Automated DNA Motif Discovery

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene. Keywords: pseudogene, short and microRNAs, non-coding transcripts, systems biology, machine learning, Bioinformatics, motif, regular expression, strongly typed genetic programming, context-free grammar.Comment: 12 pages, 2 figure

Rootstock influences postharvest anthracnose development in 'Hass' avocado

Rootstock studies conducted on ‘Hass’ avocado found that rootstock had a significant impact on postharvest anthracnose susceptibility. This is the first record of such an effect for avocado. The severity and incidence of anthracnose was significantly lower on ‘Hass’ grafted to ‘Velvick’ Guatemalan seedling rootstock compared with the ‘Duke 6’ Mexican seedling rootstock. Differences in anthracnose susceptibility were related to significant differences in concentrations of antifungal dienes in the leaves and mineral nutrients in the leaves and fruits from trees grafted to different rootstocks. Leaf diene concentrations were up to 1.5 times higher in ‘Hass’ trees on the ‘Velvick’ than the ‘Duke 6’ rootstock. In ungrafted nursery stock trees, diene concentrations were around 3 times higher in ‘Velvick’ than ‘Duke 6’ leaves. The ‘Velvick’/‘Hass’ combination also had a significantly lower leaf N concentration, a significantly higher fruit flesh Mn concentration, and significantly lower and higher leaf N/Ca and Ca+Mg/K ratios, respectively. A significant correlation (r = 0.82) between anthracnose severity and skin N/Ca ratio was also evident

Visualizing Tree Structures in Genetic Programming

This paper presents methods to visualize the structure of trees that occur in genetic programming. These methods allow for the inspection of structure of entire trees even though several thousands of nodes may be involved. The methods also scale to allow for the inspection of structure for entire populations and for complete trials even though millions of nodes may be involved. Examples are given that demonstrate how this new way of “seeing” can afford a potentially rich way of understanding dynamics that underpin genetic programming. The examples indicate further studies that might be enabled by visualizing structure at these scales.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45620/1/10710_2005_Article_7621.pd

Forward Neutral Pion Transverse Single Spin Asymmetries in p+p Collisions at \sqrt{s}=200 GeV

We report precision measurements of the Feynman-x dependence, and first measurements of the transverse momentum dependence, of transverse single spin asymmetries for the production of \pi^0 mesons from polarized proton collisions at \sqrt{s}=200 GeV. The x_F dependence of the results is in fair agreement with perturbative QCD model calculations that identify orbital motion of quarks and gluons within the proton as the origin of the spin effects. Results for the p_T dependence at fixed x_F are not consistent with pQCD-based calculations.Comment: 6 pages, 4 figure

Inhibition of transforming growth factor α (TGF-α)-mediated growth effects in ovarian cancer cell lines by a tyrosine kinase inhibitor ZM 252868

The modulating effects of the epidermal growth factor (EGF) receptor-specific tyrosine kinase inhibitor ZM 252868 on cell growth and signalling have been evaluated in four ovarian carcinoma cell lines PE01, PE04, SKOV-3 and PE01CDDP. Transforming growth factor α (TGF-α)-stimulated growth was completely inhibited by concentrations ≥ 0.3 μM in the PE01 and PE04 cell lines and by ≥ 0.1 μM in SKOV-3 cells. TGF-α inhibition of PE01CDDP growth was reversed by concentrations ≥ 0.1 μM ZM 252868. TGF-α-stimulated tyrosine phosphorylation of both the EGF receptor and c-erbB2 receptor in all four cell lines. The inhibitor ZM 252868, at concentrations ≥ 0.3 μM, completely inhibited TGF-α-stimulated tyrosine phosphorylation of the EGF receptor and reduced phosphorylation of the c-erbB2 protein. EGF-activated EGF receptor tyrosine kinase activity was completely inhibited by 3 μM ZM 252868 in PE01, SKOV-3 and PE01CDDP cells. These data indicate that the EGF receptor-targeted TK inhibitor ZM 252868 can inhibit growth of ovarian carcinoma cells in vitro consistent with inhibition of tyrosine phosphorylation at the EGF receptor. © 1999 Cancer Research Campaig

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Citation: Chaffin, A. S., Huang, Y. F., Smith, S., Bekele, W. A., Babiker, E., Gnanesh, B. N., . . . Tinker, N. A. (2016). A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. Plant Genome, 9(2), 21. doi:10.3835/plantgenome2015.10.0102Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (similar to 12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes

Exploring the Fast Ignition Approach to Fusion Energy

Probably the most famous equation in physics is Einstein's E=mc{sup 2}, which was contained within his fifth and final paper that was published in 1905. It is this relationship between energy ( E) and mass ( m) that the fusion process exploits to generate energy. When two isotopes of hydrogen (normally Deuterium and Tritium (DT)) fuse they form helium and a neutron. In this process some of the mass of the hydrogen is converted into energy. In the fast ignition approach to fusion a large driver (such as the NIF laser) is used to compress the DT fuel to extremely high densities and then is ''sparked'' by a high intensity, short-pulse laser. The short-pulse laser energy is converted to an electron beam, which then deposits its energy in the DT fuel. The energy of the electrons in this beam is so large that the electron's mass is increased according to Einstein theory of relativity. Understanding the transport of this relativistic electron beam is critical to the success of fast ignition and is the subject of this poster