The function of PAB1 in translation and in PUF3 dependent deadenylation

The involvement of the poly(A)-binding protein (PAB1) in deadenylation and translation is well known. How PAB1 inhibits deadenylation and promotes translation is not well understood. I have analyzed PAB1 variants, containing entire domain deletions and substitutions of yeast residues with human residues. Chapter I discusses and provides in vivo translation rates of strains containing PAB1 variants, defects in mRNA degradation proteins, and defects in translation components. In chapter II, I address the role of PAB1 in regulated deadenylation. For this analysis I studied the effect of PUF3, a member of the PUF family of proteins that bind specific 3\u27 UTR sequences and accelerate deadenylation and/or repress translation of the target transcript. The mechanism for PUF mediated deadenylation has recently been shown to involve recruitment of CCR4 via CAF1, suggesting PUF proteins accelerate deadenylation by increasing the local concentration of deadenylases around the mRNA. Since PUF proteins are involved in repression of translation it has been suggested that they also accelerate deadenylation through perturbation of the mRNP complex. In this work I show that PUP requires the PAB1 RRM1 domain for deadenylation of COX17 mRNA. Additionally, I show that PUP bypasses the requirement of the PAB1 P domain for deadenylation, and is required for acceleration of deadenylation through defects in the cap binding protein, elF4E. This suggests that PUP interacts with PAB1 to disturb the mRNP complex to accelerate deadenylation of COX17 mRNA

A hierarchical model of non-homogeneous Poisson processes for Twitter retweets

We present a hierarchical model of nonhomogeneous Poisson processes (NHPP) for information diffusion on online social media, in particular Twitter retweets. The retweets of each original tweet are modelled by a NHPP, for which the intensity function is a product of time-decaying components and another component that depends on the follower count of the original tweet author. The latter allows us to explain or predict the ultimate retweet count by a network centrality-related covariate. The inference algorithm enables the Bayes factor to be computed, to facilitate model selection. Finally, the model is applied to the retweet datasets of two hashtags. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplemen

SPT5 affects the rate of mRNA degradation and physically interacts with CCR4 but does not control mRNA deadenylation

The CCR4-NOT complex has been shown to have multiple roles in mRNA metabolism, including that of transcriptional elongation, mRNA transport, and nuclear exosome function, but the primary function of CCR4 and CAF1 is in the deadenylation and degradation of cytoplasmic mRNA. As previous genetic analysis supported an interaction between SPT5, known to be involved in transcriptional elongation, and that of CCR4, the physical association of SPT5 with CCR4 was examined. A two-hybrid screen utilizing the deadenylase domain of CCR4 as a bait identified SPT5 as a potential interacting protein. SPT5 at its physiological concentration was shown to immunoprecipitate CCR4 and CAF1, and in vitro purified SPT5 specifically could bind to CAF1 and the deadenylase domain of CCR4. We additionally demonstrated that mutations in SPT5 or an spt4 deletion slowed the rate of mRNA degradation, a phenotype associated with defects in the CCR4 mRNA deadenylase complex. Yet, unlike ccr4 and caf1 deletions, spt5 and spt4 defects displayed little effect on the rate of deadenylation. They also did not affect decapping or 5\u27 - 3\u27 degradation of mRNA. These results suggest that the interactions between SPT5/SPT4 and the CCR4-NOT complex are probably the consequences of effects involving nuclear events and do not involve the primary role of CCR4 in mRNA deadenylation and turnover

The Alpha-Melanocyte Stimulating Hormone Induces Conversion of Effector T Cells into Treg Cells

The neuropeptide alpha-melanocyte stimulating hormone (α-MSH) has an important role in modulating immunity and homeostasis. The production of IFN-γ by effector T cells is suppressed by α-MSH, while TGF-β production is promoted in the same cells. Such α-MSH-treated T cells have immune regulatory activity and suppress hypersensitivity, autoimmune diseases, and graft rejection. Previous characterizations of the α-MSH-induced Treg cells showed that the cells are CD4+ T cells expressing the same levels of CD25 as effector T cells. Therefore, we further analyzed the α-MSH-induced Treg cells for expression of effector and regulatory T-cell markers. Also, we examined the potential for α-MSH-induced Treg cells to be from the effector T-cell population. We found that the α-MSH-induced Treg cells are CD25+  CD4+ T cells that share similar surface markers as effector T cells, except that they express on their surface LAP. Also, the α-MSH treatment augments FoxP3 message in the effector T cells, and α-MSH induction of regulatory activity was limited to the effector CD25+ T-cell population. Therefore, α-MSH converts effector T cells into Treg cells, which suppress immunity targeting specific antigens and tissues

Vanadium(V) oxo and imido calix[8]arene complexes: synthesis, structural studies, and ethylene homo/copolymerisation capability

Interaction of p-tert-butylcalix[8]areneH₈ (L⁸H₈) with in-situ generated [NaVO(Ot-Bu)₄] (from VOCl₃ and four equivalents of NaOtBu) afforded the dark brown complex [Na(NCMe)₅][(VO)₂L⁸H]·4MeCN (1·4MeCN), in which the calix[8]arene adopts a saddle-shaped conformation. Increasing (to four equivalents per L⁸) the amount of [NaVO(Ot-Bu)₄] present in the reaction, led to the formation of the yellow octa-vanadyl complex {[(Na(VO)₄L⁸)(Na(NCMe))₃] [Na(NCMe)₆}₂·10MeCN (2·10MeCN), in which the calix[8]arene adopts a pleated loop conformation. In the presence of adventitious oxygen, reaction of four equivalents of [VO(Ot-Bu)₃] (generated from VOCl₃ and 3KOtBu) with L⁸H₈ afforded the alkali-metal free green complex [(VO)₄L⁸(μ³-O)₂] (3); the solvates 3·3MeCN and 3·3CH₂Cl₂ have been isolated. In both solvates, the L⁸ ligand adopts a shallow saddle-shaped conformation, supporting a core comprising of a (VO)₄O₄ ladder. In the case of lithium, in order to obtain crystalline material, it was found necessary to reverse the order of addition such that lithium tert-butoxide was added to L⁸H₈, and then subsequently treated (at –78 ⁰C) with two equivalents of VOCl₃; crystallization from tetrahydrofuran (THF) afforded {(VO₂)₂Li₆[L⁸](thf)₂(OtBu)₂(Et₂O)₂}·Et₂O (4·Et₂O). In the structure of 4·Et₂O, vanadium, lithium and oxygen form a central lattern-type cage, which is capped top and bottom by an Li₂O₂2 diamond; the calix[8]arene is in a ‘down, down, out, out, down, down’ conformation. When the ‘same reaction’ was extracted into acetonitrile (MeCN), the salt complex [Li(NCMe)₄][(VO)₂L⁸H]·8MeCN (5.8MeCN) was formed. In 5·8MeCN, the [Li(NCMe)₄] cations reside between the anions in the clefts of L⁸H, the latter adopting a saddle-shaped conformation. Use of the imido precursors [V(Nt-Bu)(Ot-Bu)₃] and [V(Np-tolyl)(Ot-Bu)₃] and L⁸H₈, afforded, via an imido exchange, the salt [t-BuNH₃]{[V(p-tolylN)]₂L⁸H}·3½MeCN (6·3½MeCN). The molecular structures of 1 to 6 are reported; data collections for complexes 2·10MeCN, 3·3MeCN and 3·3CH₂Cl₂ required the use of synchrotron radiation. Complexes 1, 3 and 4 have been screened as pre-catalysts for the polymerization of ethylene in the presence of a variety of co-catalysts (with and without a re-activator) at various temperatures and for the co-polymerization of ethylene with propylene; results are compared versus the benchmark catalyst VO(OEt)Cl₂. In some cases, activities as high as 136,000 g/mmol.v.h were achievable, whilst it also proved possible to obtain higher molecular weight polymers (in comparible yields) versus the use of VO(OEt)Cl₂. In the case of the co-polymerization, the incorporation of propylene was 7.1 – 10.9 mol% (cf 10 mol% for VO(OEt)Cl₂), though catalytic activities were lower versus VO(OEt)Cl₂

Biological Therapies that Target Inflammatory Cytokines to Treat Uveitis

Uveitis is a leading cause of blindness that presents a considerable challenge given that our understanding of the mechanisms of disease is still evolving. Both innate and adaptive immunity play a role in disease and mediators of these responses can serve as therapeutic targets. TNF-α and IL-1β inflammatory cytokines are central mediators of immunity and are involved in the dysregulated inflammatory response during uveitis. Because toxicity limits the use of steroids and other steroid-sparing agents, biologics that target a specific cell type or pathway are being explored for the treatment of autoimmune uveitis. This chapter begins with a broad overview of the aberrant immune response resulting in uveitis, and highlights key mediators such as TNF-α, IL-1β, IL-6, and IL-17 and their potential use as therapeutic targets. Most biological agents discussed in this review have not been FDA-approved for uveitis. However, favorable outcomes in early trials and FDA approval of these drugs for the treatment of other autoimmune diseases associated with uveitis support the potential for these biological agents in the management of uveitis. This review aims to provide an updated report on the efficacy of biologics that target TNF-α, IL-1β, IL-6, and IL-17 for the treatment of autoimmune uveitis

A complete view of galaxy evolution: panchromatic luminosity functions and the generation of metals

When and how did galaxies form and their metals accumulate? Over the last decade, this has moved from an archeological question to a live investigation: there is now a broad picture of the evolution of galaxies in dark matter halos: their masses, stars, metals and supermassive blackholes. Galaxies have been found and studied in which these formation processes are taking place most vigorously, all the way back in cosmic time to when the intergalactic medium (IGM) was still largely neutral. However, the details of how and why the interstellar medium (ISM) in distant galaxies cools, is processed, recycled and enriched in metals by stars, and fuels active galactic nuclei (AGNs) remain uncertain. In particular, the cooling of gas to fuel star formation, and the chemistry and physics of the most intensely active regions is hidden from view at optical wavelengths, but can be seen and diagnosed at mid- & far-infrared (IR) wavelengths. Rest-frame IR observations are important first to identify the most luminous, interesting and important galaxies, secondly to quantify accurately their total luminosity, and finally to use spectroscopy to trace the conditions in the molecular and atomic gas out of which stars form. In order to map out these processes over the full range of environments and large-scale structures found in the universe - from the densest clusters of galaxies to the emptiest voids - we require tools for deep, large area surveys, of millions of galaxies out to z~5, and for detailed follow-up spectroscopy. The necessary tools can be realized technically. Here, we outline the requirements for gathering the crucial information to build, validate and challenge models of galaxy evolution.Comment: A whitepaper submitted on 15th February 2009 in response to the call from the Astro2010 panel: astro2010.org; uploaded as an 8-page pdf fil

MC5r and A2Ar Deficiencies During Experimental Autoimmune Uveitis Identifies Distinct T cell Polarization Programs and a Biphasic Regulatory Response

Autoantigen-specific regulatory immunity emerges in the spleen of mice recovering from experimental autoimmune uveitis (EAU), a murine model for human autoimmune uveoretinitis. This regulatory immunity provides induced tolerance to ocular autoantigen, and requires melanocortin 5 receptor (MC5r) expression on antigen presenting cells with adenosine 2 A receptor (A2Ar) expression on T cells. During EAU it is not well understood what roles MC5r and A2Ar have on promoting regulatory immunity. Cytokine profile analysis during EAU revealed MC5r and A2Ar each mediate distinct T cell responses, and are responsible for a functional regulatory immune response in the spleen. A2Ar stimulation at EAU onset did not augment this regulatory response, nor bypass the MC5r requirement to induce regulatory immunity. The importance of this pathway in human autoimmune uveitis was assayed. PBMC from uveitis patients were assayed for MC5r expression on monocytes and A2Ar on T cells, and comparison between uveitis patients and healthy controls had no significant difference. The importance for MC5r and A2Ar expression in EAU to promote the induction of protective regulatory immunity, and the expression of MC5r and A2Ar on human immune cells, suggests that it may be possible to utilize the melanocortin-adenosinergic pathways to induce protective immunity in uveitic patients

Complex permittivity measurement system for solid materials using complementary frequency selective surfaces

This paper describes a novel method of characterizing complex permittivity using a complementary frequency selective surface (CFSS). The CFSS provides a passband behavior and the change in the passband when a material under test (MUT) is placed adjacent to the CFSS has been used for retrieving of the complex permittivity of the MUT. The complex permittivity of the MUT are determined based on the measured bandpass resonant frequency and insertion loss of the CFSS with the MUT. This is an amplitudeonly method where phase measurements are not required. This technique offers a convenient, fast, low-cost and nondestructive measurement that is not restricted by the sample size or shap