Dusp3 and Psme3 are associated with murine susceptibility to Staphylococcus aureus infection and human sepsis.

Using A/J mice, which are susceptible to Staphylococcus aureus, we sought to identify genetic determinants of susceptibility to S. aureus, and evaluate their function with regard to S. aureus infection. One QTL region on chromosome 11 containing 422 genes was found to be significantly associated with susceptibility to S. aureus infection. Of these 422 genes, whole genome transcription profiling identified five genes (Dcaf7, Dusp3, Fam134c, Psme3, and Slc4a1) that were significantly differentially expressed in a) S. aureus -infected susceptible (A/J) vs. resistant (C57BL/6J) mice and b) humans with S. aureus blood stream infection vs. healthy subjects. Three of these genes (Dcaf7, Dusp3, and Psme3) were down-regulated in susceptible vs. resistant mice at both pre- and post-infection time points by qPCR. siRNA-mediated knockdown of Dusp3 and Psme3 induced significant increases of cytokine production in S. aureus-challenged RAW264.7 macrophages and bone marrow derived macrophages (BMDMs) through enhancing NF-κB signaling activity. Similar increases in cytokine production and NF-κB activity were also seen in BMDMs from CSS11 (C57BL/6J background with chromosome 11 from A/J), but not C57BL/6J. These findings suggest that Dusp3 and Psme3 contribute to S. aureus infection susceptibility in A/J mice and play a role in human S. aureus infection.

Sea Urchin Body Plan Development and Evolution: An Integrative Transcriptomic Approach

My dissertation work integrates comparative transcriptomics and functional analyses to investigate gene expression changes underlying two significant aspects of sea urchin evolution and development: the dramatic developmental changes associated with an ecologically significant shift in life history strategy and the development of the unusual radial body plan of adult sea urchins.

In Chapter 2, I investigate evolutionary changes in gene expression underlying the switch from feeding (planktotrophic) to nonfeeding (lecithotrophic) development in sea urchins. In order to identify these changes, I used Illumina RNA-seq to measure expression dynamics across 7 developmental stages in three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and an outgroup planktotroph Lytechinus variegatus. My analyses draw on a well-characterized developmental gene regulatory network (GRN) in sea urchins to understand how the ancestral planktotrophic developmental program was altered during the evolution of lecithotrophic development. My results suggest that changes in gene expression profiles occurred more frequently across the transcriptome during the evolution of lecithotrophy than during the persistence of planktotrophy. These changes were even more pronounced within the GRN than across the transcriptome as a whole, and occurred in each network territory (skeletogenic, endomesoderm and ectoderm). I found evidence for both conservation and divergence of regulatory interactions in the network, as well as significant changes in the expression of genes with known roles in larval skeletogenesis, which is dramatically altered in lecithotrophs. I further explored network dynamics between species using coexpression analyses, which allowed me to identify novel players likely involved in sea urchin neurogenesis and endoderm patterning.

In Chapter 3, I investigate developmental changes in gene expression underlying radial body plan development and metamorphosis in H. erythrogramma. Using Illumina RNA-seq, I measured gene expression profiles across larval, metamorphic, and post-metamorphic life cycle phases. My results present a high-resolution view of gene expression dynamics during the complex transition from pre- to post-metamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases.

Collectively, my investigations provide an important foundation for future, empirical studies to investigate the functional role of gene expression change in the evolution of developmental differences between species and also for the generation of the unusual radial body plan of sea urchins.

Differential developmental trajectories of magnetic susceptibility in human brain gray and white matter over the lifespan

As indicated by several recent studies, magnetic susceptibility of the brain is influenced mainly by myelin in the white matter and by iron deposits in the deep nuclei. Myelination and iron deposition in the brain evolve both spatially and temporally. This evolution reflects an important characteristic of normal brain development and ageing. In this study, we assessed the changes of regional susceptibility in the human brain in vivo by examining the developmental and ageing process from 1 to 83 years of age. The evolution of magnetic susceptibility over this lifespan was found to display differential trajectories between the gray and the white matter. In both cortical and subcortical white matter, an initial decrease followed by a subsequent increase in magnetic susceptibility was observed, which could be fitted by a Poisson curve. In the gray matter, including the cortical gray matter and the iron-rich deep nuclei, magnetic susceptibility displayed a monotonic increase that can be described by an exponential growth. The rate of change varied according to functional and anatomical regions of the brain. For the brain nuclei, the age-related changes of susceptibility were in good agreement with the findings from R2* measurement. Our results suggest that magnetic susceptibility may provide valuable information regarding the spatial and temporal patterns of brain myelination and iron deposition during brain maturation and ageing. © 2013 Wiley Periodicals, Inc.

Wnt Protein Signaling Reduces Nuclear Acetyl-CoA Levels to Suppress Gene Expression during Osteoblast Differentiation.

Developmental signals in metazoans play critical roles in inducing cell differentiation from multipotent progenitors. The existing paradigm posits that the signals operate directly through their downstream transcription factors to activate expression of cell type-specific genes, which are the hallmark of cell identity. We have investigated the mechanism through which Wnt signaling induces osteoblast differentiation in an osteoblast-adipocyte bipotent progenitor cell line. Unexpectedly, Wnt3a acutely suppresses the expression of a large number of genes while inducing osteoblast differentiation. The suppressed genes include Pparg and Cebpa, which encode adipocyte-specifying transcription factors and suppression of which is sufficient to induce osteoblast differentiation. The large scale gene suppression induced by Wnt3a corresponds to a global decrease in histone acetylation, an epigenetic modification that is associated with gene activation. Mechanistically, Wnt3a does not alter histone acetyltransferase or deacetylase activities but, rather, decreases the level of acetyl-CoA in the nucleus. The Wnt-induced decrease in histone acetylation is independent of β-catenin signaling but, rather, correlates with suppression of glucose metabolism in the tricarboxylic acid cycle. Functionally, preventing histone deacetylation by increasing nucleocytoplasmic acetyl-CoA levels impairs Wnt3a-induced osteoblast differentiation. Thus, Wnt signaling induces osteoblast differentiation in part through histone deacetylation and epigenetic suppression of an alternative cell fate.

Optimal kinetics for quantification of antigen-induced cytokines in human peripheral blood mononuclear cells by real-time PCR and by ELISA.

Real-time polymerase chain reaction (PCR) has recently been described as a new tool to measure and accurately quantify mRNA levels. In this study, we have applied this technique to evaluate cytokine mRNA synthesis induced by antigenic stimulation with purified protein derivative (PPD) or heparin-binding haemagglutinin (HBHA) in human peripheral blood mononuclear cells (PBMC) from Mycobacterium tuberculosis-infected individuals. Whereas PPD and HBHA optimally induced IL-2 mRNA after respectively 8 and 16 to 24 h of in vitro stimulation, longer in vitro stimulation times were necessary for optimal induction of interferon-gamma (IFN-gamma) mRNA, respectively 16 to 24 h for PPD and 24 to 96 h for HBHA. IL-13 mRNA was optimally induced by in vitro stimulation after 16-48 h for PPD and after 48 to 96 h for HBHA. Comparison of antigen-induced Th1 and Th2 cytokines appears, therefore, valuable only if both cytokine types are analysed at their optimal time point of production, which, for a given cytokine, may differ for each antigen tested. Results obtained by real-time PCR for IFN-gamma and IL-13 mRNA correlated well with those obtained by measuring the cytokine concentrations in cell culture supernatants, provided they were high enough to be detected. We conclude that real-time PCR can be successfully applied to the quantification of antigen-induced cytokine mRNA and to the evaluation of the Th1/Th2 balance, only if the kinetics of cytokine mRNA appearance are taken into account and evaluated for each cytokine measured and each antigen analysed.

Dynamic evolution in information sharing networks

This study examines the roll-out of a collaborative information repository or 'knowledge-base' in a medium-sized UK professional services firm over a six year period. Data from usage logs provides the basis for analysis of the dynamic evolution of social networks around the depository during this time. The adoption pattern follows an 's-curve' and usage exhibits something of a power law distribution, both attributable to network effects and network opposition is associated with organisational performance on a number of indicators. But periodicity in usage is evident and the usage distribution displays an exponential cut-off. Fourier analysis provides some evidence of mathematical complexity in the periodicity. Some implications of complex patterns in social network data for research and management are discussed.

"The Black Imprint of Sandals in White Mosaic Floors": H.D.'s Mythomystical Poetics

My dissertation examines the traces of inverse (mytho)mysticism, more synchronous with mythical alchemy than transcendent mystery, in H.D.’s mature work (1946-1961). Whereas H.D.’s earliest works respond to a fin de siècle occultism and a collective psyche troubled by the eschatological distress that, as Susan Acheson writes, “was widespread amongst modernist writers grappling with …world events and with the implications of Nietzsche’s inaugural annunciation of modernity in terms of the death of God” (187), her later oeuvre is dedicated to the same work of soul undertaken by the “secret cult of Night” in Vale Ave. Here, her thematic scope faces two ways: backward to ancient Greek mystery cults and their palingenesic rites and forward to depth psychologists searching for the Soul of the World. Vale Ave plays a pronounced role in my study as symbolic guide; in its seventy-four sequences the layering of time in the “trilogy” of past, present, and future that H.D. had explored during the years of the Second World War in order to get behind the fallen walls of cause and effect collapses into two distinct phases of human origin—“meeting” (evolution) and “parting” (involution)—and the poem invites Lilith and Lucifer to be its archetypal guides. My method for the study is imaginal, entering such disciplines as history, philosophy, and theology and bringing psychological understanding to them. John Walsh’s introduction to Vale Ave notes H.D.’s theme “that the human psyche exists in a dimension outside of time and space as well as within them. In Vale Ave, H.D. presents the extremity of this dual-dimensionality: metempsychosis” (vii). However, the concept that H.D. investigates is more than a literary processus of characters who adopt different masks and appear at various junctures in a chronological unwinding of history. I explore H.D.'s works as part of a Modernist tradition of writing “books of the dead” designed not to guide the soul after death, but to draw the gaze upon “a nearer thing,” as H.D. writes in Erige Cor Tuum Ad Me In Caelum, the wisdom intrinsic in the spirit of life itself.

Structure and bioactivity of neuropeptide F from the human parasites Schistosoma mansoni and Schistosoma japonicum

The blood flukes Schistosoma mansoni and Schistosoma japonicum inflict immense suffering as agents of human schistosomiasis. Previous investigations have found the nervous systems of these worms contain abundant immunoreactivity to antisera targeting invertebrate neuropeptide Fs (NPFs) as well as structurally similar neuropeptides of the mammalian neuropeptide Y (NPY) family. Here, cDNAs encoding NPF in these worms were identified, and the mature neuropeptides from the two species differed by only a single amino acid. Both neuropeptides feature the characteristics common among NPFs; they are 36 amino acids long with a carboxyl-terminal Gly-Arg-X-Arg-Phe-amide and Tyr residues at positions 10 and 17 from the carboxyl terminus. Synthetic S. mansoni NPF potently inhibits the forskolin-stimulated accumulation of cAMP in worm homogenates, with significant effects at 10(-11) M. This is the first demonstration of an endogenous inhibition of cAMP by an NPF, and because this is the predominant pathway associated with vertebrate NPY family peptides, it demonstrates a conservation of downstream signaling pathways used by NPFs and NPY peptides.

DUB-3, a Cytokine inducible Deubiquitinating Enzyme That Blocks Profileration

Previous studies have identified the DUB family of cytokine-regulated murine deubiquitinating enzymes, which play a role in the control of cell proliferation and survival. Through data base analyses and cloning, we have identified a human cDNA (DUB-3) that shows significant homology to the known murine DUB family members. Northern blotting has shown expression of this gene in a number of tissues including brain, liver, and muscle, with two transcripts being apparent (1.6 and 1.7 kb). In addition, expression was observed in cell lines including those derived from a number of hematopoietic tumors such as the Burkitt's lymphoma cell line RAJI. We have also demonstrated that DUB-3, which was shown to be an active deubiquitinating enzyme, is induced in response to interleukin-4 and interleukin-6 stimulation. Finally, we have demonstrated that constitutive expression of DUB-3 blocks proliferation and can initiate apoptosis in both IL-3-dependent Ba/F3 cells and NIH3T3 fibroblasts. These findings suggest that human DUB-3, like the murine DUB family members, is transiently induced in response to cytokines and can, when constitutively expressed, block growth factor-dependent proliferation.

Nitric Oxide Produced in Response to Engagement of beta 2 Integrins on Human Neutrophils Activates the Monomeric GTPases Rap1 and Rap2 and Promotes Adhesion

We found that engagement of beta 2 integrins on human neutrophils increased the levels of GTP-bound Rap1 and Rap2. Also, the activation of Rap1 was blocked by PP1, SU6656, LY294002, GF109203X, or BAPTA-AM, which indicates that the downstream signaling events in Rap1 activation involve Src tyrosine kinases, phosphoinositide 3-kinase, protein kinase C, and release of calcium. Surprisingly, the integrin-induced activation of Rap2 was not regulated by any of the signaling pathways mentioned above. However, we identified nitric oxide as the signaling molecule involved in beta 2 integrin-induced activation of Rap1 and Rap2. This was illustrated by the fact that engagement of beta 2 integrins increased the production of nitrite, a stable end-product of nitric oxide. Furthermore, pretreatment of neutrophils with N-monomethyl-L-arginine, or 1400W, which are inhibitors of inducible nitric-oxide synthase, blocked integrin-induced activation of Rap1 and Rap2. Similarly, Rp-8pCPT-cGMPS, an inhibitor of cGMP-dependent serine/threonine kinases, also blunted the integrin-induced activation of Rap GTPases. Also nitric oxide production and its downstream activation of cGMP-dependent serine/threonine kinases were essential for proper neutrophil adhesion by beta 2 integrins. Thus, we made the novel findings that beta 2 integrin engagement on human neutrophils triggers production of nitric oxide and its downstream signaling is essential for activation of Rap GTPases and neutrophil adhesion.

The VLT-FLAMES survey of massive stars: mass loss and rotation of early-type stars in the SMC

We have studied the optical spectra of a sample of 31 O- and early B-type stars in the Small Magellanic Cloud, 21 of which are associated with the young massive cluster NGC 346. Stellar parameters are determined using an automated fitting method (Mokiem et al. 2005, A&A, 441, 711), which combines the stellar atmosphere code FASTWIND (Puls et al. 2005, A&A, 435, 669) with the genetic algorithm based optimisation routine PIKAIA (Charbonneau 1995, ApJS, 101, 309). Comparison with predictions of stellar evolution that account for stellar rotation does not result in a unique age, though most stars are best represented by an age of 1-3 Myr. The automated method allows for a detailed determination of the projected rotational velocities. The present day v(r) sin i distribution of the 21 dwarf stars in our sample is consistent with an underlying rotational velocity (v(r)) distribution that can be characterised by a mean velocity of about 160-190 km s(-1) and an effective half width of 100-150 km s(-1). The vr distribution must include a small percentage of slowly rotating stars. If predictions of the time evolution of the equatorial velocity for massive stars within the environment of the SMC are correct (Maeder & Meynet 2001, A&A, 373, 555), the young age of the cluster implies that this underlying distribution is representative for the initial rotational velocity distribution. The location in the Hertzsprung-Russell diagram of the stars showing helium enrichment is in qualitative agreement with evolutionary tracks accounting for rotation, but not for those ignoring vr. The mass loss rates of the SMC objects having luminosities of log L-star/L-circle dot greater than or similar to 5.4 are in excellent agreement with predictions by Vink et al. (2001, A&A, 369, 574). However, for lower luminosity stars the winds are too weak to determine. M accurately from the optical spectrum. Three targets were classified as Vz stars, two of which are located close to the theoretical zero-age main sequence. Three lower luminosity targets that were not classified as Vz stars are also found to lie near the ZAMS. We argue that this is related to a temperature effect inhibiting cooler from displaying the spectral features required for the Vz luminosity class.

Roche tomography of the secondary stars in CVs

The secondary stars in cataclysmic variables (CVs) are key to our understanding of the origin, evolution and behaviour of this class of interacting binary. In seeking a fuller understanding of these objects, the challenge for observers is to obtain images of the secondary star. This goal can be achieved through Roche tomography, an indirect imaging technique that can be used to map the Roche-lobe-filling secondary. The review begins with a description of the basic principles that underpin Roche tomography, including methods for determining the system parameters. Finally, we conclude with a look at the main scientific highlights to date, including the first unambiguous detection of starspots on AE Aqr B, and consider the future prospects of this technique.

Measurement of Short-Range Correlations in Shock-Compressed Plastic by Short-Pulse X-Ray Scattering

We have performed short-pulse x-ray scattering measurements on laser-driven shock-compressed plastic samples in the warm dense matter regime, providing instantaneous snapshots of the system evolution. Time-resolved and angularly resolved scattered spectra sensitive to the correlation effects in the plasma show the appearance of short-range order within a few interionic separations. Comparison with radiation-hydrodynamic simulations indicates that the shocked plastic is compressed with a temperature of a few electron volts. These results are important for the understanding of the thermodynamic behavior of strongly correlated matter for conditions relevant to both laboratory astrophysics and inertial confinement fusion research.

Role of TGF-beta1 and nitric oxide in the bystander response of irradiated glioma cells.

The radiation-induced bystander effect (RIBE) increases the probability of cellular response and therefore has important implications for cancer risk assessment following low-dose irradiation and for the likelihood of secondary cancers after radiotherapy. However, our knowledge of bystander signaling factors, especially those having long half-lives, is still limited. The present study found that, when a fraction of cells within a glioblastoma population were individually irradiated with helium ions from a particle microbeam, the yield of micronuclei (MN) in the nontargeted cells was increased, but these bystander MN were eliminated by treating the cells with either aminoguanidine (an inhibitor of inducible nitric oxide (NO) synthase) or anti-transforming growth factor beta1 (anti-TGF-beta1), indicating that NO and TGF-beta1 are involved in the RIBE. Intracellular NO was detected in the bystander cells, and additional TGF-beta1 was detected in the medium from irradiated T98G cells, but it was diminished by aminoguanidine. Consistent with this, an NO donor, diethylamine nitric oxide (DEANO), induced TGF-beta1 generation in T98G cells. Conversely, treatment of cells with recombinant TGF-beta1 could also induce NO and MN in T98G cells. Treatment of T98G cells with anti-TGF-beta1 inhibited the NO production when only 1% of cells were targeted, but not when 100% of cells were targeted. Our results indicate that, downstream of radiation-induced NO, TGF-beta1 can be released from targeted T98G cells and plays a key role as a signaling factor in the RIBE by further inducing free radicals and DNA damage in the nontargeted bystander cells.

The human prion protein residue 129 polymorphism lies within a cluster of epitopes for T cell recognition.

T cell immune responses to central nervous system-derived and other self-antigens are commonly described in both healthy and autoimmune individuals. However, in the case of the human prion protein (PrP), it has been argued that immunologic tolerance is uncommonly robust. Although development of an effective vaccine for prion disease requires breaking of tolerance to PrP, the extent of immune tolerance to PrP and the identity of immunodominant regions of the protein have not previously been determined in humans. We analyzed PrP T cell epitopes both by using a predictive algorithm and by measuring functional immune responses from healthy donors. Interestingly, clusters of epitopes were focused around the area of the polymorphic residue 129, previously identified as an indicator of susceptibility to prion disease, and in the C-terminal region. Moreover, responses were seen to PrP peptide 121-134 containing methionine at position 129, whereas PrP 121-134 [129V] was not immunogenic. The residue 129 polymorphism was also associated with distinct patterns of cytokine response: PrP 128-141 [129M] inducing IL-4 and IL-6 production, which was not seen in response to PrP 128-141 [129V]. Our data suggest that the immunogenic regions of human PrP lie between residue 107 and the C-terminus and that, like with many other central nervous system antigens, healthy individuals carry responses to PrP within the T cell repertoire and yet do not experience deleterious autoimmune reactions.