Age-related Liquefaction Resistance of Pleistocene Coastal Plain Sands in South Carolina

Soils of Pleistocene age in the South Carolina Coastal Plain have experienced liquefaction due to historic and pre-historic earthquakes. Numerous field and laboratory studies have shown that aged soil deposits maintain a greater resistance to liquefaction than younger soil deposits. The currently available methods for assessing liquefaction potential are based on cases in which soils are of Holocene age or younger (\u3c 10,000 yrs). The Pleistocene age soils that were tested and characterized varied in age from about 200,000 years old to 1,400,000 years old. Several sites were investigated using field methods that included the seismic cone penetration test, cone penetration test, standard penetration test, and flat plate dilatometer. Piezometers were installed at the sites. Undisturbed soil samples were retrieved from the subsurface and frozen ex situ to minimize sample disturbance during transportation and laboratory handling. The undisturbed samples were used for cyclic triaxial testing in the laboratory and were tested for shear wave velocity and compression wave velocity using in-cell transducers. Laboratory tests were performed to determine the specific gravity, grain size distribution, moisture content, unit weight, Atterberg limits, Unified Soil Classification, and visual-manual description. Optical petrography and scanning electron microscopy were used to determine the mineral content of the soils, to view grain characteristics, and to view microscopic features that were part of the soil aging process. Laboratory index tests showed that Pleistocene soils consisted predominately of poorly-graded fine sands, silty sands, and clayey sands. Shear wave velocities from the cyclic triaxial test specimens were comparable to the in situ shear wave velocities measured using the seismic cone penetration test. Compression wave velocities from the cyclic triaxial specimens were indicative of a saturated state in the soil prior to cyclic triaxial testing. The optical petrography showed that the dominant mineral in the sands consisted of quartz, which was accompanied by minor amounts of mica, feldspar, and opaque minerals. Scanning electron microscopy indicated the presence of kaolin, showed alteration features on quartz sand surfaces, and also showed the presence of soil fabric in the form of preferred grain orientation. Field testing using the standard penetration test and the cone penetration test indicated that the Pleistocene soils maintain a higher cyclic resistance ratio than the Holocene soils used in the current methods of analysis, however, the soils remain susceptible to liquefaction given expected peak ground accelerations where the cyclic stress ratio exceeds the cyclic resistance ratio. Based on the known ages of the soils, the two methods of analysis using the cone penetration test (Idriss and Boulanger, 2008 and Youd et al., 2001) showed out-of-sequence age versus cyclic resistance ratio for the Idriss and Boulanger method and a properly sequenced age versus cyclic resistance ratio for the Youd et al. method. The standard penetration test showed out-of-sequence age versus cyclic resistance ratio for all methods and the difference between the Holocene liquefaction curve and the Pleistocene liquefaction curve was less than the difference for the cone penetration tests. Field cyclic resistance ratios derived from the laboratory cyclic triaxial tests, which were adjusted for bi-directional motion and in situ stress, resided at or below the cyclic resistance ratios determined for the Pleistocene soils from the field tests and in some cases below the Holocene liquefaction curve

Actin Cytoskeleton Regulation by the Yeast NADPH Oxidase Yno1p Impacts Processes Controlled by MAPK Pathways

Reactive oxygen species (ROS) that exceed the antioxidative capacity of the cell can be harmful and are termed oxidative stress. Increasing evidence suggests that ROS are not exclusively detrimental, but can fulfill important signaling functions. Recently, we have been able to demonstrate that a NADPH oxidase-like enzyme (termed Yno1p) exists in the single-celled organism Saccharomyces cerevisiae. This enzyme resides in the peripheral and perinuclear endoplasmic reticulum and functions in close proximity to the plasma membrane. Its product, hydrogen peroxide, which is also produced by the action of the superoxide dismutase, Sod1p, influences signaling of key regulatory proteins Ras2p and Yck1p/2p. In the present work, we demonstrate that Yno1p-derived H2O2 regulates outputs controlled by three MAP kinase pathways that can share components: the filamentous growth (filamentous growth MAPK (fMAPK)), pheromone response, and osmotic stress response (hyperosmolarity glycerol response, HOG) pathways. A key structural component and regulator in this process is the actin cytoskeleton. The nucleation and stabilization of actin are regulated by Yno1p. Cells lacking YNO1 showed reduced invasive growth, which could be reversed by stimulation of actin nucleation. Additionally, under osmotic stress, the vacuoles of a ∆yno1 strain show an enhanced fragmentation. During pheromone response induced by the addition of alpha-factor, Yno1p is responsible for a burst of ROS. Collectively, these results broaden the roles of ROS to encompass microbial differentiation responses and stress responses controlled by MAPK pathway

Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1- Yeast Suppressed by a Dominant Mutation in ATP3

A yeast deletion mutation in the nuclear-encoded gene, AFO1, which codes for a mitochondrial ribosomal protein, led to slow growth on glucose, the inability to grow on glycerol or ethanol, and loss of mitochondrial DNA and respiration. We noticed that afo1- yeast readily obtains secondary mutations that suppress aspects of this phenotype, including its growth defect. We characterized and identified a dominant missense suppressor mutation in the ATP3 gene. Comparing isogenic slowly growing rho-zero and rapidly growing suppressed afo1- strains under carefully controlled fermentation conditions showed that energy charge was not significantly different between strains and was not causal for the observed growth properties. Surprisingly, in a wild-type background, the dominant suppressor allele of ATP3 still allowed respiratory growth but increased the petite frequency. Similarly, a slow-growing respiratory deficient afo1- strain displayed an about twofold increase in spontaneous frequency of point mutations (comparable to the rho-zero strain) while the suppressed strain showed mutation frequency comparable to the repiratory-competent WT strain. We conclude, that phenotypes that result from afo1- are mostly explained by rapidly emerging mutations that compensate for the slow growth that typically follows respiratory deficiency

Discovery and Functional Analysis of the Single-Celled Yeast NADPH Oxidase, Yno1

In this chapter, we describe the discovery of the NADPH oxidase gene and protein of the single-celled yeast Saccharomyces cerevisiae, Yno1. This enzyme was characterized with respect to mechanism of action, subcellular location, regulation of gene expression, and physiological function. Yno1 is not involved in defense and is not highly expressed in vegetatively growing cells. However, it is expressed in diverse stress situations. The signaling substance produced by Yno1 in conjunction with the superoxide dismutase Sod1, hydrogen peroxide, consequently leads through a change in the expression of target genes to the modulation of an adaptive cellular response. An example is the formation of pseudohyphae enabling invasive growth of the yeast cells, which is believed to aid in the utilization of new nutrients. The major role of Yno1 is in the switch of the mode of growth from vegetative budding to the formation of pseudohyphae, which are elongated chains of cells. Further examples that are described in this chapter are the response to osmotic stress and mating. All these pathways have in common that they exit the regular cell cycle and are associated with in parts enormous changes in cell morphology. This is accomplished involving a change in the structure of the actin cytoskeleton. Yno1 was shown to directly modulate the actin cytoskeleton

Severe influenza pneumonitis in children with inherited TLR3 deficiency

Autosomal recessive IRF7 and IRF9 deficiencies impair type I and III IFN immunity and underlie severe influenza pneumonitis. We report three unrelated children with influenza A virus (IAV) infection manifesting as acute respiratory distress syndrome (IAV-ARDS), heterozygous for rare TLR3 variants (P554S in two patients and P680L in the third) causing autosomal dominant (AD) TLR3 deficiency. AD TLR3 deficiency can underlie herpes simplex virus-1 (HSV-1) encephalitis (HSE) by impairing cortical neuron-intrinsic type I IFN immunity to HSV-1. TLR3-mutated leukocytes produce normal levels of IFNs in response to IAV. In contrast, TLR3-mutated fibroblasts produce lower levels of IFN-β and -λ, and display enhanced viral susceptibility, upon IAV infection. Moreover, the patients' iPSC-derived pulmonary epithelial cells (PECs) are susceptible to IAV. Treatment with IFN-α2b or IFN-λ1 rescues this phenotype. AD TLR3 deficiency may thus underlie IAV-ARDS by impairing TLR3-dependent, type I and/or III IFN-mediated, PEC-intrinsic immunity. Its clinical penetrance is incomplete for both IAV-ARDS and HSE, consistent with their typically sporadic nature.status: publishe

Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection

Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus. DBR1 encodes the only known RNA lariat debranching enzyme. We show that DBR1 expression is ubiquitous, but strongest in the spinal cord and brainstem. We also show that all DBR1 mutant alleles are severely hypomorphic, in terms of expression and function. The fibroblasts of DBR1-mutated patients contain higher RNA lariat levels than control cells, this difference becoming even more marked during HSV1 infection. Finally, we show that the patients\ue2\u80\u99 fibroblasts are highly susceptible to HSV1. RNA lariat accumulation and viral susceptibility are rescued by wild-type DBR1. Autosomal recessive, partial DBR1 deficiency underlies viral infection of the brainstem in humans through the disruption of tissue-specific and cell-intrinsic immunity to viruses. Autosomal recessive DBR1 deficiency underlies a cellular accumulation of RNA lariats, resulting in patient susceptibility to severe viral infections of the brainstem

Nuclear Fusion and Genome Encounter during Yeast Zygote Formation

When haploid cells of Saccharomyces cerevisiae are crossed, parental nuclei congress and fuse with each other. To investigate underlying mechanisms, we have developed assays that evaluate the impact of drugs and mutations. Nuclear congression is inhibited by drugs that perturb the actin and tubulin cytoskeletons. Nuclear envelope (NE) fusion consists of at least five steps in which preliminary modifications are followed by controlled flux of first outer and then inner membrane proteins, all before visible dilation of the waist of the nucleus or coalescence of the parental spindle pole bodies. Flux of nuclear pore complexes occurs after dilation. Karyogamy requires both the Sec18p/NSF ATPase and ER/NE luminal homeostasis. After fusion, chromosome tethering keeps tagged parental genomes separate from each other. The process of NE fusion and evidence of genome independence in yeast provide a prototype for understanding related events in higher eukaryotes