207 research outputs found

    Koinonia

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    Targeting The Neo-Trekkies: Going Where No One Has Gone Before, Paul Borden President\u27s Corner Book Review: Breaking Down Walls, A Model for Reconciliation in An Age of Racial Strife Remembering the ACSD 1993 National Conference COCCA: Film Aesthetics; Book Review: Hollywood vs. America and Hot Ideas Focus on the ACSD 1994 National Conference: Convicted Civility, Can We Be Faithful and Polite Too? Editorial Leadership Retreat Held at Milligan College ACSD New Professionals\u27 Retreat Position Changeshttps://pillars.taylor.edu/acsd_koinonia/1045/thumbnail.jp

    SNP markers retrieval for a non-model species: a practical approach

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    <p>Abstract</p> <p>Background</p> <p>SNP (Single Nucleotide Polymorphism) markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC) on 454 data from four lily genotypes and compared results with respect to SNP retrieval.</p> <p>Results</p> <p>CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs.</p> <p>Conclusion</p> <p>In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.</p

    Assessment of allelic diversity in intron-containing Mal d 1 genes and their association to apple allergenicity

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    <p>Abstract</p> <p>Background</p> <p>Mal d 1 is a major apple allergen causing food allergic symptoms of the oral allergy syndrome (OAS) in birch-pollen sensitised patients. The <it>Mal d 1 </it>gene family is known to have at least 7 intron-containing and 11 intronless members that have been mapped in clusters on three linkage groups. In this study, the allelic diversity of the seven intron-containing <it>Mal d 1 </it>genes was assessed among a set of apple cultivars by sequencing or indirectly through pedigree genotyping. Protein variant constitutions were subsequently compared with <b>S</b>kin <b>P</b>rick <b>T</b>est (SPT) responses to study the association of deduced protein variants with allergenicity in a set of 14 cultivars.</p> <p>Results</p> <p>From the seven intron-containing <it>Mal d 1 </it>genes investigated, <it>Mal d 1.01 </it>and <it>Mal d 1.02 </it>were highly conserved, as nine out of ten cultivars coded for the same protein variant, while only one cultivar coded for a second variant. <it>Mal d 1.04</it>, <it>Mal d 1.05 </it>and <it>Mal d 1.06 A, B </it>and <it>C </it>were more variable, coding for three to six different protein variants. Comparison of <it>Mal d 1 </it>allelic composition between the high-allergenic cultivar Golden Delicious and the low-allergenic cultivars Santana and Priscilla, which are linked in pedigree, showed an association between the protein variants coded by the <it>Mal d 1.04 </it>and <it>-1.06A </it>genes (both located on linkage group 16) with allergenicity. This association was confirmed in 10 other cultivars. In addition, <it>Mal d 1.06A </it>allele dosage effects associated with the degree of allergenicity based on prick to prick testing. Conversely, no associations were observed for the protein variants coded by the <it>Mal d 1.01 </it>(on linkage group 13), -<it>1.02</it>, -<it>1.06B, -1.06C </it>genes (all on linkage group 16), nor by the <it>Mal d 1.05 </it>gene (on linkage group 6).</p> <p>Conclusion</p> <p>Protein variant compositions of Mal d 1.04 and -1.06A and, in case of <it>Mal d 1.06A</it>, allele doses are associated with the differences in allergenicity among fourteen apple cultivars. This information indicates the involvement of qualitative as well as quantitative factors in allergenicity and warrants further research in the relative importance of quantitative and qualitative aspects of <it>Mal d 1 </it>gene expression on allergenicity. Results from this study have implications for medical diagnostics, immunotherapy, clinical research and breeding schemes for new hypo-allergenic cultivars.</p

    Time-averaged ventilation for optimized control of variable-air-volume systems

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    Typical Variable Air Volume (VAV) terminals spend the majority of time at their minimum airflow setpoints. These are often higher than the minimum ventilation requirements defined by code, resulting in excess energy use and a risk of over-cooling the spaces. We developed and tested a Time-Averaged Ventilation (TAV) control strategy in an institutional building on the UC Berkeley campus to address this issue. Whenever a zone does not require cooling, TAV alternates the VAV damper between partially open and fully closed so that the average airflow matches a predefined ventilation setpoint. Compared to the existing, base case scenario using single-max VAV logic, this strategy reduced the mean zone airflow fraction from 0.44 to 0.27 during the intervention period. The corresponding reductions in average heating, cooling, and fan power were 41%, 23%, and 15% respectively. In addition to being programmed directly in a native control system, TAV may be applied via sMAP as a low-cost retrofit strategy in any building that has a BACnet network and direct digital control (DDC) to each VAV terminal

    Chemical and Pb Isotope Composition of Phenocrysts from Bentonites Constrains the Chronostratigraphy around the Cretaceous-Paleogene Boundary in the Hell Creek Region, Montana

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    An excellent record of environmental and paleobiological change around the CretaceousPaleogene boundary is preserved in the Hell Creek and Fort Union Formations in the western Williston Basin of northeastern Montana. These records are present in fluvial deposits whose lateral discontinuity hampers long-distance correlation. Geochronology has been focused on bentonite beds that are often present in lignites. To better identify unique bentonites for correlation across the region, the chemical and Pb isotopic composition of feldspar and titanite has been measured on 46 samples. Many of these samples have been dated by 40Ar/39Ar. The combination of chemical and isotopic compositions of phenocrysts has enabled the identification of several unique bentonite beds. In particular, three horizons located at and above the Cretaceous-Paleogene boundary can now be traced—based on their unique compositions—across the region, clarifying previously ambiguous stratigraphic relationships. Other bentonites show unusual features, such as Pb isotope variations consistent with magma mixing or assimilation, that will make them easy to recognize in future studies. This technique is limited in some cases by more than one bentonite having compositions that cannot be distinguished, or bentonites with abundant xenocrysts. The Pb isotopes are consistent with a derivation from the Bitterroot Batholith, whose age range overlaps that of the tephra. These data provide an improved stratigraphic framework for the Hell Creek region and provide a basis for more focused tephrostratigraphic work, and more generally demonstrate that the combination of mineral chemistry and Pb isotope compositions is an effective technique for tephra correlation
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