Flexible modelling of spatial variation in agricultural field trials with the R package INLA

The objective of this paper was to fit different established spatial models for analysing agricultural field trials using the open-source R package INLA. Spatial variation is common in field trials, and accounting for it increases the accuracy of estimated genetic effects. However, this is still hindered by the lack of available software implementations. We compare some established spatial models and show possibilities for flexible modelling with respect to field trial design and joint modelling over multiple years and locations. We use a Bayesian framework and for statistical inference the integrated nested Laplace approximations (INLA) implemented in the R package INLA. The spatial models we use are the well-known independent row and column effects, separable first-order autoregressive ( AR1⊗AR1 ) models and a Gaussian random field (Matérn) model that is approximated via the stochastic partial differential equation approach. The Matérn model can accommodate flexible field trial designs and yields interpretable parameters. We test the models in a simulation study imitating a wheat breeding programme with different levels of spatial variation, with and without genome-wide markers and with combining data over two locations, modelling spatial and genetic effects jointly. The results show comparable predictive performance for both the AR1⊗AR1 and the Matérn models. We also present an example of fitting the models to a real wheat breeding data and simulated tree breeding data with the Nelder wheel design to show the flexibility of the Matérn model and the R package INLA

DNA Sequence Profiles of the Colorectal Cancer Critical Gene Set KRAS-BRAF-PIK3CA-PTEN-TP53 Related to Age at Disease Onset

The incidence of colorectal cancer (CRC) increases with age and early onset indicates an increased likelihood for genetic predisposition for this disease. The somatic genetics of tumor development in relation to patient age remains mostly unknown. We have examined the mutation status of five known cancer critical genes in relation to age at diagnosis, and compared the genomic complexity of tumors from young patients without known CRC syndromes with those from elderly patients. Among 181 CRC patients, stratified by microsatellite instability status, DNA sequence changes were identified in KRAS (32%), BRAF (16%), PIK3CA (4%), PTEN (14%) and TP53 (51%). In patients younger than 50 years (n = 45), PIK3CA mutations were not observed and TP53 mutations were more frequent than in the older age groups. The total gene mutation index was lowest in tumors from the youngest patients. In contrast, the genome complexity, assessed as copy number aberrations, was highest in tumors from the youngest patients. A comparable number of tumors from young (<50 years) and old patients (>70 years) was quadruple negative for the four predictive gene markers (KRAS-BRAF-PIK3CA-PTEN); however, 16% of young versus only 1% of the old patients had tumor mutations in PTEN/PIK3CA exclusively. This implies that mutation testing for prediction of EGFR treatment response may be restricted to KRAS and BRAF in elderly (>70 years) patients. Distinct genetic differences found in tumors from young and elderly patients, whom are comparable for known clinical and pathological variables, indicate that young patients have a different genetic risk profile for CRC development than older patients

Differential distribution of B7.1 (CD80) and B7.2 (CD86) costimulatory molecules on mucosal macrophage subsets in human inflammatory bowel disease (IBD)

The molecules B7.1 and B7.2 deliver costimulatory signals of critical importance to naive T cells, and may thus be involved in abrogation of oral tolerance in IBD. Functional disparity apparently exists among antigen-presenting cells in vivo. We wanted to examine if differential B7 expression occurs on mucosal macrophage subsets. Cryosections of bowel specimens from patients with IBD and normal controls were subjected to immunofluorescence and immunoperoxidase staining. In normal mucosa, selective subepithelial accumulation of B7.2+ cells was found. In inflamed IBD mucosa, however, subsets appeared consisting of both B7.2hi and B7.1hi cells as well as CD14hi macrophages. Notably, outside lymphoid aggregates the prominent fraction of recently recruited CD14hi macrophages comprised most (≈ 80%) of the B7.1hi cells, whereas most (≈ 70%) B7.2hi cells were identified as resident mucosal macrophages (CD14lo or CD14−). Differential expression of B7.1 and B7.2 on two functionally different subsets of intestinal macrophages implies separate immunoregulatory roles for the two molecules. This finding is in keeping with recent experimental data demonstrating that monocyte-derived cells are crucial for immune responses at mucosal surfaces. Preferential B7.1 up-regulation might be critical in breaking the immunological tolerance to luminal antigens in IBD, but it cannot be excluded that it is a secondary pathogenic event

Simple generalized reaction conditions for the conversion of primary aliphatic amines to surfactant-like guanidine salts with 1<i>H</i>-pyrazole carboxamidine hydrochloride

<p>Improved reaction conditions for the electrophilic reaction between a free aliphatic amine and 1H-pyrazole carboxamidine have been discovered. The surfactant-like guanidine salts, which are often hard to work with, were obtained in decent yields with short reaction times, minimal workup, and high level of purity.</p