Early activation of NK cells after lung infection with the intracellular bacterium, Francisella tularensis LVS

Francisella tularensis is a gram-negative intracellular bacterium that has been classified as a Category A biothreat because of its ability to induce deadly pneumonic tularemia when inhaled. In the present study, an experimental model of F. tularensis LVS intranasal infection was used to study the immune cells involved in cytokine secretion in the lungs after infection. Dramatic increases in the numbers of cells secreting IFN-gamma were observed 72 h after intranasal infection of BALB/c and C57BL/6 mice with sublethal (1000 CFU) or lethal (10,000 CFU) doses of F. tularensis LVS and the cells primarily responsible for this IFN-gamma expression were identified as CD11b+ DX5+ NK cells. The findings were further confirmed in C57BL/6 mice showing that cells responsible for IFN-gamma secretion in the lungs were CD11b+ DX5+ NK1.1+. NK cell depletion studies showed a decrease in the percentage of IFN-gamma secreting cells, due not only to a diminished proportion of IFN-gamma secreting NK cells, but also to a reduced percentage of T cells secreting IFN-gamma. The results indicate that IFN-gamma is secreted in response to respiratory infection with F. tularensis LVS, and that NK cells are the early responders responsible for IFN-gamma secretion.     

Structural basis for SH2D1A mutations in X-linked lymphoproliferative disease

X-linked lymphoproliferative disease (XLP) is a rare and severe immune deficiency, characterized by abnormal immune responses to the Epstein-Barr virus. Recently, the gene responsible for XLP, SH2D1A, has been identified and shown to code for a small cytoplasmic protein with an SH2 domain that interacts with SLAM and 2B4, two receptorial molecules involved in signal transduction in T and NK cells, respectively. A variety of SH2D1A gene mutations have been reported thus far in XLP males. Here we describe a single-strand conformation polymorphism assay for mutation analysis in XLP. Four novel patients with SH2D1A mutations are described. These mutants, and the others previously reported in the literature, have been included in a Registry (SH2D1Abase) that is fully accessible on the World Wide Web. A three-dimensional model of the SH2 domain of the SH2D1A protein has been developed, based on homology with other SH2 domains. The structural consequences of disease-causing SH2D1A mutations are discussed.     

Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers

Super enhancers (SEs) are broad enhancer domains usually containing multiple constituent enhancers that hold elevated activities in gene regulation. Disruption in one or more constituent enhancers causes aberrant SE activities that lead to gene dysregulation in diseases. To quantify SE aberrations, differential analysis is performed to compare SE activities between cell conditions. The state-of-art strategy in estimating differential SEs relies on overall activities and neglect the changes in length and structure of SEs. Here, we propose a novel computational method to identify differential SEs by weighting the combinatorial effects of constituent-enhancer activities and locations (i.e. internal dynamics). In addition to overall activity changes, our method identified four novel classes of differential SEs with distinct enhancer structural alterations. We demonstrate that these structure alterations hold distinct regulatory impact, such as regulating different number of genes and modulating gene expression with different strengths, highlighting the differentiated regulatory roles of these unexplored SE features. When compared to the existing method, our method showed improved identification of differential SEs that were linked to better discernment of cell-type-specific SE activity and functional interpretation.     

Lethal presentation of mosaic tetrasomy 12p (Pallister-Killian) syndrome

A lethally malformed neonate with mosaic tetrasomy 12p is presented. This is the third reported case of mosaic tetrasomy 12p to have died in the neonatal period. These three babies have shown a consistent phenotype characterized by dysmorphic facies and large diaphragmatic hernia. Mosaic tetrasomy 12p is usually not detectable from lymphocyte investigation, indicating that chromosome studies from cultured fibroblasts should be undertaken in neonates with multiple malformations which include a diaphragmatic defect.     

Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes

We have evaluated codon usage bias in Drosophila histone genes and have obtained the nucleotide sequence of a 5,161-bp D. hydei histone gene repeat unit. This repeat contains genes for all five histone proteins (H1, H2a, H2b, H3, and H4) and differs from the previously reported one by a second EcoRI site. These D. hydei repeats have been aligned to each other and to the 5.0-kb (i.e., long) and 4.8-kb (i.e., short) histone repeat types from D. melanogaster. In each species, base composition at synonymous sites is similar to the average genomic composition and approaches that in the small intergenic spacers of the histone gene repeats. Accumulation of synonymous changes at synonymous sites after the species diverged is quite high. Both of these features are consistent with the relatively low codon usage bias observed in these genes when compared with other Drosophila genes. Thus, the generalization that abundantly expressed genes in Drosophila have high codon bias and low rates of silent substitution does not hold for the histone genes.      

Immunocytochemical detection of lignin-related epitopes in cell walls in bryophytes and the charalean alga Nitella

Lignins are complex phenolic heteropolymers present in xylem and sclerenchyma cell walls in tracheophytes. The occurrence of lignin-like polymers in bryophytes is controversial. In this study two polyclonal antibodies against homoguaiacyl (G) and guaiacyl/syringyl (GS) synthetic lignin-like polymers that selectively labelled lignified cell walls in tracheophytes also bound to cell walls in bryophytes, the GS antibody usually giving a stronger labelling than the G antibody. In contrast to tracheophytes, the antibody binding in liverworts and mosses was not tissue-specific. In the hornworts Megaceros flagellaris and M. fuegiensis the pseudoelaters and spores were labelled more intensely than the other cell types with the GS antibody. The cell walls in Nitella were labelled with both antibodies but no binding was observed in Coleochaete. The results suggest that the ability to incorporate G or GS moieties in cell walls is a plesiomorphy (primitive character) of the land plant clade.     

Structures of bulged three-way DNA junctions.

We have studied a series of three-way DNA junctions containing unpaired bases on one strand at the branch-point of the junctions. The global conformation of the arms of the junctions has been analysed by means of polyacrylamide gel electrophoresis, as a function of conditions. We find that in the absence of added metal ions, all the results for all the junctions can be accounted for by extended structures, with the largest angle being that between the arms defined by the strand containing the extra bases. Upon addition of magnesium (II) or hexamine cobalt (III) ions, the electrophoretic patterns change markedly, indicative of ion-dependent folding transitions for some of the junctions. For the junction lacking the unpaired bases, the three inter-arm angles appear to be quite similar, suggesting an extended structure. However, the addition of unpaired bases permits the three-way junction to adopt a significantly different structure, in which one angle becomes smaller than the other two. These species also exhibit marked protection against osmium addition to thymine bases at the point of strand exchange. These results are consistent with a model in which two of the helical arms undergo coaxial stacking in the presence of magnesium ions, with the third arm defining an angle that depends upon the number of unpaired bases.