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Thin layer sediment placement (TLP) is used to build elevation in marshes, counteracting effects of subsidence and sea level rise. However, TLP success may vary due to plant stress associated with reductions in nutrient availability and hydrologic flushing or through the creation of acid sulfate soils. This study examined the influence of sediment grain size and soil amendments on plant growth, soil and porewater characteristics, and greenhouse gas exchange for three key US salt marsh plants: Spartina alterniflora (synonym Sporobolus alterniflorus), Spartina patens (synonym Sporobolus pumilus), and Salicornia pacifica. We found that bioavailable nitrogen concentrations (measured as extractable NH4+-N) and porewater pH and salinity were inversely related to grain size, while soil redox was more reducing in finer sediments. This suggests that utilizing finer sediments in TLP projects will result in a more reduced environment with higher nutrient availability, while larger grain sized sediments will be better flushed and oxygenated. We further found that grain size had a significant effect on vegetation biomass allocation and rates of gas exchange, although these effects were species-specific. We found that soil amendments (biochar and compost) did not subsidize plant growth but were associated with increases in soil respiration and methane emissions. Biochar amendments were additionally ineffective in ameliorating acid sulfate conditions. This study uncovers complex interactions between sediment type and vegetation, emphasizing limitations of soil amendments. The findings aid restoration project managers in making informed decisions regarding sediment type, target vegetation, and soil amendments for successful TLP projects. 

Many archaea encode and express histone proteins to compact their genomes. Archaeal and eukaryotic histones share a near-identical fold that permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that must be traversed by RNA polymerase (RNAP) to generate transcripts. As archaeal histones can spontaneously assemble with a single histone isoform, single-histone chromatin variants provide an idealized platform to detail the impacts of distinct histone-DNA contacts on transcription efficiencies and to detail the role of the conserved cleavage stimulatory factor, Transcription Factor S (TFS), in assisting RNAP through chromatin landscapes. We demonstrate that substitution of histone residues that modify histone-DNA contacts or the three-dimensional chromatin structure result in radically altered transcription elongation rates and pausing patterns. Chromatin-barriers slow and pause RNAP, providing regulatory potential. The modest impacts of TFS on elongation rates through chromatin landscapes is correlated with TFS-dispensability from the archaeonThermococcus kodakarensis. Our results detail the importance of distinct chromatin structures for archaeal gene expression and provide a unique perspective on the evolution of, and regulatory strategies imposed by, eukaryotic chromatin.

 

Adhesive toe pads have evolved numerous times over lizard evolutionary history, most notably in geckos. Despite significant variation in adult toe pad morphology across independent origins of toe pads, early developmental patterns of toe pad morphogenesis are similar among distantly related species. In these distant phylogenetic comparisons, toe pad variation is achieved during the later stages of development. We aimed to understand how toe pad variation is generated among species sharing a single evolutionary origin of toe pads (house geckos—Hemidactylus). We investigated toe pad functional variation and developmental patterns in three species of Hemidactylus, ranging from highly scansorial (H. platyurus), to less scansorial (H. turcicus), to fully terrestrial (H. imbricatus). We found that H. platyurus generated significantly greater frictional adhesive force and exhibited much larger toe pad area relative to the other two species. Furthermore, differences in the offset of toe pad extension phase during embryonic development results in the variable morphologies seen in adults. Taken together, we demonstrate how morphological variation is generated in a complex structure during development and how that variation relates in important functional outcomes.

 

We propose a workflow for modeling generalized mid-spatial frequency (MSF) errors in optical imaging systems. This workflow enables the classification of MSF distributions, filtering of bandlimited signatures, propagation of MSF errors to the exit pupil, and performance predictions that differentiate performance impacts due to the MSF distributions. We demonstrate the workflow by modeling the performance impacts of MSF errors for both transmissive and reflective imaging systems with near-diffraction-limited performance.

 

The theory and practice of evolutionary tree-thinking is pervasive through many scientific fields and is a critical component of biological literacy. Many elements of tree-thinking are introduced early in undergraduate biology education. However, basic concepts are often not revisited/reinforced and are assumed to have been fully conceptually grasped in upper-level courses and beyond. Here, we present a project-based activity that we developed to aid upper-level biology students to learn, conceptualize, and practice tree-thinking. This approach allows them to identify the misconceptions that they may have about tree-thinking, while reinforcing the theories and concepts that they may have encountered in introductory courses. It also integrates several pedagogical styles (instructor-led and student-centered), along with an organismal case study to make concepts concrete and realistic to students. 

In this work, we present a methodology for predicting the optical performance impacts of random and structured MSF surface errors using pupil-difference probability distribution (PDPD) moments. In addition, we show that, for random mid-spatial frequency (MSF) surface errors, performance estimates from the PDPD moments converge to performance estimates that assume random statistics. Finally, we apply these methods to several MSF surface errors with different distributions and compare estimated optical performance values to predictions based on earlier methods assuming random error distributions.

 

Personalization of a biomechanistic model of prostate cancer with mpMRI data enables the prediction of tumor progression, thereby showing promise to guide clinical decision-making during AS for each individual patient.

 

In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then re-analyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time. 

Pain is a worldwide problem requiring an effective, affordable, non-addictive therapy. Using the edible plant broccoli, a growth protocol was developed to induce a concentrated combinatorial of potential anti-inflammatories in seedlings.

A growth method was utilized to produce a phenylpropanoid-rich broccoli sprout extract, referred to as Original Extract (OE). OE was concentrated and then resuspended for study of the effects on inflammation events. A rabbit disc model of inflammation and degeneration, and, a mouse model of pain behavior were used for in vivo and in vitro tests. To address aspects of mammalian metabolic processing, the OE was treated with the S9 liver microsome fraction derived from mouse, for use in a mouse in vivo study. Analytical chemistry was performed to identify major chemical species. Continuous variables were analyzed with a number of methods including ANOVA, and two-tailedttests, as appropriate.

In a rabbit spine (disc) injury model, inflammatory markers were reduced, and levels of regenerative markers were increased as a result of OE treatment, both in vivo and in vitro. In a mouse pain behavioral model, after treatment with S9 liver microsome fraction, the resultant extract significantly reduced early and late pain behavior in response to a pain stimulus. The OE itself reduced pain behavior in the mouse pain model, but did not achieve the level of significance observed for S9-treated extract. Analytical chemistry undertaken on the extract constituents revealed identities of the chemical species in OE, and how S9 liver microsome fraction treatment altered species identities and proportions.

In vitro and in vivo results indicate that the OE, and S9-treated OE broccoli extracts are worthwhile materials to develop a non-opiate inflammation and pain-reducing treatment.