermore, the loss of a pyrimidine is more favorable than the loss of a purine in the fragmentation of ODNs associated with metal ions.

Adenine↗

PubMed2001

Isolation and mass spectrometric characterization of dimeric adenine photoproducts in oligodeoxynucleotides.

UVC irradiation of oligodeoxynucleotides (ODNs) at 254 nm generates two types of DNA photoproducts, A=A and (AA)*, at adjacent adenine sites in DNA. Kumar et al. previously proved the structure of these adducts in dinucleoside monophosphates [Kumar, S., et al. (1987) Nucleic Acids Res. 15, 1199-1216; Kumar, S., et al. (1991) Nucleic Acids Res. 19, 2841-2847]. Product-ion spectra of ESI-produced [M - 2H](2-) ions of the ODNs containing the dimeric adenine photoproducts show distinctive fragmentation that is informative of the structures of the photoproducts. The gas-phase cleavages of ODNs at sites of those photoproducts and thymine thymine or thymine adenine ((TA)*) photoproducts are analogous to cleavages induced by hot alkaline treatment. Nuclease-P1 digestions of ODNs containing dimeric adenine photoproducts give shorter pieces of ODNs bearing the photoproducts, which fragment under collisional activation conditions in a similar way to the large ODNs containing the photoproducts. The tandem mass spectrometric results show that the yield of (AA)* is lower than that of A=A when adjacent adenines are in the middle of an ODN sequence, and the yield of the latter is similar to that of (TA)*.

Adenine↗

PubMed2001

A preliminary report of the occupation of patients evaluated in patch test clinics.

BACKGROUND: The interplay between the occupational environment and worker's skin can result in contact dermatitis of both irritant and allergic types. Other forms of dermatitis can also be influenced by occupational exposures. OBJECTIVE: The aim of this study is to compare the occupations and allergens of occupational contact dermatitis cases with nonoccupational contact dermatitis cases. METHODS: Diagnostic patch testing with allergens of the North American Contact Dermatitis Group and occupational coding by the National Institute for Occupational Safety and Health methods. RESULTS: Of 2,889 patients referred for evaluation of contact dermatitis, 839 patients (29%) were found to have occupational contact dermatitis. Of the 839 cases deemed occupational, 455 cases (54%) were primarily allergic in nature and 270 cases (32%) were primarily irritant in nature. The remaining 14% were diagnoses other than contact dermatitis, aggravated by work. The occupation most commonly found to have allergic contact dermatitis was nursing. Allergens strongly associated with occupational exposure were thiuram, carbamates, epoxy, and ethylenediamine. CONCLUSION: Some contact allergens are more commonly associated with occupational contact dermatitis. Nursing and nursing support are occupations most likely to be overrepresented in contact dermatitis clinics.

Allergens↗

PubMed2001

Comparison of patch test results with a standard series among white and black racial groups.

BACKGROUND: Environmental, cultural, occupational, genetic, individual, and racial differences are important factors in the study of contact dermatitis. Some epidemiologic studies have compared overall sensitization rates among different racial groups, but similar data are lacking on individual allergens. OBJECTIVE: Determine differences in sensitization rates between 2 racial groups in North America undergoing patch testing over a period of 4 years at the Cleveland Clinic Foundation (CCF), Ohio. METHODS: Retrospective computer review of the standard screening tray results of 991 patients with an average age of 45.9 years consisting of 877 (88.5%) whites and 114 (11.5%) blacks. RESULTS: Nickel sulfate and thiomersal (both 8.0%) and nickel sulfate and p-phenylenediamine (both 10.6%) were the 2 most common sensitizers among whites and blacks respectively. There was a statistically significant difference (P =.00599) in the sensitization rate for p-phenylenediamine in blacks (10.6%) compared with whites (4.5%). There were also statistically significant differences in sensitization rates for p-phenylenediamine (21.2%; P =.00005) and imidazolidinyl urea in petrolatum (pet.) (9.1%; P =.04103) in black men compared with white men (p-phenylenediamine [4.2%] and imidazolidinyl urea [2.6% pet.]). CONCLUSION: The differences in sensitization rates, especially for p-phenylenediamine, may reflect variations in allergen exposure among racial groups or interindividual variations in the N-acetylation (N-acetyltransferase 1 [NAT1] and 2 [NAT2]) capacities of human skin for p-phenylenediamine.

Allergens↗

PubMed2001

Patch testing discordance alert: false-negative findings with rubber additives and fragrances.

From July 1996 through June 1998, the North American Contact Dermatitis Group evaluated 318 patients for suspected contact dermatitis by patch testing simultaneously with Finn Chambers and the T.R.U.E. Test allergen system. Discrepancies between the two systems were found in some of the results, particularly with fragrance and rubber allergens. These results suggest that positive reactions to fragrance, thiuram, and carba mix allergens may be missed if the T.R.U.E. Test is used alone.

Allergens↗

PubMed2001

Fellowship training and career outcomes for primary care physician-faculty.

PURPOSE: To examine associations between fellowship training and career outcomes among primary care physician-faculty. METHOD: A total of 821 full-time primary care physician-faculty from 24 representative U.S. medical schools were surveyed using a self-administered questionnaire. Primary outcomes were recent grant submissions and funding, career referred publications, rank, and salary. Findings were adjusted for demographic and professional characteristics. RESULTS: Of the 500 respondents, 234 of the physician-faculty had completed a fellowship and 266 had not. Fellowship-trained physician-faculty were more than four times as likely to have submitted a grant proposal and to have had a grant funded (both p < 0.0001) than were physician-faculty without fellowship training. They were also more likely to have had any refereed publications (OR 3.8, p < 0.0001) and to have achieved senior academic rank (OR = 1.9, p = 0.02). Among those with fellowship experience, the amount of research training was important. Those with at least one year of research experience in their fellowship program had more grant proposal submissions (OR = 1.9, p = 0.02), more grants funded (OR = 2.9, p = 0.0003), more publications (OR = 2.4, p = 0.02), and higher academic ranks (OR 2.3, p = 0.03) than did those with less research training. Salaries were similar in every comparison. CONCLUSION: Fellowship-trained primary care physician-faculty were more productive researchers and were more likely to have achieved senior academic rank than were their no-fellowship-trained peers. Even among physician-faculty with fellowship experience, more research training was associated with higher productivity and rank. Salaries were not affected by training experience.

Faculty, Medical↗

PubMed2001

Prospective evaluation of the brain in asymptomatic children with neurofibromatosis type 1: relationship of macrocephaly to T1 relaxation changes and structural brain abnormalities.

BACKGROUND AND PURPOSE: Mutation of the neurofibromatosis type 1 (NF-1) gene may be associated with abnormal growth control in the brain. Because macrocephaly could be a sign of abnormal brain development and because 30% to 50% of children with NF-1 display macrocephaly in the absence of hydrocephalus, we sought to determine the relationship between macrocephaly and other brain abnormalities in young subjects with NF-1. These subjects were free of brain tumor, epilepsy, or other obvious neurologic problems. METHODS: We prospectively screened 18 neurologically asymptomatic subjects with NF-1, ages 6 to 16 years, using clinical measures, psychometric testing, conventional MR imaging, and quantitative MR imaging to measure T1. RESULTS: Cranial circumference was 2 or more SDs above the age norm in seven (39%) of 18 subjects, a frequency of macrocephaly 17-fold higher than normal. Conventional MR imaging showed abnormalities in all 18 children, although there were more extensive abnormalities in subjects with macrocephaly. Macrocephaly in NF-1 was associated with enlargement of multiple brain structures, and brain T1 in macrocephalic subjects was reduced with respect to controls in the genu, frontal white matter, caudate, putamen, thalamus, and cortex. In normocephalic subjects, T1 was reduced only in the genu and splenium. Volumetric analysis showed that macrocephaly was associated specifically with enlargement of white matter volume. CONCLUSION: Neurologically asymptomatic children with NF-1 showed macrocephaly, cognitive deficit, enlarged brain structures, and abnormally low brain T1. Macrocephaly in children with NF-1 may be associated with characteristic alterations in brain development, marked by more widespread and significant changes in T1, greater enlargement of midline structures, and greater volume of white matter.

Adolescent↗

PubMed2001

An overview of neurolaw for the clinician: what every potential witness should know.

This article reviews the field of medical jurisprudence known as neurolaw which deals with the medicolegal ramifications of brain and spinal cord injuries. Placing emphasis upon how clinicians may work effectively with trial lawyers, it provides practical guidance to neurorehabilitation professionals who testify in personal injury cases.

Brain Concussion↗

PubMed2000

Error-prone lesion bypass by human DNA polymerase eta.

DNA lesion bypass is an important cellular response to genomic damage during replication. Human DNA polymerase eta (Pol(eta)), encoded by the Xeroderma pigmentosum variant (XPV) gene, is known for its activity of error-free translesion synthesis opposite a TT cis-syn cyclobutane dimer. Using purified human Pol(eta), we have examined bypass activities of this polymerase opposite several other DNA lesions. Human Pol(eta) efficiently bypassed a template 8-oxoguanine, incorporating an A or a C opposite the lesion with similar efficiencies. Human Pol(eta) effectively bypassed a template abasic site, incorporating an A and less frequently a G opposite the lesion. Significant -1 deletion was also observed when the template base 5' to the abasic site is a T. Human Pol(eta) partially bypassed a template (+)-trans-anti-benzo[a]pyrene-N:(2)-dG and predominantly incorporated an A, less frequently a T, and least frequently a G or a C opposite the lesion. This specificity of nucleotide incorporation correlates well with the known mutation spectrum of (+)-trans-anti-benzo[a]pyrene-N:(2)-dG lesion in mammalian cells. These results show that human Pol(eta) is capable of error-prone translesion DNA syntheses in vitro and suggest that Pol(eta) may bypass certain lesions with a mutagenic consequence in humans.

Animals↗

PubMed2000

Pyrene nucleotide as a mechanistic probe: evidence for a transient abasic site-like intermediate in the bypass of dipyrimidine photoproducts by T7 DNA polymerase.

We recently proposed a mechanism for why dAMP is primarily inserted opposite both T's of photoproducts of TT sites by T7 DNA polymerase [Smith, C. A., Baeten, J., and Taylor, J.-S. (1998) J. Biol. Chem., 273, 21933-21940] that was based on analysis of a recent crystal structure of a complex of this enzyme with a template, a primer, and a dideoxynucleotide. We proposed that indiscriminate insertion of dAMP opposite the 3'-T of each photoproducts takes place via a transient abasic site-like intermediate, with the photoproduct outside the active site, whereas insertion of dAMP opposite the 5'-T takes place with the photoproduct inside the active site. To obtain further support for this mechanism, we have investigated the selectivity of dNMP and pyrene nucleotide (dPMP) insertion opposite each T of the cis,syn, trans,syn-I, trans,syn-II, (6-4), and Dewar photoproducts of TT and opposite a tetrahydrofuran abasic site analogue by the exonuclease-deficient T7 DNA polymerase, Sequenase Version 2.0. Selectivity was determined by a direct competition assay that makes use of a stacked gel to resolve the various extension products. Pyrene nucleotide was chosen for investigation because it has been previously shown to be selectively inserted opposite abasic sites and was therefore expected to probe whether the photoproducts were inside the active site during a particular insertion step. In accord with the proposed mechanism, dPMP was inserted in preference to dAMP opposite the 3'-T of all the photoproducts with the exception of the trans,syn-I product, whereas dAMP was inserted in preference to dPMP opposite the 5'-T of all the photoproducts. In addition to supporting the proposed mechanism, these results suggest that pyrene nucleotide may be a useful probe for investigating the mechanism of DNA damage bypass by polymerases and for characterizing their active sites.

Bacteriophage T7↗

PubMed2000

Error-free and error-prone lesion bypass by human DNA polymerase kappa in vitro.

Error-free lesion bypass and error-prone lesion bypass are important cellular responses to DNA damage during replication, both of which require a DNA polymerase (Pol). To identify lesion bypass DNA polymerases, we have purified human Polkappa encoded by the DINB1 gene and examined its response to damaged DNA templates. Here, we show that human Polkappa is a novel lesion bypass polymerase in vitro. Purified human Polkappa efficiently bypassed a template 8-oxoguanine, incorporating mainly A and less frequently C opposite the lesion. Human Polkappa most frequently incorporated A opposite a template abasic site. Efficient further extension required T as the next template base, and was mediated mainly by a one-nucleotide deletion mechanism. Human Polkappa was able to bypass an acetylaminofluorene-modified G in DNA, incorporating either C or T, and less efficiently A opposite the lesion. Furthermore, human Polkappa effectively bypassed a template (-)-trans-anti-benzo[a]pyrene-N:(2)-dG lesion in an error-free manner by incorporating a C opposite the bulky adduct. In contrast, human Polkappa was unable to bypass a template TT dimer or a TT (6-4) photoproduct, two of the major UV lesions. These results suggest that Polkappa plays an important role in both error-free and error-prone lesion bypass in humans.

2-Acetylaminofluorene↗

PubMed2000

DARWIN: a program for docking flexible molecules.

A new program named "DARWIN" has been developed to perform docking calculations with proteins and other biological molecules. The program uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex. A unique feature of DARWIN is that it communicates with the molecular mechanics program CHARMM to make the energy calculations. A second important feature is its parallel interface, which allows simultaneous use of multiple stand-alone copies of CHARMM to rapidly evaluate large numbers of potential solutions. This permits an "accuracy first" approach to docking, which avoids many of the common assumptions and shortcuts often made to reduce computation time. The method was applied to three protein-carbohydrate complexes: the crystallographically determined structures of Concanavalin A and Fab Se155-4; and a model structure for Fab ME36.1. Conformations close to the crystal structures were obtained with this approach, but some "false positive" solutions were also selected. Many of these could be eliminated by introducing different methods for simulating solvent effects. An effective screening method for docking a database of compounds to a single target enzyme using DARWIN is also presented.

Algorithms↗

PubMed2000

Nucleic acid-triggered catalytic drug release.

We propose a concept for the rational design and synthesis of highly selective chemotherapeutic agents that makes direct use of genetic information about the disease state. The key idea is to use the mRNA or DNA specific to the disease state to trigger the catalytic release of a cytotoxic drug by promoting the association of a prodrug with a catalyst capable of releasing the drug. We demonstrate the feasibility of such an approach in vitro with a model system that is based on the hydrolysis of p-nitrophenyl esters by imidazole. In our model system, the catalytic component consists of an imidazole group linked to the 5' end of a 15-mer that is complementary to the 5' end of the triggering oligodeoxynucleotide. The corresponding prodrug component consists of a p-nitrophenol ester linked to the 3' end of an 8-mer oligodeoxynucleotide that is complementary to the 3' end of the triggering sequence. We show that this system efficiently releases p-nitrophenol in the presence of all three components and that the reaction is catalytic and undergoes multiple turnovers. We also show that the complex between the catalytic component and the triggering oligodeoxynucleotide behaves like an enzyme and follows Michaelis-Menten kinetics, with a K(M) of 22 microM and a k(cat) of 0.018 min(-1). Most importantly, we show that catalytic release of p-nitrophenol is sensitive to the presence of a single base-pair mismatch.

Antineoplastic Agents↗

PubMed2000

Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis.

The expression of the Escherichia coli DNA polymerases pol V (UmuD'2C complex) and pol IV (DinB) increases in response to DNA damage. The induction of pol V is accompanied by a substantial increase in mutations targeted at DNA template lesions in a process called SOS-induced error-prone repair. Here we show that the common DNA template lesions, TT (6-4) photoproducts, TT cis-syn photodimers and abasic sites, are efficiently bypassed within 30 seconds by pol V in the presence of activated RecA protein (RecA*), single-stranded binding protein (SSB) and pol III's processivity beta,gamma-complex. There is no detectable bypass by either pol IV or pol III on this time scale. A mutagenic 'signature' for pol V is its incorporation of guanine opposite the 3'-thymine of a TT (6-4) photoproduct, in agreement with mutational spectra. In contrast, pol III and pol IV incorporate adenine almost exclusively. When copying undamaged DNA, pol V exhibits low fidelity with error rates of around 10(-3) to 10(-4), with pol IV being 5- to 10-fold more accurate. The effects of RecA protein on pol V, and beta,gamma-complex on pol IV, cause a 15,000- and 3,000-fold increase in DNA synthesis efficiency, respectively. However, both polymerases exhibit low processivity, adding 6 to 8 nucleotides before dissociating. Lesion bypass by pol V does not require beta,gamma-complex in the presence of non-hydrolysable ATPgammaS, indicating that an intact RecA filament may be required for translesion synthesis.

DNA Damage↗

PubMed2000

Specificity of DNA lesion bypass by the yeast DNA polymerase eta.

DNA polymerase eta (Pol(eta), xeroderma pigmentosum variant, or Rad30) plays an important role in an error-free response to unrepaired UV damage during replication. It faithfully synthesizes DNA opposite a thymine-thymine cis-syn-cyclobutane dimer. We have purified the yeast Pol(eta) and studied its lesion bypass activity in vitro with various types of DNA damage. The yeast Pol(eta) lacked a nuclease or a proofreading activity. It efficiently bypassed 8-oxoguanine, incorporating C, A, and G opposite the lesion with a relative efficiency of approximately 100:56:14, respectively. The yeast Pol(eta) efficiently incorporated a C opposite an acetylaminofluorene-modified G, and efficiently inserted a G or less frequently an A opposite an apurinic/apyrimidinic (AP) site but was unable to extend the DNA synthesis further in both cases. However, some continued DNA synthesis was observed in the presence of the yeast Pol(zeta) following the Pol(eta) action opposite an AP site, achieving true lesion bypass. In contrast, the yeast Pol(alpha) was able to bypass efficiently a template AP site, predominantly incorporating an A residue opposite the lesion. These results suggest that other than UV damage, Pol(eta) may also play a role in bypassing additional DNA lesions, some of which can be error-prone.

2-Acetylaminofluorene↗

PubMed2000

Evolution from empirical dynamic contrast-enhanced magnetic resonance imaging to pharmacokinetic MRI.

For chemotherapy to be effective against cancers which grow as solid tumors, agents must reach all tumor cells in effective quantities. Although many clinical trials include studies of the pharmacokinetics of the agents in body fluids such as blood or cerebrospinal fluid (CSF), there is presently no widely applicable way to determine access of chemotherapeutic agents to all regions of a solid tumor in an individual patient. This review discusses a relatively new methodology in MR imaging - dynamic contrast-enhanced imaging for exploring tumor microcirculation and drug access by imaging the uptake, or leakage, of contrast agent into tumor interstitial (extracellular and extravascular) space. The aims and methods of dynamic contrast-enhanced MRI evaluations to measure contrast uptake are distinguished from dynamic contrast-enhanced MRI to measure blood volume or flow, by MR imaging of the first-pass effects of a contrast bolus. Measures of contrast uptake by dynamic MRI have demonstrated a convincing ability to aid in diagnosing the presence of viable tumor and to measure response for a range of human tumors. This body of clinical results will be summarized. While questions remain to be answered about how to extract non-invasive pharmacokinetic measures of drug access from these novel dynamic imaging methods, we are optimistic that these methods can provide important new clinical measures that reflect the range of biological variation within and between naturally-occurring solid tumors.

Blood-Brain Barrier↗