Biomedical subjects

P Keim

Publications and source records attributed to P Keim.

At least 19 recordsLinked to original sources

PubMed2006

Do high-tannin leaves require more roots?

The well-known deceleration of nitrogen (N) cycling in the soil resulting from addition of large amounts of foliar condensed tannins may require increased fine-root growth in order to meet plant demands for N. We examined correlations between fine-root production, plant genetics, and leaf secondary compounds in Populus angustifolia, P. fremontii, and their hybrids. We measured fine-root (<2 mm) production and leaf chemistry along an experimental genetic gradient where leaf litter tannin concentrations are genetically based and exert strong control on net N mineralization in the soil. Fine-root production was highly correlated with leaf tannins and individual tree genetic composition based upon genetic marker estimates, suggesting potential genetic control of compensatory root growth in response to accumulation of foliar secondary compounds in soils. We suggest, based on previous studies in our system and the current study, that genes for tannin production could link foliar chemistry and root growth, which may provide a powerful setting for external feedbacks between above- and belowground processes.

Hybridization, Genetic↗

PubMed2006

A genetic similarity rule determines arthropod community structure.

We define a genetic similarity rule that predicts how genetic variation in a dominant plant affects the structure of an arthropod community. This rule applies to hybridizing cottonwood species where plant genetic variation determines plant-animal interactions and structures a dependent community of leaf-modifying arthropods. Because the associated arthropod community is expected to respond to important plant traits, we also tested whether plant chemical composition is one potential intermediate link between plant genes and arthropod community composition. Two lines of evidence support our genetic similarity rule. First, in a common garden experiment we found that trees with similar genetic compositions had similar chemical compositions and similar arthropod compositions. Second, in a wild population, we found a similar relationship between genetic similarity in cottonwoods and the dependent arthropod community. Field data demonstrate that the relationship between genes and arthropods was also significant when the hybrids were analysed alone, i.e. the pattern is not dependent upon the inclusion of both parental species. Because plant-animal interactions and natural hybridization are common to diverse plant taxa, we suggest that a genetic similarity rule is potentially applicable, and may be extended, to other systems and ecological processes. For example, plants with similar genetic compositions may exhibit similar litter decomposition rates. A corollary to this genetic similarity rule predicts that in systems with low plant genetic variability, the environment will be a stronger factor structuring the dependent community. Our findings argue that the genetic composition of a dominant plant can structure higher order ecological processes, thus placing community and ecosystem ecology within a genetic and evolutionary framework. A genetic similarity rule also has important conservation implications because the loss of genetic diversity in one species, especially dominant or keystone species that define many communities, may cascade to negatively affect the rest of the dependent community.

Animals↗

PubMed2006

From genes to geography: a genetic similarity rule for arthropod community structure at multiple geographic scales.

We tested the hypothesis that leaf modifying arthropod communities are correlated with cottonwood host plant genetic variation from local to regional scales. Although recent studies found that host plant genetic composition can structure local dependent herbivore communities, the abiotic environment is a stronger factor than the genetic effect at increasingly larger spatial scales. In contrast to these studies we found that dependent arthropod community structure is correlated with both the cross type composition of cottonwoods and individual genotypes within local rivers up to the regional scale of 720,000 km(2) (Four Corner States region in the southwestern USA). Across this geographical extent comprising two naturally hybridizing cottonwood systems, the arthropod community follows a simple genetic similarity rule: genetically similar trees support more similar arthropod communities than trees that are genetically dissimilar. This relationship can be quantified with or without genetic data in Populus.

Animals↗

PubMed2005

Pair interaction of dislocations in two-dimensional crystals.

The pair interaction between crystal dislocations is systematically explored by analyzing particle trajectories of two-dimensional colloidal crystals measured by video microscopy. The resulting pair energies are compared to Monte Carlo data and to predictions derived from the standard Hamiltonian of the elastic theory of dislocations. Good agreement is found with respect to the distance and temperature dependence of the interaction potential, but not regarding the angle dependence where discrete lattice effects become important. Our results on the whole confirm that the dislocation Hamiltonian allows a quantitative understanding of the formation and interaction energies of dislocations in two-dimensional crystals.

Journal Article↗

PubMed2005

Anisotropic mean-square displacements in two-dimensional colloidal crystals of tilted dipoles.

Superparamagnetic colloidal particles confined to a flat horizontal air-water interface in an external magnetic field, which is tilted relative to the interface, form anisotropic two-dimensional crystals resulting from their mutual dipole-dipole interactions. Using real-space experiments and harmonic lattice theory we explore the mean-square displacements of the particles in the directions parallel and perpendicular to the in-plane component of the external magnetic field as a function of the tilt angle. We find that the anisotropy of the mean-square displacement behaves nonmonotonically as a function of the tilt angle and does not correlate with the structural anisotropy of the crystal.

Journal Article↗

PubMed2005

Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing.

AIM: Evaluation of the Escherichia coli genome for variable number tandem repeat (VNTR) loci in order to provide a subtyping tool with greater discrimination and more efficient capacity. METHODS AND RESULTS: Twenty-nine putative VNTR loci were identified from the E. coli genomic sequence. Their variability was validated by characterizing the number of repeats at each locus in a set of 56 E. coli O157:H7/HN and O55:H7 isolates. An optimized multiplex assay system was developed to facility high capacity analysis. Locus diversity values ranged from 0.23 to 0.95 while the number of alleles ranged from two to 29. This multiple-locus VNTR analysis (MLVA) data was used to describe genetic relationships among these isolates and was compared with PFGE (pulse field gel electrophoresis) data from a subset of the same strains. Genetic similarity values were highly correlated between the two approaches, through MLVA was capable of discrimination amongst closely related isolates when PFGE similar values were equal to 1.0. CONCLUSIONS: Highly variable VNTR loci exist in the E. coli O157:H7 genome and are excellent estimators of genetic relationships, in particular for closely related isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: Escherichia coli O157:H7 MLVA offers a complimentary analysis to the more traditional PFGE approach. Application of MLVA to an outbreak cluster could generate superior molecular epidemiology and result in a more effective public health response.

Alleles↗

PubMed2005

Habitat barriers limit gene flow and illuminate historical events in a wide-ranging carnivore, the American puma.

We examined the effects of habitat discontinuities on gene flow among puma (Puma concolor) populations across the southwestern USA. Using 16 microsatellite loci, we genotyped 540 pumas sampled throughout the states of Utah, Colorado, Arizona, and New Mexico, where a high degree of habitat heterogeneity provides for a wide range of connective habitat configurations between subpopulations. We investigated genetic structuring using complementary individual- and population-based analyses, the latter employing a novel technique to geographically cluster individuals without introducing investigator bias. The analyses revealed genetic structuring at two distinct scales. First, strikingly strong differentiation between northern and southern regions within the study area suggests little migration between them. Second, within each region, gene flow appears to be strongly limited by distance, particularly in the presence of habitat barriers such as open desert and grasslands. Northern pumas showed both reduced genetic diversity and greater divergence from a hypothetical ancestral population based on Bayesian clustering analyses, possibly reflecting a post-Pleistocene range expansion. Bayesian clustering results were sensitive to sampling density, which may complicate inference of numbers of populations when using this method. The results presented here build on those of previous studies, and begin to complete a picture of how different habitat types facilitate or impede gene flow among puma populations.

Animals↗

PubMed2004

Elastic behavior of a two-dimensional crystal near melting.

Using positional data from video microscopy, we determine the elastic moduli of two-dimensional colloidal crystals as a function of temperature. The moduli are extracted from the wave-vector-dependent normal-mode spring constants in the limit q-->0 and are compared to the renormalized Young's modulus of the Kosterlitz-Thouless-Halperin-Nelson-Young theory. An essential element of this theory is the universal prediction that Young's modulus must approach 16 pi at the melting temperature. This is indeed observed in our experiment.

Journal Article↗

PubMed2004

Anisotropic defect-mediated melting of two-dimensional colloidal crystals.

The melting transition of anisotropic two-dimensional (2D) crystals is studied in a model system of superparamagnetic colloids. The anisotropy of the induced dipole-dipole interaction is varied by tilting the external magnetic field off the normal to the particle plane. By analyzing the time-dependent Lindemann parameter as well as translational and orientational order we observe a 2D smecticlike phase. The Kosterlitz-Thouless-Halperin-Nelson-Young scenario of isotropic melting is modified: dislocation pairs and dislocations appear with different probabilities depending on their orientation with respect to the in-plane field.

Journal Article↗

PubMed2004

Harmonic lattice behavior of two-dimensional colloidal crystals.

Using positional data from videomicroscopy and applying the equipartition theorem for harmonic Hamiltonians, we determine the wave-vector-dependent normal mode spring constants of a two-dimensional colloidal model crystal and compare the measured band structure to predictions of the harmonic lattice theory. We find good agreement for both the transversal and the longitudinal modes. For q-->0, the measured spring constants are consistent with the elastic moduli of the crystal.

Journal Article↗

PubMed2004

Ecosystem implications of genetic variation in water-use of a dominant riparian tree.

Genetic variation in dominant species can affect plant and ecosystem functions in natural systems through multiple pathways. Our study focuses on how genetic variation in a dominant riparian tree ( Populus fremontii, P. angustifolia and their natural F(1) and backcross hybrids) affects whole-tree water use, and its potential ecosystem implications. Three major patterns were found. First, in a 12-year-old common garden with trees of known genetic makeup, hybrids had elevated daily integrated leaf-specific transpiration ( E(tl); P=0.013) and average canopy conductance ( G(c); P=0.037), with both E(tl) and G(c) approximately 30% higher in hybrid cross types than parental types. Second, delta(13)C values of leaves from these same trees were significantly more negative in hybrids ( P=0.004), and backcross hybrids had significantly more negative values than all other F(1) hybrid and parental types ( P<0.001). Third, in the wild, a similar pattern was found in leaf delta(13)C values where both hybrid cross types had the lowest values ( P<0.001) and backcross hybrids had lower delta(13)C values than any other tree type ( P<0.001). Our findings have two important implications: (1). the existence of a consistent genetic difference in whole-tree physiology suggests that whole-tree gas and water exchange could be another pathway through which genes could affect ecosystems; and (2). such studies are important because they seek to quantify the genetic variation that exists in basic physiological processes-such knowledge could ultimately place ecosystem studies within a genetic framework.

Carbon Isotopes↗

PubMed2002

Bacillus anthracis evolution and epidemiology.

Bacillus anthracis is a pathogen that is widely distributed around the globe. However, this great distribution is not accompanied by great genetic diversity. Although subtle morphological and biochemical differences exist, the underlying genetic basis for this plasticity is not known. Indeed, very few single nucleotide differences have been detected among isolates and the only documented high variable sequences are associated with variable number tandem repeated (VNTR) sequences. The differences among the VNTRs has been used to suggest phylogenetic relationships among the worldwide isolates. There is one major clonal split in B. anthracis (A and B), with two minor clusters established within the B branch and four or more minor branches within the A group. The A branch is the most common worldwide, though the B branch is locally important in certain areas. The ecology and the evolution of B. anthracis have been greatly influenced by the spore phase of the lifecycle.

Animals↗

PubMed2002

Genetic variation across the historical range of the wild turkey (Meleagris gallopavo).

Genetic differences within and among naturally occurring populations of wild turkeys (Meleagris gallopavo) were characterized across five subspecies' historical ranges using amplified fragment length polymorphism (AFLP) analysis, microsatellite loci and mitochondrial control region sequencing. Current subspecific designations based on morphological traits were generally supported by these analyses, with the exception of the eastern (M. g. silvestris) and Florida (M. g. osceola) subspecies, which consistently formed a single unit. The Gould's subspecies was both the most genetically divergent and the least genetically diverse of the subspecies. These genetic patterns were consistent with current and historical patterns of habitat continuity. Merriam's populations showed a positive association between genetic and geographical distance, Rio Grande populations showed a weaker association and the eastern populations showed none, suggesting differing demographic forces at work in these subspecies. We recommend managing turkeys to maintain subspecies integrity, while recognizing the importance of maintaining regional population structure that may reflect important adaptive variation.

Animals↗

PubMed2001

Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki).

Interspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later-generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness.

Animals↗

PubMed2001

Hybrid populations selectively filter gene introgression between species.

Hybrids have long been recognized as a potential pathway for gene flow between species that can have important consequences for evolution and conservation biology. However, few studies have demonstrated that genes from one species can introgress or invade another species over a broad geographic area. Using 35 genetically mapped restriction fragment length polymorphism (RFLP) markers of two species of cottonwoods (Populus fremontii x P. angustifolia) and their hybrids (n = 550 trees), we showed that the majority of the genome is prohibited from introgressing from one species into the other. However, this barrier was not absolute; Fremont cpDNA and mtDNA were found throughout the geographic range of narrowleaf cottonwood, and 20% of the nuclear markers of Fremont cottonwood introgressed varying distances (some over 100 km) into the recipient species' range. Rates of nuclear introgression were variable, but two nuclear markers introgressed as fast as the haploid, cytoplasmically inherited chloroplast and mitochondrial markers. Our genome-wide analysis provides evidence for positive, negative, and neutral effects of introgression. For example, we predict that DNA fragments that introgress through several generations of backcrossing will be small, because small fragments are less likely to contain deleterious genes. These results argue that recombination will be important, that introgression can be very selective, and that evolutionary forces within the hybrid population to effectively "filter" gene flow between species. A strong filter may make introgression adaptive, prevent genetic assimilation, lead to relaxed isolating mechanisms, and contribute to the stability of hybrid zones. Thus, rather than hybridization being a negative factor as is commonly argued, natural hybridization between native species may provide important genetic variation that impacts both ecological and evolutionary processes. Finally, we propose two hypotheses that contrast the likelihood of contemporary versus ancient introgression in this system.

Biological Evolution↗

PubMed2001

Fluorescent Amplified Fragment Length Polymorphism Analysis of Norwegian Bacillus cereus and Bacillus thuringiensis Soil Isolates.

We examined 154 Norwegian B. cereus and B. thuringiensis soil isolates (collected from five different locations), 8 B. cereus and 2 B. thuringiensis reference strains, and 2 Bacillus anthracis strains by using fluorescent amplified fragment length polymorphism (AFLP). We employed a novel fragment identification approach based on a hierarchical agglomerative clustering routine that identifies fragments in an automated fashion. No method is free of error, and we identified the major sources so that experiments can be designed to minimize its effect. Phylogenetic analysis of the fluorescent AFLP results reveals five genetic groups in these group 1 bacilli. The ATCC reference strains were restricted to two of the genetic groups, clearly not representative of the diversity in these bacteria. Both B. anthracis strains analyzed were closely related and affiliated with a B. cereus milk isolate (ATCC 4342) and a B. cereus human pathogenic strain (periodontitis). Across the entire study, pathogenic strains, including B. anthracis, were more closely related to one another than to the environmental isolates. Eight strains representing the five distinct phylogenetic clusters were further analyzed by comparison of their 16S rRNA gene sequences to confirm the phylogenetic status of these groups. This analysis was consistent with the AFLP analysis, although of much lower resolution. The innovation of automated genotype analysis by using a replicated and statistical approach to fragment identification will allow very large sample analyses in the future.

Bacillus cereus↗

PubMed2001

Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan.

In 1993, the Aum Shinrikyo cult aerosolized Bacillus anthracis spores over Kameido, Japan. Spore samples were obtained from the release site, cultured, and characterized by molecular genetic typing. The isolates were consistent with strain Sterne 34F2, which is used in Japan for animal prophylaxis against anthrax.

Aerosols↗

PubMed2001

Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome.

Yersinia pestis, the infamous plague-causing pathogen, appears to have emerged in relatively recent history. Evidence of this fact comes from several studies that document a lack of nucleotide diversity in the Y. pestis genome. In contrast, we report that variable-number tandem repeat (VNTR) sequences are common in the Y. pestis genome and occur frequently in gene coding regions. Larger tandem repeat arrays, most useful for phylogenetic analysis, are present at an average of 2.18 arrays per 10 kbp and are distributed evenly throughout the genome and the two virulence plasmids, pCD1 and pMT1. We examined allelic diversity at 42 chromosomal VNTR loci in 24 selected isolates (12 globally distributed and 12 from Siskiyou County, Calif.). Vast differences in diversity were observed among the 42 VNTR loci, ranging from 2 to 11 alleles. We found that the maximum copy number of repeats in an array was highly correlated with diversity (R = 0.86). VNTR-based phylogenetic analysis of the 24 strains successfully grouped isolates from biovar orientalis and most of the antiqua and mediaevalis strains. Hence, multiple-locus VNTR analysis (MLVA) appears capable of both distinguishing closely related strains and successfully classifying more distant relationships. Harnessing the power of MLVA to establish standardized databases will enable researchers to better understand plague ecology and evolution around the world.

Animals↗