Tle4 Regulates Epigenetic Silencing of Gamma Interferon Expression during Effector T Helper Cell Tolerance

In response to suboptimal activation, T cells become hyporesponsive, with a severely reduced capacity to proliferate and produce cytokines upon reencounter with antigen. Chromatin analysis of T cells made tolerant by use of different in vitro and in vivo approaches reveals that the expression of gamma interferon (IFN-γ) is epigenetically silenced in anergic effector TH1 cells. In those T cells, calcium signaling triggers the expression of Tle4, a member of the Groucho family of corepressors, which is then recruited to a distal regulatory element in the Ifng locus and causes the establishment of repressive epigenetic marks at the Ifng gene regulatory elements. Consequently, impaired Tle4 activity results in a markedly reduced capacity to inhibit IFN-γ production in tolerized T cells. We propose that Blimp1-dependent recruitment of Tle4 to the Ifng locus causes epigenetic silencing of the expression of the Ifng gene in anergic TH1 cells. These results define a novel function of Groucho family corepressors in peripheral T cells and demonstrate that specific mechanisms are activated in tolerant T helper cells to directly repress expression of effector cytokines, supporting the hypothesis that stable epigenetic imprinting contributes to the maintenance of the tolerance-associated hyporesponsive phenotype in T cells.     

Double-mixing kinetic studies of the reactions of methyl isocyanide and CO with diliganded intermediates of hemoglobin: alpha 2CO beta 2 and alpha 2 beta 2CO

Kinetics of the reactions of CO and methyl isocyanide with two diliganded intermediates of hemoglobin, alpha 2CO beta 2 and alpha 2 beta 2CO, have been studied by double-mixing and microperoxidase methods. The valency hybrids were prepared by high-pressure liquid chromatography. The reaction time courses of ligand combination and dissociation with both of the ligands were biphasic, and in CO combination reaction the zero-time amplitudes of the two phases were independent of the protein concentration. In the presence of 2 M urea the reaction time course was clearly dependent on protein concentration, as the zero-time amplitude of the fast phase increased at lower protein concentrations. These two observations indicate that little dissociation of tetramers into dimers occurs in the absence of urea. Consistent with this, the kinetic data for the reactions of CO best fit a reaction model consisting of two tetrameric species not in rapid equilibrium with each other. Various considerations, however, suggest that the reaction model is more appropriately described as 2D in equilibrium R in equilibrium T. The reaction of triliganded species (Hb4(CO)2Me1) with methyl isocyanide was monophasic, and the reaction model suggested a fast T in equilibrium R structural change after the binding of the third ligand. Although the precise structural nature of the two species remains undefined, it is concluded that the biphasicity in the reactions of the two hybrids is characteristic of the diliganded species only and is independent of the nature of the ligand.     

Sialoglycans in protozoal diseases: Their detection, modes of acquisition and emerging biological roles

Protozoan parasites including Plasmodia, Leishmania, Trypanosoma, Entamoeba, Trichomonas and others cause diseases in humans and domestic livestock having far-reaching socio-economic implications. They show remarkable propensity to survive within hostile environments encountered during their life cycle, and the identification of molecules that enable them to survive in such milieu is a subject of intense research. Currently available knowledge of the parasite cell surface architecture and biochemistry indicates that sialic acid and its principle derivatives are major components of the glycocalyx and assist the parasite to interact with its external environment through functions ranging from parasite survival, infectivity and host-cell recognition. This review highlights the present state of knowledge with regard to parasite sialobiology with an emphasis on its mode(s) of acquisition and their emerging biological roles, notably as an anti-recognition molecule thereby aiding the pathogen to evade host defense mechanisms. Published in 2004. This revised version was published online in August 2006 with corrections to the Cover Date.     

Goat testis calmodulin: Purification and physicochemical characterization

Calmodulin has been purified in large quantities from goat (Capra hiscus) testis. The procedure includes heat treatment, hydrophobic interaction chromatography, and gel filtration. Goat testis calmodulin closely resembles other mammalian testis calmodulin studied so far. The protein has an extinction coefficient value (E _1cm ^1% ) of 2.09 at 280 nm, a Stokes radius of 23.2 Å at 0.15 M KCl, and a frictional ratio of 1.38. Ca²⁺, and Tb³⁺ binding studies demonstrate that the protein has four Ca²⁺-binding sites with aK _d of 52.5 µM. Goat testis calmodulin shows close similarity to other calmodulins in the amino acid composition and in demonstrating an altered migration on SDS/PAGE upon Ca²⁺ binding. The protein also exhibits anomalously high values for molecular weight and Stokes radius as determined from the analytical gel chromatography and a change in its elution volume with the change of salt concentration in the eluant. These results have been discussed in view of the recently available knowledge from the crystallographic studies of rat testis calmodulin.     

SMARTp: A SMART design for nonsurgical treatments of chronic periodontitis with spatially referenced and nonrandomly missing skewed outcomes

This paper proposes dynamic treatment regimes (DTRs) as effective individualized treatment strategies for managing chronic periodontitis. The proposed DTRs are studied via SMARTp —a two-stage sequential multiple assignment randomized trial (SMART) design. For this design, we propose a statistical analysis plan and a novel cluster-level sample size calculation method that factors in typical features of periodontal responses such as non-Gaussianity, spatial clustering, and nonrandom missingness. Here, each patient is viewed as a cluster, and a tooth within a patient's mouth is viewed as an individual unit inside the cluster, with the tooth-level covariance structure described by a conditionally autoregressive structure. To accommodate possible skewness and tail behavior, the tooth-level clinical attachment level (CAL) response is assumed to be skew-t, with the nonrandomly missing structure captured via a shared parameter model corresponding to the missingness indicator. The proposed method considers mean comparison for the regimes with or without sharing an initial treatment, where the expected values and corresponding variances or covariance for the sample means of a pair of DTRs are derived by the inverse probability weighting and method of moments. Simulation studies are conducted to investigate the finite-sample performance of the proposed sample size formulas under a variety of outcome-generating scenarios. An R package SMARTp implementing our sample size formula is available at the Comprehensive R Archive Network for free download.     

Secondary structure at the beginning of the poly(A) sequence of mouse beta-actin messenger RNA.

A portion of the beta-actin mRNA of mammalian cells is believed to lack a poly(A) tail, because of its failure to bind to oligo(dT)-cellulose. S1 mapping and Northern blot analysis of this mRNA shows it to contain a poly(A) sequence of about 60 nucleotides. Only about 20-40 nucleotides are available for interaction with oligo(dT). The rest is masked, presumably by base-pairing with a poly(U) stretch present in the 3' non-coding region of the mRNA. A similar configuration occurs in the bulk of the actin mRNA, which carries a poly(A) tail with sizes ranging from approximately 60 to 200 nucleotides.     

Cervical cancer isolate PT3, super-permissive for adeno-associated virus replication, over-expresses DNA polymerase δ, PCNA, RFC and RPA

Background  

Adeno-associated virus (AAV) type 2 is an important virus due to its use as a safe and effective human gene therapy vector and its negative association with certain malignancies. AAV, a dependo-parvovirus, autonomously replicates in stratified squamous epithelium. Such tissue occurs in the nasopharynx and anogenitals, from which AAV has been clinically isolated. Related autonomous parvoviruses also demonstrate cell tropism and preferentially replicate in oncogenically transformed cells. Combining these two attributes of parvovirus tropism, squamous and malignant, we assayed if AAV might replicate in squamous cervical carcinoma cell isolates.     

Total free energy analysis of fully hydrated proteins

The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around $\beta$ strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.