Showing papers by "University of California, Davis published in 1986"

An all atom force field for simulations of proteins and nucleic acids.

Abstract: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.

Flow in porous media I: A theoretical derivation of Darcy's law

Abstract: Stokes flow through a rigid porous medium is analyzed in terms of the method of volume averaging. The traditional averaging procedure leads to an equation of motion and a continuity equation expressed in terms of the volume-averaged pressure and velocity. The equation of motion contains integrals involving spatial deviations of the pressure and velocity, the Brinkman correction, and other lower-order terms. The analysis clearly indicates why the Brinkman correction should not be used to accommodate ano slip condition at an interface between a porous medium and a bounding solid surface.

Constant-pressure equations of motion

Abstract: Some of the differences among several alternative formulations of constant-pressure molecular dynamics are described. The formulations all agree in the large-system limit, but differ for small systems.

Two simple methods for detecting acrosome‐reacted human sperm

Abstract: We describe two methods for detecting acrosome reactions of human sperm at the light microscopic level. The techniques include the use of a supravital stain to detect dead sperm in order to differentiate between “physiological” and “degenerative” acrosome reactions. Sperm are incubated with the supravital stain Hoechst 33258 (a fluorescent DNA-binding dye with limited membrane permeability), washed, suspended in 95% ethanol for fixation and permeabilization, and dried onto slides. The sperm are then labeled either by indirect immunofluorescence using rabbit anti-human sperm antiserum or with fluoresceinated Pisum sativum agglutinin (PSA). Both probes intensely label the acrosomal region of acrosome-intact sperm. Electron microscopy revealed the major site of PSA binding to be the acrosomal contents. Acrosome-reacted sperm have diminished acrosomal labeling by both probes; sperm with nuclei labeled by Hoechst stain are considered nonviable, and are excluded from the assay. Both assays are rapid, give similar results, and detect an increase in acrosome reactions following exposure to the ionophore A23187.

Autolytic Processing of Dimeric Plant Virus Satellite RNA

Abstract: Associated with some plant viruses are small satellite RNA's that depend on the plant virus to provide protective coat protein and presumably at least some of the proteins necessary for satellite RNA replication. Multimeric forms of the satellite RNA of tobacco ringspot virus are probable in vivo precursors of the monomeric satellite RNA. Evidence is presented for the in vitro autolytic processing of dimeric and trimeric forms of this satellite RNA. The reaction generates biologically active monomeric satellite RNA, apparently is reversible to form dimeric RNA from monomeric RNA, and does not require an enzyme for its catalysis.

Water flow and solute transport processes in the unsaturated zone

Abstract: This paper gives a review of our current conceptual understanding of the basic processes of water flow and chemical transport in the untsaturated (vadose) zone and of various deterministic mathematical models that are being used to describe these processes. During the past few decades, tremendous effort has been directed toward unravelling the complexities of various interactive physical, chemical, and microbiological mechanisms affecting unsaturated flow and transport, with contributions being made by soil scientists, geochemists, hydrologists, soil microbiologists, and others. Unfortunately, segmented, disciplinary research has contributed to a lack of experimental and theoretical understanding of the vadose zone, which, in turn, has precluded the accurate prediction and management of flow and contaminant transport through it. Thus a more unified and interdisciplinary approach is needed that considers the most pertinent physical, chemical, and biological processes operative in the unsaturated zone. Challenges for both fundamental and applied researchers to reveal the intricacies of the zone and to integrate these with currently known concepts are numerous, as is the urgency for progress inasmuch as our soil and ground water resources are increasingly subjected to the dangers of long-term pollution. Specific research areas in need of future investigation are outlined.

Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach

Abstract: We present a numerical cladistic (parsimony) analysis of seed plants plus progymnosperms, using characters from all parts of the plant body, outgroup comparison, and a method of character coding that avoids biases for or against alternative morphological theories. The robustness of the results was tested by construction of alternative trees and analysis of subsets of the data. These experiments show that although some clades are strongly supported, they can often be related to each other in very different but nearly equally parsimonious ways, apparently because of extensive homoplasy. Our results support Rothwell’s idea that coniferopsids are derived fromCallistophyton- like platyspermic seed ferns with saccate pollen, but the hypothesis that they evolved fromArchaeopteris- like progymnosperms and the seed arose twice is nearly as parsimonious. Meyen’s division of seed plants into radiospermic and primarily and secondarily platyspermic lines is highly unparsimonious, but his suggestion that ginkgos are related to peltasperms deserves attention. Angiosperms belong among the platyspermic groups, as the sister group of Bennettitales,Pentoxylon, and Gnetales, and this “anthophyte” clade is best related toCaytonia and glossopterids, although relationships with other combinations of Mesozoic seed fern taxa are nearly as parsimonious. These results imply that the angiosperm carpel can be interpreted as a modified pinnate sporophyll bearing anatropous cupules (=bitegmic ovules), while gnetalian strobili are best interpreted as aggregations of highly reduced bennettitalian flowers, as anticipated by Arber and Parkin and Crane. Our most parsimonious trees imply that the angiosperm line (though not necessarily all its modern features) extended back to the Triassic, but a later derivation of angiosperms from some species ofCaytonia or Bennettitales, which would be nearly as parsimonious, should also be considered. These results raise the possibility that many features considered key adaptations in the origin and rise of angiosperms (insectpollinated flowers, rapid reproduction, drought tolerance) were actually inherited from their gymnospermous precursors. The explosive diversification of angiosperms may instead have been a consequence of carpel closure, resulting in increased speciation rates due to potential for stigmatic isolating mechanisms and/or new means of dispersal. DNA sequencing of extant plants and better information on anatomy, chemistry, sporophyll morphology, and embryology of Bennettitales and Caytoniales and the morphological diversity of Mesozoic anthophytes could provide critical tests of relationships.

Floral evolution: Attractiveness to pollinators increases male fitness

Abstract: Because availability of resources often limits seed or fruit set, increased visits by pollinators may not always lead to increases in maternal reproduction. This observation has led evolutionary biologists to hypothesize that a plant's ability to attract pollinators may have its primary impact on male fitness achieved through the fertlization of ovules. This interpretation of angiosperm reproductive ecology is supported by field experiments. Pollinating insects strongly discriminated between two Mendelian petal-color morphs in Raphanus raphanistrum, a widespread, self-incompatible crucifer. In experimental populations composed of petal-color homozygotes. color discrimination by naturally occurring pollinators had no statistically significant effect on relative maternal function (fruit and seed production) in the two morphs. In contrast, yellow-flowered individuals were far more successful as fathers (pollen donors) than were the less visited whites. These results suggest that the evolution of floral signals such as petal color may be driven primarily by selection on male function.

Unidirectional incompatibility between populations of drosophila simulans

Abstract: Drosophila simulans females from a strain collected at Watsonville, CA produce very few offspring when mated with males from a strain collected at Riverside 510 km away. This incompatibility does not exist in the reciprocal cross. In the incompatible cross, mating and oviposition are normal, but eggs fail to hatch. A survey of other California populations indicates that unidirectional incompatibility is widespread. The incompatibility is maternally inherited over one generation. Using older Riverside males or rearing the strains at 28°C suppresses incompatibility. Culturing the strains on medium with tetracycline restores compatibility, suggesting the involvement of a microorganism.

Reduction of Serum Testosterone Levels During Chronic Glucocorticoid Therapy

Abstract: The effect of chronic glucocorticoid therapy on serum testosterone levels was studied in men aged 67 +/- 4 (SD) years with chronic pulmonary disease. The serum testosterone level was reduced in 14 of 16 patients to a mean value of 211 +/- 93 ng/dL, compared with 449 +/- 111 ng/dL in 11 age- and disease-matched control patients (p less than 0.001). The corticosteroid dosage and the serum testosterone level were inversely related (r = -0.78). Testosterone binding to serum proteins was not significantly affected. Basal gonadotrophin levels were not elevated while their secretory responses to exogenous gonadotrophin-releasing hormone (GnRH) were intact. We conclude that glucocorticoid therapy commonly reduces serum testosterone levels in older men due to alteration of hypothalamic GnRH secretion.

Combustion synthesis of titanium carbide: Theory and experiment

Abstract: The combustion synthesis of titanium carbide from elemental powders has been theoretically and experimentally studied as a model system for self -propagating high temperature synthesis (SHS) of refractory compounds. Calculations of the adiabatic temperature of combustion of graphite and titanium powders to form TiC x have been made to show the effects of stoichiometry, dilution and the initial temperature of the reactants. Experimental observations on the stability of the combustion front, combined with theoretical predictions, lead to an estimated activation energy of ≤ 117 kJ mol−1 for the process. This value is at least a factor of about four too low to correspond to a diffusion-controlled process. The combustion of graphite and titanium powders was accompanied by the evolution of gases whose primary constituent was found to be hydrogen. This observation was attributed to the reaction of adsorbed moisture with titanium powder. The titanium carbide phase resulting from the combustion of compacted mixed powders of the elements was highly porous (∼ 50% porosity). It can be obtained in high density (∼5% porosity) when pressure is applied during the combustion process.

Flow in Porous Media II: The Governing Equations for Immiscible, Two-Phase Flow

Abstract: The Stokes flow of two immiscible fluids through a rigid porous medium is analyzed using the method of volume averaging. The volume-averaged momentum equations, in terms of averaged quantities and spatial deviations, are identical in form to that obtained for single phase flow; however, the solution of the closure problem gives rise to additional terms not found in the traditional treatment of two-phase flow. Qualitative arguments suggest that the nontraditional terms may be important whenμβ/μγ is of order one, and order of magnitude analysis indicates that they may be significant in terms of the motion of a fluid at very low volume fractions. The theory contains features that could give rise to hysteresis effects, but in the present form it is restricted to static contact line phenomena.

Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA

Abstract: Small satellite RNAs1–5 of plant viruses depend on the presence of a supporting RNA virus for their propagation in vivo. Replication of the 359–nucleotide-long6 satellite RNA of tobacco ringspot virus (STobRV RNA) is detected only in tissue infected with tobacco ringspot virus (TobRV). STobRV RNA becomes encapsidated in TobRV coat protein and acts as a parasite of TobRV, reducing its accumulation and the severity of symptoms that it induces. Here we report the transcription in vitro of a circularly permuted, complementary DNA clone of STobRV RNA oriented so as to produce RNA that is complementary to the encapsidated, (+) polarity STobRV RNA. Like STobRV (+)RNA7, this dimeric, circularly permuted STobRV (−)RNA cleaves autolytically. Cleavage is at two identical sites generating monomeric-length RNA and two terminal fragments. The new termini are 5′-hydroxyl and 2′:3′-cyclic phosphodiester groups. The RNAs ligate spontaneously to give linear and, from the monomers, circular molecules. Replication of STobRV RNA may require these autoly-sis and ligation reactions, which, at least in vitro, occur without enzyme catalysis.

The genetic control and consequences of kin recognition by the larvae of a colonial marine invertebrate

Abstract: The evolution of altruism, cooperation and sociality should be favoured by mechanisms promoting interactions among relatives1,2. In turn, the opportunity for such interactions should be enhanced where related individuals are spatially associated. The simplest explanation for association of kin invokes philopatric, or limited, dispersal3. Alternatively, kin recognition—which is known from a broad array of taxa4,5—can produce similar associations. Neither the prevalence of kin recognition, nor aggregations of kin, are by themselves sufficient to demonstrate that kin recognition plays an important role in the production of nonrandom associations of relatives. To have such a role, kin recognition must promote or inhibit associations of kin beyond the effects of other processes, notably dispersal, that modify spatial patterns. Here we report the results of field experiments showing that sibling planktonic larvae of the sessile colonial ascidian Botryllus schlosseri settle in aggregations that are much stronger than expected from dispersal distance effects alone. Laboratory experiments indicate that larvae distinguish kin on the basis of shared alleles at a highly polymorphic histocompatibility locus known to regulate fusion between adult colonies. This kin recognition mechanism, along with limited dispersal of larvae, promotes co-settlement of histocompatible individuals. Consequently, the probability of fusion between adult colonies is far greater than that expected if larvae settled randomly

Measurement of spectral correlation

Abstract: Various methods for measurement/computation of spectral correlation functions for time series that exhibit cyclostationarity are described in a unifying theoretical framework. Some of these are amenable to digital hardware or software implementations, others are amenable to analog electrical or optical implementations, and other implementation types used for conventional spectral analysis are also possible. The interaction among reliability and temporal, spectral, and cycle resolutions is determined. Novel problems of computational complexity, cycle leakage and aliasing, cycle resolution, and cycle phasing are discussed. Sample spectral correlation functions are calculated with digital software for several simulated signals.

Induction of the acrosome reaction in human spermatozoa by a fraction of human follicular fluid

Abstract: Human ejaculated spermatozoa were washed through a Percoll gradient, preincubated for 10 hr in a defined medium containing serum albumin, and then induced to undergo rapid acrosome reactions by addition of human follicular fluid or a Sephadex G-75 column fraction of the fluid. Induction by follicular fluid did not occur when the spermatozoa were preincubated for only 0 or 5 hr. The reactions were detected by indirect immunofluorescence using a monoclonal antibody directed against the human sperm acrosomal region. The percentage of acrosomal loss counted by transmission electron microscopy agreed with that counted by immunofluorescence. The apparent molecular weight of the Sephadex G-75 fraction containing the peak of acrosome reaction-inducing activity was 45,000 ± 4,200 (SD). The occurrence of physiological acrosome reactions was supported by: assessing motility (no significant loss of motility occurred during the treatment period when sperm were preincubated with bovine serum albumin), transmission electron microscopy (the ultrastructural criteria for the acrosome reaction were met), and zona-free hamster oocyte binding and penetration (spermatozoa pretreated with the active fraction of follicular fluid, then washed and incubated with oocytes, showed significantly greater binding to and penetration of oocytes). The stimulation of the acrosome reaction by follicular fluid is apparently not due to blood serum contamination; treatment of preincubated spermatozoa with sera from the follicular fluid donors had no effect on the spermatozoa. The nature of the active component(s) in that fraction is currently being investigated.

The meninges in human development

Abstract: The brain and cranial meninges were studied in 61 serially sectioned embryos of stages 8-23. Much earlier stages than those examined by previous authors provided a more comprehensive view of meningeal development. As a result, the possible and probable sources of the cranial and spinal meninges are believed to be: (a) prechordal plate, (b) unsegmented paraxial (parachordal) mesoderm, (c) segmented paraxial (somitic) mesoderm, (d) mesectoderm (neural crest), (e) neurilemmal cells (neural crest), and (f) neural tube. Some of these sources (a, b, d) pertain to the cranial meninges, others (c, d, e) to the spinal coverings. The first of the future dural processes to develop is the tentorium cerebelli, which, at the end of the embryonic period proper, differs considerably in shape and composition from the later fetal and postnatal tentorium. The embryonic dural limiting layer (Duragrenzschicht) probably corresponds to the interface layer of the adult meninges. The appropriate literature was reviewed and summarized.