An Easy Construction of Generalized Neighbor Designs in Minimal Circular Blocks

Neighbor designs are used in the experiments where neighbor effects may arise. Neighbor designs neutralize these effects and are, therefore, considered to be robust against neighbor effects. Minimal neighbor designs are always most economical among the neighbor designs and are, therefore, preferred by the experimenters. Method of cyclic shifts provides these designs in circular blocks only for odd v (number of treatments). For v even, minimal circular generalized neighbor designs in which only v 2 unordered pairs of distinct treatments do not appear as neighbors will be the better alternate to the minimal neighbor designs. In this article, such minimal generalized neighbor designs are constructed in circular blocks for v even.

Theoretical analysis of RNA polymerase fidelity: a steady-state copolymerization approach

The fidelity of DNA transcription catalyzed by RNA polymerase (RNAP) has long been an important issue in biology. Experiments have revealed that RNAP can incorporate matched nucleotides selectively and proofread the incorporated mismatched nucleotides. However, systematic theoretical researches on RNAP fidelity are still lacking. In the last decade, several theories on RNA transcription have been proposed, but they only handled highly simplified models without considering the high-order neighbor effects and the oligonucleotides cleavage both of which are critical for the overall fidelity. In this paper, we regard RNA transcription as a binary copolymerization process and calculate the transcription fidelity by the steady-state copolymerization theory recently proposed by us for DNA replication. With this theory, the more realistic models considering higher-order neighbor effects, oligonucleotides cleavage, multi-step incorporation and multi-step cleavage can be rigorously handled.

Nearest-neighbor effects modulate loxP spacer DNA chemical shifts and guide oligonucleotide design for NMR studies

Cre recombinase catalyzes site-specific DNA recombination at pseudo-palindromic loxP sites through two rounds of strand cleavage, exchange, and religation. Cre is a potential gene editing tool of interest due its lack of requirements for external energy sources or host factors, as well as the fact that it does not generate potentially cytotoxic double-stranded DNA breaks. However, broader applications of Cre in editing noncanonical target sequences requires a deeper understanding of the DNA features that enable target site selection and efficient recombination. Although Cre recombines loxP DNA in a specific and ordered fashion, it makes few direct contacts to the loxP spacer, the region where recombination occurs. Furthermore, little is known about the structural and dynamic features of the loxP spacer that make it a suitable target for Cre. To enable NMR spectroscopic studies of the spacer, we have aimed to identify a fragment of the 34-bp loxP site that retains the structural features of the spacer while minimizing the spectral crowding and line-broadening seen in longer oligonucleotides. We report sequential backbone resonance assignments for loxP oligonucleotides of varying lengths and evaluate chemical shift differences, Δδ, between the oligos. Analysis of flanking sequence effects and mutations on spacer chemical shifts indicates that nearest-neighbor and next-nearest-neighbor effects dominate the chemical environment experienced by the spacer. We have identified a 16-bp oligonucleotide that adequately preserves the structural environment of the spacer, setting the stage for NMR-based structure determination and dynamics investigations.

Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory

An increasing number of field studies have shown that the phenotype of an individual plant depends not only on its genotype but also on those of neighboring plants; however, this fact is not taken into consideration in genome-wide association studies (GWAS). Based on the Ising model of ferromagnetism, we incorporated neighbor genotypic identity into a regression model, named “Neighbor GWAS”. Our simulations showed that the effective range of neighbor effects could be estimated using an observed phenotype when the proportion of phenotypic variation explained (PVE) by neighbor effects peaked. The spatial scale of the first nearest neighbors gave the maximum power to detect the causal variants responsible for neighbor effects, unless their effective range was too broad. However, if the effective range of the neighbor effects was broad and minor allele frequencies were low, there was collinearity between the self and neighbor effects. To suppress the false positive detection of neighbor effects, the fixed effect and variance components involved in the neighbor effects should be tested in comparison with a standard GWAS model. We applied neighbor GWAS to field herbivory data from 199 accessions of Arabidopsis thaliana and found that neighbor effects explained 8% more of the PVE of the observed damage than standard GWAS. The neighbor GWAS method provides a novel tool that could facilitate the analysis of complex traits in spatially structured environments and is available as an R package at CRAN (https://cran.rproject.org/package=rNeighborGWAS).

Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects

Phenotypes of sessile organisms, such as plants, rely not only on their own genotypes but also on those of neighboring individuals. Previously, we incorporated such neighbor effects into a single-marker regression using the Ising model of ferromagnetism. However, little is known regarding how neighbor effects should be incorporated in quantitative trait locus (QTL) mapping. In this study, we propose a new method for interval QTL mapping of neighbor effects, designated” neighbor QTL,” the algorithm of which includes: (i) obtaining conditional self-genotype probabilities with recombination fraction between flanking markers; (ii) calculating conditional neighbor genotypic identity using the self-genotype probabilities; and (iii) estimating additive and dominance deviations for neighbor effects. Our simulation using F2 and backcross lines showed that the power to detect neighbor effects increased as the effective range decreased. The neighbor QTL was applied to insect herbivory on Col × Kas recombinant inbred lines of Arabidopsis thaliana. Consistent with previous results, the pilot experiment detected a self-QTL effect on the herbivory at the GLABRA1 locus. Regarding neighbor QTL effects on herbivory, we observed a weak QTL on the top of chromosome 4, at which a weak self-bolting QTL was also identified. The neighbor QTL method is available as an R package ( https://cran.r-project.org/package=rNeighborQTL ), providing a novel tool to investigate neighbor effects in QTL studies.