Compensatory T-cell regulation in unaffected relatives of SLE patients, and opposite IL-2/CD25-mediated effects suggested by coreferentiality modeling

In human systemic lupus erythematosus (SLE), diverse autoantibodies accumulate over years before disease manifestation. Unaffected relatives of SLE patients frequently share a sustained production of autoantibodies with indiscriminable specificity, usually without ever acquiring the disease. We studied relations of IgG autoantibody profiles and peripheral blood activated regulatory T-cells (aTregs), represented by CD4(+)CD25(bright) T-cells that were regularly 70-90% Foxp3(+). We found consistent positive correlations of broad-range as well as specific SLE-associated IgG with aTreg frequencies within unaffected relatives, but not patients or unrelated controls. Our interpretation: unaffected relatives with shared genetic factors compensated pathogenic effects by aTregs engaged in parallel with the individual autoantibody production. To study this further, we applied a novel analytic approach named coreferentiality that tests the indirect relatedness of parameters in respect to multivariate phenotype data. Results show that independently of their direct correlation, aTreg frequencies and specific SLE-associated IgG were likely functionally related in unaffected relatives: they significantly parallelled each other in their relations to broad-range immunoblot autoantibody profiles. In unaffected relatives, we also found coreferential effects of genetic variation in the loci encoding IL-2 and CD25. A model of CD25 functional genetic effects constructed by coreferentiality maximization suggests that IL-2-CD25 interaction, likely stimulating aTregs in unaffected relatives, had an opposed effect in SLE patients, presumably triggering primarily T-effector cells in this group. Coreferentiality modeling as we do it here could also be useful in other contexts, particularly to explore combined functional genetic effects.     

Variation of 15N natural abundance in leaves and nodules of actinorhizal shrubs in Northwest Patagonia

This study was performed to assess the N₂-fixing capability of the native actinorhizal species Ochetophila trinervis (sin. Discaria trinervis) and Discaria chacaye (Rhamnaceae) in Northwest Patagonia. We measured the N concentration and ¹⁵N natural abundance in leaves and nodules of O. trinervis and D. chacaye, in leaves of associated non-actinorhizal vegetation, and in the soils under each sampled plant. O. trinervis and D. chacaye had foliar N concentrations that were about twice that of non-actinorhizal shrubs growing at the same sites, even though soils varied four-fold in total N across the sites. Leaves of both actinorhizal plants had a similar δ¹⁵N at any site and were close to atmospheric values. The foliar δ¹⁵N of non-actinorhizal plants and soil δ¹⁵N were strongly correlated across the sites. Nodules were depleted in δ¹⁵N relative to the foliage of the respective actinorhizal species. In conjunction with the uniformly high foliage N concentration of these actinorhizal plants and the universal presence of vesicles observed in root nodules, these data strongly suggest that O. trinervis and D. chacaye obtain a significant amount of their N from N₂ fixation. To calculate the proportion of N derived from atmosphere, theoretical B-values were estimated. In all cases where the δ¹⁵N of fixing and reference foliage were significantly different, O. trinervis and D. chacaye obtained almost all of their N from N₂ fixation. These results are the first to demonstrate N₂ fixation by O. trinervis and D. chacaye in the field and therefore suggest an important role for these actinorhizal plants in the N economy of ecosystems in northwest Patagonia as well as their potential use for restoration of degraded lands in this region.     

Life in soil by the actinorhizal root nodule endophyte <Emphasis Type="BoldItalic">Frankia</Emphasis>. A review

Frankia is a genus of soil actinomycetes famous for its ability to form N₂-fixing root nodule symbioses with actinorhizal plants. Although Frankia strains display a high diversity in terms of ecological niches in soil, current knowledge about Frankia is dominated by its life as an endophyte in root nodules. Increased use of molecular methods has refined and expanded insights into endophyte-host specificities and Frankia phylogeny. This review has focus on Frankia as a soil organism, including its part of microbial consortia, and how to study Frankia in soil. We highlight the use of nodulation tests and molecular methods to reveal population size and genetic diversity of Frankia in soil and discuss how autoregulation of nodulation and interactions with other soil microorganisms may influence the results. A comprehensive record of published interactions between Frankia and other soil microbes is summarized.     

Using scales to clarify the transition from blue-phase to brown-phase fingerling in Notothenia rossii from the South Shetland Islands

Scales and whole otoliths were read for age determination in early stages of Notothenia rossii caught in Potter Cove, South Shetland Islands, in summer seasons 2003–2006 and 2008. The sample comprised blue-phase pelagic fingerlings of 7.0–7.6 cm (TL) of age group 0 year and demersal brown-phase fingerlings/juveniles of 8.5–20.9 cm and predominant age groups 1–2 years. Counting of sclerites facilitated the interpretation of the rings, particularly in the central scale. To clarify two previous issues of controversy, we deduce that the duration of the offshore pelagic blue-phase fingerling stage is less than one year before migration to the nearshore demersal habitat. Furthermore, the first well-defined ring in scales corresponded to the first annulus, while a contiguous ring was a secondary ring sometimes deposited after the first winter during the second year of life, attributable to a shift of habitat from pelagic to demersal. A von Bertalanffy growth curve was computed by combining age/length data of the juvenile phase of N. rossii from this and a previous study at Potter Cove with literature data from the offshore adult population, resulting in the following equation: L_t = 8 6. 9  ( 1- \texte ^{- 0. 0 9 1 (t - 0. 6 6 8 )} ) L_{t} = 8 6. 9 \,\left( { 1- {\text{e}}^{{ - 0. 0 9 1 (t - 0. 6 6 8 )}} } \right) _.     

Distinct Roles of the ATR Kinase and the Mre11-Rad50-Nbs1 Complex in the Maintenance of Chromosomal Stability in Arabidopsis

Signaling of chromosomal DNA breaks is of primary importance for initiation of repair and, thus, for global genomic stability. Although the Mre11-Rad50-Nbs1 (MRN) complex is the first sensor of double-strand breaks, its role in double-strand break (DSB) signaling is not fully understood. We report the absence of γ-ray–induced, ATM/ATR-dependent histone H2AX phosphorylation in Arabidopsis thaliana rad50 and mre11 mutants, confirming that the MRN complex is required for H2AX phosphorylation by the ATM and ATR kinases in response to irradiation-induced DSB in Arabidopsis. rad50 and mre11 mutants spontaneously activate a DNA damage response, as shown by the presence of γ-H2AX foci and activation of cell cycle arrest in nonirradiated plants. This response is ATR dependent as shown both by the absence of these spontaneous foci and by the wild-type mitotic indices of double rad50 atr and mre11 atr plants. EdU S-phase labeling and fluorescence in situ hybridization analysis using specific subtelomeric probes point to a replicative S-phase origin of this chromosome damage in the double mutants and not to telomere destabilization. Thus, the data presented here show the exclusive involvement of ATR in DNA damage signaling in MRN mutants and provide evidence for a role for ATR in the avoidance of S-phase DNA damage.     

Genomic markers reveal introgressive hybridization in the Indo-West Pacific mangroves: a case study

Biodiversity of mangrove ecosystems is difficult to assess, at least partly due to lack of genetic verification of morphology-based documentation of species. Natural hybridization, on the one hand, plays an important role in evolution as a source of novel gene combinations and a mechanism of speciation. However, on the other hand, recurrent introgression allows gene flow between species and could reverse the process of genetic differentiation among populations required for speciation. To understand the dynamic evolutionary consequences of hybridization, this study examines genomic structure of hybrids and parental species at the population level. In the Indo-West Pacific, Bruguiera is one of the dominant mangrove genera and species ranges overlap extensively with one another. Morphological intermediates between sympatric Bruguiera gymnorrhiza and Bruguiera sexangula have been reported as a variety of B. sexangula or a new hybrid species, B. × rhynchopetala. However, the direction of hybridization and extent of introgression are unclear. A large number of species-specific inter-simple sequence repeat (ISSR) markers were found in B. gymnorrhiza and B. sexangula, and the additive ISSR profiling of B. × rhynchopetala ascertained its hybrid status and identified its parental origin. The varying degree of scatterness among hybrid individuals in Principal Coordinate Analysis and results from NewHybrids analysis indicate that B. × rhynchopetala comprises different generations of introgressants in addition to F(1)s. High genetic relatedness between B. × rhynchopetala and B. gymnorrhiza based on nuclear and chloroplast sequences suggests preferential hybrid backcrosses to B. gymnorrhiza. We conclude that B. × rhynchopetala has not evolved into an incipient hybrid species, and its persistence can be explained by recurrent hybridization and introgression. Genomic data provide insights into the hybridization dynamics of mangrove plants. Such information can assist in biodiversity assessment by helping detect novel taxa and/or define species boundaries.     

The clathrin adaptor complex AP-1 binds HIV-1 and MLV Gag and facilitates their budding

Retroviral assembly is driven by Gag, and nascent viral particles escape cells by recruiting the machinery that forms intralumenal vesicles of multivesicular bodies. In this study, we show that the clathrin adaptor complex AP-1 is involved in retroviral release. The absence of AP-1mu obtained by genetic knock-out or by RNA interference reduces budding of murine leukemia virus (MLV) and HIV-1, leading to a delay of viral propagation in cell culture. In contrast, overexpression of AP-1mu enhances release of HIV-1 Gag. We show that the AP-1 complex facilitates retroviral budding through a direct interaction between the matrix and AP-1mu. Less MLV Gag is found associated with late endosomes in cells lacking AP-1, and our results suggest that AP-1 and AP-3 could function on the same pathway that leads to Gag release. In addition, we find that AP-1 interacts with Tsg101 and Nedd4.1, two cellular proteins known to be involved in HIV-1 and MLV budding. We propose that AP-1 promotes Gag release by transporting it to intracellular sites of active budding, and/or by facilitating its interactions with other cellular partners.