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B P Davis

Publications and source records attributed to B P Davis.

At least 19 recordsLinked to original sources
PubMed2000

The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.

The Yeast Proteome Database (YPDtrade mark) has been for several years a resource for organized and accessible information about the proteins of Saccharomyces cerevisiae. We have now extended the YPD format to create a database containing complete proteome information about the model organism Caenorhabditis elegans (WormPDtrade mark). YPD and WormPD are designed for use not only by their respective research communities but also by the broader scientific community. In both databases, information gleaned from the literature is presented in a consistent, user-friendly Protein Report format: a single Web page presenting all available knowledge about a particular protein. Each Protein Report begins with a Title Line, a concise description of the function of that protein that is continually updated as curators review new literature. Properties and functions of the protein are presented in tabular form in the upper part of the Report, and free-text annotations organized by topic are presented in the lower part. Each Protein Report ends with a comprehensive reference list whose entries are linked to their MEDLINE s. YPD and WormPD are seamlessly integrated, with extensive links between the species. They are freely accessible to academic users on the WWW at http://www. proteome.com/databases/index.html, and are available by subscription to corporate users.

Animals↗
PubMed1999

Lack of association of a common polymorphism of the plasminogen activator inhibitor-1 gene with coronary artery disease and myocardial infarction.

OBJECTIVES: The study was done to assess whether the common polymorphic allele (4G) of the plasminogen activator inhibitor-1 (PAI-1) gene is associated with coronary artery disease (CAD) or myocardial infarction (MI). BACKGROUND: Impaired fibrinolytic function has been associated with CAD and MI. Plasminogen activator inhibitor-1 plays a central role in intravascular thrombosis and thrombolysis; the common insertion/deletion polymorphism (4G/5G) of PAI-1 has been correlated with altered PAI-1 levels and proposed as a coronary risk factor. METHODS: Blood was drawn and DNA extracted from 1,353 consenting patients undergoing coronary angiography. The 4G and 5G alleles of PAI-1 were amplified using specific primers. Amplified products were visualized by staining with ethidium bromide after electrophoresis in 1.5% agarose. RESULTS: Patient age averaged 63.5 (SD 11.7) years; 70% were men, 28% had a history of MI, 66% had severe CAD (>60% stenosis), and 23% had no CAD or MI. Overall, the frequency of the 4G allele was 54.2%, and 78% of patients were 4G carriers. Genotypic distributions were: 4G/4G = 30.1%, 4G/5G = 47.9%, and 5G/5G = 21.8%. Neither carriage of 4G (CAD odds ratio [OR] = 1.08 [0.80 to 1.46], MI OR = 1.11 [0.83 to 1.49]) nor 4G/4G homozygosity (CAD OR = 1.07, MI OR = 0.98) was associated with CAD or MI. In multivariate analyses, risk factors associated with CAD were (in order): gender, age, smoking, diabetes, cholesterol, and hypertension; for MI, they were gender, smoking, and cholesterol. CONCLUSIONS: A common PAI-1 polymorphism (4G) was not importantly associated with angiographic CAD or history of MI in a Caucasian population. Modest risk (i.e., OR <1.5), especially for MI, or risk in association with other factors, cannot be excluded.

Aged↗
PubMed1999

The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data.

The Yeast Proteome Database (YPD) is a model for the organization and presentation of comprehensive protein information. Based on the detailed curation of the scientific literature for the yeast Saccharomyces cerevisiae, YPD contains more than 50 000 annotations lines derived from the review of 8500 research publications. The information concerning each of the approximately 6100 yeast proteins is structured around a convenient one-page format, the Yeast Protein Report, with additional information provided as pop-up windows. Protein classification schema have been revised this year, defining each protein's cellular role, function and pathway, and adding a Functional to the Yeast Protein Report. These changes provide the user with a succinct summary of the protein's function and its place in the biology of the cell, and they enhance the power of YPD Search functions. Precalculated sequence alignments have been added, to provide a crossover point for comparative genomics. The first transcript profiling data has been integrated into the YPD Protein Reports, providing the framework for the presentation of genome-wide functional data. The Yeast Proteome Database can be accessed on the Web at http://www.proteome.com/YPDhome.html

Computational Biology↗
PubMed1998

Cloning and disruption of the beta-isopropylmalate dehydrogenase gene (LEU2) of Pichia stipitis with URA3 and recovery of the double auxotroph.

Transformation of Pichia stipitis is required to advance genetic studies and development of xylose metabolism in this yeast. To this end, we used P. stipitis URA3 (PsURA3) to disrupt P. stipitis LEU2 in a P. stipitis ura3 mutant. A highly fermentative P. stipitis mutant (FPL-DX26) was selected for resistance to 5'-fluoroorotic acid to obtain P. stipitis FPL-UC7 (ura3-3). A URA3:lacZ "pop-out" cassette was constructed containing PsURA3 flanked by direct repeats from segments of the lacZ reading frame. The P. stipitis LEU2 gene (PsLEU2) was cloned from a P. stipitis CBS 6054 genomic library through homology to Saccharomyces cerevisiae LEU2, and a disruption cassette was constructed by replacing the PsLEU2 reading sequence with the PsURA3:lacZ cassette. FPL-UC7 (ura3-3) was transformed with the disruption cassette, and a site-specific integrant was identified by selecting for the Leu- Ura+ phenotype. The ura3 marker was recovered from this strain by plating cells onto 5'-fluoroorotate and screening for spontaneous URA3 deletion mutants. Excision of the flanked PsURA3 gene resulted in the Leu- Ura- phenotype. The double auxotrophs are stable and can be transformed at a high frequency by PsLEU2 or PsURA3 carried on autonomous-replication-sequence-based plasmids.

3-Isopropylmalate Dehydrogenase↗
PubMed1998

Cloning and characterization of two pyruvate decarboxylase genes from Pichia stipitis CBS 6054.

In Pichia stipitis, fermentative and pyruvate decarboxylase (PDC) activities increase with diminished oxygen rather than in response to fermentable sugars. To better characterize PDC expression and regulation, two genes for PDC (PsPDC1 and PsPDC2) were cloned and sequenced from P. stipitis CBS 6054. Aside from Saccharomyces cerevisiae, from which three PDC genes have been characterized, P. stipitis is the only organism from which multiple genes for PDC have been identified and characterized. PsPDC1 and PsPDC2 have diverged almost as far from one another as they have from the next most closely related known yeast gene. PsPDC1 contains an open reading frame of 1,791 nucleotides encoding 597 amino acids. PsPDC2 contains a reading frame of 1,710 nucleotides encoding 570 amino acids. An 81-nucleotide segment in the middle of the beta domain of PsPDC1 codes for a unique segment of 27 amino acids, which may play a role in allosteric regulation. The 5' regions of both P. stipitis genes include two putative TATA elements that make them similar to the PDC genes from S. cerevisiae, Kluyveromyces marxianus, and Hanseniaspora uvarum.

Amino Acid Sequence↗
PubMed1997

Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase.

The cyclic interactions that occur between the subunits of the yeast mitochondrial RNA polymerase can serve as a simple model for the more complex enzymes in prokaryotes and the eukaryotic nucleus. We have used two-hybrid and fusion protein constructs to analyze the requirements for interaction between the single subunit core polymerase (Rpo41p), and the sigma-like promoter specificity factor (Mtf1p). We were unable to define any protein truncations that retained the ability to interact, indicating that multiple regions encompassing the entire length of the proteins are involved in interactions. We found that 9 of 15 nonfunctional (petite) point mutations in Mtf1p isolated in a plasmid shuffle strategy had lost the ability to interact. Some of the noninteracting mutations are temperature-sensitive petite (ts petite); this phenotype correlates with a precipitous drop in mitochondrial transcript abundance when cells are shifted to the nonpermissive temperature. One temperature-sensitive mutant demonstrated a striking pH dependence for core binding in vitro, consistent with the physical properties of the amino acid substitution. The noninteracting mutations fall into three widely spaced clusters of amino acids. Two of the clusters are in regions with amino acid sequence similarity to conserved regions 2 and 3 of sigma factors and related proteins; these regions have been implicated in core binding by both prokaryotic and eukaryotic sigma-like factors. By modeling the location of the mutations using the partial structure of Escherichia coli sigma70, we find that two of the clusters are potentially juxtaposed in the three-dimensional structure. Our results demonstrate that interactions between sigma-like specificity factors and core RNA polymerases require multiple regions from both components of the holoenzymes.

Amino Acid Sequence↗
PubMed1996

Increased xylose reductase activity in the xylose-fermenting yeast Pichia stipitis by overexpression of XYL1.

The Pichia stipitis xylose reductase gene (XYL1) was inserted into an autonomous plasmid that P. stipitis maintains in multicopy. The plasmid pXOR with the XYL1 insert or a control plasmid pJM6 without XYL1 was introduced into P. stipitis. When grown on xylose under aerobic conditions, the strain with pXOR had up to 1.8-fold higher xylose reductase (XOR) activity than the control strain. Oxygen limitation led to higher XOR activity in both experimental and control strains grown on xylose. However, the XOR activities of the two strains grown on xylose were similar under oxygen limitation. When grown on glucose under aerobic or oxygen-limited conditions, the experimental strain had XOR activity up to 10 times higher than that of the control strain. Ethanol production was not improved, but rather it decreased with the introduction of pXOR compared to the control, and this was attributed to nonspecific effects of the plasmid.

Aldehyde Reductase↗
PubMed1994

High-efficiency transformation of Pichia stipitis based on its URA3 gene and a homologous autonomous replication sequence, ARS2.

This paper describes the first high-efficiency transformation system for the xylose-fermenting yeast Pichia stipitis. The system includes integrating and autonomously replicating plasmids based on the gene for orotidine-5'-phosphate decarboxylase (URA3) and an autonomous replicating sequence (ARS) element (ARS2) isolated from P. stipitis CBS 6054. Ura- auxotrophs were obtained by selecting for resistance to 5-fluoroorotic acid and were identified as ura3 mutants by transformation with P. stipitis URA3. P. stipitis URA3 was cloned by its homology to Saccharomyces cerevisiae URA3, with which it is 69% identical in the coding region. P. stipitis ARS elements were cloned functionally through plasmid rescue. These sequences confer autonomous replication when cloned into vectors bearing the P. stipitis URA3 gene. P. stipitis ARS2 has features similar to those of the consensus ARS of S. cerevisiae and other ARS elements. Circular plasmids bearing the P. stipitis URA3 gene with various amounts of flanking sequences produced 600 to 8,600 Ura+ transformants per micrograms of DNA by electroporation. Most transformants obtained with circular vectors arose without integration of vector sequences. One vector yielded 5,200 to 12,500 Ura+ transformants per micrograms of DNA after it was linearized at various restriction enzyme sites within the P. stipitis URA3 insert. Transformants arising from linearized vectors produced stable integrants, and integration events were site specific for the genomic ura3 in 20% of the transformants examined. Plasmids bearing the P. stipitis URA3 gene and ARS2 element produced more than 30,000 transformants per micrograms of plasmid DNA. Autonomously replicating plasmids were stable for at least 50 generations in selection medium and were present at an average of 10 copies per nucleus.

Amino Acid Sequence↗
PubMed1992

Selective expression of trypsin fusion genes in acinar cells of the pancreas and stomach of transgenic mice.

Fusion genes combining the 5'-transcriptional regulatory region of the rat trypsin I gene and the structural gene of human growth hormone as a reporter were expressed to the high levels characteristic of the endogenous trypsin I gene selectively in the acinar cells of the pancreas of transgenic mice. As little as 232 base pairs of trypsin gene sequences containing the transcriptional start site and upstream promoter elements were sufficient to direct pancreatic expression. The tissue-specific expression was controlled transcriptionally. Trypsin-human growth hormone fusion transgenes also were expressed, although at low levels, in the stomach, an unexpected site for the expression of pancreatic digestive enzymes. Expression in the stomach of endogenous trypsin, elastase, and amylase genes in both normal and transgenic mice verified that transgene expression was consistent with normal expression of pancreatic genes. Endogenous amylase colocalizes with pepsinogen in the acinar cell-like Chief cells of the glandular portion of the mouse stomach. The expression of pancreatic genes in stomach cells is probably the consequence of similar developmental origins of pancreatic and gastric acinar cells from the primordial gut.

Animals↗
PubMed1991

Otitis media in early childhood and later language.

The relationship between early otitis media with effusion (OME) experience and later language development was examined in a prospective cohort study of 30 children from middle-class families and 33 children from low-income families. Ear status was monitored using otoscopy and tympanometry during wellness and illness periods between birth and 3 years of age. Language was assessed using standardized tests and a language sample between 4 1/2 and 6 years. Findings suggested no reliable relationship between early OME experience and later language development.

Child, Preschool↗
PubMed1989

Skin accelerometer displacement and relative bone movement of adjacent vertebrae in response to chiropractic percussion thrusts.

The authors studied relative bone movements in response to manipulative light taps to the spine. Piezoelectric accelerometers attached to bone of an anesthetized dog measured transverse, X-Z plane, movements of L2-L3 adjacent vertebrae while percussion thrusts of an instrument used for manipulation made inputs three vertebrae above and five vertebrae below the L2-L3 joint interface. Small, relative 1-mm translations and 0.5 degree rotations occurred during the first 19 msec. When one set of accelerometers were stabilized on the skin surface, half of the skin-bone translation maxima erred less than 2%. However, skin translations averaged 77% (SD = 2%) of bone translations and skin rotations averaged 95% (SD = 26%) of bone rotations. The results suggest the possibility that, with further development, piezoelectric accelerometers can be a noninvasive tool to study dynamic, relative, bone movement.

Animals↗
PubMed1988

Limited transcription of rat elastase I transgene repeats in transgenic mice.

The rat elastase I (EI) regulatory region is an enhancer that directs efficient pancreas-specific transcription of linked genes integrated in the chromosomes of transgenic mice. However, with increasing numbers of tandemly repeated EI transgenes, the transcription rate per gene decreased. This decrease was not due to a titration of essential transcription factors, because transgenic mice with as many as 250 copies of the rat EI enhancer continued transcription of the endogenous mouse EI gene at its normal rate. Furthermore, when transgenic mice bearing 250 EI genes and mice bearing 7 copies of an EI enhancer-directed human growth hormone (hGh) gene were mated to produce mice with two unlinked arrays of EI enhancer-driven transgenes, each array was transcribed at the same rate as in mice bearing each array separately. Long tandem arrays of transgenes may inhibit efficient transcription despite the presence of ample amounts of essential transcription factors. Although the transcription rate of the mouse EI gene was not affected by the presence of large numbers of transgenes, the amounts of mouse elastase I and elastase II mRNAs were decreased in the presence of high levels of transgene mRNA, indicating an adjustment of the cell mRNA population.

Animals↗
PubMed1988

Biomechanical analysis by chiropractic radiography: Part I. A simple method for determining X-ray projectional distortion.

Projectional distortion is known to produce artifactual disrelationships between the images of osseous segments on X-ray film. Apparatus and methods were developed to measure the effect of projectional distortion on a human third lumbar vertebra. The procedures for mathematical analysis of such distortion are outlined, and the results of studies to determine the accuracy of the procedure are presented.

Biomechanical Phenomena↗
PubMed1988

Biomechanical analysis by chiropractic radiography: Part III. Lack of effect of projectional distortion on Gonstead vertebral endplate lines.

Projectional distortion is known to produce artifactual dysrelationships between images of osseous segments on X-ray films. According to Gonstead, lines constructed parallel to the adjacent vertebral endplates will converge if a lateral flexion malposition is present and will be parallel if no such subluxation exists. To test the accuracy of these lines, we mounted two vertebrae on supports so that the superior vertebra could be laterally flexed by a known amount upon the fixed inferior vertebra. The specimen was X rayed with no flexion or with various degrees of right or left lateral flexion of the superior vertebra. Lateral and inferior off-centering, rotation about the z axis, and object-film distance were also varied systematically. In every instance, off-centering produced no measurable effect on the position of the constructed Gonstead lines. We therefore conclude that these lines can be confidentially used to indicate structural dysrelationship during lateral flexion. No correction for projectional distortion appears to be necessary.

Biomechanical Phenomena↗
PubMed1988

Biomechanical analysis by chiropractic radiography: Part II. Effects of X-ray projectional distortion on apparent vertebral rotation.

Projectional distortion in an X-ray image can produce artifacts that cause error in the measurement of vertebral rotation. By means of a stereotaxic positioning device, the effect of varying object-film distance, vertical and horizontal off-centering, rotation, and lateral flexion on the amount of distortion in the image of a third lumbar vertebra was determined. Mathematical analysis of the results revealed that projectional distortion due to vertical off-centering does not affect the apparent rotation of the vertebra measurably; that there is a linear relationship between apparent vertebral rotation and horizontal off-centering; for the object-film distances of 35.64 + 0.12 cm and 19.48 + 0.08 cm, the vertebra displayed 1 mm of apparent rotation for every 2 to 3 cm of lateral off-centering regardless of whether the vertebra is rotated or laterally flexed; and that as long as a given osseous segment is compared to its adjacent segment (as in analysis for subluxation), the apparent vertebral rotation may be regarded as a sufficiently accurate representation of the actual rotation of the vertebra.

Biomechanical Phenomena↗
PubMed1986

Transgenic progeny inherit tissue-specific expression of rat elastase I genes.

Six different lines of transgenic mice bearing rat elastase I genes stably inherit both the high-level pancreatic expression and low-level nonpancreatic expression characteristic of each original founding mouse. The high pancreatic expression of the introduced rat genes is transcriptionally determined. In response to high rat elastase I mRNA content in the pancreas, rat elastase I protein is synthesized and secreted at high levels. The stable inheritance of expression of the foreign rat elastase I genes in transgenic mice allows the development of animal lines that synthesize and secrete high levels of foreign protein by the pancreas.

Animals↗