Biomedical subjects

M L Peterson

Publications and source records attributed to M L Peterson.

At least 19 recordsLinked to original sources

PubMed1999

Cryptic intron activation within the large exon of the mouse polymeric immunoglobulin receptor gene: cryptic splice sites correspond to protein domain boundaries.

The fourth exon of the mouse polymeric immuno-globulin receptor (pIgR) is 654 nt long and, despite being surrounded by large introns, is constitutively spliced into the mRNA. Deletion of an 84 nt sequence from this exon strongly activated both cryptic 5' and 3' splice sites surrounding a 78 nt cryptic intron. The 84 nt deletion is just upstream of the cryptic 3' splice site; the cryptic 3' splice site was likely activated because the deletion created a better 3' splice site. However, the cryptic 5' splice site was also required to activate the cryptic splice reaction; point mutations in either of the cryptic splice sites that decreased their match to the consensus splice site sequence inactivated the cryptic splice reaction. The activation and inactivation of these cryptic splice sites as a pair suggests that they are being co-recognized by the splicing machinery. Interestingly, the large fourth exon of the pIgR gene encodes two immunoglobulin-like extracellular protein domains; the cryptic 3' splice site coincides with the junction between these protein domains. The cryptic 5' splice site is located between protein subdomains where an intron is found in another gene of the immunoglobulin superfamily.

Animals↗

PubMed1999

Pyriform augmentation as an ancillary procedure in facial rejuvenation surgery.

A patient is presented in whom augmentation of the pyriform aperture of the maxilla was performed with porous hydroxyapatite in concert with a face and brow lift. Basic research has recently shown that remodeling of the facial skeleton continues throughout life and that this remodeling process leads to changes in the position of several key areas. The pyriform aperture was identified as one region that remodels in a posterior direction, leading to retrusion of the alar base in the older individual. This skeletal retrusion occurs in a very site-specific fashion, and its effects are reflected on the overlying soft tissues of the face. With aging, remodeling of the pyriform aperture posteriorly causes the alar base to appear recessed and decreases the nasolabial angle, changes that are noted on the profile of the older individual. Augmentation of the pyriform aperture can be achieved through a buccal sulcus incision and, when used in conjunction with standard facial rejuvenation procedures, can improve the overall result in facial cosmetic surgery.

Female↗

PubMed1999

Fluoroquinolone resistance in Bacteroides fragilis following sparfloxacin exposure.

In vitro pharmacodynamic studies investigating the antimicrobial properties of five fluoroquinolones, (trovafloxacin, sparfloxacin, clinafloxacin, levofloxacin, and ciprofloxacin) against Bacteroides fragilis ATCC 23745 were conducted. The times required to reduce the viable counts by 3 log units were as follows: clinafloxacin, 2.9 h; levofloxacin, 4.6 h; trovafloxacin, 6 h; and sparfloxacin, 10 h. Exposure to ciprofloxacin did not achieve a 3-log decrease in viable counts. The susceptibility of B. fragilis was determined both prior to exposure and following 24 h of exposure to each of the five fluoroquinolones tested. The MICs of clinafloxacin, levofloxacin, trovafloxacin, sparfloxacin, ciprofloxacin, metronidazole, cefoxitin, chloramphenicol, and clindamycin were determined by the broth microdilution method. The MICs for B. fragilis preexposure were as follows: clinafloxacin, 0.25 microg/ml; trovafloxacin, 0.5 microg/ml; sparfloxacin, 2 microg /ml; levofloxacin, 2 microg/ml; and ciprofloxacin, 8 microg/ml. Similar pre- and postexposure MICs were obtained for cultures exposed to trovafloxacin, clinafloxacin, levofloxacin, and ciprofloxacin. However, following 24 h of exposure to sparfloxacin, a fluoroquinolone-resistant strain emerged. The MICs for this strain were as follows: clinafloxacin, 1 microg/ml; trovafloxacin, 4 microg/ml; sparfloxacin, 16 microg/ml; levofloxacin, 16 microg/ml; and ciprofloxacin, 32 microg/ml. No changes in the susceptibility of B. fragilis pre- and postexposure to sparfloxacin were noted for metronidazole (MIC, 1 microg/ml), cefoxitin (MIC, 4 microg /ml), chloramphenicol (MIC, 4 microg/ml), and clindamycin (MIC, 0.06 microg/ml). Resistance remained stable as the organism was passaged on antibiotic-free agar for 10 consecutive days. Mutant B. fragilis strains with decreased susceptibility to clinafloxacin, trovafloxacin, sparfloxacin, levofloxacin, and ciprofloxacin were selected on brucella blood agar containing 8x the MIC of levofloxacin at a frequencies of 6.4 x 10(-9), 4x the MICs of trovafloxacin and sparfloxacin at frequencies of 2.2 x 10(-9) and 3. 3 x 10(-10), respectively, and 2x the MIC of clinafloxacin at a frequency of 5.5 x 10(-11); no mutants were selected with ciprofloxacin. The susceptibilities of strains to trovafloxacin, levofloxacin, clinafloxacin, sparfloxacin, and ciprofloxacin before and after exposure to sparfloxacin were modestly affected by the presence of reserpine (20 microg/ml), an inhibitor of antibiotic efflux. The mechanism of fluoroquinolone resistance is being explored, but it is unlikely to be efflux due to a lack of cross-resistance to unrelated antimicrobial agents and to the fact that the MICs for strains before and after exposure to sparfloxacin are minimally affected by reserpine.

Anti-Infective Agents↗

PubMed1998

Deconvolution by omission libraries.

Omission libraries, synthesized by omitting one amino acid in all coupling positions, are very efficient tools for the rapid identification of the amino acid components of bioactive peptides. Based on the determined amino acids, an occurrence library can be defined and prepared which is much less complex than the full one while still comprising the bioactive peptide.

Amino Acid Sequence↗

PubMed1998

A waveguide-based acoustic microscope.

A new instrument is presented which is capable of high resolution acoustic imaging at relatively low frequencies. This approach results in increased complexity of the signal processing required and reduced throughput of the instrument. However, these disadvantages are amply compensated by the ability to create velocity scan images of materials with either high attenuation or low material velocities. These measurements are not possible using traditional/acoustic microscopes. The initial performance of the new instrument is demonstrated using thin samples of shim materials to show that acceptable spatial resolution and highly accurate time delay measurements are possible. An application is then shown using the instrument to evaluate subchondral sclerosis in horse bones. It has been hypothesized that changes in the elastic modulus may be associated with fatigue-induced microdamage. The modulus change may further represent bone damage which precedes the development of microcracking. Thin samples are used to allow complementary microradiography to be performed on the bone slices. Because of the low material velocity, surface wave interference methods (so called V(z) curves) are not well suited for use in some bone samples. The thickness of the samples eliminates the potential for the samples to be evaluated using pulse-echo time delay measurements. The new instrument is thus unique in its ability to create velocity scans of these samples.

Animals↗

PubMed1998

A nonimmunoglobulin transgene and the endogenous immunoglobulin mu gene are coordinately regulated by alternative RNA processing during B-cell maturation.

The immunoglobulin (Ig) genes have been extensively studied as model systems for developmentally regulated alternative RNA processing. Transcripts from these genes are alternatively processed at their 3' ends to yield a transcript that is either cleaved and polyadenylated at a site within an intron or spliced to remove the poly(A) site and subsequently cleaved and polyadenylated at a downstream site. Results obtained from expressing modified genes in established tissue culture cell lines that represent different stages of B-lymphocyte maturation have suggested that the only requirement for regulation is that a pre-mRNA contain competing cleavage-polyadenylation and splice reactions whose efficiencies are balanced. Since several non-Ig genes modified to have an Ig gene-like structure are regulated in cell lines, Ig-specific sequences are not essential for this control. This strongly implies that changes in the amounts or activities of general RNA processing components mediate the processing regulation. Despite numerous studies in cell lines, this model of Ig gene regulation has never been tested in vivo during normal lymphocyte maturation. We have now introduced a non-Ig gene with an Ig gene-like structure into the mouse germ line and demonstrate that RNA from the transgene is alternatively processed and regulated in murine splenic B cells. This establishes that the balance and arrangement of competing cleavage-polyadenylation reactions are sufficient for RNA processing regulation during normal B-lymphocyte development. These experiments also validate the use of tissue culture cell lines for studies of Ig processing regulation. This is the first transgenic mouse produced to test a specific model for regulated mRNA processing.

Alternative Splicing↗

PubMed1997

Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels.

The erbAalpha gene encodes two alpha-thyroid hormone receptor isoforms, TRalpha1 and TRalpha2, which arise from alternatively processed mRNAs, erbAalpha1 (alpha1) and erb alpha2 (alpha2). The splicing and alternative polyadenylation patterns of these mRNAs resemble that of mRNAs encoding different forms of immunoglobulin heavy chains, which are regulated at the level of alternative processing during B cell differentiation. This study examines the levels of erbAalpha mRNA in eight B cell lines representing four stages of differentiation in order to determine whether regulation of the alternatively processed alpha1 and alpha2 mRNAs parallels the processing of immunoglobulin heavy chain mRNAs. Results show that the pattern of alpha1 and alpha2 mRNA expression is clearly different from that observed for immunoglobulin heavy chain mRNAs. B cell lines display characteristic ratios of alpha1/alpha2 mRNA at distinct stages of differentiation. Furthermore, expression of an overlapping gene, Rev-ErbAalpha (RevErb), was found to correlate strongly with an increase in the ratio of alpha1/alpha2 mRNA. These results suggest that alternative processing of erbAalpha mRNAs is regulated by a mechanism which is distinct from that regulating immunoglobulin mRNA. The correlation between RevErb and erbAalpha mRNA is consistent with negative regulation of alpha2 via antisense interactions with the complementary RevErb mRNA.

Alternative Splicing↗

PubMed1997

Origin of genes encoding multi-enzymatic proteins in eukaryotes.

In several biosynthetic pathways of eukaryotes, multiple steps are catalyzed by enzymes physically linked as domains of multi-enzymatic proteins. The same steps in prokaryotes are frequently carried out by mono-enzymatic proteins. If genes encoding mono-enzymatic proteins are the precursors to those genes encoding multi-enzymatic proteins, how these genes fused remains an open question. However, the recent discovery of a cleavage-polyadenylation signal within an intron of the GART gene provides clues to this process and might also have more general implications for the origin of genes that contain alternative RNA processing reactions at their 5' or 3' ends.

Amino Acid Sequence↗

PubMed1996

The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation.

The switch from membrane-bound to secreted-form IgM that occurs during differentiation of B lymphocytes has long been known to involve regulated processing of the heavy chain pre-mRNA. Here, we show that accumulation of one subunit of an essential polyadenylation factor (CstF-64) is specifically repressed in mouse primary B cells and that overexpression of CstF-64 is sufficient to switch heavy chain expression from membrane-bound (microm) to secreted form (micros). We further show that CstF-64 is limiting for formation of intact CstF, that CstF has a higher affinity for the microm poly(A) site than for the micros site, and that the microm site is stronger in a reconstituted in vitro processing reaction. Our results indicate that CstF-64 plays a key role in regulating IgM heavy chain expression during B cell differentiation.

Alternative Splicing↗

PubMed1996

Circulating thrombopoietin concentrations in thrombocytopenic patients, including cancer patients following chemotherapy, with or without peripheral blood progenitor cell transplantation.

Thrombopoietin, the ligand for the c-mpl receptor, promotes proliferation and maturation of megakaryocytes. An ELISA using a chimaeric receptor, mpl-IgG, for capture, and rabbit antibody to thrombopoietin for detection was developed for the quantitation of thrombopoietin in human serum or plasma. This ELISA preferentially detects full-length thrombopoietin compared to the bioactive N-terminal half of the molecule which has homology to erythropoietin. Thrombopoietin was not detected (< 0.16 ng/ml) in 88/89 healthy individuals. However, elevated thrombopoietin concentrations of up to 3 ng/ml were detected in 59/63 thrombocytopenic patients, including cancer patients following chemotherapy. In cancer patients receiving chemotherapy with (n = 12) or without (n = 6) peripheral blood progenitor cell transplantation, thrombopoietin concentrations varied inversely with platelet counts throughout the treatment period. In general, patients who received myeloablative chemotherapy on days -7 to -2 and peripheral blood progenitor cell transplantation on day 0 had high thrombopoietin levels (0.6-2.9 ng/ml) around day 5. Low platelet counts (< 20 x 10(9)/l) occurred between days 4 and 9. Patients who received high-dose chemotherapy on day 1 (equivalent to day -7 for transplantation patients) to day 6 without transplantation had high thrombopoietin concentrations (1.4-2.3 ng/ml) around day 13 and low platelet counts occurred between days 7 and 17.

Adult↗

PubMed1995

Conformational energy downward driver (CEDD): characterization and calibration of the method.

A method has been developed that allows one to drive a molecule to conformations of lowest energy given the starting conformation, the identity of the rotatable bonds and the step size. This method has proved useful in our hands in the drug design arena where it is frequently more important to get 'low-energy' conformers of a molecule that match some other (e.g. pharmacophoric or enzyme pocket) requirements than to exhaustively enumerate all possible low-energy conformations for each of the molecules to be studied. The method has been shown to work in the test cases studied to date. Furthermore, so far it has been shown to be sufficiently fast to be used for molecules containing up to 70 rotatable bonds.

Algorithms↗

PubMed1995

Alternative processing of IgA pre-mRNA responds like IgM to alterations in the efficiency of the competing splice and cleavage-polyadenylation reactions.

Both the membrane-associated and -secreted Ig proteins are encoded by a single gene whose primary transcript is alternatively processed at its 3' end. The relative use of the alternative processing pathways is regulated during B cell maturation. This alternative RNA processing involves two competing reactions, splicing from the last constant region exon to the membrane exon(s) and cleavage-polyadenylation at the secretory-specific poly(A) site. Studies with the IgM-encoding mu gene have shown that cell-specific regulation requires that the efficiencies of these two reactions be balanced; any gene modifications that substantially improve or reduce the efficiency of either reaction also abrogate the regulatory shift in alternative processing pathways. All of the Ig isotypes that undergo a membrane-to-secreted switch during B cell maturation have a similar gene structure, thus suggesting that they might all be regulated by the same mechanism. We show that RNA processing of chimeric mu alpha genes containing modifications in the C alpha 3 exon size and the C alpha 3-alpha m intron size respond to these modifications as predicted by previous mu gene studies. In addition, RNA expression ratios from the chimeric mu alpha genes are regulated in B cells and plasma cells. This provides good evidence that splicing and cleavage-polyadenylation in the alpha gene are balanced reactions that are regulated in the same way as in the mu gene.

Alternative Splicing↗

PubMed1995

A sensitive lacZ-based expression vector for analyzing transcriptional control elements in eukaryotic cells.

We have developed a eukaryotic expression vector that provides a rapid and sensitive measure of transcriptional activity modulated by general and tissue-specific regulatory motifs. The lacZ structural gene has been linked to the minimal promoter of the human liver/bone/kidney alkaline phosphatase gene. In addition, a trimerized cassette of the SV40 polyadenylation region has been placed 5' of this promoter to reduce plasmid-initiated transcripts extending through the lacZ gene that would contribute to background beta-galactosidase (beta-Gal) activity. By combining the weak promoter and the poly(A) cassette, only a very low level of lacZ activity is detected in the absence of additional regulatory sequences. Regulatory domains can be inserted into this vector via a unique Bam HI restriction site and their activity can be rapidly monitored in situ via a colorimetric 5-bromo-4-chloro-3-indolyl-beta-D-galactoside (X-Ga) staining protocol. Also, the activity of linked regulatory domains can be measured quantitatively by assaying beta-Gal levels in cell extracts. We show that derivatives of this vector can be used to monitor the activity of general and tissue-specific control elements and can be transactivated by a single transcription factor in cotransfection experiments.

Alkaline Phosphatase↗

PubMed1994

A very low intake of fat is required to decrease fecal bile acid concentrations in rats.

The purpose of this study was to determine the effect of different amounts of dietary fat on colonic cell proliferation and fecal bile acid concentrations. Thirty-nine male Sprague-Dawley rats were randomly assigned to three diets (13 rats per diet) containing 5, 10 and 20 g butter/100 g diet. Diets were fed for 3 wk. As fat intake increased, total fecal fat excretion remained constant. When dietary fat was decreased from 20 to 10 g/100 g diet, total fecal bile acid concentrations tended to increase 14.5%. However, a further reduction to 5 g butter/100 g diet significantly decreased fecal total bile acid concentration by 48% from the concentration in feces of rats fed 10 g butter/100 g diet. The concentration of deoxycholate (considered a highly promotive bile acid) was not reduced unless the amount of fat in the diet was reduced to 5 g/100 g. Labeling index was used as an intermediate marker for colon carcinogenesis. For deoxycholate, a decrease of fat intake to 5 g/100 g diet decreased the cecal labeling index relative to those of rats fed 10 or 20 g butter/100 g diet. These data indicate that decreasing the dietary fat from 20 to 10 g/100 g does not decrease fecal bile acid concentration or colonic cell proliferation, but some effects are seen in rats fed 5 g butter/100 g diet.

Animals↗

PubMed1994

Rats fed high fat diets with increased calcium levels have fecal bile acid concentrations similar to those of rats fed a low fat diet.

The mechanism by which calcium may protect against colon carcinogenesis was studied in rats fed three levels of calcium (0.5, 1.0 and 1.5 g/100 g diet) and a high butter diet (20 g/100 g). Results were compared with values obtained using a low butter diet (5 g/100 g) supplemented with 0.5 g Ca/100 g diet. Concentration and relative proportions of individual fecal bile acids were determined by gas chromatography, and in vivo colonic cell proliferation was assessed using [3H]thymidine. Total fecal output and total fecal lipids increased as dietary calcium increased. When calcium supplementation remained at 0.5%, raising the level of fat in the diet increased the fecal concentrations of deoxycholate, omega-muricholate and total bile acids. However, when the level of fat supplementation remained constant at 20 g/100 g diet, but dietary calcium was 1.0 or 1.5 g/100 g, the concentration of these bile acids returned to the level found in feces of rats fed the low fat diet. Despite the significant decrease in the concentrations of certain fecal bile acids with increasing calcium supplementation, these differences were not reflected in substantive changes in epithelial cytokinetics. These data show that in rats fed high butter diets, 1.0% calcium is sufficient to lower total bile acid concentration and the concentrations of certain individual bile acids to those found in feces of rats fed low fat diets. Despite the significant effects of calcium on bile acid concentrations, minimal effects were observed on indices of colonic cell proliferation.

Animals↗

PubMed1994

Exon size affects competition between splicing and cleavage-polyadenylation in the immunoglobulin mu gene.

The alternative RNA processing of microseconds and microns mRNAs from a single primary transcript depends on competition between a cleavage-polyadenylation reaction to produce microseconds mRNA and a splicing reaction to produce microns mRNA. The ratio of microseconds to microns mRNA is regulated during B-cell maturation; relatively more spliced microns mRNA is made in B cells than in plasma cells. The balance between the efficiencies of splicing and cleavage-polyadenylation is critical to the regulation. The mu gene can be modified to either reduce or improve the efficiency of each reaction and thus alter the ratio of the two RNAs produced. However, as long as neither reaction is so strong that it totally dominates, expression of the modified mu genes is regulated in B cells and plasma cells. The current experiments reveal a relationship between the C mu 4 exon size and the microseconds/microns expression ratio. The shorter the distance between the C mu 4 5' splice site and the nearest upstream 3' splice site, the more spliced microns mRNA was produced. Conversely, when this exon was expanded, more microseconds mRNA was produced. Expression from these mu genes with altered exon sizes were regulated between B cells and plasma cells. Since RNA processing in the mu gene can be considered a competition between defining the C mu 4 exon as an internal exon (in microns mRNA) versus a terminal exon (in microseconds mRNA), exon size may affect the competition among factors interacting with this exon.

Animals↗

PubMed1994

Regulated immunoglobulin (Ig) RNA processing does not require specific cis-acting sequences: non-Ig RNA can be alternatively processed in B cells and plasma cells.

Alternative RNA processing of the heavy-chain immunoglobulin mu gene is regulated during B-cell maturation and requires competition between splice and cleavage-polyadenylation reactions that have balanced efficiencies. Studies with modified mu genes have failed to identify gene-specific sequences required for regulation. Thus, the only important feature for regulation may be the balanced competing splice and cleavage-polyadenylation reactions themselves. If this is so, then alternative RNA processing from any gene with similar competitive RNA processing pathways should also be regulated when expression is compared between B cells and plasma cells. To test this prediction, two nonimmunoglobulin genes engineered to have competing splice and cleavage-polyadenylation reactions were expressed in B cells and plasma cells. The ratios of alternative RNAs produced from both genes are different in the two cell types; like the mu gene, relatively more spliced RNA is produced in B cells than in plasma cells. Also, in a survey of mu gene expression in nine non-B-cell lines, only a T-cell line had an expression pattern similar to that of B cells; the expression patterns of all other lines resembled that of the plasma cells. Therefore, regulated mu RNA processing must be mediated by changes in general processing factors whose activity or abundance is regulated, most likely, in B cells.

Alternative Splicing↗

PubMed1993

The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents.

The inability to reliably predict relative orientations of drug molecules within our series of antipicornavirus agents has severely limited the usefulness of available structure-activity data in the drug design process. A reported method of overlapping molecules has been evaluated to see if it could provide a solution to this problem. Although it initially succeeded remarkably well with a series of molecules whose bound X-ray structures were known, this success was shown to be only a function of the bound conformation of these molecules. Thus, this method did not provide a general solution to the problem at hand.

Algorithms↗