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Biomedical subjects

J B Cooper

Publications and source records attributed to J B Cooper.

At least 55 records · Page 3Linked to original sources
PubMed2000

Heritability of clinical mastitis incidence and relationships with sire transmitting abilities for somatic cell score, udder type traits, productive life, and protein yield.

The objective of this study was to determine the relationships among daughter clinical mastitis during first and second lactations and sire transmitting abilities for somatic cell score, udder type traits, productive life, and protein yield. Data on clinical mastitis during first lactation were available for 1795 daughters (in six Pennsylvania herds, one Minnesota herd, and one Nebraska herd) of 283 Holstein sires. Data on clinical mastitis during second lactation were available for 1055 of these daughters. A total of 479 cows had 864 clinical episodes during first lactation, and 230 cows had 384 clinical episodes during second lactation. Clinical mastitis incidence and the total number of clinical episodes during each lactation were regressed on herd-season of calving (a classification variable), age at first calving, lactation length, and sire transmitting abilities taken one at a time. Linear effects, nonlinear effects, and odds ratios were estimated for sire transmitting abilities. Separate analyses were conducted on dependent variables that considered clinical mastitis from: all organisms, coagulase-negative staphylococci, coliform species, streptococci other than Streptococcus agalactiae, and the most common environmental organisms (coliform species and streptococci other than Streptococcus agalactiae). Heritability of clinical mastitis ranged from 0.01 to 0.42. Daughters of sires that transmit the lowest somatic cell score had the lowest incidence of clinical mastitis and the fewest clinical episodes during first and second lactations. Daughters of sires that transmit longer productive life, shallower udders, deeper udder cleft, and strongly attached fore udders had either fewer clinical episodes or lower clinical mastitis incidence during first and second lactations. The incidence of clinical mastitis and the number of clinical episodes per lactation may be reduced by selection for lower somatic cell score, longer productive life, shallower udders, deeper udder cleft, or strongly attached fore udders.

Animals↗
PubMed1999

High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase.

Common to the biosynthesis of all known tetrapyrroles is the condensation of two molecules of 5-aminolevulinic acid to the pyrrole porphobilinogen catalyzed by the enzyme porphobilinogen synthase (PBGS). Two major classes of PBGS are known. Zn2+-dependent PBGSs are found in mammals, yeast and some bacteria including Escherichia coli, while Mg2+-dependent PBGSs are present mainly in plants and other bacteria. The crystal structure of the Mg2+-dependent PBGS from the human pathogen Pseudomonas aeruginosa in complex with the competitive inhibitor levulinic acid (LA) solved at 1.67 A resolution shows a homooctameric enzyme that consists of four asymmetric dimers. The monomers in each dimer differ from each other by having a "closed" and an "open" active site pocket. In the closed subunit, the active site is completely shielded from solvent by a well-defined lid that is partially disordered in the open subunit. A single molecule of LA binds to a mainly hydrophobic pocket in each monomer where it is covalently attached via a Schiff base to an active site lysine residue. Whereas no metal ions are found in the active site of both monomers, a single well-defined and highly hydrated Mg2+is present only in the closed form about 14 A away from the Schiff base forming nitrogen atom of the active site lysine. We conclude that the observed differences in the active sites of both monomers might be induced by Mg2+-binding to this remote site and propose a structure-based mechanism for this allosteric Mg2+in rate enhancement.

Allosteric Site↗
PubMed1999

X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0 A resolution.

5-Aminolevulinic acid dehydratase (ALAD), an early enzyme of the tetrapyrrole biosynthesis pathway, catalyzes the dimerization of 5-aminolevulinic acid to form the pyrrole, porphobilinogen. ALAD from Escherichia coli is shown to form a homo-octameric structure with 422 symmetry in which each subunit adopts the TIM barrel fold with a 30-residue N-terminal arm. Pairs of monomers associate with their arms wrapped around each other. Four of these dimers interact, principally via their arm regions, to form octamers in which each active site is located on the surface. The active site contains two lysine residues (195 and 247), one of which (Lys 247) forms a Schiff base link with the bound substrate analogue, levulinic acid. Of the two substrate binding sites (referred to as A and P), our analysis defines the residues forming the P-site, which is where the first ALA molecule to associate with the enzyme binds. The carboxyl group of the levulinic acid moiety forms hydrogen bonds with the side chains of Ser 273 and Tyr 312. In proximity to the levulinic acid is a zinc binding site formed by three cysteines (Cys 120, 122, and 130) and a solvent molecule. We infer that the second substrate binding site (or A-site) is located between the triple-cysteine zinc site and the bound levulinic acid moiety. Two invariant arginine residues in a loop covering the active site (Arg 205 and Arg 216) appear to be appropriately placed to bind the carboxylate of the A-site substrate. Another metal binding site, close to the active site flap, in which a putative zinc ion is coordinated by a carboxyl and five solvent molecules may account for the activating properties of magnesium ions.

Binding Sites↗
PubMed1999

Right median nerve electrical stimulation to hasten awakening from coma.

Electrical stimulation of the right median nerve may hasten the awakening of closed head injured, comatose patients. A series of 25 comatose patients have been treated. These patients made better recoveries than similar individuals reported in the literature. In a double-blind pilot project patients in the treated group scored better on interval Glasgow Coma Scale scores, spent fewer days in the intensive care unit, and showed better Glasgow Outcome Scores at 1 month post-injury. Peripheral electrical stimulation of the right median nerve, through activation of the ascending reticular activating system, may be sufficient to arouse the moderate to severely comatose patient.

Adolescent↗
PubMed1999

The molecular structure of an unusual cytochrome c2 determined at 2.0 A; the cytochrome cH from Methylobacterium extorquens.

Cytochrome cH is the electron donor to the oxidase in methylotrophic bacteria. Its amino acid sequence suggests that it is a typical Class 1 cytochrome c, but some features of the sequence indicated that its structure might be of special interest. The structure of oxidized cytochrome cH has been solved to 2.0 A resolution by X-ray diffraction. It has the classical tertiary structure of the Class 1 cytochromes c but bears a closer gross resemblance to mitochondrial cytochrome c than to the bacterial cytochrome c2. The left-hand side of the haem cleft is unique; in particular, it is highly hydrophobic, the usual water is absent, and the "conserved" Tyr67 is replaced by tryptophan. A number of features of the structure demonstrate that the usual hydrogen bonding network involving water in the haem channel is not essential and that other mechanisms may exist for modulation of redox potentials in this cytochrome.

Amino Acid Sequence↗
PubMed1999

The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid.

The X-ray structure of the complex formed between yeast 5-aminolaevulinic acid dehydratase (ALAD) and the inhibitor laevulinic acid has been determined at 2.15 A resolution. The inhibitor binds by forming a Schiff base link with one of the two invariant lysines at the catalytic center: Lys263. It is known that this lysine forms a Schiff base link with substrate bound at the enzyme's so-called P-site. The carboxyl group of laevulinic acid makes hydrogen bonds with the side-chain-OH groups of Tyr329 and Ser290, as well as with the main-chain >NH group of Ser290. The aliphatic moiety of the inhibitor makes hydrophobic interactions with surrounding aromatic residues in the protein including Phe219, which resides in the flap covering the active site. Our analysis strongly suggests that the same interactions will be made by P-side substrate and also indicates that the substrate that binds at the enzyme's A-site will interact with the enzyme's zinc ion bound by three cysteines (133, 135, and 143). Inhibitor binding caused a substantial ordering of the active site flap (residues 217-235), which was largely invisible in the native electron density map and indicates that this highly conserved yet flexible region has a specific role in substrate binding during catalysis.

Binding Sites↗
PubMed1999

Clinical mastitis in primiparous Holsteins: comparisons of bovine leukocyte adhesion deficiency carriers and noncarriers.

The objective of this study was to determine the impact of bovine leukocyte adhesion deficiency on clinical mastitis incidence, severity, and duration in Holstein cows. Genomic DNA from milk of 847 Holstein cows in six Pennsylvania herds was used to determine bovine leukocyte adhesion deficiency genotypes (82 or 9.7% carriers). Data on clinical mastitis incidence, severity, duration, and pathogen involved were collected during first lactation for the project cows. One hundred ninety-four cows had one or more clinical mastitis episodes; milk samples from each quarter with clinical mastitis were collected at discovery of the episode and were cultured following National Mastitis Council recommendations. The overall incidence of clinical mastitis was significantly affected by sire and herd-year-season of calving. In addition, incidence of clinical mastitis tended to increase with age at first calving. Severity and duration of clinical mastitis were impacted by the pathogen involved. Incidence of clinical mastitis from all pathogens, from coagulase-negative staphylococci, and from coliform bacteria was not significantly related to bovine leukocyte adhesion deficiency status. Carriers tended to have lower rates of mastitis from streptococci other than Streptococcus agalactiae when compared with noncarriers, but this result should be interpreted with caution because of the low frequency of mastitis from the streptococci. Bovine leukocyte adhesion deficiency status was unrelated to severity or duration of clinical episodes. Bovine leukocyte adhesion deficiency carriers are probably similar to noncarriers in resistance to clinical mastitis.

Aging↗
PubMed1998

Identification of an opioid kappa receptor subtype-selective N-substituent for (+)-(3R,4R)-dimethyl-4-(3-hydroxyphenyl)piperidine.

A three-component library of compounds was prepared in parallel using multiple simultaneous solution-phase synthetic methodology. The compounds were biased toward opioid receptor antagonist activity by incorporating (+)-(3R,4R)-dimethyl-4-(3-hydroxyphenyl)piperidine (a potent, nonselective opioid pure antagonist) as one of the monomers. The other two monomers, which included N-substituted or unsubstituted Boc-protected amino acids and a range of substituted aryl carboxylic acids, were selected to add chemical diversity. Screening of these compounds in competitive binding experiments with the kappa opioid receptor selective ligand [3H]U69,593 led to the discovery of a novel kappa opioid receptor selective ligand, N-¿(2'S)-[3-(4-hydroxyphenyl)propanamido]-3'-methylbutyl¿-(3R, 4R)-dimethyl-4-(3-hydroxyphenyl)piperidine (8, RTI-5989-29). Additional structure-activity relationship studies suggested that 8 possesses lipophilic and hydrogen-bonding sites that are important to its opioid receptor potency and selectivity. These sites appear to exist predominantly within the kappa receptor since the selectivity arises from a 530-fold loss of affinity of 8 for the mu receptor and an 18-fold increase in affinity for the kappa receptor relative to the mu-selective ligand, (+)-N-[trans-4-phenyl-2-butenyl]-(3R, 4R)-dimethyl-4-(3-hydroxyphenyl)piperidine (5a). The degree of selectivity observed in the radioligand binding experiments was not observed in the functional assay. According to its ability to inhibit agonist stimulated binding of [35S]GTPgammaS at all three opioid receptors, compound 8 behaves as a mu/kappa opioid receptor pure antagonist with negligible affinity for the delta receptor.

Animals↗
PubMed1998

Engineering a change in metal-ion specificity of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis-- X-ray structure analysis of site-directed mutants.

We have refined the X-ray structures of two site-directed mutants of the iron-dependent superoxide dismutase (SOD) from Mycobacterium tuberculosis. These mutations which affect residue 145 in the enzyme (H145Q and H145E) were designed to alter its metal-ion specificity. This residue is either Gln or His in homologous SOD enzymes and has previously been shown to play a role in active-site interactions since its side-chain helps to coordinate the metal ion via a solvent molecule which is thought to be a hydroxide ion. The mutations were based on the observation that in the closely homologous manganese dependent SOD from Mycobacterium leprae, the only significant difference from the M. tuberculosis SOD within 10 A of the metal-binding site is the substitution of Gln for His at position 145. Hence an H145Q mutant of the M. tuberculosis (TB) SOD was engineered to investigate this residue's role in metal ion dependence and an isosteric H145E mutant was also expressed. The X-ray structures of the H145Q and H145E mutants have been solved at resolutions of 4.0 A and 2.5 A, respectively, confirming that neither mutation has any gross effects on the conformation of the enzyme or the structure of the active site. The residue substitutions are accommodated in the enzyme's three-dimensional structure by small local conformational changes. Peroxide inhibition experiments and atomic absorption spectroscopy establish surprisingly the H145E mutant SOD has manganese bound to it whereas the H145Q mutant SOD retains iron as the active-site metal. This alteration in metal specificity may reflect on the preference of manganese ions for anionic ligands.

Amino Acid Sequence↗
PubMed1998

Lead poisoning, haem synthesis and 5-aminolaevulinic acid dehydratase.

In mammals and yeast, 5-aminolaevulinic acid dehydratase is a zinc-dependent enzyme that catalyses the synthesis of porphobilinogen-the pyrrole building block that is incorporated into all modified tetrapyrroles, including haem, chlorophyll and vitamin B12. The X-ray structure of this enzyme reveals how substitution of the catalytically important zinc ion by lead inactivates the enzyme and causes a form of pseudo-porphyria.

Animals↗
PubMed1998

An analysis of structural similarity in the iron and manganese superoxide dismutases based on known structures and sequences.

There are two types of homologous enzymes catalysing the dismutation of the superoxide radical--Cu-Zn superoxide dismutases, and manganese or iron superoxide dismutases. In the latter two forms there is a high percentage of identity in the primary structures, and the tertiary structures are very similar particularly in the areas of the active site and in the residues responsible for the formation of the dimer. The quaternary structure of the dimer is also highly conserved. However, it has been found that despite this conservation there is strong metal ion specificity and many enzymes in the family will only be active if the correct metal ion is present. The purpose of this study has been to analyse solved X-ray structures for interactions common in both the manganese and iron forms and those that are specific to each, which may indicate reasons for the metal ion specificity. Initial analysis points to the probability that it is a combination of a number of residues, and not necessarily the same ones in every instance, which confer the specificity. In addition we have identified some anomalies in the currently available Fe/MnSOD structures which may require further remodelling and refinement.

Amino Acid Sequence↗
PubMed1998

An epitope delivery system for use with recombinant mycobacteria.

We have developed a novel epitope delivery system based on the insertion of peptides within a permissive loop of a bacterial superoxide dismutase molecule. This system allowed high-level expression of heterologous peptides in two mycobacterial vaccine strains, Mycobacterium bovis bacille Calmette-Guérin (BCG) and Mycobacterium vaccae. The broader application of the system was analyzed by preparation of constructs containing peptide epitopes from a range of infectious agents and allergens. We report detailed characterization of the immunogenicity of one such construct, in which an epitope from the Der p1 house dust mite allergen was expressed in M. vaccae. The construct was able to stimulate T-cell hybridomas specific for Der p1, and it induced peptide-specific gamma interferon responses when used to immunize naive mice. This novel expression system demonstrates new possibilities for the use of mycobacteria as vaccine delivery vehicles.

Amino Acid Sequence↗
PubMed1998

Intramammary infections in primiparous Holsteins: heritabilities and comparisons of bovine leukocyte adhesion deficiency carriers and noncarriers.

The objective of this study was to determine the impact of bovine leukocyte adhesion deficiency on intramammary infection (IMI) in Holstein cows at first calving. Quarter milk samples were collected between 3 d prepartum and 4 d postpartum from 756 Holstein cows in first lactation. These samples were frozen and subsequently cultured using National Mastitis Council recommendations. Sixty-eight carriers of bovine leukocyte adhesion deficiency were identified (9.0% of cows) from an additional milk sampling collected in early lactation. Binary variables (infected or uninfected) for each quarter were defined as dependent variables to evaluate IMI incidence from all bacterial species and major species groups: coliforms, coagulase-negative staphylococci, and streptococci other than Streptococcus agalactiae. The model included herd-season of calving, days in milk when samples were collected, age at calving, quarter, cow (random effect), and bovine leukocyte adhesion deficiency. Sire was included as a random effect (instead of cow), and bovine leukocyte adhesion deficiency was dropped from the model to estimate heritabilities. Heritabilities for IMI incidence from the various groups of organisms ranged from 0.02 to 0.66 (0.21 from all bacterial species). No differences were observed between carriers of bovine leukocyte adhesion deficiency and homozygous normal noncarriers for IMI from coliform, coagulase-negative staphylococci, streptococci other than Streptococcus agalactiae, or all bacterial species combined.

Aging↗
PubMed1997

The three-dimensional structure at 2.4 A resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae.

The crystal structures of glycosylated native proteinase A, an aspartic proteinase found in the vacuole of Saccharomyces cerevisiae, and its complex with a difluorostatone-containing tripeptide have been determined by molecular replacement to 3.5 A and 2.4 A resolutions, respectively. Superposition of the bound and native forms gave an r.m.s. difference of 0.6 A largely reflecting the poor resolution of the native crystal structure. The secondary and tertiary structures are highly similar to those found in porcine pepsin and lysosomal cathepsin D; superposition of the structure of proteinase A bound to the difluorostatone inhibitor on those of pepsin and cathepsin D gave pairwise r.m.s. differences for C(alpha) atoms of 1.36 A and 0.88 A. Most differences occur in loop regions. Comparison of the structure of the proteinase A-difluorostatone complex with that of endothiapepsin bound with the same inhibitor shows that the conformation and hydrogen bond interactions of the inhibitor in the active site are very similar, even though the enzymes have only 27% sequence identity. Electron density for the crystal structure of the proteinase A complex reveals five residues of the oligosaccharide structure attached to Asn67: Man-(1 --> 2)-alpha-Man-(1 --> 3)-beta-Man-(1 --> 4)-beta-GlcNAc-(1 --> 4)-beta-GlcNAc-Asn-67. The first three residues of the oligosaccharide cover the same region of the protein surface as those of the oligosaccharide attached to the equivalent position in cathepsin D. The second carbohydrate attachment site is disordered beyond the first carbohydrate residue in both enzymes.

Aspartic Acid Endopeptidases↗
PubMed1997

X-ray structure of 5-aminolaevulinate dehydratase, a hybrid aldolase.

5-Aminolaevulinate dehydratase (ALAD) is a homo-octameric metallo-enzyme that catalyses the formation of porphobilinogen from 5-aminolaevulinic acid. The structure of the yeast enzyme has been solved to 2.3 A resolution, revealing that each subunit adopts a TIM barrel fold with a 39 residue N-terminal arm. Pairs of monomers wrap their arms around each other to form compact dimers and these associate to form a 422 symmetric octamer. All eight active sites are on the surface of the octamer and possess two lysine residues (210 and 263), one of which, Lys 263, forms a Schiff base link to the substrate. The two lysine side chains are close to two zinc binding sites one of which is formed by three cysteine residues (133, 135 and 143) while the other involves Cys 234 and His 142. ALAD has features at its active site that are common to both metallo- and Schiff base-aldolases and therefore represents an intriguing combination of both classes of enzyme. Lead ions, which inhibit ALAD potently, replace the zinc bound to the enzyme's unique triple-cysteine site.

Amino Acid Sequence↗