Evaluation of a New Method for Large-Scale and Gene-targeted Next Generation DNA Sequencing in Nonmodel Species

The efficient method called exon capture provides for sequencing genes genome-wide, targeting candidate genes, and sampling specific exons within genes. Although developed for model species with available whole genome sequences, the method can capture exons in nonmodel species using the genomic resources of a related model species. How close the relatives must be for effective exon capture is not known. The work herein demonstrates cross-taxa capture in ungulates, using the domestic cow genome as a reference. It also describes a computer program designed for collecting exon sequences for exon capture, allowing users to set per-gene and overall base pair (bp) limits, and to prefer internal or external exons. Cross-taxa exon capture was tested with subject-reference divergence times from 0 to ~60 million years. Sequencing success decreased with increasing subject-reference phylogenetic divergence. With the domestic cow genome as reference, American bison exons, at 1-2 million years (MY) of divergence, were captured as successfully as those of a domestic cow. The cow and bison captures each yielded sequence from ~80% of the 3.6 million bp targeted. Two bighorn sheep, 7 mule deer, and 4 pigs at about 20, 30, and 60 MY of divergence from the cow, respectively, yielded averages of ~70%, ~60%, and ~55% of the targeted bp. A gene family with many closely related, duplicated loci was expected to show reduced success compared to the whole collection. This prediction was supported, as 63 exons in the MHC gene family sequences yielded 62% fully sequenced in the cow, and 32%, 20%, and 4% for the bighorn, deer, and pigs, respectively. A comparison of two sequence alignment programs showed that Stampy, designed for high sample-reference divergence, was dramatically better than BWA, designed for low divergence, only in the pig capture, in which Stampy yielded ~30% more bp than did BWA. A universal ungulate exon capture array could be developed using the 8,999 exons that were fully sequenced in all species, including the pig at ~60 MY. As this method helps us understand the genetic basis of evolutionary processes, so it can contribute to an informed study and stewardship of our ecological endowment

The Impact of Spiritual Mentoring Among African American Males at Eastern Kentucky University

the findings of this study demonstrated that mentoring had a significant impact on African American males who attended the spiritual mentoring program at Eastern Kentucky University. these findings demonstrated mentoring can play a significant role in the life of a person and encourage growth and balance. Mentoring can bring about positive change and empower those being mentored to discover their identity and spiritual direction

Genetic component of flammability variation in a Mediterranean shrub

Recurrent fires impose a strong selection pressure in many ecosystems worldwide. In such ecosystems, plant flammability is of paramount importance because it enhances population persistence, particularly in non‐resprouting species. Indeed, there is evidence of phenotypic divergence of flammability under different fire regimes. Our general hypothesis is that flammability‐enhancing traits are adaptive; here, we test whether they have a genetic component. To test this hypothesis, we used the postfire obligate seeder Ulex parviflorus from sites historically exposed to different fire recurrence. We associated molecular variation in potentially adaptive loci detected with a genomic scan (using AFLP markers) with individual phenotypic variability in flammability across fire regimes. We found that at least 42% of the phenotypic variation in flammability was explained by the genetic divergence in a subset of AFLP loci. In spite of generalized gene flow, the genetic variability was structured by differences in fire recurrence. Our results provide the first field evidence supporting that traits enhancing plant flammability have a genetic component and thus can be responding to natural selection driven by fire. These results highlight the importance of flammability as an adaptive trait in fire‐prone ecosystems

Exome-wide DNA capture and next generation sequencing in domestic and wild species

<p>Abstract</p> <p>Background</p> <p>Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses.</p> <p>We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (<it>Bos taurus</it>) to capture (enrich for), and subsequently sequence, thousands of exons of <it>B. taurus</it>, <it>B. indicus</it>, and <it>Bison bison </it>(wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits.</p> <p>Results</p> <p>We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the <it>B. taurus </it>genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes.</p> <p>Conclusions</p> <p>This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.</p

A comparison of a direct electron detector and a high-speed video camera for a scanning precession electron diffraction phase and orientation mapping

A scanning precession electron diffraction system has been integrated with a direct electron detector to allow the collection of improved quality diffraction patterns. This has been used on a two-phase α–β titanium alloy (Timetal® 575) for phase and orientation mapping using an existing pattern-matching algorithm and has been compared to the commonly used detector system, which consisted of a high-speed video-camera imaging the small phosphor focusing screen. Noise is appreciably lower with the direct electron detector, and this is especially noticeable further from the diffraction pattern center where the real electron scattering is reduced and both diffraction spots and inelastic scattering between spots are weaker. The results for orientation mapping are a significant improvement in phase and orientation indexing reliability, especially of fine nanoscale laths of α-Ti, where the weak diffracted signal is rather lost in the noise for the optically coupled camera. This was done at a dose of ~19 e−/Å2, and there is clearly a prospect for reducing the current further while still producing indexable patterns. This opens the way for precession diffraction phase and orientation mapping of radiation-sensitive crystalline materials

Art/Act: A WGS Online Magazine

22 pages“Art, Activism, and Popular Culture” (WGS 199) investigates how art and activism intersect to address pressing contemporary social issues concerning gender, race, and sexuality. In particular, the course focuses on how art is utilized as feminist activism, and vice versa, to address social issues such as the prison industrial complex, sexual assault, media production, institutional critique, and HIV/AIDS. The course takes on a special emphasis on how artists-activists-students have utilized art to organize and create change on the college campus. Along with rigorous reading and writing, in the Winter 2016 term, students also engaged in the topic of art and activism through constructionist learning— learning through creating—in a special lab component of the class. In collaboration with the Jordan Schnitzer Museum of Art, students participated in a special museum activity to explore art history and the politics of institutional critique on campus

The Switchgrass Genome: Tools and Strategies

Switchgrass ( L.) is a perennial grass species receiving significant focus as a potential bioenergy crop. In the last 5 yr the switchgrass research community has produced a genetic linkage map, an expressed sequence tag (EST) database, a set of single nucleotide polymorphism (SNP) markers that are distributed across the 18 linkage groups, 4x sampling of the AP13 genome in 400-bp reads, and bacterial artificial chromosome (BAC) libraries containing over 200,000 clones. These studies have revealed close collinearity of the switchgrass genome with those of sorghum [ (L.) Moench], rice ( L.), and (L.) P. Beauv. Switchgrass researchers have also developed several microarray technologies for gene expression studies. Switchgrass genomic resources will accelerate the ability of plant breeders to enhance productivity, pest resistance, and nutritional quality. Because switchgrass is a relative newcomer to the genomics world, many secrets of the switchgrass genome have yet to be revealed. To continue to efficiently explore basic and applied topics in switchgrass, it will be critical to capture and exploit the knowledge of plant geneticists and breeders on the next logical steps in the development and utilization of genomic resources for this species. To this end, the community has established a switchgrass genomics executive committee and work group ( [verified 28 Oct. 2011])