Shaping of the autoreactive regulatory T cell repertoire by thymic cortical positive selection

The main function of regulatory T lymphocytes is to keep autoimmune responses at bay. Accordingly, it has been firmly established that the repertoire of CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs) is enriched in autospecific cells. Differences in thymic-positive and/or -negative selection may account for selection of the qualitatively distinct regulatory and conventional T cell (Tconv) repertoires. It has previously been shown that precursors for Tregs are less sensitive to negative selection than Tconv precursors. Studies with TCR/ligand doubly transgenic mice suggested that an agonist ligand might induce positive selection of Treg (but not Tconv) cells. However, massive deletion of Tconv (but not Treg) cell precursors observed in these mice renders interpretation of such data problematic and a potential role for positive selection in generation of the autospecific Treg repertoire has remained therefore incompletely understood. To study this important unresolved issue and circumvent use of TCR/ligand-transgenic mice, we have developed transgenic mice expressing a single MHC class II/peptide ligand on positively selecting thymic cortical epithelial cells. We found that functional Treg (but not Tconv) cells specific for the single ligand were preferentially selected from the naturally diverse repertoire of immature precursors. Our data therefore demonstrate that thymic cortical positive selection of regulatory and Tconv precursors is governed by distinct rules and that it plays an important role in shaping the autoreactive Treg repertoire.     

Identification of blottin: a novel gastric trefoil factor family-2 binding protein

The trefoil factor family (TFF) peptides are important in gastro-intestinal mucosal protection and repair. Their mechanism of action remains unclear and receptors are sought. We aimed to identify and characterise proteins binding to TFF2. A fusion protein of mouse TFF2 with alkaline phosphatase was generated and used to probe 2-D protein blots of mouse stomach. The resulting spots were analysed by MS. The protein identified was characterised by bioinformatics, rapid amplification of cDNA ends, in situ hybridisation (ISH) and immunohistochemistry (IHC). Functional assays were performed in gastrointestinal cell lines. A single major murine protein was identified and named blottin. It was previously unknown as a translated product. Blottin is also present in rat and human; the latter gene is also known as GDDR. The predicted full-length proteins are 184 amino acids long (20 kDa), reducing to 164 amino acids (18 kDa) after signal peptide cleavage. ISH of gastrointestinal tissues shows abundant blottin mRNA in gastric surface and foveolar epithelium. IHC shows cytoplasmic staining for blottin protein, and by immunoelectron microscopy in mucus granules and Golgi stacks. Previous work showed that blottin is down-regulated in gastric cancers. Blottin contains a BRICHOS domain, and has 56% similarity with gastrokine-1. Cultured HT-29 cells express blottin and show increased DNA synthesis with antiblottin antibody; however, this effect is reversed by the immunising peptide. We have identified and characterised a TFF2-binding protein produced by gastric epithelium. Blottin may play a role in gastrointestinal mucosal protection and modulate gut epithelial cell proliferation.     

Srf-dependent paracrine signals produced by myofibers control satellite cell-mediated skeletal muscle hypertrophy

Adult skeletal muscles adapt their fiber size to workload. We show that serum response factor (Srf) is required for satellite cell-mediated hypertrophic muscle growth. Deletion of Srf from myofibers and not satellite cells blunts overload-induced hypertrophy, and impairs satellite cell proliferation and recruitment to pre-existing fibers. We reveal a gene network in which Srf within myofibers modulates interleukin-6 and cyclooxygenase-2/interleukin-4 expressions and therefore exerts a paracrine control of satellite cell functions. In Srf-deleted muscles, in vivo overexpression of interleukin-6 is sufficient to restore satellite cell proliferation but not satellite cell fusion and overall growth. In contrast cyclooxygenase-2/interleukin-4 overexpression rescue satellite cell recruitment and muscle growth without affecting satellite cell proliferation, identifying altered fusion as the limiting cellular event. These findings unravel a role for Srf in the translation of mechanical cues applied to myofibers into paracrine signals, which in turn will modulate satellite cell functions and support muscle growth.     

Extensive natural variation for cellular hydrogen peroxide release is genetically controlled

Natural variation in DNA sequence contributes to individual differences in quantitative traits. While multiple studies have shown genetic control over gene expression variation, few additional cellular traits have been investigated. Here, we investigated the natural variation of NADPH oxidase-dependent hydrogen peroxide (H₂O₂ release), which is the joint effect of reactive oxygen species (ROS) production, superoxide metabolism and degradation, and is related to a number of human disorders. We assessed the normal variation of H₂O₂ release in lymphoblastoid cell lines (LCL) in a family-based 3-generation cohort (CEPH-HapMap), and in 3 population-based cohorts (KORA, GenCord, HapMap). Substantial individual variation was observed, 45% of which were associated with heritability in the CEPH-HapMap cohort. We identified 2 genome-wide significant loci of Hsa12 and Hsa15 in genome-wide linkage analysis. Next, we performed genome-wide association study (GWAS) for the combined KORA-GenCord cohorts (n = 279) using enhanced marker resolution by imputation (>1.4 million SNPs). We found 5 significant associations (p<5.00×10−8) and 54 suggestive associations (p<1.00×10−5), one of which confirmed the linked region on Hsa15. To replicate our findings, we performed GWAS using 58 HapMap individuals and ∼2.1 million SNPs. We identified 40 genome-wide significant and 302 suggestive SNPs, and confirmed genome signals on Hsa1, Hsa12, and Hsa15. Genetic loci within 900 kb from the known candidate gene p67phox on Hsa1 were identified in GWAS in both cohorts. We did not find replication of SNPs across all cohorts, but replication within the same genomic region. Finally, a highly significant decrease in H₂O₂ release was observed in Down Syndrome (DS) individuals (p<2.88×10−12). Taken together, our results show strong evidence of genetic control of H₂O₂ in LCL of healthy and DS cohorts and suggest that cellular phenotypes, which themselves are also complex, may be used as proxies for dissection of complex disorders.     

Gene maps linearization using genomic rearrangement distances.

A preliminary step to most comparative genomics studies is the annotation of chromosomes as ordered sequences of genes. Different genetic mapping techniques often give rise to different maps with unequal gene content and sets of unordered neighboring genes. Only partial orders can thus be obtained from combining such maps. However, once a total order O is known for a given genome, it can be used as a reference to order genes of a closely related species characterized by a partial order P. Our goal is to find a linearization of P that is as close as possible to O, in term of a given genomic distance. We first prove NP-completeness complexity results considering the breakpoint and the common interval distances. We then focus on the breakpoint distance and give a dynamic programming algorithm whose running time is exponential for general partial orders, but polynomial when the partial order is derived from a bounded number of genetic maps. A time-efficient greedy heuristic is then given for the general case and is empirically shown to produce solutions within 10% of the optimal solution, on simulated data. Applications to the analysis of grass genomes are presented.     

Cuticular differences of the exoskeleton relative to habitat preferences among three terrestrial isopods

Terrestrial isopods have adapted to land life by diverse morphological, physiological and behavioral changes. Isopod species exhibit a large variety of preferences ranging from moist to dry habitats. Isopod cuticle is an interesting model for studying adaptations to terrestrial life. The cuticle consists of a hierarchically organized material which provides protection and sites for muscle attachment. The present paper aimed to investigate the structure of the cuticle in three isopod species in order to relate some peculiar features to an adaptive process to environmental constraints. Results showed that general thickness of Ligia italica cuticle was quite similar to that observed in Porcellio lamellatus. Nevertheless, this cuticle was half as thick as in Porcellio laevis. Although the positive relationship found between total body lengths and the total thickness of the cuticle, the exocuticle did not show any differences between the three species. However, it is the development of a thicker endocuticle in P. laevis which make its total cuticle thickness more important.     

Interphase Clinical Trials: Phase III/Phase IV

In this paper we investigate ways in which the results of a controlled Phase III clinical trial can be used in subsequent Phase IV, and possibly further Phase III studies. Specifically we are interested in; 1) developing particular hypothesis relating to a modified study population, 2) studying how changes in the particularities of the Phase III study group can influence certain outcome variables of interest and 3) using the results of the Phase III study applied to specific target groups, having particular characteristics, to updating observations from the Phase III study with information obtained at a later stage. These issues are all concerned with the way in which we can exploit information from a Phase III trial, information that is of high quality but not necessarily directly related to the way in which many post Phase III studies, focussing on different patient population groups, are carried out. Since it is often these post Phase III studies that have the strongest influence on clinical practice we aim to develop a framework around which the post Phase III studies might be structured.