Consistency and Change in Participatory Action Research: Reflections on a Focus Group Study about How Farmers Learn

The purpose of this paper is to reflect on our efforts to balance consistency in our multi-year participatory action research study with the need to adapt our research protocol to what we are learning along the way. While both are important, we share several examples of how our flexibility and openness to adapt our protocol to our research findings has lead to methodological refinements and serendipitous learnings. We discuss implications for both agricultural education and research

Abelian Gauge Fluxes and Local Models in F-Theory

We analyze the Abelian gauge fluxes in local F-theory models with G_S=SU(6) and SO(10). For the case of G_S=SO(10), there is a no-go theorem which states that for an exotic-free spectrum, there are no solutions for U(1)^2 gauge fluxes. We explicitly construct the U(1)^2 gauge fluxes with an exotic-free bulk spectrum for the case of G_S=SU(6). We also analyze the conditions for the curves supporting the given field content and discuss non-minimal spectra of the MSSM with doublet-triplet splitting.Comment: 43 pages, 15 tables; typos corrected, reference adde

U(n) Spectral Covers from Decomposition

We construct decomposed spectral covers for bundles on elliptically fibered Calabi-Yau threefolds whose structure groups are S(U(1) x U(4)), S(U(2) x U(3)) and S(U(1) x U(1) x U(3)) in heterotic string compactifications. The decomposition requires not only the tuning of the SU(5) spectral covers but also the tuning of the complex structure moduli of the Calabi-Yau threefolds. This configuration is translated to geometric data on F-theory side. We find that the monodromy locus for two-cycles in K3 fibered Calabi-Yau fourfolds in a stable degeneration limit is globally factorized with squared factors under the decomposition conditions. This signals that the monodromy group is reduced and there is a U(1) symmetry in a low energy effective field theory. To support that, we explicitly check the reduction of a monodromy group in an appreciable region of the moduli space for an $E_6$ gauge theory with (1+2) decomposition. This may provide a systematic way for constructing F-theory models with U(1) symmetries.Comment: 41 pages, 14 figures; v2: minor improvements and a reference adde

On Global Flipped SU(5) GUTs in F-theory

We construct an SU(4) spectral divisor and its factorization of types (3,1) and (2,2) based on the construction proposed in [1]. We calculate the chiral spectra of flipped SU(5) GUTs by using the spectral divisor construction. The results agree with those from the analysis of semi-local spectral covers. Our computations provide an example for the validity of the spectral divisor construction and suggest that the standard heterotic formulae are applicable to the case of F-theory on an elliptically fibered Calabi-Yau fourfold with no heterotic dual.Comment: 45 pages, 12 tables, 1 figure; typos corrected, footnotes added, and a reference adde

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication

The genome-wide mapping of gene-regulatory motifs remains a major goal that will facilitate the modelling of gene-regulatory networks and their evolution. The repressor element 1 is a long, conserved transcription factor-binding site which recruits the transcriptional repressor REST to numerous neuron-specific target genes. REST plays important roles in multiple biological processes and disease states. To map RE1 sites and target genes, we created a position specific scoring matrix representing the RE1 and used it to search the human and mouse genomes. We identified 1301 and 997 RE1s inhuman and mouse genomes, respectively, of which >40% are novel. By employing an ontological analysis we show that REST target genes are significantly enriched in a number of functional classes. Taking the novel REST target gene CACNA1A as an experimental model, we show that it can be regulated by multiple RE1s of different binding affinities, which are only partially conserved between human and mouse. A novel BLAST methodology indicated that many RE1s belong to closely related families. Most of these sequences are associated with transposable elements, leading us to propose that transposon-mediated duplication and insertion of RE1s has led to the acquisition of novel target genes by REST during evolution

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Lack of HLA predominance and HLA shared epitopes in biliary Atresia

Biliary atresia (BA) is characterized by progressive inflammation and fibrosis of bile ducts. A theory of pathogenesis entails autoimmune-mediated injury targeting bile duct epithelia. One of the strongest genetic associations with autoimmunity is with HLA genes. In addition, apparently dissimilar HLA alleles may have similar antigen-binding sites, called shared epitopes, that overlap in their capacity to present antigens. In autoimmune disease, the incidence of the disease may be related to the presence of shared epitopes, not simply the HLA allelic association. Aim: To determine HLA allele frequency (high-resolution genotyping) and shared epitope associations in BA. Results: Analysis of every allele for HLA-A, -B, -C, -DRB1, -DPB1 and -DQB1 in 180 BA and 360 racially-matched controls did not identify any significant HLA association with BA. Furthermore, shared epitope analysis of greater than 10 million possible combinations of peptide sequences was not different between BA and controls. Conclusions: This study encompasses the largest HLA allele frequency analysis for BA in the United States and is the first study to perform shared epitope analysis. When controlling for multiple comparisons, no HLA allele or shared epitope association was identified in BA. Future studies of genetic links to BA that involve alterations of the immune response should include investigations into defects in regulatory T cells and non-HLA linked autoinflammatory diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2193-1801-2-42) contains supplementary material, which is available to authorized users