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Open Access Publications from the University of California

Scholarly Works (56 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2010)
Cell motility plays an essential role in many physiological and pathological processes, yet we still lack information about the spatio-temporal coordination between regulatory biochemical processes and mechanics of cell migration. This dissertation has investigated the mechanics of amoeboid cell migration through intensive analysis of the traction forces exerted and shapes adopted by single Dictyostelium discoideum cells migrating chemotactically, focusing on wild-type (WT) and contractility-defective cells lacking either protein myosin II (mhcA⁻) or the myosin II essential light chains (mlcE⁻). We have developed an improved traction force cytometry method to calculate cell traction stresses which considers the finite thickness of the substrate. We have shown that the strain energy exerted by locomoting cells on the substrate evolves quasi-periodically and correlates with cell length, and thus it can be used as a quantitative indicator of the cell motility cycle. The periodicity (T) of the oscillations in the traction forces correlates strongly with the average velocity of migration (V) of cells according to the hyperbolic law V T=[lambda], where the constant [lambda] is independent of the strain analyzed and corresponds to the average distance a cell travels per cycle. Given the quasi-periodic character of both cell length and strain energy, we have performed a phase statistical analysis to obtain a spatio-temporal representation of the canonical motility cycle divided into four phases: protrusion, contraction, retraction, and relaxation. This analysis has elucidated the role that protein myosin II plays in enhancing the kinetics of the four stages of the cycle and in controlling the spatial distribution of the traction forces regulating that process. We have used principal component analysis to dissect the mechanics of locomotion of amoeboid cells into a reduced set of dominant components of cellular traction forces and shape changes. The dominant traction force component accounts for 40% of the strain energy performed by these cells, and its temporal evolution correlates with the quasi-periodic variations of cell length and strain energy exerted on the substrate. Finally, we have developed two analytic assays for the calculation of cell traction stresses in configurations of interest to further understand the mechanosensing machinery of cells
    Cover page: Force and shape coordination in amoeboid cell motility
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2018)
    In temperate climates, transmission of West Nile virus (WNV) is detectable rarely during the coldest months (late fall through early spring), yet the virus has reappeared consistently during the next warm season. Several mechanisms may contribute to WNV persistence through winter, including bird-to-bird transmission among highly viremic species. Here we consider whether, under realistic scenarios supported by field and laboratory evidence, a winter bird community could sustain WNV through the winter in the absence of mosquitoes. With this purpose we constructed a deterministic model for a community of susceptible birds consisting of communally roosting crows, raptors and other birds. We simulated WNV introduction and subsequent transmission dynamics during the winter under realistic initial conditions and model parameterizations, including plausible contact rates for roosting crows. Model results were used to determine whether the bird community could yield realistic outbreaks that would result in WNV infectious individuals at the end of the winter, which would set up the potential for onward horizontal transmission into summer. Our findings strongly suggest that winter crow roosts could allow for WNV persistence through the winter, and our model results provide synthesis to explain inconclusive results from field studies on WNV overwintering in crow roosts.
      • Thesis
      • Peer Reviewed
      UC Berkeley Electronic Theses and Dissertations (2022)

      The genitalia of males evolves rapidly and divergently in most animal groups. Explanations for this pattern typically evoke mechanisms of post-copulatory sexual selection, such as sperm competition, cryptic female choice, and sexual conflict. While the fossil record often allows for the documentation of patterns of evolutionary change, the predominantly soft-tissue nature of the genitalia is rarely observed in the fossil record. However, the baculum (os penis or os priapi), a bone located at the distal end of the penis of most mammalian species, offers the opportunity of examining the evolution of male genitalia, and thus may contribute to our understanding of post-copulatory sexual selection and the evolution of reproductive biology within mammals. Bacula are rare in the fossil record and thus difficult to be identified and classified when in isolation. Nonetheless, sometimes they are preserved in association with other skeletal material allowing accurate species-level taxonomic assignments. Here, I focus on the bacula of the Canidae, which consists of three subfamilies, the extant Caninae (wolves, coyotes, jackals, foxes, etc.) and two extinct subfamilies, the Borophaginae and the Hesperocyoninae, both of which have rich fossil records that reveal high taxonomic and ecomorphological diversity.

      This dissertation consists of four chapters. In the first chapter, I briefly contextualize the theory of post-copulatory sexual selection and then I review the evidence that it acts on the baculum from a combination of studies that used functional, experimental, and comparative data.

      In Chapter 2 I describe the morphology of fossil bacula of five species of Borophaginae. These descriptions add substantial knowledge regarding the baculum of extinct canids, which was previously known for only two extinct species. The five bacula were found associated with other skeletal elements that were already described in the literature and have enabled identification to the species level. These borophagine bacula share many similarities with extant canines such as being robust, having a urethral groove, and a simple distal end. Because these features have been associated with reproductive strategies in extant carnivorans it is possible to use the baculum of Borophaginae to draw implications for their reproductive biology.

      In Chapter 3 I quantify variation in morphology of the baculum of canids in 2D using elliptic Fourier analysis. First, I show that the baculum of 26 (out of ~35) extant species is morphologically conserved and that the intraspecific morphological variation is larger than the interspecific differences, and therefore it is difficult to distinguish among species using bacular morphology alone. However, four extinct canids that have completely preserved bacula show morphological differences from the extant canids. In particular, one morphological feature, the primary curvature of the baculum, differentiates the baculum of three stem group canids from those of extant species. I used phylogenetic ancestral state reconstruction to show that it would be unlikely to predict the arched curvature of the baculum observed in the stem fossils from the morphology observed in extant species.

      Finally, in Chapter 4, I examine the relative size of the canid baculum. Using a linear regression corrected for phylogeny, I show a slightly negative allometric relationship between baculum length and body size in canids.Further, an isometric relationship cannot be rejected. These results are in contrast with the strong negative allometric relationships that have been described for other mammalian clades. Of particular interest are the relative size of fossil bacula. The baculum of Hesperocyon gregarius, the only known in the Hesperocyoninae, is significantly longer than expected for its body size and suggests a different allometric curve for this species in comparison with other canid groups. The bacula of two borophagine species are within the same allometric line of extant canids. Finally, the baculum of the extinct dire wolf (Aenocyon dirus) is longer than expected based on its body size, suggesting that its reproductive strategies could be different from those of extant canines.

        Cover page: The evolution of the baculum in the extant and extinct Canidae
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (1986)
        The colonization of the New World by the Palearctic species Drosophila subobscura was first detected in 1978 in South America and around 1982 in western North America. The ensuing dramatic expansion of the species, in territory as well as numbers, provides an opportunity for studying evolution in a scale rarely possible. We have used 10 restriction endonucleases to analyze the mitochondrial DNA (mtDNA) of individuals from 23 widely dispersed localities. Only two mtDNA composite morphs have been detected in the Americas. None of the two morphs has been found in Africa, and only one in the Atlantic islands; but both are widespread in Europe, which provides no clue of the precise geographic origin of the colonizers. The amount of nucleotide-substitution polymorphism detected in D. subobscura is typical for animals, but it is greater in the Old than in the New World, presumably due to the recent colonization by a limited number of colonizers. Assuming standard evolutionary rates of mtDNA base substitution, the mtDNA morphs found in D. subobscura can be traced to a single one that existed no less than one million years ago. We argue against the inference that the D. subobscura flies now living descend from only one or a few females that lived at that time. This type of inference, which we call the "Mother Eve hypothesis," has been made to conclude that the human population went through a severe constriction about 200,000 years ago, so that all living humans descend from only one or a few women who lived at that time. The Mother Eve hypothesis is fallacious.
        • 1 supplemental PDF
        Cover page: Evolution of mitochondrial DNA in Drosophila subobscuraCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (1994)
        A Cu/Zn superoxide dismutase-encoding gene (Sod) from Drosophila willistoni was cloned and sequenced. The gene shows a typical structure for a fruit-fly Sod gene, with a coding region of 462 bp in two exons separated by a 417-bp intron. Comparison of the Sod sequences from D. willistoni and D. melanogaster suggests that these species are only remotely related. Downstream from the Sod gene, there is an ORF on the opposite strand that putatively encodes the last exon of an unidentified gene. The polyadenylation signals of the two genes are separated by only 61 bp in D. willistoni, conforming to the common picture of compact dipteran genomes.
          Cover page: Characterization of a Cu/Zn Superoxide dismutase-encoding gene region in Drosophila willistoniCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2024)
          Placerias hesternus, a Late Triassic dicynodont, is one of the last megafaunal synapsids of the Mesozoic. The species has a tusk-like projection on its maxillary bone, known as the caniniform process. This process has been hypothesized to be sexually dimorphic since the 1950s, however this claim has not been thoroughly investigated quantitatively. Here, we examined maxillae, premaxillae, quadrates, and fibulae from a single population from the Placerias Quarry in the Blue Mesa Member of the Chinle Formation, near St. Johns, Arizona, USA to determine if the caniniform process is dimorphic. We made a total of 25 measurements from the four bones and used a maximum likelihood framework to compare the fit of unimodal versus bimodal distributions for each set of measurements. Our results from complete maxillae reveal that the caniniform process has two distinct morphs, with a shorter and longer form. This interpretation is substantiated both by strong statistical support for bimodal distribution of caniniform lengths, and by clustering analysis that clearly distinguishes two morphs for the maxillae. Clustering analysis also shows support for potential dimorphism in the shape of the quadrate. However, no measurements from elements other than the maxilla have a strong likelihood of bimodal distribution. These results support the long-standing hypothesis that the caniniform in Placerias was dimorphic. Alternative explanations to sexual dimorphism that could account for the dimorphism among these fossils include the presence of juveniles in the sample or time-averaged sampling of a chronospecies, but both have been previously rejected for the Placerias Quarry population. The lack of strong dimorphism in non-maxilla elements and increased variation in caniniform length of the large-caniniform morph suggest that the caniniform is a secondary sexual trait, possibly used in intraspecific competition.
            Cover page: Quantitative evidence for dimorphism suggests sexual selection in the maxillary caniniform process of Placerias hesternus.
            • Article
            • Peer Reviewed
            Dermatology Online Journal, Volume 17, Issue 5 (2011)
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2001)
              In Shaker K(+) channel, the amino terminus deletion Delta6-46 removes fast inactivation (N-type) unmasking a slow inactivation process. In Shaker Delta6-46 (Sh-IR) background, two additional mutations (T449V-I470C) remove slow inactivation, producing a noninactivating channel. However, despite the fact that Sh-IR-T449V-I470C mutant channels remain conductive, prolonged depolarizations (1 min, 0 mV) produce a shift of the QV curve by about -30 mV, suggesting that the channels still undergo the conformational changes typical of slow inactivation. For depolarizations longer than 50 ms, the tail currents measured during repolarization to -90 mV display a slow component that increases in amplitude as the duration of the depolarizing pulse increases. We found that the slow development of the QV shift had a counterpart in the amplitude of the slow component of the ionic tail current that is not present in Sh-IR. During long depolarizations, the time course of both the increase in the slow component of the tail current and the change in voltage dependence of the charge movement could be well fitted by exponential functions with identical time constant of 459 ms. Single channel recordings revealed that after prolonged depolarizations, the channels remain conductive for long periods after membrane repolarization. Nonstationary autocovariance analysis performed on macroscopic current in the T449V-I470C mutant confirmed that a novel open state appears with increasing prepulse depolarization time. These observations suggest that in the mutant studied, a new open state becomes progressively populated during long depolarizations (>50 ms). An appealing interpretation of these results is that the new open state of the mutant channel corresponds to a slow inactivated state of Sh-IR that became conductive.
                Cover page: A Conducting State with Properties of a Slow Inactivated State in a Shaker K+ Channel Mutant
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2015)
                Wildlife are increasingly recognized as important biological reservoirs of zoonotic species of Cryptosporidium that might contaminate water and cause human exposure to this protozoal parasite. The habitat range of the yellow-bellied marmot (Marmota flaviventris) overlaps extensively with the watershed boundaries of municipal water supplies for California communities along the foothills of the Sierra Nevada. We conducted a cross-sectional epidemiological study to estimate the fecal shedding of Cryptosporidium oocysts by yellow-bellied marmots and to quantify the environmental loading rate and determine risk factors for Cryptosporidium fecal shedding in this montane wildlife species. The observed proportion of Cryptosporidium positive fecal samples was 14.7% (33/224, positive number relative to total number samples) and the environmental loading rate was estimated to be 10,693 oocysts animal(-1) day(-1). Fecal shedding was associated with the elevation and vegetation status of their habitat. Based on a portion of the 18s rRNA gene sequence of 2 isolates, the Cryptosporidium found in Marmota flaviventris were 99.88%-100% match to multiple isolates of C. parvum in the GenBank.
                  Cover page: Elevation and vegetation determine Cryptosporidium oocyst shedding by yellow-bellied marmots (Marmota flaviventris) in the Sierra Nevada Mountains
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (1997)
                  Prolonged depolarization induces a slow inactivation process in some K+ channels. We have studied ionic and gating currents during long depolarizations in the mutant Shaker H4-Delta(6-46) K+ channel and in the nonconducting mutant (Shaker H4-Delta(6-46)-W434F). These channels lack the amino terminus that confers the fast (N-type) inactivation (Hoshi, T., W.N. Zagotta, and R.W. Aldrich. 1991. Neuron. 7:547-556). Channels were expressed in oocytes and currents were measured with the cut-open-oocyte and patch-clamp techniques. In both clones, the curves describing the voltage dependence of the charge movement were shifted toward more negative potentials when the holding potential was maintained at depolarized potentials. The evidences that this new voltage dependence of the charge movement in the depolarized condition is associated with the process of slow inactivation are the following: (a) the installation of both the slow inactivation of the ionic current and the inactivation of the charge in response to a sustained 1-min depolarization to 0 mV followed the same time course; and (b) the recovery from inactivation of both ionic and gating currents (induced by repolarizations to -90 mV after a 1-min inactivating pulse at 0 mV) also followed a similar time course. Although prolonged depolarizations induce inactivation of the majority of the channels, a small fraction remains non-slow inactivated. The voltage dependence of this fraction of channels remained unaltered, suggesting that their activation pathway was unmodified by prolonged depolarization. The data could be fitted to a sequential model for Shaker K+ channels (Bezanilla, F., E. Perozo, and E. Stefani. 1994. Biophys. J. 66:1011-1021), with the addition of a series of parallel nonconducting (inactivated) states that become populated during prolonged depolarization. The data suggest that prolonged depolarization modifies the conformation of the voltage sensor and that this change can be associated with the process of slow inactivation.
                    Cover page: Correlation between Charge Movement and Ionic Current during Slow Inactivation in Shaker K+ Channels
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