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P Keim

Publications and source records attributed to P Keim.

At least 55 records · Page 3Linked to original sources
PubMed1997

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates.

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five polymorphisms differed by the presence of two to six copies of the 12-bp tandem repeat 5'-CAATATCAACAA-3'. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations.

Bacillus anthracis↗
PubMed1997

Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers.

Bacillus anthracis causes anthrax and represents one of the most molecularly monomorphic bacteria known. We have used AFLP (amplified fragment length polymorphism) DNA markers to analyze 78 B. anthracis isolates and six related Bacillus species for molecular variation. AFLP markers are extremely sensitive to even small sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Using this approach, we examined ca. 6.3% of the Bacillus genome for length mutations and ca. 0.36% for point mutations. Extensive variation was observed among taxa, and both cladistic and phenetic analyses were used to construct a phylogeny of B. anthracis and its closest relatives. This genome-wide analysis of 357 AFLP characters (polymorphic fragments) indicates that B. cereus and B. thuringiensis are the closest taxa to B. anthracis, with B. mycoides slightly more distant. B. subtilis, B. polymyxa, and B. stearothermophilus shared few AFLP markers with B. anthracis and were used as outgroups to root the analysis. In contrast to the variation among taxa, only rare AFLP marker variation was observed within B. anthracis, which may be the most genetically uniform bacterial species known. However, AFLP markers did establish the presence or absence of the pXO1 and pXO2 plasmids and detected 31 polymorphic chromosomal regions among the 79 B. anthracis isolates. Cluster analysis identified two very distinct genetic lineages among the B. anthracis isolates. The level of variation and its geographic distribution are consistent with a historically recent African origin for this pathogenic organism. Based on AFLP marker similarity, the ongoing anthrax epidemic in Canada and the northern United States is due to a single strain introduction that has remained stable over at least 30 years and a 1,000-mile distribution.

Animals↗
PubMed1996

Characterization and application of soybean YACs to molecular cytogenetics.

Yeast artificial chromosomes (YACs) are widely used in the physical analysis of complex genomes. In addition to their value in chromosome walking for map-based cloning, YACs represent excellent probes for chromosome mapping using fluorescence in situ hybridization (FISH). We have screened such a library for low-copy-number clones by hybridization to total genomic DNA. Four clones were chosen for chromosome tagging based upon their low or moderate signal. By using degenerate oligonucleotide-primed PCR (DOP-PCR), we were able to use relatively small amounts of soybean YAC DNA, isolated directly by preparative pulsed-field gel electrophoresis, as FISH probes for both metaphase chromosome spreads and interphase nuclei. FISH chromosomal analysis using the three of the clones as probes resulted in relatively simple hybridization patterns consistent with a single homologous locus or two homoeologous loci. The fourth YAC probe resulted in a diffuse hybridization pattern with signal on all metaphase chromosomes. We conclude that YACs represent a valuable source of probes for chromosomal analysis in soybean.

Chromosomes, Artificial, Yeast↗
PubMed1996

Increased regional cerebral glucose metabolism and semantic memory performance in Alzheimer's disease: a pilot double blind transdermal nicotine positron emission tomography study.

Nicotinic receptor dysfunction and impaired semantic memory occur early in Alzheimer's disease patients (AD). Previous research implied that nicotine's ability to enhance alertness, arousal, and cognition in a number of nonclinical populations was a function of its ability to stimulate CNS nicotinic cholinergic receptors. In this study it was hypothesized that transdermal administration of nicotine would increase both regional cerebral glucose metabolism (rCMRglc) and semantic memory (as assessed by verbal fluency). Two mild AD and two elderly controls underwent positron emission tomography scanning during a double blind nicotinic agonist verbal fluency challenge procedure. rCMRglc increases occurred in both AD patients, but not controls. In the two AD patients, verbal fluency scores increased by an average of 17%. One elderly control's verbal fluency increased, and the other decreased. These findings suggest that nicotine's effect on metabolism and verbal fluency is due to its ability to stimulate the cholinergic system.

Alzheimer Disease↗
PubMed1996

An analysis of genetic variation in Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using AFLP markers.

A recently developed molecular technique (amplified fragment length polymorphisms, AFLP) was used for characterizing genetic heterogeneity within and among populations of a critically endangered species of plant, Astragalus cremnophylax var. cremnophylax. Using AFLP, up to 50 polymorphic genetic markers per AFLP-PCR amplification were generated, and a total of 220 variable markers overall. This information was used first to assess genetic diversity within each of the three known populations of Astragalus cremnophylax var. cremnophylax from Grand Canyon National Park in Arizona, USA: North Rim (NR; n = 970), South Rim Site 1 (SR1; n = 500), and South Rim Site 2 (SR2; n = 2). Diversity in the form of average heterozygosity [symbol: see text] H [symbol: see text] and the proportion of polymorphic genes [symbol: see text] P [symbol: see text] was greatest in the NR population ([symbol: see text] H [symbol: see text] = 0.13 and [symbol: see text] P [symbol: see text] = 0.38) and least in the SR2 population ([symbol: see text] H [symbol: see text] = 0.02 and [symbol: see text] P [symbol: see text] = 0.04). Diversity was also quite low for the SR1 population ([symbol: see text] H [symbol: see text] = 0.04 and [symbol: see text] P [symbol: see text] = 0.10). In addition, substantial genetic differentiation among populations was indicated by both phenetic (AMOVA) and genetic analyses (overall corrected FST = 0.41). This finding was corroborated by the results of several multivariate analyses which utilized the genetic data, including a UPGMA cluster analysis and a principal coordinate analysis which revealed the existence of discrete groups corresponding to the populations. Population structure was further revealed within the NR population which was known to consist of four spatially separated groups of plants. Several recommendations for the future management of the species are discussed.

Genetic Markers↗
PubMed1996

RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south-western USA.

Amphibians in the south-western United States are currently experiencing population declines. Causal explanations for these population changes as well as the implementation of sound management practices requires an understanding of the genetic structure of natural amphibian populations. To this end, we estimated genetic differences within and among seven isolated populations of northern leopard frogs, Rana pipiens, from Arizona and southern Utah using random amplified polymorphic DNA (RAPD) analyses. Fourteen arbitrarily designed primers detected 38 polymorphic loci in 85 individual frogs. Three types of population structure were observed in this study. (i) Two populations showed low genetic diversity (D = 0.10 and 0.04) and may have been established by relatively recent events. (ii) Two were not genetically distinct and exhibited a high degree of within-population diversity (D = 0.35). The possibility of gene flow between these populations is high due to their geographical proximity and their shared genetic structure. (iii) Three populations were genetically distinct from each other and the other populations, and exhibited intermediate within-population variation (D = 0.19, 0.17, 0.14). Genetic distances among the seven populations ranged from 0.00 to 0.20, suggesting that some of these leopard frog populations are genetically distinct. Although based on relatively small samples, these data suggest that leopard frog populations in the south-west are likely to represent unique genetic entities worthy of conservation. The management implications of these results are that isolated leopard frog populations should be evaluated on an individual basis to best preserve them.

Animals↗
PubMed1995

Genomic organization and evolution of the soybean SB92 satellite sequence.

Repetitive DNA sequences comprise a large percentage of plant genomes, and their characterization provides information about both species and genome evolution. We have isolated a recombinant clone containing a highly repeated DNA element (SB92) that is homologous to ca. 0.9% of the soybean genome or about 10(5) copies. This repeated sequence is tandemly arranged and is found in four or five major genomic locations. FISH analysis of metaphase chromosomes suggests that two of these locations are centromeric. We have determined the sequence of two cloned repeats and performed genomic sequencing to obtain a consensus sequence. The consensus repeat size was 92 bp and exhibited an average of 10% nucleotide substitution relative to the two cloned repeats. This high level of sequence diversity suggests an ancient origin but is inconsistent with the limited phylogenetic distribution of SB92, which is found at high copy number only in the annual soybeans. It therefore seems likely that this sequence is undergoing very rapid evolution.

Base Sequence↗
PubMed1994

Hypomethylated sequences: characterization of the duplicate soybean genome.

Soybean is believed to be a diploidized tetraploid generated from an allotetraploid ancestor. In this study, we used hypomethylated genomic DNA as a source of probes to investigate the genomic structure and methylation patterns of duplicated sequences. Forty-five genomic clones from Phaseolus vulgaris and 664 genomic clones from Glycine max were used to examine the duplicated regions in the soybean genome. Southern analysis of genomic DNA using probes from both sources revealed that greater than 15% of the hypomethylated genomic regions were only present once in the soybean genome. The remaining ca. 85% of the hypomethylated regions comprise duplicated or middle repetitive DNA sequences. If only the ratio of single to duplicate probe patterns is considered, it appears that 25% of the single-copy sequences have been lost. By using a subset of probes that only detected duplicated sequences, we examined the methylation status of the homeologous genomes with the restriction enzymes MspI and HpaII. We found that in all cases both copies of these regions were hypomethylated, although there were examples of low-level methylation. It appears that duplicate sequences are being eliminated in the diploidization process. Our data reveal no evidence that duplicated sequences are being "silenced" by inactivation correlated with methylation patterns.

DNA, Plant↗
PubMed1993

Characterization of beta-amyloid peptide from human cerebrospinal fluid.

beta-Amyloid peptide (A beta) is one of the main components of senile plaques in the brain tissue of Alzheimer's disease (AD) patients. A beta is proteolytically cleaved from the amyloid precursor protein (APP), an integral membrane protein possessing a large extracellular N-terminal domain followed by a single membrane-spanning region and a short cytoplasmic C-terminal tail. A beta has been isolated from senile plaques and cerebral vascular tissue of AD brain and characterized as a heterogeneous peptide containing 28-43 amino acids whose sequence begins in the extracellular domain of APP and extends into the putative transmembrane sequence. It has long been speculated that A beta may also be present in body fluids, such as CSF, that contact neuritic plaques. Recently using a specific enzyme-linked immunosorbent assay we were able to quantify one form of A beta in CSF. In this report, using one of these antibodies covalently bound as an affinity matrix, multiple complex forms of A beta have been isolated and characterized from CSF derived from patients with either meningitis or other neurological disorders. Amino acid sequencing reveals A beta species with N-termini of Asp1, Glu3, His6, Glu11, and Val12, although on a molar basis, Asp1 represents the predominant aminoterminus. Laser desorption mass spectrometry confirmed the presence in CSF of A beta species containing 27, 28, 30, 34, 35, 40, 42, and 43 amino acids, all beginning at Asp1; two stable trimers, (Asp1-Met35)3 and (His6-Ala42)3; and one stable dimer containing (Asp1-Val40)2.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1992

Big game species identification by deoxyribonucleic acid (DNA) probes.

Species identification is important in many big game forensic science cases but cannot always be accomplished because of the lack of adequate techniques. The authors have developed deoxyribonucleic acid (DNA) probes for elk, deer, and antelope by isolating highly repeated satellite sequences. These DNA probes distinguish among deer, elk, and antelope, although not between different species of deer. Because of the high number of sequence copies per genome, these probes are extremely sensitive, requiring less than 10 ng of total genomic DNA. The developmental protocol for these probes is relatively simple and is applicable to many other species.

Animals↗
PubMed1990

RFLP mapping in soybean: association between marker loci and variation in quantitative traits.

We have constructed a genetic map for soybean and identified associations between genetic markers and quantitative trait loci. One-hundred-fifty restriction fragment length polymorphisms (RFLPs) were used to identify genetic linkages in an F2 segregating population from an interspecific cross (Glycine max x Glycine soja). Twenty-six genetic linkage groups containing ca. 1200 recombination units are reported. Progeny-testing of F2-derived families allowed quantitative traits to be evaluated in replicated field trials. Genomic regions, which accounted for a portion of the genetic variation (R2 = 16 to 24%) in several reproductive and morphological traits, were linked to RFLP markers. Significant associations between RFLP markers and quantitative trait loci were detected for eight of nine traits evaluated. The ability to identify genes within a continuously varying trait has important consequences for plant breeding and for understanding evolutionary processes.

Chromosome Mapping↗
PubMed1989

Genetic analysis of an interspecific hybrid swarm of Populus: occurrence of unidirectional introgression.

Restriction fragment length polymorphisms were used to distinguish genotypes of two species of Populus, P. fremontii ('Fremont') and P. angustifolia ('narrowleaf'). Both inter- and intraspecific polymorphisms were detected in these cottonwood trees. The interspecific variation was much greater than the intraspecific variation. This permitted identification of parental genotypes within individual trees of a hybrid swarm which exists in an overlap zone between the two species. Within this hybrid swarm, individual trees are either F1 hybrids or backcrosses with a pure 'narrowleaf' parent; no progeny were found that could be attributed to crossing between F1 hybrid trees, or to backcrossing between F1 hybrid trees and 'Fremont'.

Crosses, Genetic↗
PubMed1988

Isolation of two neuropeptides in the AKH/RPCH-family from horseflies (Diptera).

Two neuropeptides (DCCI and DCCII) in the adipokinetic/red pigment concentrating hormone-family have been isolated and purified from the corpora cardiaca of horseflies (Diptera : Tabanidae). Both peptides were purified by a sequence of three reversed phase-high performance liquid chromatographic steps. Amino acid analysis of the purified peptides indicated the following composition for DCCI: Glx(l), Gly(1), Leu(1), Phe(1), Pro(1), Thr(2) and for DCCII: Glx(1), Gly(2), Leu(1), Phe(1), Pro(1), Thr(2), and Tyr(1). Photodiode array ultraviolet spectroscopy indicated the presence of tryptophan in both DCCI and II. Both DCCI and II had red pigment concentrating hormone activity in the crab, Uca pugilator.

Amino Acids↗
PubMed1987

The sequence of the 3.3-kilobase repetitive element from Dipodomys ordii suggests a mechanism for its amplification and interspersion.

DNA from the kangaroo rat, Dipodomys ordii, contains a 3.3-kb, highly repeated sequence that is interspersed throughout the genome in small tandem clusters. One 3.3-kb unit has been cloned into pBR322 and the nucleotide sequence determined. The clone used was shown to be representative of the bulk of such sequences found in the genomic DNA. The sequence contains 10 homologous subunits each ca. 260 bp in length. Comparison of these to one another yielded a 258-bp consensus sequence containing a 35-bp terminal inverted repeat. Two unique stretches also occur. One of these contains a region that could serve as a promoter for RNA polymerase III; the other contains a sequence related to the ARS sequences of yeast. It is proposed that an ancestral sequence similar to the consensus sequence was amplified to 10 or more units, and that, subsequently, two other sequences were inserted. The properties of these insertions may have led to the dispersal of the sequence throughout the genome.

Animals↗
PubMed1981

Purification, physical characterization, and NH2-terminal sequence of glutamine synthetase from the cyanobacterium Anabaena 7120.

A procedure for the complete purification of glutamine synthetase (L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.2) from the cyanobacterium (blue-green alga) Anabaena 7120 is described. The enzyme has structural characteristics in common with glutamine synthetases from other sources: a subunit molecular weight of approximately 50,000 and a native structure, determined by low dose exposure electron microscopy, consisting of a two-layered regular hexagon made up of 12 subunits. Sequence analysis suggests that the subunits are identical. There was no indication that the enzyme from cyanobacteria is adenylylated, a feature shared with the glutamine synthetase from Bacillus subtilis but not with the enzyme from Escherichia coli. NH2-terminal sequence analysis and the predicted conformation of the NH2-terminal regions showed definite homology among the enzymes from all three sources. The limited analysis suggested a stronger structural homology between the enzyme from Anabaena 7120 and that from E. coli.

Amino Acid Sequence↗