Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450

Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection. We have created an artificial family comprising ~3,000 P450 heme proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven crossover locations chosen to minimize structural disruption. Members of this protein family differ from any known sequence at an average of 72 and by as many as 109 amino acids. Most (>73%) of the properly folded chimeric P450 heme proteins are catalytically active peroxygenases; some are more thermostable than the parent proteins. A multiple sequence alignment of 955 chimeras, including both folded and not, is a valuable resource for sequence-structure-function studies. Logistic regression analysis of the multiple sequence alignment identifies key structural contributions to cytochrome P450 heme incorporation and peroxygenase activity and suggests possible structural differences between parents CYP102A1 and CYP102A2

Compost Carryover: Nitrogen Phosphorous and FT-IR Analysis of Soil Organic Matter

Compost plays a central role in organic soil fertility plans but is bulky and costly to apply. Determining compost carryover is therefore important for cost-effective soil fertility planning. This study investigated two aspects of nutritive carryover [nitrogen and phosphorus (P)], and an indicator of non-nutritive carryover [soil organic matter (SOM)] to determine the residual effect of a one-time compost application applied at four rates in a corn-squash rotation. Crop yield was measured as an integrated carryover indicator of nutritive and non-nutritive effects. Functional groups of compost and SOM were investigated using FT-IR spectroscopy and soil organic carbon (SOC). While year to year variability was great, compost had a persistent positive effect on crop yields, evident 3 years after application with no reduction in magnitude over time. Soil nitrate was low, and additions of compost at any rate generally did not increase levels beyond the year of application, with the exception of year four. Olsen P was also low, yet was higher in amended soils than in non-amended soils 3 years after application. Pronounced polysaccharide peaks, evident in compost spectra and absent in control soil, were apparent in compost-amended soils 3 years after compost treatment and SOC was greater 2 years afterwards. Compost carryover was most pronounced in year four following the incorporation of a nitrogen-fixing cover crop. These results show that compost can influence nutritive and non-nutritive soil properties many years after incorporation, thereby reinforcing the importance of including compost in organic fertility plans despite the unpredictability of year-to-year response

Semi-classical twists for sl(3) and sl(4) boundary r-matrices of Cremmer-Gervais type

We obtain explicit formulas for the semi-classical twists deforming the coalgebraic structure of U(sl(3)) and U(sl(4)). In rank 2 and 3 the corresponding universal R-matrices quantize the boundary r-matrices of Cremmer-Gervais type defining Lie Frobenius structures on the maximal parabolic subalgebras in sl(n)

Cremmer-Gervais r-matrices and the Cherednik Algebras of type GL2

We give an intepretation of the Cremmer-Gervais r-matrices for sl(n) in terms of actions of elements in the rational and trigonometric Cherednik algebras of type GL2 on certain subspaces of their polynomial representations. This is used to compute the nilpotency index of the Jordanian r-matrices, thus answering a question of Gerstenhaber and Giaquinto. We also give an interpretation of the Cremmer-Gervais quantization in terms of the corresponding double affine Hecke algebra.Comment: 6 page

The non-dynamical r-matrices of the degenerate Calogero-Moser models

A complete description of the non-dynamical r-matrices of the degenerate Calogero-Moser models based on $gl_n$ is presented. First the most general momentum independent r-matrices are given for the standard Lax representation of these systems and those r-matrices whose coordinate dependence can be gauged away are selected. Then the constant r-matrices resulting from gauge transformation are determined and are related to well-known r-matrices. In the hyperbolic/trigonometric case a non-dynamical r-matrix equivalent to a real/imaginary multiple of the Cremmer-Gervais classical r-matrix is found. In the rational case the constant r-matrix corresponds to the antisymmetric solution of the classical Yang-Baxter equation associated with the Frobenius subalgebra of $gl_n$ consisting of the matrices with vanishing last row. These claims are consistent with previous results of Hasegawa and others, which imply that Belavin's elliptic r-matrix and its degenerations appear in the Calogero-Moser models. The advantages of our analysis are that it is elementary and also clarifies the extent to which the constant r-matrix is unique in the degenerate cases.Comment: 25 pages, LaTeX; expanded by an appendix detailing the proof of Theorem 1 and a concluding section in version

Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids.

Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model

Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation

Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis