Understanding the Behavior of Embankment Dams Under Blast Loading

This purpose of this study is to investigate the deformation-induced stability of earthen embankment dams to explosive airblast loading. This study specifically investigated the effects of close-in explosive airblast loads on the downstream toe of a homogeneous earthen embankment dam composed of cohesive soils. Small-scale explosive airblast experiments were performed on cohesive soils to obtain an experimental data set with which to compare numerical analyses. Experimental measurements included crater geometry, ground vibration energy, and air overpressure from the blast events. Laboratory tests were conducted on the experiment soils to obtain engineering properties including shear strength and compressibility indices. Finite element simulations of airblast loading on a cohesive soil embankment dam were performed using Multi-Material Arbitrary Lagrangian Eulerian (MM-ALE) methods in LS-DYNA and compared to experimental results. Blast effects on varying reservoir levels and engineered drainage were investigated to determine the impact on dam stability. The airblast simulations created craters on the downstream slope and reduced the toe length. While larger explosive masses removed more material, crater dimensions did not significantly increase with explosive mass due to energy loss in air. Circular slip surfaces intersected the crater and reduced stability for dams with no engineered drainage. A horizontal toe drain effectively lowered the phreatic surface away from the blast crater and increased structural stability. Failure (as defined by a factor of safety less than unity) was induced in dams with no engineered drainage at reservoir levels of 80 percent reservoir capacity or greater. Dams with lower reservoir levels did not experience failure from an explosive airblast event. In addition, failure could not be induced in dams with engineered drainage. It was concluded that explosive airblasts posed a possibility of slope failure only for dams with no engineered drainage that were close to full reservoir capacity

DNA mismatch repair and response to oxidative stress in the extremely halophilic archaeon Halobacterium sp. strain NRC-1

Halobacterium is an extremely halophilic archaeon that has homologs of the key proteins, MutS and MutL used in DNA mismatch repair in both Bacteria and Eukarya. To determine whether Halobacterium has a functional mismatch repair system, we calculated the spontaneous mutation rate and determined the spectrum of mutation in Halobacterium using fluctuation tests targeting genes of the UMP biosynthesis pathway and we performed a sequence analysis of the mutated genes. We found that Halobacterium has a low incidence of mutation indicating that some form of DNA repair is taking place, however the mutational spectrum in the Archaea is different from that seen in Bacteria and Eukarya suggesting differences between the archaeal, bacterial, and eukaryal repair systems. To test if the MutS and MutL homologs in Halobacterium are essential for the low incidence of mutation, we used in-frame targeted gene deletion and characterized the mutant phenotypes. We found no phenotypic differences between the mutant strains and the background strain indicating that the MutS and MutL protein homologs found in Halobacterium are not essential for maintaining the low incidence of mutation. Since much of the replication and repair processes in Halobacterium are similar to that of Eukarya, deciphering how MMR occurs in the Archaea could lead to a new understanding of pathway interactions based on the recruitment of repair enzymes from both bacterial and eukaryal counterparts. In addition, we elucidated the oxidative stress response in Halobacterium to hydrogen peroxide and paraquat using a whole genome transcriptional array, in-frame targeted gene deletion, and survival analysis of mutant phenotypes. We showed an overall effort of the cells to scavenge reactive oxygen species and repair damages to the DNA, which has also been seen in response to gamma irradiation. From the mutant analyses, we were able to deduce that Sod1 and PerA proteins played an essential role in removing oxidative stress in Halobacterium. Deciphering the stress response to hydrogen peroxide and paraquat in an extreme halophile that lives in an environment subject to long periods of desiccation can further our understanding of the DNA repair and protection systems to oxidative stress in general

MutS and MutL Are Dispensable for Maintenance of the Genomic Mutation Rate in the Halophilic Archaeon Halobacterium salinarum NRC-1

BACKGROUND: The genome of the halophilic archaeon Halobacterium salinarum NRC-1 encodes for homologs of MutS and MutL, which are key proteins of a DNA mismatch repair pathway conserved in Bacteria and Eukarya. Mismatch repair is essential for retaining the fidelity of genetic information and defects in this pathway result in the deleterious accumulation of mutations and in hereditary diseases in humans. METHODOLOGY/PRINCIPAL FINDINGS: We calculated the spontaneous genomic mutation rate of H. salinarum NRC-1 using fluctuation tests targeting genes of the uracil monophosphate biosynthesis pathway. We found that H. salinarum NRC-1 has a low incidence of mutation suggesting the presence of active mechanisms to control spontaneous mutations during replication. The spectrum of mutational changes found in H. salinarum NRC-1, and in other archaea, appears to be unique to this domain of life and might be a consequence of their adaption to extreme environmental conditions. In-frame targeted gene deletions of H. salinarum NRC-1 mismatch repair genes and phenotypic characterization of the mutants demonstrated that the mutS and mutL genes are not required for maintenance of the observed mutation rate. CONCLUSIONS/SIGNIFICANCE: We established that H. salinarum NRC-1 mutS and mutL genes are redundant to an alternative system that limits spontaneous mutation in this organism. This finding leads to the puzzling question of what mechanism is responsible for maintenance of the low genomic mutation rates observed in the Archaea, which for the most part do not have MutS and MutL homologs

Cloning, Purification, and Partial Characterization of the Halobacterium sp. NRC-1 Minichromosome Maintenance (MCM) Helicase

The MCM gene from the archaeon Halobacterium, with and without its intein, was cloned into an Escherichia coli expression vector, overexpressed and the protein was purified and antibodies were generated. The antibodies were used to demonstrate that in vivo only the processed enzyme, without the intein, could be detected

Coordination of frontline defense mechanisms under severe oxidative stress

Inference of an environmental and gene regulatory influence network (EGRINOS) by integrating transcriptional responses to H2O2 and paraquat (PQ) has revealed a multi-tiered oxidative stress (OS)-management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids and gas vesicles, metal trafficking, and various other aspects of metabolism.ChIP-chip, microarray, and survival assays have validated important architectural aspects of this network, identified novel defense mechanisms (including two evolutionarily distant peroxidase enxymes), and showed that general transcription factors of the transcription factor B family have an important function in coordinating the OS response (OSR) despite their inability to directly sense ROS.A comparison of transcriptional responses to sub-lethal doses of H2O2 and PQ with predictions of these responses made by an EGRIN model generated earlier from responses to other environmental factors has confirmed that a significant fraction of the OSR is made up of a generalized component that is also observed in response to other stressors.Analysis of active regulons within environment and gene regulatory influence network for OS (EGRINOS) across diverse environmental conditions has identified the specialized component of oxidative stress response (OSR) that is triggered by sub-lethal OS, but not by other stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of γ rays

Identification of a novel gene regulating amygdala-mediated fear extinction.

Recent years have seen advances in our understanding of the neural circuits associated with trauma-related disorders, and the development of relevant assays for these behaviors in rodents. Although inherited factors are known to influence individual differences in risk for these disorders, it has been difficult to identify specific genes that moderate circuit functions to affect trauma-related behaviors. Here, we exploited robust inbred mouse strain differences in Pavlovian fear extinction to uncover quantitative trait loci (QTL) associated with this trait. We found these strain differences to be resistant to developmental cross-fostering and associated with anatomical variation in basolateral amygdala (BLA) perineuronal nets, which are developmentally implicated in extinction. Next, by profiling extinction-driven BLA expression of QTL-linked genes, we nominated Ppid (peptidylprolyl isomerase D, a member of the tetratricopeptide repeat (TPR) protein family) as an extinction-related candidate gene. We then showed that Ppid was enriched in excitatory and inhibitory BLA neuronal populations, but at lower levels in the extinction-impaired mouse strain. Using a virus-based approach to directly regulate Ppid function, we demonstrated that downregulating BLA-Ppid impaired extinction, while upregulating BLA-Ppid facilitated extinction and altered in vivo neuronal extinction encoding. Next, we showed that Ppid colocalized with the glucocorticoid receptor (GR) in BLA neurons and found that the extinction-facilitating effects of Ppid upregulation were blocked by a GR antagonist. Collectively, our results identify Ppid as a novel gene involved in regulating extinction via functional actions in the BLA, with possible implications for understanding genetic and pathophysiological mechanisms underlying risk for trauma-related disorders

Invasive Haemophilus influenzae Disease, Europe, 1996–2006

Incidence and case-fatality ratios are higher for non–type b than for type b infection

Phosphoinositide-binding interface proteins involved in shaping cell membranes

The mechanism by which cell and cell membrane shapes are created has long been a subject of great interest. Among the phosphoinositide-binding proteins, a group of proteins that can change the shape of membranes, in addition to the phosphoinositide-binding ability, has been found. These proteins, which contain membrane-deforming domains such as the BAR, EFC/F-BAR, and the IMD/I-BAR domains, led to inward-invaginated tubes or outward protrusions of the membrane, resulting in a variety of membrane shapes. Furthermore, these proteins not only bind to phosphoinositide, but also to the N-WASP/WAVE complex and the actin polymerization machinery, which generates a driving force to shape the membranes

Embracing translational HRD research for evidence-based management: let’s talk about how to bridge the research-practice gap

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