Incomplete recovery of seeds from scatterhoards by granivorous rodents: Implications for plant establishment.

Granivorous rodents are important components of ecosystems not only because they consume seeds but also because some aid in seed dispersal through seed-caching behaviors. Some rodents bury seeds in shallow pits throughout territories, called scatterhoards, that individuals recover, pilfer, or transfer to other caches. We suspect some single-seed caches in environments represent missed seeds from reclaiming or pilfering caches. We documented the sloppiness of seed removal from scatterhoards of soapweed yucca (Yucca glauca) seeds by Ord's kangaroo rats (Dipodomys ordii). We quantified the frequency and location of seeds remaining. In an experiment with artificial caches of three sizes, kangaroo rats harvested 51% of caches after one night, and 53% had incomplete recovery with at least one seed remaining. The greater the number of seeds in caches, the greater frequency of incomplete recovery. In another experiment with natural and artificial caches, 75% of caches were excavated after 8 days, with at least 70% having at least one seed remaining. Regardless of original cache size, a single seed represented the mode for seeds remaining. Incomplete recovery of seeds likely benefits plant establishment, potentially significantly in some systems. Remaining seeds, especially those buried at bottoms of caches, likely will stay undetected in landscapes, yielding propagules for subsequent plant generations. Soapweed yucca has large but light, flat wind-dispersed seeds, and removal of caches with smaller seeds might have greater frequency of missed seeds during recovery and pilfering by rodents. Our results suggest that scatter-hoarding granivores also contribute to plant establishment by leaving limited numbers of seeds behind when removing caches, at least in some systems.

A Selection of Macrocyclic Peptides That Bind STING From an mRNA-Display Library With Split Degenerate Codons.

Recent improvements in mRNA display have enabled the selection of peptides that incorporate non-natural amino acids, thus expanding the chemical diversity of macrocycles beyond what is accessible in nature. Such libraries have incorporated non-natural amino acids at the expense of natural amino acids by reassigning their codons. Here we report an alternative approach to expanded amino-acid diversity that preserves all 19 natural amino acids (no methionine) and adds 6 non-natural amino acids, resulting in the highest sequence complexity reported to date. We have applied mRNA display to this 25-letter library to select functional macrocycles that bind human STING, a protein involved in immunoregulation. The resulting STING-binding peptides include a 9-mer macrocycle with a dissociation constant (KD ) of 3.4 nM, which blocks binding of cGAMP to STING and induces STING dimerization. This approach is generalizable to expanding the amino-acid alphabet in a library beyond 25 building blocks.

Boreal chorus frog (Pseudacris maculata) spring calling activity, habitat metrics, and associated environmental data.

Data were collected using multimodal monitoring technologies pairing sound recorders with time-lapse camera systems. In the spring of 2015, 2016, and 2017, sound recordings and imagery were collected at a wet meadow and forested slough in the Central Platte River Valley of Nebraska. Boreal chorus frog (Pseudacris maculata) calling activity was obtained from analysing sound recordings. Habitat metrics including vegetation phenology and wet meadow hydropattern were derived from image analysis. This dataset can be used to assess phenology, anuran vocalization activity, and environmental change, as well as to further understanding of wetland ecology. Data are co-submitted with manuscript Brinley Buckley, E. M., Gottesman, B. L., Caven, A. J., Harner, M. J., and Pijanowski, B. C., Assessing ecological and environmental influences on Boreal Chorus Frog (Pseudacris maculata) spring calling phenology using multimodal passive monitoring technologies. Ecological Indicators (In Press).

Biological and environmental datasets from the August 2017 total solar eclipse.

The datasets in this article are associated with the research article 'Assessing biological and environmental effects of a total solar eclipse with passive multimodal technologies' (Brinley Buckley et al., 2018). We documented biotic and abiotic changes during a total solar eclipse on 21 August 2017, in south-central Nebraska, USA, with a multimodal suite of tools, including time-lapse camera systems, data loggers, and sound recording devices. Time-lapse images were used to approximate changes in light, data loggers were used to record temperature and humidity, and sound recordings were used to calculate acoustic indices characterizing variation in the soundscape, as well as to manually identify and estimate avian vocalization activity.

NMR in drug design.

The use of NMR as a tool to determine 3 dimensional protein solution structures, once a darling of the pharmaceutical industry, has largely given way to study of the interaction of prospective drugs with macromolecular targets. Many of these approaches involve ligand-centered studies, which have the advantage of speed and efficiency, but there are also many approaches that take directly from our learnings in macromolecular NMR and provide greater structural detail yet are still optimized for rapid turn-around of information. In the evolution of NMR in the pharmaceutical industry, the unique strengths of NMR to provide dynamic and atomic level information continue to be exploited to discover and design new drugs. Numerous methods have been developed over the past two decades that fall into the categories of fragment-based pre-lead discovery, ligand binding studies and qualitative structural screening.

Fragment-based screening of the bromodomain of ATAD2.

Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. Fragment hits were identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.

Fragment-based drug discovery using NMR spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience.

Decomposition of leaf litter from a native tree and an actinorhizal invasive across riparian habitats.

Dynamics of nutrient exchange between floodplains and rivers have been altered by changes in flow management and proliferation of nonnative plants. We tested the hypothesis that the nonnative, actinorhizal tree, Russian olive (Elaeagnus angustifolia), alters dynamics of leaf litter decomposition compared to native cottonwood (Populus deltoides ssp. wislizeni) along the Rio Grande, a river with a modified flow regime, in central New Mexico (U.S.A.). Leaf litter was placed in the river channel and the surface and subsurface horizons of forest soil at seven riparian sites that differed in their hydrologic connection to the river. All sites had a cottonwood canopy with a Russian olive-dominated understory. Mass loss rates, nutrient content, fungal biomass, extracellular enzyme activities (EEA), and macroinvertebrate colonization were followed for three months in the river and one year in forests. Initial nitrogen (N) content of Russian olive litter (2.2%) was more than four times that of cottonwood (0.5%). Mass loss rates (k; in units of d(-1)) were greatest in the river (Russian olive, k = 0.0249; cottonwood, k = 0.0226), intermediate in subsurface soil (Russian olive, k = 0.0072; cottonwood, k = 0.0031), and slowest on the soil surface (Russian olive, k = 0.0034; cottonwood, k = 0.0012) in a ratio of about 10:2:1. Rates of mass loss in the river were indistinguishable between species and proportional to macroinvertebrate colonization. In the riparian forest, Russian olive decayed significantly faster than cottonwood in both soil horizons. Terrestrial decomposition rates were related positively to EEA, fungal biomass, and litter N, whereas differences among floodplain sites were related to hydrologic connectivity with the river. Because nutrient exchanges between riparian forests and the river have been constrained by flow management, Russian olive litter represents a significant annual input of N to riparian forests, which now retain a large portion of slowly decomposing cottonwood litter with a high potential for N immobilization. As a result, retention and mineralization of litter N within these forests is controlled by hydrologic connectivity to the river, which affects litter export and in situ decomposition.

Climate, hydrologic disturbance, and succession: drivers of floodplain pattern.

Floodplains are among the world's most threatened ecosystems due to the pervasiveness of dams, levee systems, and other modifications to rivers. Few unaltered floodplains remain where we may examine their dynamics over decadal time scales. Our study provides a detailed examination of landscape change over a 60-year period (1945-2004) on the Nyack floodplain of the Middle Fork of the Flathead River, a free-flowing, gravel-bed river in northwest Montana, USA. We used historical aerial photographs and airborne and satellite imagery to delineate habitats (i.e., mature forest, regenerative forest, water, cobble) within the floodplain. We related changes in the distribution and size of these habitats to hydrologic disturbance and regional climate. Results show a relationship between changes in floodplain habitats and annual flood magnitude, as well as between hydrology and the cooling and warming phases of the Pacific Decadal Oscillation (PDO). Large magnitude floods and greater frequency of moderate floods were associated with the cooling phases of the PDO, resulting in a floodplain environment dominated by extensive restructuring and regeneration of floodplain habitats. Conversely, warming phases of the PDO corresponded with decreases in magnitude, duration, and frequency of critical flows, creating a floodplain environment dominated by late successional vegetation and low levels of physical restructuring. Over the 60-year time series, habitat change was widespread throughout the floodplain, though the relative abundances of the habitats did not change greatly. We conclude that the long- and short-term interactions of climate, floods, and plant succession produce a shifting habitat mosaic that is a fundamental attribute of natural floodplain ecosystems.