Different properties of ACPA and IgM-RF derived from a large dataset: further evidence of two distinct autoantibody systems

Introduction  

The aim of this study was to examine seroconversion and the relationship with age and inflammation of autoantibodies in a large group of patients attending an outpatient rheumatology clinic.     

Antibody-mediated targeting of liposomes. Binding to lymphocytes does not ensure incorporation of vesicle contents into the cells

Small sonicated lipid vesicles containing the water-souble fluorescent dye 6-carboxyfluorescein were formed from dioleoyl phosphatidylcholine and the antigenic lipid N-dinitrophenylaminocaproyl phosphatidylethanolamine. When these vesicles were incubated with trinitrophenyl-modified human lymphocytes and divalent anti-trinitrophenyl antibody, the antibody bound 5000 to 15 000 vesicles to each cell. Binding was detected by fluorescence microscopy and quantitated by fluorometry and flow microfluorometry. Binding was three times greater with F(ab')2 fragments than with the whole antibody and, as expected, was almost absent with the monovalent F(ab') fragments. It was also absent or greatly reduced, (i) with control immunoglobulin G, (ii) in the presence of excess soluble trintrophenyl hapten, or (iii) if hapten was omitted from either cells or vesicles. It was unaffected by sodium azide and 2-deoxy-D-glucose but was markedly decreased at 3 degrees C. It was not reversed by incubation at 3 degrees C with excess trinitrophenyl lysine. Self-quenching of the fluorescence of 6-carboxyfluorescein was used to distinguish between release of vesicle contents into the cells and simple binding of intact vesicles (Weinstein, J.N., Yoshikami, S., Henkart, P., Blumenthal, R. and Gagins, W.A. (1977) Science 195, 489--491). Antibody-mediated binding led to little or no increase over spontaneous background levels in the amount of vesicle contents released into the lymphocytes.     

Reducing bias in bacterial community analysis of lower respiratory infections

High-throughput pyrosequencing and quantitative PCR (Q-PCR) analysis offer greatly improved accuracy and depth of characterisation of lower respiratory infections. However, such approaches suffer from an inability to distinguish between DNA derived from viable and non-viable bacteria. This discrimination represents an important step in characterising microbial communities, particularly in contexts with poor clearance of material or high antimicrobial stress, as non-viable bacteria and extracellular DNA can contribute significantly to analyses. Pre-treatment of samples with propidium monoazide (PMA) is an effective approach to non-viable cell exclusion (NVCE). However, the impact of NVCE on microbial community characteristics (abundance, diversity, composition and structure) is not known. Here, adult cystic fibrosis (CF) sputum samples were used as a paradigm. The effects of PMA treatment on CF sputum bacterial community characteristics, as analysed by pyrosequencing and enumeration by species-specific (Pseudomonas aeruginosa) and total bacterial Q-PCR, were assessed. At the local community level, abundances of both total bacteria and of P. aeruginosa were significantly lower in PMA-treated sample portions. Meta-analysis indicated no overall significant differences in diversity; however, PMA treatment resulted in a significant alteration in local community membership in all cases. In contrast, at the metacommunity level, PMA treatment resulted in an increase in community evenness, driven by an increase in diversity, predominately representing rare community members. Importantly, PMA treatment facilitated the detection of both recognised and emerging CF pathogens, significantly influencing ‘core'' and ‘satellite'' taxa group membership. Our findings suggest failure to implement NVCE may result in skewed bacterial community analyses.     

Subpopulations of mouse Lyt-2+ T cells defined by the expression of an Ly-6-linked antigen, B4B2

The production and characterization of a rat mu,kappa monoclonal anti-mouse T cell subset antibody, B4B2, is reported in this paper. B4B2 typing of lymphoid tissues of commonly used inbred mouse strains revealed two types of reactivity patterns. They can be characterized as C57BL/6-like (B6-like) or C3H/He-like (C3H-like). Among B6-like strains, B4B2 recognizes 5 to 10% of spleen cells, 30 to 50% of bone marrow cells, and less than 2 to 3% of thymocytes. In C3H-like strains, B4B2 reacts with less than 1% of spleen cells, 2 to 8% of bone marrow cells, and less than 1% of thymocytes. B4B2 recognizes a T cell subset differentiation antigen expressed by B6-like strains but not by C3H-like strains. Typing of BXH recombinant inbred strains showed linked expression of B4B2 and the Ly-6 antigen. The expression of B4B2 antigen appears to be under codominant control as the median fluorescence distribution of B4B2+ cells in C57BL/6 was approximately twice that of (C57BL/6xC3H)F1. B4B2 was shown to react with approximately 40 to 50% of Lyt-2+ T cells and less than 1% of L3T4+ T cells. No staining of resting or activated B cells by B4B2 was detected. The ratio of B4B2+:Lyt-2+ cells was similar for resting T cells and activated T cells obtained from mitogen-stimulated cultures or mixed lymphocyte cultures. In neonatal spleen, substantially more B4B2+ than Lyt-2+ cells were found. With increasing age, however, a rapid decline in B4B2+ cells and a corresponding increase of Lyt-2+ cells was observed. By approximately 1 mo of age, the relative proportion of these subsets had reversed so that Lyt-2+ cells became more numerous than B4B2+ cells.     

Phylogeography of Plathymenia reticulata (Leguminosae) reveals patterns of recent range expansion towards northeastern Brazil and southern Cerrados in Eastern Tropical South America

Little is known about past vegetation dynamics in Eastern Tropical South America (ETSA). Here we describe patterns of chloroplast (cp) DNA variation in Plathymenia reticulata, a widespread tree in the ETSA Atlantic Forest and Cerrado biomes, but not found in the xeromorphic Caatinga. Forty one populations, comprising 220 individuals, were analysed by sequencing the trnS‐trnG and trnL‐trnL‐trnF cpDNA regions. Combined, they resulted in 18 geographically structured haplotypes. The central region of the sampling area, comprising Minas Gerais and Goiás Brazilian states, is a centre of genetic diversity and probably the most longstanding area of the distribution range of the species. In contrast, populations from northeastern Brazil and the southern Cerrados showed very low diversity levels, almost exclusively with common haplotypes which are also found in the central region. Coupled with a long‐branched star‐like network, these patterns suggest a recent range expansion of P. reticulata to those regions from central region sources. The recent origin of the species (in the early Pleistocene) or the extinction of some populations due to drier and cooler climate during the last glacial maximum could have been responsible for that phylogeographic pattern. The populations from northeastern Brazil originated from two colonization routes, one eastern (Atlantic) and one western (inland). Due to its high diversity and complex landscape, the central region, especially central‐north Minas Gerais (between 15°–18° S and 42°–46° W), should be given the highest priority for conservation.     

Levels of anti-citrullinated protein antibodies and IgM rheumatoid factor are not associated with outcome in early arthritis patients: a cohort study

Introduction  

To investigate whether baseline levels of anti-citrullinated protein antibody (ACPA) or IgM rheumatoid factor (IgM-RF) and changes in the year thereafter are associated with disease activity, functional and radiographic outcome in early arthritis patients, and provide additional information over baseline autoantibody status.     

Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish

Background  

The fish, Erythrinus erythrinus, shows an interpopulation diversity, with four karyomorphs differing by chromosomal number, chromosomal morphology and heteromorphic sex chromosomes. Karyomorph A has a diploid number of 2n = 54 and does not have differentiated sex chromosomes. Karyomorph D has 2n = 52 chromosomes in females and 2n = 51 in males, and it is most likely derived from karyomorph A by the differentiation of a multiple X₁X₂Y sex chromosome system. In this study, we analyzed karyomorphs A and D by means of cytogenetic approaches to evaluate their evolutionary relationship.     

Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs

Background  

The canonical core promoter elements consist of the TATA box, initiator (Inr), downstream core promoter element (DPE), TFIIB recognition element (BRE) and the newly-discovered motif 10 element (MTE). The motifs for these core promoter elements are highly degenerate, which tends to lead to a high false discovery rate when attempting to detect them in promoter sequences.