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Biomedical subjects

K A Johnson

Publications and source records attributed to K A Johnson.

At least 37 records · Page 2Linked to original sources

The effect of oilseeds in diets of lactating cows on milk production and methane emissions.

Thirty-six lactating multiparous Holstein cows were assigned to diets that contained 2.3, 4.0, and 5.6% fat for an entire lactation to determine the effect of oilseeds on milk composition, production, and methane emissions. The diets were formulated so that whole cottonseeds and canola oilseeds provided equal amounts of added fat. Methane emissions were measured every 3 mo from two replicates of four cows per treatment using a room tracer approach. Dry matter intakes and yields of milk and FCM were greater for cows fed the diets containing oilseeds. Although the concentration of protein in milk was reduced, yields of both protein and fat tended to be increased by the addition of fat. Within the milk fat, the concentrations of C10, C12, C14:0, and C16:0 were reduced and concentrations of C18, C18:1, and trans-C18:1 were increased in response to dietary oilseeds. In serum, urea-N was increased by the dietary oilseeds. Supplementation of diets with oilseeds did not affect methane emissions but tended to increase the efficiency of milk produced per unit of methane emitted. A 1.7% addition of fat to the control diet from a combination of oilseed types increased yields of milk without reducing methane emission rates. The strategy of using unsaturated fats from oilseeds to substantially reduce methane emissions was ineffective, although yield of milk was increased.

Animal Feed↗

Toxicity of antiviral nucleoside analogs and the human mitochondrial DNA polymerase.

To examine the role of the mitochondrial polymerase (Pol gamma) in clinically observed toxicity of nucleoside analogs used to treat AIDS, we examined the kinetics of incorporation catalyzed by Pol gamma for each Food and Drug Administration-approved analog plus 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-iodouracil (FIAU), beta-L-(-)-2',3'-dideoxy-3'-thiacytidine (-)3TC, and (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA). We used recombinant exonuclease-deficient (E200A), reconstituted human Pol gamma holoenzyme in single turnover kinetic studies to measure K(d) (K(m)) and k(pol) (k(cat)) to estimate the specificity constant (k(cat)/K(m)) for each nucleoside analog triphosphate. The specificity constants vary more than 500,000-fold for the series ddC > ddA (ddI) > 2',3'-didehydro-2',3'-dideoxythymidine (d4T) >> (+)3TC >> (-)3TC > PMPA > azidothymidine (AZT) >> Carbovir (CBV). Abacavir (prodrug of CBV) and PMPA are two new drugs that are expected to be least toxic. Notably, the higher toxicities of d4T, ddC, and ddA arose from their 13-36-fold tighter binding relative to the normal dNTP even though their rates of incorporation were comparable with PMPA and AZT. We also examined the rate of exonuclease removal of each analog after incorporation. The rates varied from 0.06 to 0.0004 s(-1) for the series FIAU > (+)3TC approximately equal to (-)3TC > CBV > AZT > PMPA approximately equal to d4T >> ddA (ddI) >> ddC. Removal of ddC was too slow to measure (<0.00002 s(-1)). The high toxicity of dideoxy compounds, ddC and ddI (metabolized to ddA), may be a combination of high rates of incorporation and ineffective exonuclease removal. Conversely, the more effective excision of (-)3TC, CBV, and AZT may contribute to lower toxicity. FIAU is readily extended by the next correct base pair (0.13 s(-1)) faster than it is removed (0.06 s(-1)) and, therefore, is stably incorporated and highly mutagenic. We define a toxicity index for chain terminators to account for relative rates of incorporation versus removal. These results provide a method to rapidly screen new analogs for potential toxicity.

Base Sequence↗

Fidelity of nucleotide incorporation by human mitochondrial DNA polymerase.

We have examined the fidelity of polymerization catalyzed by the human mitochondrial DNA polymerase using wild-type and exonuclease-deficient (E200A mutation) forms of recombinant, reconstituted holoenzyme. Each of the four nucleotides bind and incorporate with similar kinetics; the average dissociation constant for ground state binding is 0.8 microm, and the average rate of polymerization is 37 x s(-1), defining a specificity constant kcat/Km = 4.6 x 10(7) x m(-1) x s(-1). Mismatched nucleotides show weaker ground-state nucleotide binding affinities ranging from 57 to 364 microm and slower rates of polymerization ranging from 0.013 to 1.16 x s(-1). The kinetic parameters yield fidelity estimates of 1 error out of 260,000 nucleotides for a T:T mismatch, 3563 for G:T, and 570,000 for C:T. The accessory subunit increases fidelity 14-fold by facilitating both ground-state binding and the incorporation rate of the correct A:T base pair compared with a T:T mismatch. Correctly base-paired DNA dissociates from the polymerase at a rate of 0.02 x s(-1) promoting processive polymerization. Thus, the mitochondrial DNA polymerase catalyzed incorporation with an average processivity of 1850, defined by the ratio of polymerization rate to the dissociation rate (37/0.02) and with an average fidelity of one error in 280,000 base pairs.

Base Pair Mismatch↗

Exonuclease proofreading by human mitochondrial DNA polymerase.

We have examined the ability of the human mitochondrial DNA polymerase to correct errors in DNA sequence using single turnover kinetic methods. The rate of excision of single-stranded DNA ranged from 0.07 to 0.17 x s(-1), depending on the identity of the 3'-base. Excision of the 3'-terminal base from correctly base paired DNA occurred at a rate of 0.05 x s(-1), indicating that the cost of proofreading is minimal, as defined by the ratio of the k(exo) for correctly base-paired DNA divided by the rate of forward polymerization (0.05/37 = 0.14%). Excision of duplex DNA containing 1-7 mismatches was biphasic, and the rate and amplitude of the fast phase increased with the number of mismatches, reaching a maximum of 9 x s(-1). We showed that transfer of DNA from the polymerase to the exonuclease active site and back again occurs through an intramolecular reaction, allowing for a complete cycle of reactions for error correction. For DNA containing a buried mismatch (T:T followed by C:G base pairs), the 3' base was removed at a rate of 3 x s(-1). The addition of nucleotide to the reaction that is identical to the 3' base increased the rate of excision 7-fold to 21 x s(-1). We propose that the free nucleotide enhances the rate of transfer of the DNA to the exonuclease active site by interrupting the correct 3' base pair through interaction with the template base. The exonuclease contribution to fidelity is minimal if the calculation is based on hydrolysis of a single mismatch: (k(exo) + k(pol,over))/(k(pol,over)) = 10, but this value increases to approximately 200 when examining error correction in the presence of nucleotides.

Base Pair Mismatch↗

Presenilin-1-associated abnormalities in regional cerebral perfusion.

OBJECTIVE: To investigate the influence of the presenilin-1 gene (PS-1) mutation on regional cerebral perfusion, SPECT was evaluated in 57 individuals. The subjects were members of a large pedigree from Colombia, South America, many of whom carry a PS-1 mutation for early-onset AD. METHODS: Members of this large kindred who were cognitively normal and did not carry the PS-1 mutation (n = 23) were compared with subjects who were carriers of the mutation but were asymptomatic (n = 18) and with individuals with the mutation and a clinical diagnosis of AD (n = 16). Cerebral perfusion was measured in each subject using hexamethylpropyleneamine oxime SPECT. The data were analyzed in two ways: 1) Mean cerebral perfusion in each of 4320 voxels in the brain was compared among the groups using t-tests (t-maps); and 2) each individual received a weighted score on 20 vectors (factors), based on a large normative sample (n = 200), using a method known as singular value decomposition (SVD). RESULTS: Based on t-maps, subjects with the PS-1 mutation who were asymptomatic demonstrated reduced perfusion in comparison with the normal control subjects in the hippocampal complex, anterior and posterior cingulate, posterior parietal lobe, and anterior frontal lobe. The AD patients demonstrated decreased perfusion in the posterior parietal and superior frontal cortex in comparison with the normal control subjects. Discriminant function analysis of the vector scores derived from SVD (adjusted for age and gender) accurately discriminated 86% of the subjects in the three groups (p < 0.0005). CONCLUSION: Regional cerebral perfusion abnormalities based on SPECT are detectable before development of the clinical symptoms of AD in carriers of the PS-1 mutation.

Adult↗

Insights into the molecular mechanism of mitochondrial toxicity by AIDS drugs.

Several of the nucleoside analogs used in the treatment of AIDS exhibit a delayed clinical toxicity limiting their usefulness. The toxicity of nucleoside analogs may be related to their effects on the human mitochondrial DNA polymerase (Pol gamma), the polymerase responsible for mitochondrial DNA replication. Among the AIDS drugs approved by the FDA for clinical use, two are modified cytosine analogs, Zalcitabine (2',3'-dideoxycytidine (ddC)) and Lamivudine (beta-d-(+)-2',3'-dideoxy-3'-thiacytidine ((-)3TC])). (-)3TC is the only analog containing an unnatural l(-) nucleoside configuration and is well tolerated by patients even after long term administration. In cell culture (-)3TC is less toxic than its d(+) isomer, (+)3TC, containing the natural nucleoside configuration, and both are considerably less toxic than ddC. We have investigated the mechanistic basis for the differential toxicity of these three cytosine analogs by comparing the effects of dideoxy-CTP), (+)3TC-triphosphate (TP), and (-)3TC-TP on the polymerase and exonuclease activities of recombinant human Pol gamma. This analysis reveals that Pol gamma incorporates (-)3TC-triphosphate 16-fold less efficiently than the corresponding (+)isomer and 1140-fold less efficiently than dideoxy-CTP, showing a good correlation between incorporation rate and toxicity. The rates of excision of the incorporated analogs from the chain-terminated 3'-end of the DNA primer by the 3'-5'-exonuclease activity of Pol gamma were similar (0.01 s(-)1) for both 3TC analogs. In marked contrast, the rate of exonuclease removal of a ddC chain-terminated DNA occurs at least 2 orders of magnitude slower, suggesting that the failure of the exonuclease to remove ddC may play a major role in its greater toxicity. This study demonstrates that direct analysis of the mitochondrial DNA polymerase structure/function relationships may provide valuable insights leading to the design of less toxic inhibitors.

Acquired Immunodeficiency Syndrome↗

Chemical and on-line electrochemical reduction of metalloproteins with high-resolution electrospray ionization mass spectrometry detection.

The observation of the reduced forms of several metal-containing proteins using electrospray ionization (ESI) is reported for the first time. High-resolution mass analysis using Fourier transform ion cyclotron resonance mass spectrometry allows the oxidized and reduced forms of the proteins to be distinguished. The metalloproteins are reduced both chemically and electrochemically. Under normal sample handling conditions, the proteins that are reduced in solution appear in their oxidized form in their ESI mass spectra. Rigorous exclusion of oxygen from the solution of the reduced protein allows the observation of the reduced form in the gas phase. The metal centers investigated include heme and non-heme iron proteins, copper, and a manganese-substituted iron-sulfur cluster of the form [3FeMn-4S]. The electrochemical method is shown to provide several advantages over chemical reduction. The oxidation state of the metal center is stable with respect to electrospray ionization in both positive and negative ionization modes.

Electrochemistry↗

Crystal structure and catalytic mechanism of the MJ0109 gene product: a bifunctional enzyme with inositol monophosphatase and fructose 1,6-bisphosphatase activities.

Inositol monophosphatase (EC 3.1.3.25) in hyperthermophilic archaea is thought to play a role in the biosynthesis of di-myo-inositol-1,1'-phosphate (DIP), an osmolyte unique to hyperthermophiles. The Methanococcus jannaschii MJ109 gene product, the sequence of which is substantially homologous to that of human inositol monophosphatase, exhibits inositol monophosphatase activity but with substrate specificity that is broader than those of bacterial and eukaryotic inositol monophosphatases (it can also act as a fructose bisphosphatase). To understand its substrate specificity as well as the poor inhibition by Li(+) (a potent inhibitor of the mammalian enzyme), we have crystallized the enzyme and determined its three-dimensional structure. The overall fold, as expected, is similar to that of the mammalian enzyme, but the details suggest a closer relationship to fructose 1,6-bisphosphatases. Three complexes of the MJ0109 protein with substrate and/or product and inhibitory as well as activating metal ions suggest that the phosphatase mechanism is a three-metal ion assisted catalysis which is in variance with that proposed previously for the human inositol monophosphatase.

Amino Acid Sequence↗

Selection bias in Teratology Information Service pregnancy outcome studies.

BACKGROUND: Pregnancy outcome studies conducted through Teratology Information Services (TIS) rely on volunteer subjects. If these subjects tend to have different risk profiles than the population from which they are drawn, the results of TIS studies may have limited generalizability. METHODS: We selected all subjects who enrolled in the California Teratogen Information Service (CTIS) pregnancy outcome study for prenatal exposure to carbamazepine or valproic acid between 1990 and 1997 and who received prenatal care through Kaiser Permanente of Southern California (n = 13). We compared these subjects to Kaiser patients identified through the Maternal Serum Alpha Fetoprotein Program with exposure to carbamazepine or valproic acid but who had not enrolled in the CTIS project. The controls were matched by Kaiser location and pregnancy year using a 2:1 ratio (n = 26). Medical records were reviewed and the prevalence of 14 pregnancy risk factors was compared between the two groups. RESULTS: There were no significant differences between the groups on any one risk factor; however, a notably higher proportion of women who did not enroll in the CTIS study used tobacco or had a positive family history of congenital anomalies. CONCLUSIONS: Although the sample was small, and results may not apply to other exposures in different health care environments, these data provide some evidence that women who enroll in TIS pregnancy outcome studies do not have a substantially different pregnancy risk profile than women who do not. Efforts to address possible selection bias should be incorporated in future TIS study design.

Abnormalities, Drug-Induced↗

Bimanual coordination in chronic schizophrenia.

Anomalies of movement are observed both clinically and experimentally in schizophrenia. While the basal ganglia have been implicated in its pathogenesis, the nature of such involvement is equivocal. The basal ganglia may be involved in bimanual coordination through their input to the supplementary motor area (SMA). While a neglected area of study in schizophrenia, a bimanual movement task may provide a means of assessing the functional integrity of the motor circuit. Twelve patients with chronic schizophrenia and 12 matched control participants performed a bimanual movement task on a set of vertically mounted cranks at different speeds (1 and 2 Hz) and phase relationships. Participants performed in-phase movements (hands separated by 0 degrees ) and out-of-phase movements (hands separated by 180 degrees ) at both speeds with an external cue on or off. All participants performed the in-phase movements well, irrespective of speed or cueing conditions. Patients with schizophrenia were unable to perform the out-of-phase movements, particularly at the faster speed, reverting instead to the in-phase movement. There was no effect of external cueing on any of the movement conditions. These results suggest a specific problem of bimanual coordination indicative of SMA dysfunction per se and/or faulty callosal integration. A disturbance in the ability to switch attention during the out-of-phase task may also be involved.

Adult↗

Movement-related potentials in Huntington's disease: movement preparation and execution.

Movement-related potentials (MRPs) reflect increasing cortical activity related to the preparation and execution of voluntary movement. Execution and preparatory components may be separated by comparing MRPs recorded from actual and imagined movement. Imagined movement initiates preparatory processes, but not motor execution activity. MRPs are maximal over the supplementary motor area (SMA), an area of the cortex involved in the planning and preparation of movement. The SMA receives input from the basal ganglia, which are affected in Huntington's disease (HD), a hyperkinetic movement disorder. In order to further elucidate the effects of the disorder upon the cortical activity relating to movement, MRPs were recorded from ten HD patients, and ten age-matched controls, whilst they performed and imagined performing a sequential button-pressing task. HD patients produced MRPs of significantly reduced size both for performed and imagined movement. The component relating to movement execution was obtained by subtracting the MRP for imagined movement from the MRP for performed movement, and was found to be normal in HD. The movement preparation component was found by subtracting the MRP found for a control condition of watching the visual cues from the MRP for imagined movement. This preparation component in HD was reduced in early slope, peak amplitude, and post-peak slope. This study therefore reported abnormal MRPs in HD, particularly in terms of the components relating to movement preparation, and this finding may further explain the movement deficits reported in the disease.

Adult↗

Seasonal bioavailability of sediment-associated heavy metals along the Mississippi river floodplain.

A value of simultaneously extracted metal to acid-volatile sulfide (SEM-AVS) can provide important information regarding metal availability in anaerobic sediment. SEM and AVS concentrations were obtained by the cold-acid purge-and-trap technique during spring and summer at six locations along the Mississippi River floodplain. SEM-AVS values and AVS concentrations did not vary significantly between locations during both seasons. AVS concentrations were significantly greater during summer than spring, resulting in significantly lower SEM-AVS values in summer. Total SEM concentrations did not significantly vary between seasons or specific locations. SEM-AVS values were greater than one at each location during both seasons. Sediment metal toxicity was predicted to be absent for benthic organisms along the river floodplain.

Animals↗

First observation by mass spectrometry of a 3+ oxidation state for a [4Fe-4S] metalloprotein: an ESI-FTICR mass spectrometry study of the high potential iron-sulfur protein from Chromatium vinosum.

Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR) is used to measure the molecular weight of the high potential iron-sulfur protein (HiPIP) from Chromatium vinosum (C. vinosum) and its corresponding apoprotein. By accurate mass measurement of the metalloprotein, the oxidation state of the [4Fe-4S] metal center is assigned as 3+. This is the highest oxidation state yet observed by mass spectrometry for a [4Fe-4S] cluster, which usually appears in the 2+ oxidation state. In order to make this assignment correctly, the mass spectrum of the apoprotein was acquired, and a 1 Da difference was found between the molecular mass of the apoprotein and its published amino acid sequence. The mass spectra of the trypsin and cyanogen bromide digests of the alkylated apoprotein were obtained, and the data suggests that the C-terminal glycine residue is amidated.

Amino Acid Sequence↗