Homologous recombination is required for genome stability in the absence of DOG-1 in Caenorhabditis elegans

In C. elegans, DOG-1 prevents deletions that initiate in polyG/polyC tracts (G/C tracts), most likely by unwinding secondary structures that can form in G/C tracts during lagging-strand DNA synthesis. We have used the dog-1 mutant to assay the in vivo contribution of various repair genes to the maintenance of G/C tracts. Here we show that DOG-1 and the BLM ortholog, HIM-6, act synergistically during replication; simultaneous loss of function of both genes results in replicative stress and an increase in the formation of small deletions that initiate in G/C tracts. Similarly, we demonstrate that the C. elegans orthologs of the homologous recombination repair genes BARD1, RAD51, and XPF and the trans-lesion synthesis polymerases poleta and polkappa contribute to the prevention of deletions in dog-1 mutants. Finally, we provide evidence that the small deletions generated in the dog-1 background are not formed through homologous recombination, nucleotide excision repair, or nonhomologous end-joining mechanisms, but appear to result from a mutagenic repair mechanism acting at G/C tracts. Our data support the hypothesis that absence of DOG-1 leads to replication fork stalling that can be repaired by deletion-free or deletion-prone mechanisms.     

Using shared goal setting to improve access and equity: a mixed methods study of the Good Goals intervention in children's occupational therapy

ABSTRACT: BACKGROUND: Access and equity in children's therapy services may be improved by directing clinicians' use of resources toward specific goals that are important to patients. A practice-change intervention (titled 'Good Goals') was designed to achieve this. This study investigated uptake, adoption, and possible effects of at intervention in children's occupational therapy services. METHODS: Mixed methods case studies (n = 3 services, including 46 therapists and 558 children) were conducted. The intervention was delivered over 25 weeks through face-to-face training, team workbooks, and 'tools for change'. Data were collected before, during, and after the intervention on a range of factors using interviews, a focus group, case note analysis, routine data, document analysis, and researchers' observations. RESULTS: Factors related to uptake and adoptions were: mode of intervention delivery, competing demands on therapists' time, and leadership by service manager. Service managers and therapists reported that the intervention: helped therapists establish a shared rationale for clinical decisions; increased clarity in service provision; and improved interactions with families and schools. During the study period, therapists' behaviours changed: identifying goals, odds ratio 2.4 (95% CI 1.5 to 3.8); agreeing goals, 3.5 (2.4 to 5.1); evaluating progress, 2.0 (1.1 to 3.5). Children's LoT decreased by two months [95% CI [MINUS SIGN]8 to +4 months] across the services. Cost per therapist trained ranged from [POUND SIGN]1,003 to [POUND SIGN]1,277, depending upon service size and therapists' salary bands. CONCLUSIONS: Good Goals is a promising quality improvement intervention that can be delivered and adopted in practice and may have benefits. Further research is required to evaluate its: (i) impact on patient outcomes, effectiveness, cost-effectiveness, and (ii) transferability to other clinical contexts.     

Specific expression of an extensin-like gene in the style of Nicotiana alata.

cDNAs and corresponding genomic clones encoding a putative proline-rich protein (NaPRP3) were isolated from libraries prepared from Nicotiana alata style mRNA and genomic DNA. The predicted NaPRP3 protein is structurally similar to extensin in containing six copies of the characteristic extensin sequence Ser-Pro4, but differs in being smaller (151 residues compared with greater than 300 residues) and lacking Tyr residues. In contrast to most extensin genes, the NaPRP3 gene is not induced by mechanical wounding, and its expression is restricted to cells of the transmitting tract of the style.     

Prostaglandin E2 affects T cell responses through modulation of CD46 expression

The ubiquitous protein CD46, a regulator of complement activity, promotes T cell activation and differentiation toward a regulatory Tr1-like phenotype. The CD46-mediated differentiation pathway is defective in several chronic inflammatory diseases, underlying the importance of CD46 in controlling T cell function and the need to understand its regulatory mechanisms. Using an RNA interference-based screening approach in primary T cells, we have identified that two members of the G protein-coupled receptor kinases were involved in regulating CD46 expression at the surface of activated cells. We have investigated the role of PGE(2), which binds to the E-prostanoid family of G protein-coupled receptors through four subtypes of receptors called EP 1-4, in the regulation of CD46 expression and function. Conflicting roles of PGE(2) in T cell functions have been reported, and the reasons for these apparent discrepancies are not well understood. We show that addition of PGE(2) strongly downregulates CD46 expression in activated T cells. Moreover, PGE(2) differentially affects T cell activation, cytokine production, and phenotype depending on the activation signals received by the T cells. This was correlated with a distinct pattern of the PGE(2) receptors expressed, with EP4 being preferentially induced by CD46 activation. Indeed, addition of an EP4 antagonist could reverse the effects observed on cytokine production after CD46 costimulation. These data demonstrate a novel role of the PGE(2)-EP4 axis in CD46 functions, which might at least partly explain the diverse roles of PGE(2) in T cell functions.     

Contingency in the direction and mechanics of soil organic matter responses to increased rainfall

Background and Aims

Rainfall is expected to show greater and more variable changes in response to anticipated rising of earth surface temperatures than most other climatic variables, and will be a major driver of ecosystem change.

Methods

We studied the effects of predicted changes in California’s rainy season for storage and stabilization mechanisms of soil organic matter (SOM). In a controlled and replicated experiment, we amended rainfall over large plots of natural grassland in accordance with alternative scenarios of future climate change.

Results

We found that increases in annual rainfall have important consequences for soil carbon (C) storage, but that the strength and even direction of these effects depend critically on seasonal timing. Additional rainfall during the winter rainy season led to C loss from soil while additions after the typical rainy season increased soil C content. Analysis of MIneral-Organic Matter (OM) associations reveals a potentially powerful mechanism underlying this difference: increased winter rainfall greatly diminished the role of Fe and Al oxides in SOM stabilization. Dithionite extractable crystalline Fe oxides explained more than 35% of the variability in C storage under ambient control and extended spring rainfall conditions, compared to less than 0.01% under increased winter rainfall. Likewise, poorly crystalline Fe and Al oxides explained more than 25 and 40% of the variability in C storage in the control and extended spring rainfall treatments, respectively, but less than 5% in the increased winter rainfall treatment.

Conclusions

Increases in annual precipitation identical in amount but at three-month offsets produced opposite effects on soil C storage. Such clear differences in the amount and chemical composition of SOM, and in the vertical distribution of oxides in the soil profile in response to treatment timing carry important implications for the C sequestration trajectory of this ecosystem.     

Inhibitors of hepatitis C virus NS3/4A: α-Ketoamide based macrocyclic inhibitors

A novel series of hepatitis C virus (HCV) NS3/4A protease inhibitors bearing a P2-P4 macrocycle and a P1-P1′ α-ketoamide serine trap is reported. The NS3 protease, which is essential for viral replication, is considered one of the most attractive targets for developing novel anti-HCV therapies. The optimization of both the macrocycle and the warhead portions led to the discovery of compounds 8b and 8g with a good activity both in the enzyme as well as in the cell based (replicon) assays with favorable PK profile in a preclinical species.     

Trf1 Is Not Required for Proliferation or Functional Telomere Maintenance in Chicken DT40 Cells

The telomere end-protection complex prevents the ends of linear eukaryotic chromosomes from degradation or inappropriate DNA repair. The homodimeric double-stranded DNA-binding protein, Trf1, is a component of this complex and is essential for mouse embryonic development. To define the requirement for Trf1 in somatic cells, we deleted Trf1 in chicken DT40 cells by gene targeting. Trf1-deficient cells proliferated as rapidly as control cells and showed telomeric localization of Trf2, Rap1, and Pot1. Telomeric G-strand overhang lengths were increased in late-passage Trf1-deficient cells, although telomere lengths were unaffected by Trf1 deficiency, as determined by denaturing Southern and quantitative FISH analysis. Although we observed some clonal variation in terminal telomere fragment lengths, this did not correlate with cellular Trf1 levels. Trf1 was not required for telomere seeding, indicating that de novo telomere formation can proceed without Trf1. The Pin2 isoform and a novel exon 4, 5–deleted isoform localized to telomeres in Trf1-deficient cells. Trf1-deficient cells were sensitive to DNA damage induced by ionizing radiation. Our data demonstrate that chicken DT40 B cells do not require Trf1 for functional telomere structure and suggest that Trf1 may have additional, nontelomeric roles involved in maintaining genome stability.