Identification of the expressome by machine learning on omics data.

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes

Investigation into the Role of Platelet Derived Growth Factor (PDGF) in Type I Collagen Glomerulopathy

Progressive accumulation of collagen and extracellular matrix (ECM) proteins within renal glomeruli have implications for or result in renal fibrosis and glomerulosclerosis, with both events culminating in renal failure. To model this accumulation the Col1a2-deficient mouse model was used. The Col1a2-deficientmouse model is characterized by a mutation in the a2(I) chain, preventing incorporation into the type I collagen molecule. As a result, an α1(I) collagen chain incorporates into the collagen triple helix forming homotrimeric type I collagen, as opposed to heterotrimeric type I collagen. This change is due to the secondary wound healing response in response to ECM accumulation, fibrosis, or damage. Transforming growth factor-beta (TGF-β) has been studied within this model and demonstrated it was not the initiating molecule in collagen deposition. This study looks at Tumor Necrosis Factor-Alpha (TNF-a) and Platelet Derived Growth Factor (PDGF) as potential mediators of this hypothesized secondary wound healing response. TNF-ais an inflammatory cytokine produced following tissue damage, released by mesangial cells, and has been shown to induce epithelial-to-mesenchymal transition (EMT). Recently, PDGF receptors and ligand upregulation has been shown in other mouse models of renal fibrosis. However, TNF-ashowed no differential staining upon Picrosirius Red (PSR) between experimental and control groups. PDGFR-ββ and PDGF-BB displayed differential labeling in Col1a2-deficient in comparison to age matched wild type animals. The results for PDGF-DD mice were less conclusive when comparing the Col1a2-deficient mice to that of their wild type counterparts

Complexified sigma model and duality

We show that the equations of motion associated with a complexified sigma-model action do not admit manifest dual SO(n,n) symmetry. In the process we discover new type of numbers which we called `complexoids' in order to emphasize their close relation with both complex numbers and matroids. It turns out that the complexoids allow to consider the analogue of the complexified sigma-model action but with (1+1)-worldsheet metric, instead of Euclidean-worldsheet metric. Our observations can be useful for further developments of complexified quantum mechanics.Comment: 15 pages, Latex, improved versio

Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes

High temperature–high pressure thermal conductivities of ethylene and propane

Thermal conductivities λ of ethylene and propane were measured in the temperature and pressure ranges 400–750 K and 0.1–2.65 MPa (ethylene) and 400–725 K and 0.1 to 0.6 MPa (propane). The data were correlated by expressions of the form λ=λ0(T) ×λp(P), with λ0 being a second order polynomial in temperature and λp a third (ethylene) or a fourth (propane) order polynomial in pressure. The results obtained were compared with previous thermal conductivity measurements.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71313/2/JCPSA6-70-8-3948-1.pd

Quantum affine Cartan matrices, Poincare series of binary polyhedral groups, and reflection representations

We first review some invariant theoretic results about the finite subgroups of SU(2) in a quick algebraic way by using the McKay correspondence and quantum affine Cartan matrices. By the way it turns out that some parameters (a,b,h;p,q,r) that one usually associates with such a group and hence with a simply-laced Coxeter-Dynkin diagram have a meaningful definition for the non-simply-laced diagrams, too, and as a byproduct we extend Saito's formula for the determinant of the Cartan matrix to all cases. Returning to invariant theory we show that for each irreducible representation i of a binary tetrahedral, octahedral, or icosahedral group one can find a homomorphism into a finite complex reflection group whose defining reflection representation restricts to i.Comment: 19 page