Dynamic cofilin phosphorylation in the control of lamellipodial actin homeostasis

During animal cell chemotaxis, signalling at the plasma membrane induces actin polymerisation to drive forward cell movement. Since the cellular pool of actin is limited, efficient protrusion formation also requires the coordinated disassembly of pre-existing actin filaments. To search for proteins that can monitor filamentous and globular actin levels to maintain the balance of polymerisation and disassembly, we followed changes in the proteome induced by RNA interference (RNAi)mediated alterations in actin signalling. This unbiased approach revealed an increase in the levels of an inactive, phosphorylated form of the actin-severing protein cofilin in cells unable to generate actin-based lamellipodia. Conversely, an increase in F-actin levels induced the dephosphorylation and activation of cofilin via activation of the Ssh phosphatase. Similarly, in the context of acute phosphoinositide 3-kinase (PI3K) signalling, dynamic changes in cofilin phosphorylation were found to depend on the Ssh phosphatase and on changes in lamellipodial Factin. These results indicate that changes in the extent of cofilin phosphorylation are regulated by Ssh in response to changes in the levels and/or organisation of F-actin. Together with the recent finding that Ssh phosphatase activity is augmented by F-actin binding, these results identify Ssh-dependent regulation of phosphorylated cofilin levels as an important feedback control mechanism that maintains actin filament homeostasis during actin signalling

Shock Deformation in Zircon, a Comparison of Results from Shock-Reverberation and Single-Shock Experiments

The utility of the mineral zircon, ZrSiO4, as a shock-metamorphic geobarometer and geochronometer, has been steadily growing within the planetary science community. Zircon is an accessory phase found in many terrestrial rock types, lunar samples, lunar meteorites, martian meteorites and various other achondrites. Because zircon is refractory and has a high closure temperature for Pb diffusion, it has been used to determine the ages of some of the oldest material on Earth and elsewhere in the Solar System. Furthermore, major (O) and trace-element (REE, Ti, Hf) abundances and isotope compositions of zircon help characterize the petrogenetic environments and sources from which they crystallized. The response of zircon to impact-induced shock deformation is predominantly crystallographic, including dislocation creep and the formation of planar and sub-planar, low-angle grain boundaries; the formation of mechanical {112} twins; transformation to the high pressure polymorph reidite; the development of polycrystalline microtextures; and dissociation to the oxide constituents SiO2 and ZrO2. Shock microstructures can also variably affect the U- Pb isotope systematics of zircon and, in some instances, be used to constrain the impact age. While numerous studies have characterized shock deformation in zircon recovered from a variety of terrestrial impact craters and ejecta deposits and Apollo samples, experimental studies of shock deformation in zircon are limited to a handful of examples in the literature. In addition, the formation conditions (e.g., P, T) of various shock microstructures, such as planar-deformation bands, twins, and reidite lamellae, remain poorly con-strained. Furthermore, previous shocked-zircon experimental charges have not been analyzed using modern analytical equipment. This study will therefore under-take an new set of zircon shock experiments, which will then be microstructurally characterized using state-of-the-art instrumentation within the Astromaterials Research and Exploration Science Division (ARES), NASA Johnson Space Center

Shocked Quartz in Polymict Impact Breccia from the Upper Cretaceous Yallalie Impact Structure in Western Australia

Yallalie is a ~12 km diameter circular structure located ~200 km north of Perth, Australia. Previous studies have proposed that the buried structure is a complex impact crater based on geophysical data. Allochthonous breccia exposed near the structure has previously been interpreted as proximal impact ejecta; however, no diagnostic indicators of shock metamorphism have been found. Here we report multiple (27) shocked quartz grains containing planar fractures (PFs) and planar deformation features (PDFs) in the breccia. The PFs occur in up to five sets per grain, while the PDFs occur in up to four sets per grain. Universal stage measurements of all 27 shocked quartz grains confirms that the planar microstructures occur in known crystallographic orientations in quartz corresponding to shock compression from 5 to 20 GPa. Proximity to the buried structure (~4 km) and occurrence of shocked quartz indicates that the breccia represents either primary or reworked ejecta. Ejecta distribution simulated using iSALE hydrocode predicts the same distribution of shock levels at the site as those found in the breccia, which supports a primary ejecta interpretation, although local reworking cannot be excluded. The Yallalie impact event is stratigraphically constrained to have occurred in the interval from 89.8 to 83.6 Ma based on the occurrence of Coniacian clasts in the breccia and undisturbed overlying Santonian to Campanian sedimentary rocks. Yallalie is thus the first confirmed Upper Cretaceous impact structure in Australia

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

Effects of prenatal exposure to xenobiotic estrogen and the development of endometriosis in adulthood

Abstract only availableEndometriosis is an estrogen-dependent disease that affects millions of women worldwide, causing pain and infertility. While it is known that retrograde menstruation places endometrial tissue in the peritoneal cavity, it is unclear why it invades and proliferates in women with endometriosis. Studies have shown that other hormone-dependent diseases have a fetal basis (e.g. breast cancer), suggesting that the presence of different hormones before birth may alter the incidence of endometriosis in adulthood. For example, women whose mothers took the synthetic estrogen diethylstilbestrol (DES) during pregnancy had an eighty percent increased incidence of endometriosis. Thus, our hypothesis is that prenatal exposure to xenobiotic estrogen will increase the severity of endometriosis in adulthood in a mouse model of surgically-induced endometriosis. To test this hypothesis, mice were time mated and dosed with vehicle control, 100 ng/kg DES or 10,000 ng/kg DES from days 11-17 of gestation. Surgical induction of endometriosis was performed in adulthood by autotransplantation of one uterine horm. The horn was removed, opened, divided into three pieces, and sutured to the arterial cascade of the intestinal mesentery. The implants became vascularized and formed endometriotic lesions. The mice were then collected at 2 or 4 weeks post-surgery, and the following endpoints were measured: 1) uterine weight; 2) implant size; and 3) implant weight. Additionally, implants were set aside for further analysis of 1) histology; 2) estrogen receptor indicator reporter gene activity; and 3) endometriosis-related gene expression. At the conclusion of this ongoing study, we expect to show whether there is an estrogen-mediated fetal component to endometriosis.Life Sciences Undergraduate Research Opportunity Progra

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

© 2015 Roulis et al. Background: The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results: In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions: Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates

Neonatal exposure to xenobiotic estrogen alters the adult immune response and exacerbates endometriosis in mice [abstract]

Faculty Mentor: Dr. Susan C. Nagel, Obstetrics/Gynecology, and Women's HealthAbstract only availableEndometriosis is a common medical condition affecting 5-10% of women worldwide, and results in severe cramps, pelvic pain, and infertility. The cause of the disease is still unknown. Endometriosis occurs when endometrial tissue, which escapes into the peritoneal cavity via retrograde menstruation, adheres to other tissues in the cavity and causes irritated, inflamed lesions. Studies have suggested that the risk of developing endometriosis increases in women who have been exposed to xenobiotic (foreign to the body) estrogens during developmental stages of life. Thus, it is our hypothesis that programming of the immune system by xenoestrogens during development could potentially exacerbate endometriosis. This could occur by altering the peritoneal environment and/or the invading endometrial tissue. Therefore, it is our goal to study the effects of neonatal xenoestrogen exposure on the immune system; and ultimately, on the establishment of endometriosis in adulthood. In order to study this response, we dosed two strains of mice (CD1 and C57) with xenobiotic estrogens on postnatal days 2-14. In experiment A, CD1 mice were dosed with vehicle control (corn oil), 20 µg/kg/day, or 200 µg/kg/day bisphenol A. In experiment B, C57 mice were dosed with a vehicle control (corn oil) or 0.1 µg/kg/day diethylstilbestrol. At 8 weeks of age, endometriosis was induced in each strain via both a surgical induction and an injection technique. At 12 weeks, the endometriotic implants were counted and weighed to determine which mice had a greater susceptibility to the condition. Our next objective will be to analyze peritoneal fluid from the treated mice to identify key immune functions (for example, the release of certain cytokines) that may have been programmed by developmental xenoestrogen exposure.Endometriosis is a common medical condition affecting 5-10% of women worldwide, and results in severe cramps, pelvic pain, and infertility.  The cause of the disease is still unknown.  Endometriosis occurs when endometrial tissue, which escapes into the peritoneal cavity via retrograde menstruation, adheres to other tissues in the cavity and causes irritated, inflamed lesions.  Studies have suggested that the risk of developing endometriosis increases in women who have been exposed to xenobiotic (foreign to the body) estrogens during developmental stages of life.  Thus, it is our hypothesis that programming of the immune system by xenoestrogens during development could potentially exacerbate endometriosis.  This could occur by altering the peritoneal environment and/or the invading endometrial tissue.  Therefore, it is our goal to study the effects of neonatal xenoestrogen exposure on the immune system; and ultimately, on the establishment of endometriosis in adulthood.  In order to study this response, we dosed two strains of mice (CD1 and C57) with xenobiotic estrogens on postnatal days 2-14.  In experiment A, CD1 mice were dosed with vehicle control (corn oil), 20 µg/kg/day, or 200 µg/kg/day bisphenol A.  In experiment B, C57 mice were dosed with a vehicle control (corn oil) or 0.1 µg/kg/day diethylstilbestrol.  At 8 weeks of age, endometriosis was induced in each strain via both a surgical induction and an injection technique.  At 12 weeks, the endometriotic implants were counted and weighed to determine which mice had a greater susceptibility to the condition.  Our next objective will be to analyze peritoneal fluid from the treated mice to identify key immune functions (for example, the release of certain cytokines) that may have been programmed by developmental xenoestrogen exposure

Dynamic Bayesian belief network to model the development of walking and cycling schemes

This paper aims to describe a model which represents the formulation of decision-making processes (over a number of years) affecting the step-changes of walking and cycling (WaC) schemes. These processes can be seen as being driven by a number of causal factors, many of which are associated with the attitudes of a variety of factors, in terms of both determining whether any scheme will be implemented and, if it is implemented, the extent to which it is used. The outputs of the model are pathways as to how the future might unfold (in terms of a number of future time steps) with respect to specific pedestrian and cyclist schemes. The transitions of the decision making processes are formulated using a qualitative simulation method, which describes the step-changes of the WaC scheme development. In this article a Bayesian belief network (BBN) theory is extended to model the influence between and within factors in the dynamic decision making process

Lath Structured Monazite from Haughton Dome, Canada Reveals Shock-Induced Tetragonal High Pressure Polymorph of REEPO4

Shock deformed monazite, mono-clinic rare earth element (REE) phosphate, from the Haughton Dome impact structure, Nunavut, Canada, contain lath-structured lamellae. Microstructural phase heritage indicate the former presence of a previously unreported, shock-produced, tetragonal-structured, high pressure polymorph of REEPO4. This study presents an electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM) study of shock deformed monazite from the historic sample DIG-9, a shock stage III, biotite sillimanite gneiss sample from near the central uplift of the Haughton Dome (7522'20"N, 8940'50"W), in which shock features in monazite were first described

Phase Heritage: Deciphering Evidence of Pre-Existing Phases via Inherited Crystallographic Orientations

The concept of 'phase heritage' (e.g., Timms et al., 2017a) involves microstructural recognition of the former presence of a phase that has since transformed to another via evidence encoded in crystallographic orientations. Phase heritage relies on the phenomenon that newly grown (daughter) phases nucleate with particular crystallographic orientation relationships with the preceding (parent) phase. This phenomenon is common for displacive (i.e., shear or martensitic) transformations, well documented in the metals and ceramics literature, but is relatively uncommon in geosciences. This presentation outlines the concepts behind this approach, showcases results from software for automated analysis of EBSD data, and illustrates examples of polymorphic and dissociation phase transformations in the ZrSiO4-ZrO2-SiO2 system, which has particularly useful applications for 'extreme thermobarometry' in impact environments (Timms et al., 2017a)