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Biomedical subjects

J Knowles

Publications and source records attributed to J Knowles.

At least 19 recordsLinked to original sources
PubMed2000

No association between a presenilin 1 polymorphism and Alzheimer disease.

BACKGROUND: Homozygosity of allele 1 of a presenilin 1 intron 8 polymorphism (PS1-1) has been associated with doubling of the risk of sporadic late-onset Alzheimer disease (LOAD), in some, but not all studies. OBJECTIVE: To genotype the PS1 intron 8 polymorphism in predominantly Hispanic families with LOAD to test for association and for linkage between this polymorphism and LOAD. DESIGN: A family-based, case-control, genetic-linkage study. SETTING: Predominantly Hispanic families were selected from probands who were part of a random sample of 2128 Medicare beneficiaries aged 65 years or older who were residing in the community of Washington Heights, which is located in the northern part of Manhattan, NY. PARTICIPANTS: Fifty-one families with 103 affected family members, 67 unaffected family members, and 7 family members with other diagnoses were genotyped for the PS1 polymorphism. All patients met National Institute of Neurological and Communicative Disorders and Stroke-Alzheimer's Disease and Related Disorders Association criteria for either probable or possible Alzheimer disease. Age was truncated at 55 years or older. MAIN OUTCOME MEASURES: Association analyses, conditional logistic regression, and traditional linkage methods were applied to the families for the PS1 polymorphism and for the presence of the gene for apolipoprotein E (APOE). Results of the association and conditional logistic regression analyses of PS1 intron 8 polymorphism were subsequently adjusted for the effect of APOE-epsilon4, sex, age, and education of each sibling. RESULTS: No association between the PS1 intron 8 polymorphism and LOAD was observed (relative risk, 0.99; 95% confidence interval, 0.3-3.4). An association between presence of the APOE-epsilon4 allele and LOAD (relative risk 4.05; 95% confidence interval, 1.3-12.5) was observed. CONCLUSION: We could not confirm the relationship between the PS1 intron 8 polymorphism and LOAD in this collection of families.

Aged↗
PubMed2000

Behaviour in early treated phenylketonuria: a systematic review.

UNLABELLED: A search was made of the literature on behaviour in early treated phenylketonuria (PKU). Some 34 publications were selected for systematic review in order to answer the following questions: (1) does behaviour in early treated subjects with PKU differ from that in the general population?, (2) if so, do the differences show any consistent pattern?, matter in real life?, relate to intellectual status, phenylalanine (Phe) control or social factors? and (3) can behavioural problems be precipitated or reversed by changes in Phe control?. Eleven reports based on four studies of > 20 subjects provided the most useful data. There was good evidence of differences between subjects with PKU and their unaffected peers in behaviour and perception of self. The pattern of results was consistent across nations and age groups (higher scores on emotional/neurotic items and lower scores on anti-social/aggressive items) and suggested that subjects with PKU are more prone to depression, anxiety, phobic tendencies, isolation from their peers and a less "masculine" self image. Features of attention deficit hyperactivity disorder and associations between behaviour problems and both lower IQ and a worse quality of Phe control were well documented in several studies. CONCLUSION: The literature did not allow for definite conclusions on the cause of the behavioural problems but, taken together, the findings suggest that both the stressful dietary intervention and a degree of neurobiological impairment are likely to play a part.

Adolescent↗
PubMed2000

Continuous circadian measurements of ventilation in behaving adult rats.

Body temperature (Tb) and oxygen consumption (V(O(2))) are important determinants of ventilation (VE). While the circadian rhythms in Tb and V(O(2)) have been well described, the daily pattern of VE has not due to limitations in the available methods for measuring VE. Here we describe an adaptation of the barometric method using a chamber in which a large flow through very small restrictions was generated by the combined action of a positive pressure pump on the entrance and a negative pressure pump at the outlet. In this way the chamber effectively behaved as a closed system, despite having a high enough flow for long-term recording in freely moving, undisturbed small animals. This system was then used to test the hypothesis that VE oscillates with a circadian pattern similar to that of Tb(.) Measurements of tidal volume (VT) and breathing rate (f), in combination with Tb and activity by telemetry, were made in eight adult rats over 4-6 days under 12:12 light:dark conditions. Both VT, f, and thus VE, showed a circadian pattern similar to that of Tb and activity; that is, values were higher during the dark compared to the light phase. The differences in VE levels according to the time of the day suggest that mechanisms involved in the control of breathing may also have circadian patterns.

Animals↗
PubMed1999

Statistical mechanical simulation of polymeric DNA melting with MELTSIM.

MOTIVATION: MELTSIM is a windows-based statistical mechanical program for simulating melting curves of DNAs of known sequence and genomic dimensions under different conditions of ionic strength with great accuracy. The program is useful for mapping variations of base compositions of sequences, conducting studies of denaturation, establishing appropriate conditions for hybridization and renaturation, determinations of sequence complexity, and sequence divergence. RESULTS: Good agreement is achieved between experimental and calculated melting curves of plasmid, bacterial, yeast and human DNAs. Denaturation maps that accompany the calculated curves indicate non-coding regions have a significantly lower (G+C) composition than coding regions in all species examined. Curves of partially sequenced human DNA suggest the current database may be heavily biased with coding regions, and excluding large (A+T)-rich elements. AVAILABILITY: MELTSIM 1.0 is available at: //www.uml.edu/Dept/Chem/UMLBIC/Apps/MEL TSIM/MELTSIM-1.0-Win/meltsim. zip. Melting curve plots in this paper were made with GNUPLOT 3.5, available at: http://www.cs.dartmouth.edu/gnuplot_inf o.html Contact : blake@maine.maine.edu;

Base Composition↗
PubMed1998

Effect of heat treatment on pulsed laser deposited amorphous calcium phosphate coatings.

Amorphous calcium phosphate coatings were produced by pulsed laser deposition from targets of nonstoichiometric hydroxyapatite (Ca/P = 1.70) at a low substrate temperature of 300 degrees C. They were heated in air at different temperatures: 300, 450, 525 and 650 degrees C. Chemical and structural analyses of these coatings were performed using X-ray diffraction (XRD), FTIR, and SEM, XRD analysis of the as-deposited and heated coatings revealed that their crystallinity improved as heat treatment temperature increased. The main phase was apatitic, with some beta-tricalcium phosphate in the coatings heated at 525 and 600 degrees C. In the apatitic phase there was some carbonate substitution for phosphate and hydroxyl ions at 450 degrees C and almost solely for phosphate at 525 and 600 degrees C as identified by FTIR. This was accompanied by a higher hydroxyl content at 525 and 600 degrees C. At 450 degrees C a texture on the coating surface was observable by SEM that was attributable to a calcium hydroxide and calcite formation by XRD. These phases almost disappeared at 600 degrees C, probably due to a transformation into calcium oxide.

Calcium Phosphates↗
PubMed1997

Fluorescent labeling of NK2 receptor at specific sites in vivo and fluorescence energy transfer analysis of NK2 ligand-receptor complexes.

A fluorescent unnatural amino acid was introduced biosynthetically at known sites into the G protein-coupled neurokinin (tachykinin) NK2 receptor by suppression of UAG nonsense codons with the aid of a chemically misacylated synthetic tRNA specifically designed for the incorporation of unnatural amino acids during heterologous expression in Xenopus oocytes. A systematic UAG-scanning mutagenesis in NK2 extra- or intracellular loops and proximal transmembrane domains established that readthrough at some UAG sites may represent a limitation to the range of applicability of the nonsense suppression methodology. Fluorescence-labeled NK2 mutants containing an unique fluorescent nitrobenzoxadiazoyl-diaminopropionic acid residue at known sites were shown to be functionnally active. Intermolecular distances were determined by measuring the fluorescence resonance energy transfer (FRET) between the fluorescent unnatural amino acid and a fluorescently labeled NK2 heptapeptide antagonist in a native membrane environment. These distances confirmed the seven transmembrane topology for G protein-coupled receptors and determined a structural model for NK2 ligand-receptor interactions. The peptide is inserted between the fifth and sixth transmembrane domains, thus suggesting that antagonism may be caused by preventing correct packing of the helices required for receptor function.

Amino Acid Sequence↗
PubMed1996

Probing the structure and function of the tachykinin neurokinin-2 receptor through biosynthetic incorporation of fluorescent amino acids at specific sites.

A general method for understanding the mechanisms of ligand recognition and activation of G protein-coupled receptors has been developed. A study of ligand-receptor interactions in the prototypic seven-transmembrane neurokinin-2 receptor (NK2) using this fluorescence-based approach is presented. A fluorescent unnatural amino acid was introduced at known sites into NK2 by suppression of UAG nonsense codons with the aid of a chemically misacylated synthetic tRNA specifically designed for the incorporation of unnatural amino acids during heterologous expression in Xenopus oocytes. Fluorescence-labeled NK2 mutants containing an unique 3-N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-2,3-diaminopropionic acid (NBD-Dap) residue at either site 103, in the first extracellular loop, or 248, in the third cytoplasmic loop, were functionally active. The fluorescent NK2 mutants were investigated by microspectrofluorimetry in a native membrane environment. Intermolecular distances were determined by measuring the fluorescence resonance energy transfer (FRET) between the fluorescent unnatural amino acid and a fluorescently labeled NK2 heptapeptide antagonist. These distances, calculated by the theory of Förster, permit to fix the ligand in space and define the structure of the receptor in a molecular model for NK2 ligand-receptor interactions. Our data are the first report of the incorporation of a fluorescent unnatural amino acid into a membrane protein in intact cells by the method of nonsense codon suppression, as well as the first measurement of experimental distances between a G protein-coupled receptor and its ligand by FRET. The method presented here can be generally applied to the analysis of spatial relationships in integral membrane proteins such as receptors or channels.

Animals↗
PubMed1996

Velocity distributions in glottal models.

Velocity distributions within three models of the human larynx, namely, a rigid plexiglas model, an excised canine larynx, and a computational model are investigated with experimental and theoretical analyses. A plexiglas wind tunnel with interchangeable glottal constrictions was used as a two-dimensional steady-flow model to measure velocity and pressure for various glottal shapes. A canine excised larynx was used as a prototype pulsatile flow model to study pressure and velocity variations during phonation. Results of the plexiglas modelling indicated a parabolic laminar velocity profiles upstream of the glottal constriction and turbulent and asymmetric velocity profile downstream of the glottal constriction. The time-averaged velocities of the excised larynx had similarities with the plexiglas model results, and instabilities and asymmetries were also demonstrated by the computational method.

Animals↗
PubMed1995

A thermolabile triosephosphate isomerase from the psychrophile Vibrio sp. strain ANT-300.

We report the isolation of a gene encoding triosephosphate isomerase (TIM; EC 5.3.1.1) from Vibrio sp. strain ANT-300, a psychrophilic marine eubacterium that grows optimally at 7 degrees C. The deduced primary sequence of this isomerase is 50% identical to Escherichia coli TIM and 37% identical to the isomerase of the psychrotroph Moraxella sp. TA137. Transformation with this gene allowed growth of a TIM-deficient E. coli strain on selective media, but only at temperatures below 30 degrees C. The temperature dependence of this complementation is likely to result from an intrinsic thermolability of the isomerase. Indeed, the TIM activity present in ANT-300 lysates is markedly heat-sensitive, with a half-life of inactivation of 520 s at 25 degrees C.

Amino Acid Sequence↗
PubMed1994

Conformational properties of four peptides corresponding to alpha-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein.

Four peptides corresponding to alpha-helical regions delimited by residues 63-73 and 97-112 of cytochrome c2 (Rhodospirillum) and residues 24-36 and 45-55 of bovine calcium binding protein are predicted to be alpha-helical by a recently developed method [Rooman, M., Kocher, J.P., & Wodak, S.J. (1991) J. Mol. Biol. 221, 961-979], synthesized by solid phase methods, and purified by HPLC, and their solution conformations are determined by NMR and CD. The observed conformational properties of these peptides in solution confirmed prediction results: in water/TFE (60/40, v/v) at room temperature, these peptides adopt an alpha-helical conformation, as shown by an extended pattern of strong, sequential dNN(i,i + 1) NOE cross-peaks, d alpha N(i,i + 1) NOEs of reduced intensity, several medium-range [d alpha N(i,i + 3), d alpha N(i,i + 4), d alpha beta-(i,i + 3)] NOE connectivities, small 3JH alpha N values, and more upfield alpha-proton chemical shifts. CD studies at different TFE concentrations and at room temperature provide further evidence of the propensity of these peptides to adopt an alpha-helical conformation in solution, as determined by the ellipticity values at 222 nm, and by deconvolution of the CD spectra. According to the method used, helicities in the range 34-50% and 55-75% are found for the 63-73 and 97-112 fragments of cytochrome c2, respectively, and in the range 53-80% and 42-65% for the fragments 24-36 and 45-55 of calcium binding protein in water/TFE (60/40, v/v) at 298 K. In addition, the experiments and predictions agree for those residues that are more flexible. Finally, the relevance of our results for the protein folding pathways is discussed.

Algorithms↗
PubMed1994

The precursor of the Streptomyces R61 DD-peptidase containing a C-terminal extension is inactive.

The Streptomyces R61 DD-peptidase gene encodes a 26-residue C-terminal extension which is not found in the mature protein. When the gene was expressed in Escherichia coli, the extension was not cleaved and the precursor protein was not enzymatically active. It also reacted with penicillins significantly more slowly than the mature protein. The introduction of a 'stop' codon after that corresponding to the C-terminal residue of the mature protein resulted in the production of an active protein in the periplasm of E. coli.

Amino Acid Sequence↗
PubMed1994

Knee function after patellectomy. A 12- to 48-year follow-up.

We describe 83 knees (69 patients) which had had patellectomy for anterior knee pain (52), patellofemoral osteoarthritis (25) or comminuted fractures (6) between 1942 and 1978. The patients were questioned about their symptoms and the function of the operated knee 14 to 50 years after operation. In the group with anterior knee pain, 76% achieved good results and were satisfied with the operation. Only 54% of the osteoarthritis group had satisfactory relief of pain and most had progressive deterioration of function. Sixteen patients who had had unilateral patellectomy were assessed by dynamometry, ultrasound and radiography. The average quadriceps muscle power was 60% of that on the normal side although two patients had stronger muscles in their operated than in their unoperated legs.

Adult↗