Cloning of the chicken RNA polymerase I promoter and use for reverse genetics of influenza A viruses in avian cells

Reverse genetics techniques to rescue influenza viruses have thus far been based on the use of a human polymerase I (PolI) promoter to direct the synthesis of the eight viral RNAs. They can only be used on cells from primate origin due to the species specificity of the PolI promoter. Here we report the cloning of the chicken PolI promoter sequence and the generation of recombinant influenza virus upon transfection of bidirectional PolI/PolII plasmids in avian cells. Potential contributions of this new reverse genetics system in the fields of influenza virus research and influenza vaccine production are discussed.     

X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis

Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the loss of the Y-linked homologs.     

LY6A/E (SCA-1) expression in the mouse testis

Recently, it was found by two research groups that LY6A, known widely in the stem cell community as stem cell antigen-1 or SCA-1, is expressed on testicular side population (SP) cells. Whether these SP cells are spermatogonial stem cells is a point of disagreement and, therefore, the identity of the LY6A-positive cells as well. We studied the expression pattern of LY6A in testis by immunohistochemistry and found it to be expressed in the interstitial tissue on peritubular myoid, endothelial, and spherical-shaped peritubular mesenchymal cells. To address the question whether LY6A has a function in spermatogenesis or testis development, we studied the testis of Ly6a(-/-) mice (allele Ly6a(tm1Pmf)). We found no morphological abnormalities or differences in numbers of spermatogonia, spermatocytes, Leydig cells, or macrophages in relation to the number of Sertoli cells. Therefore, we conclude that LY6A expression does not influence testis development or spermatogenesis and that spermatogonial stem cells are LY6A negative.     

Solution structure of a conserved domain of antizyme: a protein regulator of polyamines

Antizyme and its isoforms are members of an unusual yet broadly conserved family of proteins, with roles in regulating polyamine levels within cells. Antizyme has the ability to bind and inhibit the enzyme ornithine decarboxylase (ODC), targeting it for degradation at the proteasome; antizyme is also known to affect the transport of polyamines and interact with the antizyme inhibitor protein (AZI), as well as the cell-cycle protein cyclin D1. In the present work, NMR methods were used to determine the solution structure of a stable, folded domain of mammalian antizyme isoform-1 (AZ-1), consisting of amino acid residues 87-227. The protein was found to contain eight beta strands and two alpha helices, with the strands forming a mixed parallel and antiparallel beta sheet. At the level of primary sequence, antizyme is not similar to any protein of known structure, and results show that antizyme exhibits a novel arrangement of its strands and helices. Interestingly, however, the fold of antizyme is similar to that found in a family of acetyl transferases, as well as translation initiation factor IF3, despite a lack of functional relatedness between these proteins. Structural results, combined with amino acid sequence comparisons, were used to identify conserved features among the various homologues of antizyme and their isoforms. Conserved surface residues, including a cluster of acidic amino acids, were found to be located on a single face of antizyme, suggesting this surface is a possible site of interaction with target proteins such as ODC. This structural model provides an essential framework for an improved future understanding of how the different parts of antizyme play their roles in polyamine regulation.     

In vitro T-cell immunogenicity of oligopeptides derived from the region 92-110 of the 16-kDa protein of Mycobacterium tuberculosis

The 16-kDa protein of Mycobacterium tuberculosis provokes specific immune responses; it is thus a target for the development of peptide-based diagnostic reagents and subunit vaccines. Previous studies have demonstrated the presence of several regions containing murine and human T-cell epitopes. Within the 91-110 immunodominant domain, we found that peptides comprising the sequence of 91SEFAYGSFVRTVSL104 elicit specific T-cell responses in both human T-cell clones and human peripheral blood mononuclear cells (PBMC) from PPD+ (purified protein derivative) individuals. Elongation of this peptide towards the C-terminal end did not provide more effective peptides, but the removal of residue 91Ser resulted in an almost complete loss of functionality. However, the introduction of an acetyl group at the N-terminal of residue 92Glu produced a shorter peptide (Ac-92EFAYGSFVRTVSL104) exhibiting properties required for efficient T-cell responses. CD measurements indicated that peptide 91SEFAYGSFVRTVSLPVGADE110 adopts a helical conformation in trifluoroethanol. We found that the N-terminal part of this sequence plays a major role in the induction of proliferative T-cell responses and is responsible for the highly ordered, helical secondary structure. The "lead" structure described here could also be considered in the development of synthetic peptides or multicomponent peptide mixtures for the early detection, monitoring, or preventing Mycobacterium tuberculosis infection with optimized T-cell response-provoking capacity.     

Expression and characterization of the isolated glycosyltransferase module of Escherichia coli PBP1b

The enzymes involved in the biosynthesis of peptidoglycan are targets for the development of new antibiotics. The bifunctional high molecular weight (HMW) penicillin-binding proteins (PBPs), which contain both glycosyltransferase (GTase) and transpeptidase (TPase) activities, are particularly attractive targets because of their extracellular location. However, there is limited mechanistic or structural information about the GTase modules of these enzymes. In this paper, we describe the overexpression and characterization of the GTase module of Escherichia coli PBP1b, a paradigm of the HMW PBPs. We define the C-terminal boundary of the GTase module and show that the isolated module can be overexpressed at significantly higher levels than the full-length protein. The catalytic efficiency and other characteristics of the isolated module are comparable in most respects to the full-length enzyme. This work lays the groundwork for mechanistic and structural analysis of GTase modules.     

Prevention of diabetes in nonobese diabetic mice mediated by CD1d-restricted nonclassical NKT cells

A role for regulatory lymphocytes has been demonstrated in the pathogenesis of type 1 diabetes in the NOD mouse but the nature of these cells is debated. CD1d-restricted NKT lymphocytes have been implicated in this process. Previous reports of reduced diabetes incidence in NOD mice in which the numbers of NKT cells are artificially increased have been attributed to the enhanced production of IL-4 by these cells and a role for classical NKT cells, using the Valpha14-Jalpha18 rearrangement. We now show that overexpression in NOD mice of CD1d-restricted TCR Valpha3.2(+)Vbeta9(+) NKT cells producing high levels of IFN-gamma but low amounts of IL-4 leads to prevention of type 1 diabetes, demonstrating a role for nonclassical CD1d-restricted NKT cells in the regulation of autoimmune diabetes.     

Human dendritic cells respond to Helicobacter pylori, promoting NK cell and Th1-effector responses in vitro

Helicobacter pylori infection leads to chronic gastric inflammation. The current study determined the response of human APCs, NK cells, and T cells toward the bacteria in vitro. Human monocyte-derived dendritic cells (DC) were incubated with bacteria for 48 h. Intact H. pylori at a multitude of infection 5 stimulated the expression of MHC class II (4- to 7-fold), CD80, and CD86 B7 molecules (10- to 12-fold) and the CD83 costimulatory molecule (>30-fold) as well as IL-12 secretion (>50-fold) in DCs, and thereby, strongly induced their maturation and activation. CD56(+)/CD4(-) NK cells, as well as CD4(+)/CD45RA(+) naive T cells, were isolated and incubated with DCs pulsed with intact bacteria or different cellular fractions. Coculture of H. pylori-pulsed DCs with NK cells strongly potentiated the secretion of TNF-alpha and IFN-gamma. Coculture of naive T cells with H. pylori-pulsed DCs significantly enhanced TNF-alpha, IFN-gamma, and IL-2 secretion as well as T-bet mRNA levels, while GATA-3 mRNA was lowered. However, the effect appeared attenuated compared with coculture with Escherichia coli. A greater stimulation was seen with naive T cells and DCs pulsed with H. pylori membrane preparations. Intact H. pylori potently induced the maturation and activation of human monocyte-derived DC and thereby promote NK and Th1 effector responses. The strong activation of NK cells may be important for the innate immune response. Th1-polarized T cells were induced especially by incubation with membrane preparations of H. pylori, suggesting that membrane proteins may account for the specific adaptive immune response.     

Enhanced activation of and increased production of matrix metalloproteinase-9 by human blood monocytes upon adhering to carbamylated collagen

Carbamylation refers to chemical modification of protein side chains by cyanate derived e.g. from urea. It alters their structural and functional properties. We have studied the influence of the carbamylation of type I collagen in vitro on its interactions with elutriated human monocytes, and its potential role in atherosclerosis. Adhesion of monocytes onto carbamylated collagen was significantly enhanced compared to native collagen. There was no change in superoxide anion production. On the other hand, there was an increase in the production and the activation of matrix metalloproteinase-9. No effect was found on tissue inhibitor of metalloproteinase-1 production. Thus, the presence of carbamylated collagen may stimulate the remodelling of extracellular matrix mediated by activated monocytes. Such alterations may contribute to enhanced atherosclerosis in renal insufficiency, a pathological condition associated with elevated levels of carbamylation.     

High-throughput non-heme iron assay for animal tissues

Iron has been widely studied in nearly every realm of biology. However, current methodologies, such as genetic mapping or mutation screening, have been difficult to apply due to the lack of robust high-throughput methods for quantifying iron levels from cells or tissues. The measurement of total iron levels in tissues, usually done with atomic absorption spectroscopy, is impractical for large numbers of samples and includes the contribution of heme iron from hemoglobin contained in red blood cells. The measurement of non-heme iron by reaction with a bathophenanthroline reagent, a commonly used assay reported more than 30 years ago, is also not feasible for large-scale analyses because it is cuvette-based. We therefore have modified this method to a microplate format that will facilitate large-scale analysis. The microplate assay is highly sensitive and specific, and is a simple and effective method for the measurement of non-heme iron for animal tissues that will enable the application of high-throughput of genetic methodologies.