Isotopes from Fecal Material Provides Evidence of Recent Diet of Prairie Deer Mice

Prairie deer mice are important predators in many agricultural systems, and through their diet they can help to regulate pest insect and weed populations. Our objective was to test whether fecal material is an effective means of detailing the foraging ecology of small mammals. We conducted three studies to evaluate the efficacy of this technique: 1) field-collected fecal material from unknown deer mice from late winter to early spring, 2) fecal material collected in an enclosure with mice fed a mix of C3 and C4 plant seeds, and 3) fecal material from tagged female mice in the field. We detected significant shifts in δ13C in one study and δ15N in another relative to spring thaw (δ13C: –13.34 vs. –10.72, P = 0.01, δ15N: 4.92 vs. 4.09, P = 0.03), a significant correlation between the relative amounts of two seed types and δ13C (slope = 5.46, SE = 1.82, P \u3c 0.01), and a significant decrease in δ15N due to nursing (4.57 ± 0.19 vs 3.28 ± 0.47, P = 0.02). Use of this technique will help to clarify foraging of this economically important species in agroecosystems

Isotopes from Fecal Material Provides Evidence of Recent Diet of Prairie Deer Mice

Prairie deer mice are important predators in many agricultural systems, and through their diet they can help to regulate pest insect and weed populations. Our objective was to test whether fecal material is an effective means of detailing the foraging ecology of small mammals. We conducted three studies to evaluate the efficacy of this technique: 1) field-collected fecal material from unknown deer mice from late winter to early spring, 2) fecal material collected in an enclosure with mice fed a mix of C3 and C4 plant seeds, and 3) fecal material from tagged female mice in the field. We detected significant shifts in δ13C in one study and δ15N in another relative to spring thaw (δ13C: –13.34 vs. –10.72, P = 0.01, δ15N: 4.92 vs. 4.09, P = 0.03), a significant correlation between the relative amounts of two seed types and δ13C (slope = 5.46, SE = 1.82, P \u3c 0.01), and a significant decrease in δ15N due to nursing (4.57 ± 0.19 vs 3.28 ± 0.47, P = 0.02). Use of this technique will help to clarify foraging of this economically important species in agroecosystems

Perspectives of Extension Agents and Farmers Toward Multifunctional Agriculture in the United States Corn Belt

We surveyed the perspectives of farmers, crop professionals, and Extension agents and found that they have positive perspectives concerning multifunctional agriculture, including a positive effect of a nearby prairie to cropland productivity. The survey was conducted in central Iowa and included individuals predominantly from Iowa involved in commodity research and production. Our results are preliminary and provide a baseline for further research into the perspectives of change agents in the U.S. Corn Belt. They also provide insight into similarities among key links in the diffusion of innovation chain

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (KD). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA at sites complementary to a 20-base-pair guide RNA. The Cas9 system has been used to modify genomes in multiple cells and organisms, demonstrating its potential as a facile genome-engineering tool. We used in vitro selection and high-throughput sequencing to determine the propensity of eight Cas9:guide RNA complexes to cleave each of 10^12 potential off-target DNA sequences. The selection results predicted five off-target sites in the human genome that were confirmed to undergo genome cleavage in HEK293T cells upon expression of one of two Cas9:guide RNA complexes. In contrast to previous models, our results show that Cas9:guide RNA specificity extends past a 7- to 12-base pair seed sequence. Our results also suggest a tradeoff between activity and specificity both in vitro and in cells as a shorter, less-active guide RNA is more specific then a longer, more-active guide RNA. High concentrations of Cas9:guide RNA complexes can cleave off-target sites containing mutations near or within the PAM that are not cleaved when enzyme concentrations are limiting

Rapid Morphological Change in the Masticatory Structures of an Important Ecosystem Service Provider.

Humans have altered the biotic and abiotic environmental conditions of most organisms. In some cases, such as intensive agriculture, an organism's entire ecosystem is converted to novel conditions. Thus, it is striking that some species continue to thrive under such conditions. The prairie deer mouse (Peromyscus maniculatus bairdii) is an example of such an organism, and so we sought to understand what role evolutionary adaptation played in the success of this species, with particular interest in adaptations to novel foods. In order to understand the evolutionary history of this species' masticatory structures, we examined the maxilla, zygomatic plate, and mandible of historic specimens collected prior to 1910 to specimens collected in 2012 and 2013. We found that mandibles, zygomatic plates, and maxilla have all changed significantly since 1910, and that morphological development has shifted significantly. We present compelling evidence that these differences are due to natural selection as a response to a novel and ubiquitous food source, waste grain (corn, Zea mays and soybean, Glycine max)

Summary of variation explained by PC axes.

<p>This table shows the percent of variation explained by the first 8 PC axes of mandible and upper jaw shape.</p><p>Summary of variation explained by PC axes.</p

Landmarks used for morphological analysis.

<p>Landmarks follow Myers et al. and McPhee [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127218#pone.0127218.ref026" target="_blank">26</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127218#pone.0127218.ref025" target="_blank">25</a>]. Landmarks follow the same numbering as seen in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127218#pone.0127218.g002" target="_blank">Fig 2</a>.</p><p>Landmarks used for morphological analysis.</p

Size differences in mouse upper jaws and mandibles.

<p>All data depict average centroid size, which is calculated using all landmarks included in the morphometric analysis. Figures depict mandible and upper jaw size differences by location and year. Site abbreviations and sample sizes are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127218#pone.0127218.t001" target="_blank">Table 1</a>. Sites with greater than or equal to 75% corn-soybean cover in the landscape are depicted in red, while sites with less than or equal to 33% corn-soybean cover are depicted in black. Bottom graphs illustrate the average size and 1 SE by time period.</p

Landmarks (circles) and semilandmarks (triangles) digitized onto each specimen.

<p>Landmarks are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127218#pone.0127218.t002" target="_blank">Table 2</a>.</p