Showing papers by "University of Colorado Boulder published in 1986"

β -Glucuronidase from Escherichia coli as a Gene-Fusion Marker

Abstract: We have developed a gene-fusion system based on the Escherichia coli beta-glucuronidase gene (uidA). The uidA gene has been cloned from E. coli K-12 and its entire nucleotide sequence has been determined. beta-Glucuronidase has been purified to homogeneity and characterized. The enzyme has a subunit molecular weight of 68,200, is very stable, and is easily and sensitively assayed using commercially available substrates. We have constructed gene fusions of the E. coli lacZ promoter and coding region with the coding region of the uidA gene that show beta-glucuronidase activity under lac control. Plasmid vectors have been constructed to facilitate the transfer of the beta-glucuronidase coding region to heterologous control regions, using many different restriction endonuclease cleavage sites. There are several biological systems in which uidA-encoded beta-glucuronidase may be an attractive alternative or complement to previously described gene-fusion markers such as beta-galactosidase or chloramphenicol acetyltransferase.

Reassessing the reliability and validity of self-report delinquency measures

Abstract: Several issues related to the reliability and validity of self-report delinquency measures are raised and discussed. These include problems associated with the use of internal consistency as the measure of reliability, the level of reliability or precision required for different types of analyses, problems with the content validity of self-report measures, problems of overreporting and underreporting, problems with the use of official records as a validity check on self-reports, and the lack of any good criterion as a major obstacle in assessing the empirical validity of self-report measures. In the light of these problems, some cautions about the use of self-report measures are made.

Efficient algorithms for finding minimum spanning trees in undirected and directed graphs

Abstract: Recently, Fredman and Tarjan invented a new, especially efficient form of heap (priority queue). Their data structure, theFibonacci heap (or F-heap) supports arbitrary deletion inO(logn) amortized time and other heap operations inO(1) amortized time. In this paper we use F-heaps to obtain fast algorithms for finding minimum spanning trees in undirected and directed graphs. For an undirected graph containingn vertices andm edges, our minimum spanning tree algorithm runs inO(m logβ (m, n)) time, improved fromO(mβ(m, n)) time, whereβ(m, n)=min {i|log(i) n ≦m/n}. Our minimum spanning tree algorithm for directed graphs runs inO(n logn + m) time, improved fromO(n log n +m log log log(m/n+2) n). Both algorithms can be extended to allow a degree constraint at one vertex.

The intervening sequence RNA of Tetrahymena is an enzyme.

Abstract: A shortened form of the self-splicing ribosomal RNA (rRNA) intervening sequence of Tetrahymena thermophila acts as an enzyme in vitro. The enzyme catalyzes the cleavage and rejoining of oligonucleotide substrates in a sequence-dependent manner with Km = 42 microM and kcat = 2 min-1. The reaction mechanism resembles that of rRNA precursor self-splicing. With pentacytidylic acid as the substrate, successive cleavage and rejoining reactions lead to the synthesis of polycytidylic acid. Thus, the RNA molecule can act as an RNA polymerase, differing from the protein enzyme in that it uses an internal rather than an external template. At pH 9, the same RNA enzyme has activity as a sequence-specific ribonuclease.

Toxicity of Nitrite to Fish: A Review

Abstract: Nitrite, an intermediate in the oxidation of ammonium to nitrate, changes hemoglobin to methemoglobin, which does not carry oxygen; nitrite may thus cause anoxia in fish and other aquatic organisms. The published literature on nitrite toxicity to fish, which consists of about 40 papers, shows that the ratio of the 24-h LC50 (concentration lethal to half of the test organisms in 24 h) to the 96-h LC50 has a median value of 2.0 and is fairly uniform across species; toxicity tests of differing duration can therefore be standardized to a common duration. In general, chronic effects are difficult to detect at concentrations below one-fifth of the 96-h LC50. Most fish concentrate nitrite in fresh water; chloride in the external environment offsets the toxicity of nitrite by competing with nitrite for uptake through the chloride cells of the gills. The strength of the chloride effect is greatest for the least-sensitive species and smallest for the most-sensitive species. The addition of 1 mg/L chloride ...

Advances in ultrarapid freezing for the preservation of cellular ultrastructure

Abstract: Most of our current knowledge of cellular ultrastructure is derived from studies of chemically fixed and chemically cryoprotected preparations. In the first part of this review, we document the many artifacts associated with chemical techniques that render them unsuitable for further refinement of our understanding of cellular ultrastructure. The best method currently available for the preservation of cellular ultrastructure is ultrarapid freezing. The second part of this review is a consideration of the physics of ice crystal formation in biological systems, which suggests that ice crystals will be present in any frozen, uncryoprotected specimen. We define an ultrarapidly frozen preparation as one in which the ice crystals are so small as to be invisible at the electron microscopic level. Improvements in the ease of application and reliability of ultrarapid freezing techniques have reached the point that these techniques can be used by anyone requiring the best achievable preservation of cellular ultrastructure. In the third part of this review, we describe and critique the five methods of ultrarapid freezing in current use.

The elastohydrodynamic collision of two spheres

Abstract: The dynamic deformation of a solid elastic sphere which is immersed in a viscous fluid and in close motion toward another sphere or a plane solid surface is presented. The deformed shape of the solid surfaces and the pressure profile in the fluid layer separating these surfaces are determined simultaneously via asymptotic and numerical techniques. This research provides the first steps in establishing rational criteria for predicting whether a solid particle will stick or rebound subsequent to impact during filtration or coagulation when viscous forces are important.

The Neglect of Experiment

Abstract: Acknowledgments List of abbreviations Introduction 1. The discovery of parity nonconservation 2. The nondiscovery of parity nonconservation 3. CP or not CP 4. The role of experiment 5. Do experiments tell us about the world? 6. The epistemology of experiment 7. The epistemology of experiment: case studies 8. Forging, cooking, trimming and riding on the bandwagon: fraud in science Conclusion Notes Index.

Steric interactions in a model multimembrane system: A synchrotron x-ray study.

Abstract: We report a high-resolution x-ray study of a model multilayer fluid membrane system in the lyotropic L/sub ..cap alpha../ phase of a quaternary microemulsion system. The structure factor exhibits power-law behavior characteristic of a Landau-Peierls system. As a function of intermembrane distance 3.8 nmless than or equal todless than or equal to16.3 nm, the exponent eta(d) which describes the algebraic decay of layer correlations is predicted by the model of Helfrich where entropic steric repulsions dominate intermembrane interactions.

Long-term enhancement of hippocampal synaptic transmission and the acquisition of spatial information

Abstract: The hypothesis that memories are stored as a specific distribution of strengths in a population of modifiable synapses was examined by the bilateral induction of long-term enhancement in synapses of the main afferent fiber system to the hippocampal formation in rats. Brief, high- frequency activation of the perforant pathway in chronically prepared animals resulted in a persistent increase in the field EPSP and population spike, measured extracellularly in fascia dentata. This treatment resulted in a profound and persistent deficit in the acquisition of new spatial information in a task requiring spatial “reference” memory, and disruption of recently acquired spatial information. Well-established spatial memory was completely unaffected, however, as was the acquisition of spatial information into short-term “working” memory. These results support the hypothesis that, during the formation of “cognitive maps,” spatial information must be temporarily stored at modifiable synapses at the input stage to the hippocampal formation, but that this information is not needed once the representation of the environment is well established. Spatial working memory, in a familiar environment, appears not to depend on the distribution of synaptic strengths in this system at all.

The Tetrahymena ribozyme acts like an RNA restriction endonuclease

Abstract: A shortened form of the Tetrahymena self-splicing ribosomal RNA intervening sequence acts as an endoribonuclease, catalysing the cleavage of large RNA molecules by a mechanism involving guanosine transfer. The sequence specificity approaches that of the DNA restriction endonucleases. Site-specific mutagenesis of the enzyme active site alters the substrate sequence specificity in a predictable manner, so that endoribonucleases can be synthesized to cut at a variety of tetranucleotide sequences.

Disruption of a coronal streamer by an eruptive prominence and coronal mass ejection

Abstract: The coronal mass ejection of August 18, 1980 is analyzed using images from the coronagraph on the Solar Maximum Mission (SMM) satellite. The event occurred at the site of a large coronal helmet streamer and evolved into the three-part structure of a bright frontal shell, followed by a relatively dark space surrounding a bright filamentary core as seen in many mass ejections of the SMM epoch. The bright core can be identified as material from a prominence whose eruption was observed from the ground. The mass of the frontal shell is equal to that of the coronal helmet streamer, indicating that the shell is the coronal material previously in the helmet streamer, displaced and set into motion by the erupting prominence and surrounding cavity. The mass ejected in the bright core (or prominences) is estimated to be 50 percent larger than the 'coronal' material in the front loop.

Efficient estimation of sensory thresholds

Abstract: Laboratory computers permit detection and discrimination thresholds to be measured rapidly, efficiently, and accurately. In this paper, the general natures of psychometric functions and of thresholds are reviewed, and various methods for estimating sensory thresholds are summarized. The most efficient method, in principle, using maximum-likelihood threshold estimations, is examined in detail. Four techniques are discussed that minimize the reported problems found with the maximum-likelihood method. A package of FORTRAN subroutines, ML-TEST, which implements the maximum-likelihood method, is described. These subroutines are available on request from the author.

Memory Constraints and Flower Choice in Pieris rapae.

Abstract: Darwin hypothesized that flower constancy in insects that feed on nectar results from the need to learn how to extract nectar from a flower of a given species. In laboratory tests, Pieris rapae, the cabbage butterfly, showed flower constancy by continuing to visit flower species with which it had experience. The time required by individuals to find the source of nectar in flowers decreased with successive attempts, the performance following a learning curve. Learning to extract nectar from a second species interfered with the ability to extract nectar from the first. Insects that switch species thus experience a cost in time to learn. These results support recent suggestions on the importance of learning in animal foraging.

Transcription factor Sp1 recognizes a DNA sequence in the mouse dihydrofolate reductase promoter

Abstract: Human (HeLa) cells contain a host-cell-encoded transcription factor, Sp1, which is required for transcription of simian virus 40 (SV40) promoters. Since the discovery of Sp1 we have been interested in learning what role this factor plays in uninfected cells. A monkey cellular gene promoter interacts with Sp1, but no gene products linked to this promoter have yet been identified. The finding that the sequence of the 5'-flanking DNA of the mouse dihydrofolate reductase (DHFR) gene contains several regions showing strong homology to the Sp1 binding region of simian virus 40 (SV40) prompted us to undertake experiments with dhfr. We report here that Sp1 binds to these regions in the dhfr promoter, and that Sp1-containing preparations stimulate transcription from the dhfr promoter in an in vitro reaction. Our results suggest that in addition to its interactions with the SV40 viral promoter, one function of Sp1 is to direct the expression of the cellular DHFR gene.

The effective thermal conductivity of a composite material with spherical inclusions

Abstract: A new method is presented for calculating the effective thermal conductivity of a composite material containing spherical inclusions. The surface of a large body is assumed kept at a uniform temperature. This body is in contact with a composite material of infinite extent having a lower temperature far from the heated body. Green's theorem is then used to calculate the rate of heat transfer from the heated body to the composite material, yielding $$k_e /k = 1 + \frac{{3(\alpha - 1)}}{{[\alpha + 2 - (\alpha - 1)\phi ]}}\{ \phi + f(\alpha )\phi ^2 + 0(\phi ^3 )\} $$ where ke is the effective thermal conductivity, k is the thermal conductivity of the continuous phase, α is the ratio of the thermal conductivity of the spherical inclusions to k, and φ is the volume fraction occupied by the dispersed phase. The function f(α) is presented in this work. Although a similar result has been found previously by renormalization techniques, the method presented in this paper has merit in that a decaying temperature field is used. As a result, only convergent integrals are encountered, and a renormalization factor is not needed. This method is more straightforward than its predecessors and sheds additional light on the basic properties of two-phase materials.

Self-Reported Violent Offending A Descriptive Analysis of Juvenile Violent Offenders and Their Offending Careers

Abstract: Serious violent offenders are identified on the basis of self-reported involvement in violent FBI Index Offenses from a large representative sample of adolescents in the United States. The study involves a longitudinal prospective design with five annual waves of data on this national youth panel. Estimates of four basic parameters of violent offending are presented: prevalence rates, individual offending rates, career lengths, and crime mix patterns. These estimates are then compared to estimates based upon official arrest data. Self-reported estimates are substantially greater than those based upon arrest data, suggesting that those arrested for serious violent offenses constitute only a fraction of youth actually involved in serious violent behavior. The analysis also indicated that compared to self-reported data, arrest data overstate the magnitude of sex, race, and age differentials in the prevalence of serious violent offending. Further, self-reported individual offending rates were also substantial...

Evaluating alternative linear programming models to solve the two-group discriminant problem

Abstract: The two-group discriminant problem has applications in many areas, for example, differentiating between good credit risks and poor ones, between promising new firms and those likely to fail, or between patients with strong prospects for recovery and those highly at risk. To expand our tools for dealing with such problems, we propose a class of nonpara-metric discriminant procedures based on linear programming (LP). Although these procedures have attracted considerable attention recently, only a limited number of computational studies have examined the relative merits of alternative formulations. In this paper we provide a detailed study of three contrasting formulations for the two-group problem. The experimental design provides a variety of test conditions involving both normal and nonnormal populations. Our results establish the LP model which seeks to minimize the sum of deviations beyond the two-group boundary as a promising alternative to more conventional linear discriminant techniques.

Social Ecology and Behavior of Coyotes

Abstract: Publisher Summary Behavioral patterns are subject to natural selection and behavior like any other attributes of an animal, which contributes to individual survival The chapter summarizes a long-term study of coyotes that was conducted in the Grand Teton National Park, in the northwest comer of Wyoming There is remarkable agreement in the results stemming from a limited number of field projects concerned with the social behavior and behavioral ecology of coyotes, and some general principles concerning social ecology, scent marking, predatory behavior, time budgeting, and reproductive and care-giving patterns can be developed that are applicable not only to coyotes but to many other carnivores

Size effects of electrical breakdown in quenched random media.

Abstract: Two percolation models for electrical breakdown in quenched random media, a fuse-wire network and a dielectric network, are introduced and studied. A combination of Lifshitz and scaling arguments leads to a size dependence given by $\frac{{V}_{b}}{L}\ensuremath{\sim}\frac{a(p)}{[1+b(p){(\mathrm{ln}L)}^{\ensuremath{\beta}}]}$, where $\frac{\ensuremath{\beta}=1}{(d\ensuremath{-}1)}$ for the fuse network and $\ensuremath{\beta}=1$ for the dielectric network. Simulations support this hypothesis in the 2D fuse network. We argue that any finite fraction of quenched defects qualitatively reduces the breakdown strength of a wide variety of electrical and mechanical systems in both two and three dimensions.

Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: experimental approaches to the determination of thermodynamic parameters.

Abstract: Many biologically important proteins bind nonspecifically, and often cooperatively, to single-or double-stranded nucleic acid lattices in discharging their physiological functions. This binding can generally be described in thermodynamic terms by three parameters: n, the binding site size; K, the intrinsic binding constant; omega, the binding cooperativity parameter. The experimental determination of these parameters often appears to be straightforward but can be fraught with conceptual and methodological difficulties that may not be readily apparent. In this paper we describe and analyze a number of approaches that can be used to measure these protein-nucleic acid interaction parameters and illustrate these methods with experiments on the binding of T4-coded gene 32 (single-stranded DNA binding) protein to various nucleic acid lattices. We consider the following procedures: (i) the titration of a fixed amount of lattice (nucleic acid) with added ligand (protein); (ii) the titration of a fixed amount of ligand with added lattice; (iii) the determination of ligand binding affinities at very low levels of lattice saturation; (iv) the analysis of ligand cluster size distribution on the lattice; (v) the analysis of ligand binding to lattices of finite length. The applicability and limitations of each approach are considered and discussed, and potential pitfalls are explicitly pointed out.