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Biomedical subjects

P A Bartlett

Publications and source records attributed to P A Bartlett.

At least 19 recordsLinked to original sources
PubMed2002

Measurement of amygdala T2 relaxation time in temporal lobe epilepsy.

OBJECTIVES: To implement and validate the use of coronal dual echo T2 maps for the measurement of T2 relaxation time of the amygdala (AT2) as a rapid and reproducible method for identifying amygdala abnormality. METHODS: 20 healthy subjects and 25 patients with known hippocampal sclerosis (HS) were studied using a dual echo CSE sequence on a 1.5T MRI GE scanner. The T2 relaxation time of the amygdala was calculated and measured using a previously validated method. RESULTS: The mean control AT2 was 88.1 ms (SD 2 ms). The coefficient of reliability was good at 6.3% test-retest and 7.4% inter-rater. The upper limit of normal AT2 was 92 ms. AT2 was abnormal ipsilaterally in six, and bilaterally in three, of 20 patients with unilateral HS. Two of five patients with bilateral HS had unilateral abnormal AT2. CONCLUSION: Reliable T2 measurements can be obtained in the amygdala, and may be useful in the detection of amygdala abnormality.

Amygdala↗
PubMed2001

Five-membered ring analogues of shikimic acid.

Shikimate and other intermediates of the shikimate-chorismate pathway are densely functionalized structures that seem to offer limited options for skeletal modification. We designed and synthesized cyclopentylidenes 1 and 2, as well as cyclopentenes 3 and 4, as novel ring-contracted analogues of shikimic acid. Enzymatic studies showed that analogues 1-3 are indeed processed by shikimate kinase to give phosphates 1-P, 2-P, and 3-P as five-membered ring analogues of shikimate-3-phosphate. In particular, analogue 1 is converted by the enzyme at a rate only 3.5-fold slower than that of the native substrate, while analogue 3 binds to shikimate kinase with an apparent Km of 1.7 mM, compared to 0.14 mM for shikimate.

Kinetics↗
PubMed2001

A fast FLAIR dual-echo technique for hippocampal T2 relaxometry: first experiences in patients with temporal lobe epilepsy.

To evaluate the use of cerebrospinal fluid (CSF) signal nulling in MR T2 measurements of the hippocampus in normal control subjects and patients with temporal lobe epilepsy (TLE), dual-echo acquisitions covering the whole brain were used. T2 relaxation times were estimated in 12 standard Eurospin II MR test objects and in the hippocampi of 10 control subjects, using T2 maps constructed from conventional spin-echo (CSE), fast spin-echo (FSE), and fast FLAIR (FF) dual-echo sequences on a 1.5-T MR scanner. Hippocampal T2 values (HCT2) were measured on contiguous coronal 5-mm slices throughout the antero-posterior extent of each hippocampus in the 10 controls and 12 TLE patients, using both CSE and FF. Scan-rescan reproducibility in Eurospin II standard MR test objects was high for all sequences. There was a good correlation between T2 values from CSE, FF, and FSE sequences in test objects and in control hippocampi. In controls, the coefficient of variation of mean HCT2 values differed between slice positions, but was lowest for FF, followed by CSE data. The intrarater coefficient of reliability between repeated measurements in control subjects was lowest for FF HCT2, at 2.3%. The interrater coefficient of reliability for CSE HCT2 measurements in controls (4.8%) was slightly lower than the interrater coefficient for FF HCT2 (5.4%). HCT2 measurement with both CSE and FF identified abnormal values in the same 10 hippocampi of 12 patients. Hippocampal dual-echo T2 relaxometry using CSF nulling is reliable in control subjects, and identifies the abnormal hippocampi in patients with TLE. The increases in hippocampal T2 signal demonstrated using FF HCT2 measurements are unlikely to be partial volume effects from CSF.

Adult↗
PubMed2001

A longitudinal quantitative MRI study of community-based patients with chronic epilepsy and newly diagnosed seizures: methodology and preliminary findings.

Experimental and human data suggest that progressive cerebral damage may result from the cumulative effect of brief recurrent seizures. Longitudinal studies addressing this fundamental question, however, are lacking. We have addressed this need with a large prospective community-based observational study, which aims to rescan 154 patients with chronic active epilepsy and 90 patients with newly diagnosed seizures, after an interval of 3.5 years. Here, we describe the quantitative magnetic resonance methods used to identify subtle volume changes in hippocampal, cerebellar, and neocortical structures over time and report preliminary findings. Using this methodology, we have previously shown that we can reliably detect individual hippocampal volume (HV) and cerebellar volume (CBV) changes greater than 3.1 and 3.0%, respectively (Lemieux et al, 2000). Analysis of the first 53 subjects (24 patients with chronic active epilepsy, 9 patients with newly diagnosed seizures, and 20 controls) has demonstrated significant HV losses in 4 individuals. Automated and semiautomated calculation has detected significant reductions in CBV, total brain volume, and gray matter volume in 2, 3, and 1 subject, respectively. There were no significant white matter volume losses detected. Data collected from rescanning the entire cohorts will help to provide further information on the relationship between recurrent seizures and secondary brain damage.

Adult↗
PubMed2001

Quantitative short echo time proton magnetic resonance spectroscopic imaging study of malformations of cortical development causing epilepsy.

In patients with malformations of cortical development (MCD), widespread structural abnormalities of the brain have been demonstrated using volumetric MRI, and associated with poor post-surgical outcome in patients with localization-related epilepsy. Proton magnetic resonance spectroscopic imaging (1H-MRSI) studies permit the non-invasive measurement of concentrations of a variety of cerebral metabolites implicated in cerebral structure and function. There is a dearth of quantitative 1H-MRSI studies of MCD. Ten controls and 10 patients with localization-related epilepsy who were found to have MCD on high resolution MRI underwent 1H-MRSI on a 1.5 T GE Signa scanner [TE (echo time) = 30 ms, TR (repetition time) = 3 s]. In all patients, the axial area studied contained lesional and perilesional tissue. In seven unilaterally affected patients, the area studied contained also apparently normal contralateral grey and white matter; in three patients with bilateral but asymmetrical MCD, it contained visually normal and abnormal tissue from both hemispheres. N-acetyl aspartate + N-acetyl aspartyl glutamate (NAA), creatine + phosphocreatine (Cr), choline-containing compounds (Cho), glutamate + glutamine (Glx) and myo-inositol (Ins) were automatically quantified in voxels covering these different regions. Metabolite concentrations were corrected for CSF content and correlated with the grey and white matter of the MRSI voxels. In control subjects, there were significant positive correlations between grey matter content and concentrations of NAA, Glx, Ins and Cr. Compared with a normal range that took grey matter content into account, defined as the control mean +/- 2 SD, all lesions but one showed metabolic abnormalities. The most common abnormality was a decrease in NAA, but findings were heterogeneous and there was increased NAA in one lesion. Perilesional tissue was abnormal in eight patients, with increased NAA in three. Tissue contralateral to the main MCD was abnormal in all three patients with bilateral but asymmetrical MCD, and in six of the seven apparently unilaterally affected patients. Spectroscopic grey and white matter abnormalities in patients with MCD exceeded the apparently focal abnormality shown by MRI, indicating widespread abnormalities of cerebral function.

Adult↗
PubMed2000

Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.

The refined crystal structure of the complex between human pepsin and a synthetic phosphonate inhibitor, Iva-Val-Val-Leu(P)-(O)Phe-Ala-Ala-OMe [Iva = isovaleryl, Leu(P) = the phosphinic acid analog of L-leucine, (O)Phe = L-3-phenyllactic acid, OMe = methyl ester], is presented. The structure was refined using diffraction data between 30 and 1.96 A resolution to a final R factor ( summation operator| |F(o)| - |F(c)| | / summation operator|F(o)|, where |F(o)| and |F(c)| are the observed and calculated structure-factor amplitudes, respectively) of 20.0%. The interactions of the inhibitor with the enzyme show the locations of the binding sites on the enzyme from S4 to S3'. Modeling of the inhibitor binding to porcine pepsin shows very similar binding sites, except at S4. Comparison of the complex structure with the structures of related inhibitors bound to penicillopepsin helps to rationalize the observed differences in the binding constants. The convergence of reaction mechanisms and geometries in different families of proteinases is also discussed.

Aspartic Acid Endopeptidases↗
PubMed1999

Short echo time single-voxel 1H magnetic resonance spectroscopy in magnetic resonance imaging-negative temporal lobe epilepsy: different biochemical profile compared with hippocampal sclerosis.

Single-voxel proton magnetic resonance spectroscopy (1H MRS) has shown abnormalities in patients with temporal lobe epilepsy (TLE) and hippocampal sclerosis (HS). Many TLE patients, however, do not have HS or other lesions on quantitative magnetic resonance imaging (MRI) (MRI-negative). Fifteen control subjects, 15 patients with unilateral HS, and 15 MRI-negative TLE patients underwent 1H MRS at an echo time of 30 msec on a 1.5-T GE Signa scanner. Voxels were tailored to the individual hippocampi. N-Acetylaspartate (NAA), creatine, choline, total glutamate plus glutamine (Glx), and myo-inositol (Ins) were quantitated by using an external standard and LCModel, a user-independent quantitation method. Normal ranges were defined as the control mean +/- 2.5 SD. In HS patients, 12 of 15 had abnormally low NAA in sclerotic hippocampi; 3 of these 12 also had abnormally low NAA contralaterally. Abnormally low NAA/Ins ratios lateralized the side affected by HS in 7 of 15 patients, without any bilateral abnormalities. In 15 MRI-negative TLE patients, 4 had abnormally low hippocampal NAA ipsilateral to seizure onset, 1 of whom had abnormally low NAA bilaterally. Analysis of groups of subjects showed a bilateral decrease in NAA, most marked in patients with HS and on the side of seizure onset. The mean NAA/Ins ratio was lower in patients with HS than in control subjects and in MRI-negative patients. The concentration of Glx was higher ipsilateral to seizure onset in MRI-negative patients than in HS patients. Quantitative short echo time 1H MRS identified abnormalities in 87% of patients with HS and 27% of MRI-negative TLE patients in concordance with other lateralizing data. In individual and group comparisons, 1H MRS described a metabolite profile in the hippocampi of MRI-negative TLE patients that was different from patients with HS, with an increase in Glx and a less marked decrease in NAA than was seen in HS.

Adult↗
PubMed1998

Lowering the entropic barrier for binding conformationally flexible inhibitors to enzymes.

The design of inhibitors with enhanced potency against proteolytic enzymes has many applications for the treatment of human diseases. In addition to the optimization of chemical interactions between the enzyme and inhibitor, the binding affinity can be increased by constraining the inhibitor to the conformation that is recognized by the enzyme, thus lowering the entropic barrier to complex formation. We have structurally characterized the complexes of a macrocyclic pentapeptide inhibitor and its acyclic analogue with penicillopepsin, an aspartic proteinase, to study the effect of conformational constraint on the binding affinity. The phosphonate-based macrocycle PPi4 (Ki = 0.10 nM) is covalently linked at the P2-Asn and P1'-Phe side chains [nomenclature of Schechter and Berger, Biochim. Biophys. Res. Commun. (1967) 27, 157-162] via an amide bond, relative to the acyclic compound PPi3 (Ki = 42 nM). Comparisons of the high-resolution crystal structures of PPi4-penicillopepsin (0.95 A) and PPi3-penicillopepsin (1.45 A) reveal that the conformations of the inhibitors and their interactions with the enzyme are similar. The 420-fold increase in the binding affinity of PPi4 is attributed to a reduction in its conformational flexibility, thus providing the first rigorous measure of the entropic contribution to the binding energy in a protein-ligand complex and stressing the advantages of the design strategy.

Aspartic Acid Endopeptidases↗
PubMed1998

Fast fluid-attenuated inversion-recovery imaging: first experience with a 3D version in epilepsy.

We developed a 3D version of fast fluid-attenuated inversion-recovery imaging (FLAIR) which provides images with a slice thickness of 1.5 mm. We present our initial experience with 3D fast FLAIR in patients with epilepsy. We compared 3D fast FLAIR (slice thickness 1.5 mm), 2D fast FLAIR (slice thickness 5 mm) and a 3D spoiled GRASS (IRSPGR) sequence (slice thickness 1.5 mm) in 10 patients with lesional epilepsy (head injury 1, hippocampal sclerosis 2, low-grade glioma 2, dysembryoplastic neuroepithelial tumour 2, polymicrogyria 1, perinatal infarct 1 and presumed thrombosed aneurysm 1). Both 2D and 3D fast FLAIR sequences yielded higher conspicuity for lesions than the T1-weighted IRSPGR sequence, except in the patient with polymicrogyria. The extent of the lesion, in particular that of low-grade tumours, was best assessed on 3D fast FLAIR images. 3D fast FLAIR may be a useful additional tool especially for imaging low-grade tumours.

Artifacts↗
PubMed1997

Synthetic strategies in combinatorial chemistry.

Different synthetic strategies are required for the two kinds of libraries being developed for combinatoral chemistry. Preparation of a 'focused' library involves conversion of a known synthetic route to the solid-phase or automated format, whereas generation of a 'prospecting' library is driven more by availability of input materials and considerations of structural novelty. While both types can be identified over the history of combinatorial chemistry, elaborating syntheses of novel, nonoligomeric, 'drug-like' molecules for use in prospecting libraries is a relatively recent development.

Chemistry, Organic↗
PubMed1997

Development of hippocampal atrophy: a serial magnetic resonance imaging study in a patient who developed epilepsy after generalized status epilepticus.

PURPOSE: To investigate changes in hippocampal volume. METHODS: We used serial magnetic resonance imaging (MRI) in a patient who developed chronic epilepsy after having generalized tonic-clonic status epilepticus (SE). Five MRI investigations were performed during SE and a 58-month follow-up period. Hippocampal volumetric measurements and coregistration of scans were performed to detect hippocampal atrophy. RESULTS: During status both mesiotemporal regions returned a high signal on T2-weighted images. Two months after the onset of SE, bilateral hippocampal atrophy was detected. Further progressive hippocampal atrophy was detected in the subsequent 58 months by both hippocampal volumetric measurements and coregistration of scans. CONCLUSIONS: Our findings suggest that hippocampal atrophy is a process that may continue after the end of the SE.

Adult↗
PubMed1996

Synthesis and evaluation of inhibitors of bacterial D-alanine:D-alanine ligases.

BACKGROUND: D-Alanine:D-alanine ligase is essential for bacterial cell wall synthesis, assembling one of the subunits used for peptidoglycan crosslinking. The resulting aminoacyl-D-Ala-D-Ala strand is the Achilles' heel of vancomycin-susceptible bacteria; binding of vancomycin to this sequence interferes with crosslinking and blocks cell-wall synthesis. A mutant enzyme (VanA) from vancomycin-resistant Enterococcus faecium has been found to incorporate alpha-hydroxy acids at the terminal site instead of D-Ala; the resulting depsipeptides do not bind vancomycin, yet function in the crosslinking reaction. To investigate the binding specificity of these ligases, we examined their inhibition by a series of substrate analogs. RESULTS: Phosphinate and phosphonate dipeptide analogs (which, after phosphorylation by the enzyme, mimic intermediates in the ligation reaction) were prepared and evaluated as reversible inhibitors of the wild-type ligases DdlA and DdlB from Escherichia coli and of the mutant enzyme VanA. Ki values were calculated for the first stage of inhibitor binding according to a mechanism in which inhibitor competes with D-Ala for both substrate binding sites. DdlA is potently inhibited by phosphinates but not by phosphonates, while DdlB and VanA show little discrimination; both series of compounds inhibit DdlB strongly and VanA weakly. CONCLUSIONS: VanA has greatly reduced affinity for all the ligands studied. The relative affinities of the inhibitors in the reversible binding step are not, however, consistent with the substrate specificities of the enzymes. We propose a mechanism in which proton transfer from the attacking nucleophile to the departing phosphate occurs directly, without intervention of the enzyme.

Bacteria↗
PubMed1996

A convenient method for determining cyclic peptide conformation from 1D 1H-NMR information.

A rapid and convenient method for determining the backbone conformation of cyclic peptides results from the combination of 1D 1H NMR information and molecular modeling. phi Angle torsional constraints calculated from 3JHN.H alpha coupling constants are used to determine the position of multiple-welled potential energy penalty functions that are imposed on the force field used in the structure refinement (Amber* with GB/SA solvation model). Monte Carlo searches and minimizations lead to a collection of structures that are clustered by backbone similarity and then filtered according to hydrogen-bonding constraints determined by the chemical shift temperature dependencies of the amide protons. This approach was applied to five cyclic peptides whose structures had been determined previously using more extensive 2D NMR techniques, and the importance of the torsional, H-bonding, and solvation restraints were assessed. For the four peptides that adopt a predominant conformation, this method reproduced the reported structures closely; lack of convergence for the fifth structure reflected the multiple backbone conformations that this macrocycle adopts.

Hydrogen Bonding↗
PubMed1996

Magnetic resonance imaging in epilepsy with a fast FLAIR sequence.

OBJECTIVE: To assess the diagnostic value of the fast FLAIR sequence in patients with epilepsy. METHODS: One hundred and twenty eight patients with epilepsy and 10 control subjects were scanned with the fast FLAIR sequence with 5 mm slices, a coronal gradient echo (GRE) T1 weighted sequence with 1.5 mm slices and spin echo (SE) or fast spin echo (FSE) proton density and T2 weighted sequences with 5 mm slices. All images were compared by an unblinded neuroradiologist and neurologist. Fast FLAIR images of patients with hippocampal sclerosis (HS) and normal control subjects were also evaluated by two blinded independent raters. RESULTS: Fast FLAIR provided a high conspicuity of neocortical damage, hamartomas, dysembryoplastic neuroepithelial tumours, and clear cut hippocampal sclerosis. However, the same information could be obtained from the coronal T1 and T2 weighted images. In three patients fast FLAIR showed a clearly abnormal signal when SE T2 weighted images had not been definitely abnormal. Heterotopia was less conspicuous on fast FLAIR than GRE T1 weighted images. The two blinded raters detected all but one of the patients with clear cut hippocampal sclerosis on fast FLAIR images but missed all borderline cases of hippocampal atrophy and there were two false positives. Clear cut hippocampal sclerosis was more conspicuous on fast FLAIR images than on SE T2 weighted images in most patients, but additional patients were not identified. CONCLUSION: Fast FLAIR has the advantage of identifying neocortical lesions and definite hippocampal sclerosis with a short scanning time and may also demonstrate lesions when other sequences are normal in a limited number of cases. The technique was not useful, however, for identifying mild hippocampal sclerosis or heterotopia.

Clinical Protocols↗
PubMed1994

Substrate analogs as mechanistic probes for the bifunctional chorismate synthase from Neurospora crassa.

Analogs of EPSP (4-8) have been prepared, and their activity as substrates for the chorismate synthase from Neurospora crassa has been characterized kinetically. The enzyme appears to show strict discrimination against substitution at the Z-position of the enol ether side chain as well as against substitution at the S-position of the reduced analogs. Both the glycolyl and (R)-lactyl analogs 4 and (R)-5 are good substrates, with (R)-5 having a higher V value than the natural substrate. Three substrates, including EPSP, have been found to show significant substrate inhibition with this enzyme, which at present can be explained by a noncompetitive model involving formation of a catalytically incompetent, ternary ES2 complex. A significant secondary kinetic isotope effect on V of 1.10 +/- 0.02 has been observed at C-3 with EPSP, indicating that C-O bond cleavage is kinetically significant at saturating substrate concentration; this effect is severely depressed at limiting substrate, with D(V/K) = 0.97 +/- 0.02. A similar effect is found for the primary deuterium isotope effect at C-6R, as observed previously [Balasubramanian, S., Davies, G. M., Coggins, J. R., & Abell, C. (1991) J. Am. Chem. Soc. 113, 8945-8946]. The primary isotope effects at C-6R with reduced analogs (R)-5 and (S)-6 are significantly larger than those with EPSP. The larger values of V and DV for (R)-5, when compared to EPSP, are evidence that release of chorismate is partially rate-limiting under saturating conditions. Incubation of the enzyme with reduced 5-deazaFMN does not result in any observable formation of chorismate, consistent with previous results indicating that reduced flavin is chemically involved in the synthesis of chorismate from EPSP [Ramjee, M. N., Balasubramanian, S., Abell, C., Coggins, J. R., Davies, G. M., Hawkes, T. R., Lowe, D. J., & Thorneley, R. N. F. (1992) J. Am. Chem. Soc. 114, 3151-3153].

Deuterium↗
PubMed1994

CAVEAT: a program to facilitate the design of organic molecules.

A frequently encountered problem in the design of enzyme inhibitors and other biologically active molecules is the identification of molecular frameworks to serve as templates or linking units that can position functional groups in specific relative orientations. The program CAVEAT was designed to address this problem by searching 3D databases for such molecular fragments. Key innovations introduced in CAVEAT are a focus on relationships between bonds and the provision of automated methods to identify and classify structural frameworks. Performance has been a particular concern in formulating CAVEAT, since it is intended to be used in an interactive manner. The focus in this report is the design and implementation of the principal algorithms and the performance achieved.

Amino Acid Sequence↗