Response of a rare endemic, Penstemon clutei, to burning and reduced belowground competition

Penstemon clutei, a rare perennial beard tongue endemic to the ponderosa pine forest of the Sunset Crater volcanic field of northern Arizona, presents an opportunity to test the hypothesis that restoration of historic ecosystem conditions may enhance the sustainability of a rare species. We tested prescribed burning and root trenching treatments as proxies for the surface fires and reduced tree densities characteristic of historic ponderosa pine ecosystems in a study area at OLeary Peak, part of the Sunset Crater volcanic field (Coconino National Forest, AZ). Prescribed burning killed many mature P. clutei plants and negatively affected density for at least 3 years post-burn. In contrast, trenching to cut root competition of overstory trees led to a 1200 percent increase in P. clutei plants. Precipitation influenced the response. Seed germination experiments showed that P. clutei does not have innate dormancy. Germination rates in the lab ranged from 5 to 70 percent under a range of environmental and fire-related conditions (i.e., cold stratification, light, exposure to ash, NH4), but these factors were not statistically significant. Tested seedling establishment rates in situ were very low (0.4(percent)). These experiments suggest that the observed P. clutei population increase following severe wildfires (1973 Burnt fire, 1996 Hochderffer fire) may have been due primarily to the removal of tree competition rather than to direct fire effects. Further experimentation is suggested to develop ecological information for thoughtful integration of ecosystem restoration with the habitat needs of rare plants

Working paper 18: Prescribed and wildland use fires in the southwest: Do frequency and timing matter?

Support for the use of prescribed fire and wildland fire use has increased in the Southwest in recent decades. However, the frequency and seasonality of these contemporary fires is typically different than historical fires, which burned during late spring and early summer in the driest and windiest time of the year. Contemporary changes in the landscape, including unprecedented fuel loads and human development in and around forests, now limit the ability to use fire during those times of the year. Most managed fire now occurs outside the windy fire season because it is safer and allows managers to provide greater protection to susceptible cultural or natural resources, such as historic structures or dry snags

Group actions on central simple algebras: a geometric approach

We study actions of linear algebraic groups on central simple algebras using algebro-geometric techniques. Suppose an algebraic group G acts on a central simple algebra A of degree n. We are interested in questions of the following type: (a) Do the G-fixed elements form a central simple subalgebra of A of degree n? (b) Does A have a G-invariant maximal subfield? (c) Does A have a splitting field with a G-action, extending the G-action on the center of A? Somewhat surprisingly, we find that under mild assumptions on A and the actions, one can answer these questions by using techniques from birational invariant theory (i.e., the study of group actions on algebraic varieties, up to equivariant birational isomorphisms). In fact, group actions on central simple algebras turn out to be related to some of the central problems in birational invariant theory, such as the existence of sections, stabilizers in general position, affine models, etc. In this paper we explain these connections and explore them to give partial answers to questions (a)-(c).Comment: 33 pages. Final version, to appear in Journal of Algebra. Includes a short new section on Brauer-Severi varietie

Seeding versus natural regeneration: a comparison of vegetation change following thinning and burning in ponderosa pine

The decision whether to seed with native species following restoration treatments should be based on existing vegetation, species present in or absent from the soil seed bank, past management history, microclimate conditions and soils. We installed three permanent monitoring plots in two areas (total 18.6 ha) at Mt. Trumbull, AZ. Trees were thinned and the sites burned in 1996 and 1997. A 5 ha area was seeded with native shrub, grass and forb species; the remaining 13.6 ha were unseeded. Pretreatment species richness ranged from none to five species per plot. We recorded 13 graminoid and eight shrub species in the seeded area, and four graminoid and four shrub species in the unseeded area. The greatest increase in species richness in both seeded and unseeded plots occurred approximately 1.8 years posttreatment. Perennial native species dominated plant cover by 2.8 years, although annual native forbs dominate the soil seed bank. Perennial grasses are nearly absent from the seed bank. The seeded area had the highest diversity, but it also had twice as many nonnative species (14 versus 7 in the unseeded plots). By August 1999, maximum species richness reached 51 species on the seeded plot. Of these species, 80 percent were native. Although seeding increases diversity, it may also have the long-term tradeoff of introducing new genotypes and species, both native and nonnative

An effective mesh strategy for CFD modelling of polymer electrolyte membrane fuel cells

Computational fluid dynamics (CFD) is a major tool in PEM fuel cell research. Typical three-dimensional PEM fuel cell models involve more than 106 mesh elements. This makes the computation very intense and necessitates a methodology to mesh the computational domain that can keep the number of elements to a minimum while maintaining good accuracy. In this study, the effect of computational mesh in each direction on the accuracy of the solution is investigated in a systematic way. It is found that the mesh in different directions has a different degree of influence on the solution suggesting that the mesh in one direction can be coarser than the other. The proposed mesh strategy is capable of greatly reducing the number of mesh elements, hence computation time, while preserving the characteristics of important flow-field variables. Moreover, it is applicable to a wide range of cell sizes and flow-field configurations and should be used as a guideline for mesh generation

Changes in ponderosa pine forests of the Mt. Trumbull Wilderness

Ponderosa pine forests in the Mt. Trumbull Wilderness on the Arizona Strip have become dense with young trees and highly susceptible to catastrophic wildfire due to exclusion of the natural frequent-fire regime. As part of a broader regional ecological restoration study, the Mt. Trumbull Wilderness was sampled for fire scarred trees, vegetation, and fuels in 1997 and 1999. Reconstructed fire histories show that fires recurred about every 4.4 years prior to settlement, with larger fires burning every 9.5 years. Frequent fires ceased after 1863 in the Mt. Trumbull Wilderness, coincident with the time of Euro-American settlement around 1870, beginning a fire-free period that has lasted up to the present except for a few small fires and a larger 1989 wildfire. Current forests are dense, averaging approximately 1,200 trees/ha, and dominated by small trees. Throughout the wilderness, tree canopy cover averages over 65(percent) and tree basal area is high, 35- 36 m2/ha. Understory plant cover is about 20(percent) and understory species diversity averages 11.4 species/sample plot. Living and dead fuels, including plants, woody debris, and the forest floor, will easily support high-intensity wildfires. In contrast, the presettlement forest was relatively open, with tree density of approximately 62 trees/ha and basal area averaging 8.9 m2/ha, dominated by large ponderosa pine trees. In ecological terms, prospects are good for restoring the Mt. Trumbull Wilderness to emulate the ecological structure and fire disturbance regime of the presettlement reference condition. The current forest condition is perhaps least affected by recent degradation of any site in the Uinkaret Mountains. However, ecological information is only one component contributing to the debate over appropriate management values and practices in wilderness areas on public lands

Small molecules inhibit STAT3 activation, autophagy, and cancer cell anchorage-independent growth

Triple-negative breast cancers (TNBCs) lack the signature targets of other breast tumors, such as HER2, estrogen receptor, and progesterone receptor. These aggressive basal-like tumors are driven by a complex array of signaling pathways that are activated by multiple driver mutations. Here we report the discovery of 6 (KIN-281), a small molecule that inhibits multiple kinases including maternal leucine zipper kinase (MELK) and the non-receptor tyrosine kinase bone marrow X-linked (BMX) with single-digit micromolar IC50s. Several derivatives of 6 were synthesized to gain insight into the binding mode of the compound to the ATP binding pocket. Compound 6 was tested for its effect on anchorage-dependent and independent growth of MDA-MB-231 and MDA-MB-468 breast cancer cells. The effect of 6 on BMX prompted us to evaluate its effect on STAT3 phosphorylation and DNA binding. The compound’s inhibition of cell growth led to measurements of survivin, Bcl-XL, p21WAF1/CIP1, and cyclin A2 levels. Finally, LC3B-II levels were quantified following treatment of cells with 6 to determine whether the compound affected autophagy, a process that is known to be activated by STAT3. Compound 6 provides a starting point for the development of small molecules with polypharmacology that can suppress TNBC growth and metastasis

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

Citation: Mei, W. B., Liu, S. Z., Schnable, J. C., Yeh, C. T., Springer, N. M., Schnable, P. S., & Barbazuk, W. B. (2017). A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize. Frontiers in Plant Science, 8, 19. https://doi.org/10.3389/fpls.2017.00694Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 X Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize

The transition between stochastic and deterministic behavior in an excitable gene circuit

We explore the connection between a stochastic simulation model and an ordinary differential equations (ODEs) model of the dynamics of an excitable gene circuit that exhibits noise-induced oscillations. Near a bifurcation point in the ODE model, the stochastic simulation model yields behavior dramatically different from that predicted by the ODE model. We analyze how that behavior depends on the gene copy number and find very slow convergence to the large number limit near the bifurcation point. The implications for understanding the dynamics of gene circuits and other birth-death dynamical systems with small numbers of constituents are discussed.Comment: PLoS ONE: Research Article, published 11 Apr 201