ATP-dependent remodeling by SWI/SNF and ISWI proteins stimulates V(D)J cleavage of 5 S arrays

Control of V(D)J recombination is critical for the generation of a fully developed immune repertoire. The molecular mechanisms underlying the regulation of antigen receptor gene assembly are beginning to be revealed. Here we studied the influence of chromatin modifications on V(D)J cleavage of a polynucleosomal substrate, in which V(D)J cleavage is greatly reduced compared with naked DNA. ATP-dependent remodeling by human SWI/SNF (hSWI/SNF) in the presence of HMG1 led to a substantial increase of cleavage by the recombination activation gene (RAG) proteins. Either BRG1, the ATPase subunit of hSWI/SNF, or SNF2h, the ATPase of human ISWI complexes, was capable of stimulating V(D)J cleavage of the array, although these remodelers act by different mechanisms. No effect of histone hyperacetylation was detectable in this system. As is observed on naked DNA, in the presence of core RAG1, the full-length RAG2 protein proved to be more active than core RAG2 on these polynucleosomal arrays, reinforcing the importance of the RAG2 C-terminal domain for efficient recombination. Comparison of 5 S array cleavage by the RAG proteins or by the restriction enzyme HhaI after remodeling by hSWI/SNF suggested that RAG proteins and HhaI might have different requirements for maximal accessibility of the substrate.     

Ordered DNA release and target capture in RAG transposition

Following V(D)J cleavage, the newly liberated DNA signal ends can be either fused together into a signal joint or used as donor DNA in RAG-mediated transposition. We find that both V(D)J cleavage and release of flanking coding DNA occur before the target capture step of transposition can proceed; no coding DNA is ever detected in the target capture complex. Separately from its role in V(D)J cleavage, the DDE motif of the RAG1/2 active site is specifically required for target DNA capture. The requirement for cleavage and release of coding DNA prior to either physical target binding or functional target commitment suggests that the RAG1/2 transposase contains a single binding site for non-RSS DNA that can accommodate either target DNA or coding DNA, but not both together. Perhaps the presence of coding DNA may aid in preventing transpositional resolution of V(D)J recombination intermediates.     

Reconstructing atoll-like mounds from the Frasnian of Belgium

A succession of Frasnian mounds on the southern border of the Dinant Synclinorium (Belgium) was investigated for their facies architecture, sedimentary dynamics and palaeogeographic evolution. Seven mound facies were defined from the Arche (A) and Lion (L) members, each characterized by a specific range of textures and association of organisms (A2/L2: red or pink limestone with stromatactis, corals and crinoids; A3/L3: grey, pink or green limestone with stromatactis, corals and stromatoporoids; A4/L4: grey limestone with corals, peloids and dasycladaceens; A5/L5: grey microbial limestone; A6/L6: grey limestone with dendroid stromatoporoids; A7/L7: grey laminated limestone with fenestrae; and A8/L8: grey bioturbated limestone). Laterally equivalent sediments include substantial reworked material from the buildups and background sedimentation. Textures and fossils suggest that A2/L2 and A3/L3 facies developed close to storm wave base, in a subphotic environment. Facies A4/L4, occurring near fair weather wave base in the euphotic zone, includes lenses of A5/L5 with stromatolitic coatings and thrombolithes. A6/L6 corresponds to a slightly restricted environment and shows a progressive transition to fenestral limestone of A7/L7. This facies was deposited in a moderately restricted intertidal area. A8/L8 developed in a quiet lagoonal subtidal environment. The mounds started with A2/L2 or A3/L3 in which microbial lenses and algal facies A4/L4 became progressively more abundant upwards. Following 20 m of laterally undifferentiated facies, more restricted facies occur in the central part of the buildups. This geometry suggests the initiation of restricted sedimentation, sheltered by bindstone or floatstone facies. The facies interpretation shows that after construction of the lower part of the mounds during a transgression and a sea-level highstand, a lowstand forced reef growth to the margin of the buildups, initiating the development of atoll-like crowns during the subsequent transgressive stage. The persistence of restricted facies results from the balance between sea-level rise and reef growth.     

FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression

Background  

While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes.     

Dynamics of Memory B-Cell Populations in Blood,Lymph Nodes,and Bone Marrow during Antiretroviral Therapy and Envelope Boosting in Simian Immunodeficiency Virus SIVmac251-Infected Rhesus Macaques

Human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection causes B-cell dysregulation and the loss of memory B cells in peripheral blood mononuclear cells (PBMC). These effects are not completely reversed by antiretroviral treatment (ART). To further elucidate B-cell changes during chronic SIV infection and treatment, we investigated memory B-cell subpopulations and plasma cells/plasmablasts (PC/PB) in blood, bone marrow, and lymph nodes of rhesus macaques during ART and upon release from ART. Macaques previously immunized with SIV recombinants and the gp120 protein were included to assess the effects of prior vaccination. ART was administered for 11 weeks, with or without gp120 boosting at week 9. Naïve and resting, activated, and tissue-like memory B cells and PC/PB were evaluated by flow cytometry. Antibody-secreting cells (ASC) and serum antibody titers were assessed. No lasting changes in B-cell memory subpopulations occurred in bone marrow and lymph nodes, but significant decreases in numbers of activated memory B cells and increases in numbers of tissue-like memory B cells persisted in PBMC. Macaque PC/PB were found to be either CD27⁺ or CD27⁻ and therefore were defined as CD19⁺ CD38^hi CD138⁺. The numbers of these PC/PB were transiently increased in both PBMC and bone marrow following gp120 boosting of the unvaccinated and vaccinated macaque groups. Similarly, ASC numbers in PBMC and bone marrow of the two macaque groups also transiently increased following envelope boosting. Nevertheless, serum binding titers against SIVgp120 remained unchanged. Thus, even during chronic SIV infection, B cells respond to antigen, but long-term memory does not develop, perhaps due to germinal center destruction. Earlier and/or prolonged treatment to allow the generation of virus-specific long-term memory B cells should benefit ART/therapeutic vaccination regimens.     

Portable microsatellite primers for Ficus (Moraceae)

? Premise of the study: Highly portable microsatellite primers were developed for Ficus to facilitate investigation of genetic structure of complete regional floras using a single set of markers. ? Methods and Results: Pyrosequencing of five species of Ficus produced a library of 5723 potential primers. Potential primers found in at least two species and presenting identical annealing temperatures were tested on a set of five additional Ficus species. A set of 20 primer pairs producing well-defined and easily readable peaks was retained and tests showed their potential utility for analyzing population genetic structure of 24 Ficus species from Taiwan. Numbers of alleles per locus ranged from one to six in the least variable species and from one to 17 in the most variable species. ? Conclusions: The results indicate that our set of primers can be used to analyze polymorphism and compare levels of polymorphism among Ficus species.