Instanton induced charged fermion and neutrino masses in a minimal Standard Model scenario from intersecting D-branes

String instanton Yukawa corrections from Euclidean D-branes are investigated in an effective Standard Model theory obtained from the minimal U(3)xU(2)xU(1) D-brane configuration. In the case of the minimal chiral and Higgs spectrum, it is found that superpotential contributions are induced by string instantons for the perturbatively forbidden entries of the up and down quark mass matrices. Analogous non-perturbative effects generate heavy Majorana neutrino masses and a Dirac neutrino texture with factorizable Yukawa couplings. For this latter case, a specific example is worked out where it is shown how this texture can reconcile the neutrino data.Comment: 17 pages, 3 figure

Cave Levels, Marine Terraces, Paleoshorelines, and the Water Table in Peninsular Florida

Levels of passages are a common feature of many cave systems around the world. Likewise, coastal and marine terraces are common in coastal plain settings. This paper extends the discussion of cave levels from traditional research sites in the interior lowlands of the United States to the Atlantic Coastal Plains, namely peninsular Florida. Are there levels in Florida caves, and is there a link between the elevation of cave levels, marine terraces, paleoshorelines, and thus the water table, above and below present sea level in peninsular Florida

Non-Transgenic CRISPR-Mediated Knockout of Entire Ergot Alkaloid Gene Clusters in Slow-Growing Asexual Polyploid Fungi

The Epichloë species of fungi include seed-borne symbionts (endophytes) of cool-season grasses that enhance plant fitness, although some also produce alkaloids that are toxic to livestock. Selected or mutated toxin-free endophytes can be introduced into forage cultivars for improved livestock performance. Long-read genome sequencing revealed clusters of ergot alkaloid biosynthesis (EAS) genes in Epichloë coenophiala strain e19 from tall fescue (Lolium arundinaceum) and Epichloë hybrida Lp1 from perennial ryegrass (Lolium perenne). The two homeologous clusters in E. coenophiala—a triploid hybrid species—were 196 kb (EAS1) and 75 kb (EAS2), and the E. hybrida EAS cluster was 83 kb. As a CRISPR-based approach to target these clusters, the fungi were transformed with ribonucleoprotein (RNP) complexes of modified Cas9 nuclease (Cas9-2NLS) and pairs of single guide RNAs (sgRNAs), plus a transiently selected plasmid. In E. coenophiala, the procedure generated deletions of EAS1 and EAS2 separately, as well as both clusters simultaneously. The technique also gave deletions of the EAS cluster in E. hybrida and of individual alkaloid biosynthesis genes (dmaW and lolC) that had previously proved difficult to delete in E. coenophiala. Thus, this facile CRISPR RNP approach readily generates non-transgenic endophytes without toxin genes for use in research and forage cultivar improvement

Does allochthonous disscolved organic matter increase during summer algal bloom conditions in an agricultural reservoir?

Cyanobacterial harmful algal blooms (cyanoHABs) are increasing in frequency worldwide. CyanoHABs can produce toxins (e.g., microcystin), which can be a contaminant in recreational and drinking water reservoirs. Reservoirs have been increasing worldwide, highlighting the importance of understanding their biogeochemical processes. Dissolved organic matter (DOM) is a reactive and readily available source of nitrogen (N) and carbon (C) for microbes in aquatic systems, however, the relationships between DOM and cyanoHABs remain relatively unexplored in agricultural reservoirs. Our primary objective is to determine if an increase in allochthonous DOM leads to an increase in autochthonous DOM during a summer cyanobacterial bloom event in a warm monomictic agricultural reservoir. Water samples were collected two to three times per week from June 21st until October 5th, 2018 and analyzed for algal biomass and community composition, DOM quality and quantity. A variety of spectral parameters were used to determine DOM quality. One cyanobacterial bloom event was detected on July 16th. Maximum microcystin concentration for the sampling period was 0.68 [mu]gL-1 which is well under the EPA recommended recreational limit (8 [mu]gL-1). Dissolved organic carbon (DOC) concentrations were positively correlated with high amounts of terrestrial DOM. DOC concentrations and a350 also correlated positively with microcystin concentrations. Specific UV absorbance at 254nm (SUVA254) correlated positively with Chl-a (r=0.37, p=0.033). Our findings indicate that high DOM quantity has a significant relationship to microcystin concentration, which has negative implications for recreation and drinking water quality.Kyra M. Flora, Ruchi Bhattacharya, and Rebecca L. North (School of Natural Resources, University of Missouri, Columbia

A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups

<p>Abstract</p> <p>Background</p> <p>As the amount of genome sequencing data grows, so does the problem of computational gene identification, and in particular, the splicing signals that flank exon borders. Traditional methods for identifying splicing signals have been created and optimized using sequences from model organisms, mostly vertebrate and yeast species. However, as genome sequencing extends across the animal kingdom and includes various invertebrate species, the need for mechanisms to recognize splice signals in these organisms increases as well. With that aim in mind, we generated a model for identifying donor and acceptor splice sites that was optimized using sequences from the purple sea urchin, <it>Strongylocentrotus purpuratus</it>. This model was then used to assess the possibility of alternative or cryptic splicing within the highly variable immune response gene family known as <it>185/333</it>.</p> <p>Results</p> <p>A donor splice site model was generated from <it>S. purpuratus </it>sequences that incorporates non-adjacent dependences among positions within the 9 nt splice signal and uses position weight matrices to determine the probability that the site is used for splicing. The <it>Purpuratus </it>model was shown to predict splice signals better than a similar model created from vertebrate sequences. Although the <it>Purpuratus </it>model was able to correctly predict the true splice sites within the <it>185/333 </it>genes, no evidence for alternative or trans-gene splicing was observed.</p> <p>Conclusion</p> <p>The data presented herein describe the first published analyses of echinoderm splice sites and suggest that the previous methods of identifying splice signals that are based largely on vertebrate sequences may be insufficient. Furthermore, alternative or trans-gene splicing does not appear to be acting as a diversification mechanism in the <it>185/333 </it>gene family.</p

Chromosome-End Knockoff Strategy to Reshape Alkaloid Profiles of a Fungal Endophyte

Molecular genetic techniques to precisely eliminate genes in asexual filamentous fungi require the introduction of a marker gene into the target genome. We developed a novel strategy to eliminate genes or gene clusters located in subterminal regions of chromosomes, and then eliminate the marker gene and vector backbone used in the transformation procedure. Because many toxin gene clusters are subterminal, this method is particularly suited to generating nontoxic fungal strains. We tested this technique on Epichloë coenophiala, a seed-transmissible symbiotic fungus (endophyte) of the important forage grass, tall fescue (Lolium arundinaceum). The endophyte is necessary for maximal productivity and sustainability of this grass but can produce ergot alkaloids such as ergovaline, which are toxic to livestock. The genome sequence of E. coenophiala strain e19 revealed two paralogous ergot alkaloid biosynthesis gene clusters, designated EAS1 and EAS2. EAS1 was apparently subterminal, and the lpsB copy in EAS2 had a frame-shift mutation. We designed a vector with a fungal-active hygromycin phosphotransferase gene (hph), an lpsA1 gene fragment for homologous recombination at the telomere-distal end of EAS1, and a telomere repeat array positioned to drive spontaneous loss of hph and other vector sequences, and to stabilize the new chromosome end. We transformed E. coenophiala with this vector, then selected “knockoff” endophyte strains, confirmed by genome sequencing to lack 162 kb of a chromosome end including most of EAS1, and also to lack vector sequences. These ∆EAS1 knockoff strains produced no detectable ergovaline, whereas complementation with functional lpsB restored ergovaline production

Silicon microcantilever sensors to detect the reversible conformational change of a molecular switch, Spiropyan

The high sensitivity of silicon microcantilever sensors has expanded their use in areas ranging from gas sensing to bio-medical applications. Photochromic molecules also represent promising candidates for a large variety of sensing applications. In this work, the operating principles of these two sensing methods are combined in order to detect the reversible conformational change of a molecular switch, spiropyran. Thus, arrays of silicon microcantilever sensors were functionalized with spiropyran on the gold covered side and used as test microcantilevers. The microcantilever deflection response was observed, in five sequential cycles, as the transition from the spiropyran (SP) (CLOSED) to the merocyanine (MC) (OPEN) state and vice-versa when induced by UV and white light LED sources, respectively, proving the reversibility capabilities of this type of sensor. The microcantilever deflection direction was observed to be in one direction when changing to the MC state and in the opposite direction when changing back to the SP state. A tensile stress was induced in the microcantilever when the SP to MC transition took place, while a compressive stress was observed for the reverse transition. These different type of stresses are believed to be related to the spatial conformational changes induced in the photochromic molecule upon photo-isomerisation