Floristic Inventory of Woollen’s Gardens Nature Preserve, Indianapolis, Marion County, Indiana, USA, With Quantitative Vegetation Sampling of Permanent Plots in 2003 and 2016

Urban forest fragments face challenges to habitat quality due to small size, isolation from larger natural areas, and close association with anthropogenic disturbance. Monitoring changes in vegetation can inform management practices targeted at preserving biodiversity in the face of these threats. Woollen’s Gardens is a high-quality mesic upland forest preserve in the city of Indianapolis, Indiana, USA, with a beechmaple older-growth forest and a significant display of showy spring wildflowers. The entire preserve was inventoried and quantitative vegetation analysis along seven 100 m transects was conducted in 2003 and again in 2016 to track changes. Data from both years document a high-quality flora with few non-native plants. Floristic Quality Index values for native species, derived from Floristic Quality Assessment, were 50.2 in 2003 and 47.3 in 2016. Native mean C-values of 4.5 and 4.3 for each year support that the site is comparable to the highest quality natural areas in central Indiana. Values declined little when non-natives were included, indicating non-natives are having little negative impact on the flora. Although non-natives comprised less than 10% of the flora, 11 of the 16 species are considered invasive in Indiana. In 2003, invasive Amur honeysuckle (Lonicera maackii) was among species in plots with the highest relative importance value. In 2016, invasive wintercreeper (Euonymus fortunei) was among these species. Limited public access to Woollen’s Gardens minimizes human disturbance, but invasive species are a threat to vegetation quality. Continuation of eradication efforts is strongly recommended before populations of these non-natives become more difficult to control

Winter wheat roots grow twice as deep as spring wheat roots, is this important for N uptake and N leaching losses?

Cropping systems comprising winter catch crops followed by spring wheat could reduce N leaching risks compared to traditional winter wheat systems in humid climates. We studied the soil mineral N (Ninorg) and root growth of winter- and spring wheat to 2.5 m depth during three years. Root depth of winter wheat (2.2 m) was twice that of spring wheat, and this was related to much lower amounts of Ninorg in the 1 to 2.5 m layer after winter wheat (81 kg Ninorg ha-1 less). When growing winter catch crops before spring wheat, N content in the 1 to 2.5 m layer after spring wheat was not different from that after winter wheat. The results suggest that by virtue of its deep rooting, winter wheat may not lead to high levels of leaching as it is often assumed in humid climates. Deep soil and root measurements (below 1 m) in this experiment were essential to answer the questions we posed

Three-dimensional low Reynolds number flows near biological filtering and protective layers

Mesoscale filtering and protective layers are replete throughout the natural world. Within the body, arrays of extracellular proteins, microvilli, and cilia can act as both protective layers and mechanosensors. For example, blood flow profiles through the endothelial surface layer determine the amount of shear stress felt by the endothelial cells and may alter the rates at which molecules enter and exit the cells. Characterizing the flow profiles through such layers is therefore critical towards understanding the function of such arrays in cell signaling and molecular filtering. External filtering layers are also important to many animals and plants. Trichomes (the hairs or fine outgrowths on plants) can drastically alter both the average wind speed and profile near the leaf's surface, affecting the rates of nutrient and heat exchange. In this paper, dynamically scaled physical models are used to study the flow profiles outside of arrays of cylinders that represent such filtering and protective layers. In addition, numerical simulations using the Immersed Boundary Method are used to resolve the 3D flows within the layers. The experimental and computational results are compared to analytical results obtained by modeling the layer as a homogeneous porous medium with free flow above the layer. The experimental results show that the bulk flow is well described by simple analytical models. The numerical results show that the spatially averaged flow within the layer is well described by the Brinkman model. The numerical results also demonstrate that the flow can be highly 3D with fluid moving into and out of the layer. These effects are not described by the Brinkman model and may be significant for biologically relevant volume fractions. The results of this paper can be used to understand how variations in density and height of such structures can alter shear stresses and bulk flows.Comment: 28 pages, 10 figure

Two CYP82D Enzymes Function as Flavone Hydroxylases in the Biosynthesis of Root-Specific 4′-Deoxyflavones in Scutellaria baicalensis

Baicalein, wogonin, and their glycosides are major bioactive compounds found in the medicinal plant Scutellaria baicalensis Georgi. These flavones can induce apoptosis in a variety of cancer cell lines but have no effect on normal cells. Furthermore, they have many additional benefits for human health, such as anti-oxidant, antiviral, and liver-protective properties. Here, we report the isolation and characterization of two CYP450 enzymes, SbCYP82D1.1 and SbCYP82D2, which function as the flavone 6-hydroxylase (F6H) and flavone 8-hydroxylase (F8H), respectively, in S. baicalensis. SbCYP82D1.1 has broad substrate specificity for flavones such as chrysin and apigenin and is responsible for biosynthesis of baicalein and scutellarein in roots and aerial parts of S. baicalensis, respectively. When the expression of SbCYP82D1.1 is knocked down, baicalin and baicalein levels are reduced significantly while chrysin glycosides accumulate in hairy roots. SbCYP82D2 is an F8H with high substrate specificity, accepting only chrysin as its substrate to produce norwogonin, although minor 6-hydroxylation activity can also be detected. Phylogenetic analysis suggested that SbCYP82D2 might have evolved from SbCYP82D1.1 via gene duplication followed by neofunctionalization, whereby the ancestral F6H activity is partially retained in the derived SbCYP82D2. We report the characterization of two CYP450 enzymes, which 6- and 8-hydroxylate chrysin to form the 4′-deoxyflavone bioactives in roots of Scutellaria baicalensis. Like the main 4′-deoxyflavone enzymes, these decorating enzymes have evolved their functionalities by convergence with the more ubiquitous 4′-hydroxyflavone pathway enzymes. Key words: Scutellaria baicalensis; Huangqin; baicalein; wogonin; flavone 6-hydroxylase; flavone 8-hydroxylas

From segment to somite: segmentation to epithelialization analyzed within quantitative frameworks

One of the most visually striking patterns in the early developing embryo is somite segmentation. Somites form as repeated, periodic structures in pairs along nearly the entire caudal vertebrate axis. The morphological process involves short- and long-range signals that drive cell rearrangements and cell shaping to create discrete, epithelialized segments. Key to developing novel strategies to prevent somite birth defects that involve axial bone and skeletal muscle development is understanding how the molecular choreography is coordinated across multiple spatial scales and in a repeating temporal manner. Mathematical models have emerged as useful tools to integrate spatiotemporal data and simulate model mechanisms to provide unique insights into somite pattern formation. In this short review, we present two quantitative frameworks that address the morphogenesis from segment to somite and discuss recent data of segmentation and epithelialization

Molecular cloning and expression profiling of a chalcone synthase gene from hairy root cultures of Scutellaria viscidula Bunge

A cDNA encoding chalcone synthase (CHS), the key enzyme in flavonoid biosynthesis, was isolated from hairy root cultures of Scutellaria viscidula Bunge by rapid amplification of cDNA ends (RACE). The full-length cDNA of S. viscidula CHS, designated as Svchs (GenBank accession no. EU386767), was 1649 bp with a 1170 bp open reading frame (ORF) that corresponded to a deduced protein of 390 amino acid residues, a calculated molecular mass of 42.56 kDa and a theoretical isoelectric point (pI) of 5.79. Multiple sequence alignments showed that SvCHS shared high homology with CHS from other plants. Functional analysis in silico indicated that SvCHS was a hydrophilic protein most likely associated with intermediate metabolism. The active sites of the malonyl-CoA binding motif, coumaroyl pocket and cyclization pocket in CHS of Medicago sativa were also found in SvCHS. Molecular modeling indicated that the secondary structure of SvCHS contained mainly α-helixes and random coils. Phylogenetic analysis showed that SvCHS was most closely related to CHS from Scutellaria baicalensis. In agreement with its function as an elicitor-responsive gene, the expression of Svchs was induced and coordinated by methyl jasmonate. To our knowledge, this is the first report to describe the isolation and expression of a gene from S. viscidula

Flux analysis in central carbon metabolism in plants: 13C NMR experiments and analysis

Metabolic flux analysis is crucial in metabolic engineering. This research concentrated on improvements in 13C labeling-based flux analysis, a powerful flux quantification method, particularly oriented toward application to plants. Furthermore, systemic 13C flux analyses were performed on two model plant systems: Glycine max (soybean) embryos, and Catharanthus roseus hairy roots.;The concepts \u27bond integrity\u27, \u27bondomer\u27 and the algorithm \u27Boolean function mapping\u27 were introduced, to facilitate efficient flux evaluation from carbon bond labeling experiments, and easier flux identifiability analysis.;13C labeling experiments were performed on developing soybean (Glycine max) embryos and C. roseus hairy roots. A computer program, NMR2Flux, was developed to automatically calculate fluxes from the labeling data. This program accepts a user-defined metabolic network model, and incorporates recent mathematical advances toward accurate and efficient evaluation of fluxes and their standard deviations. Several physiological insights were obtained from the flux results. For instance, in soybean embryos, the reductive pentose phosphate pathway was active in the plastid and negligible in the cytosol. Also, unknown fluxes (such as plastidic fructose-1,6-bisphosphatase) could be identified and quantified. To the best of the author\u27s knowledge, this is the most comprehensive flux analysis of a plant system to date.;Investigations on flux identifiability were carried out for the soybean embryo system. Using these, optimal labeling experiments were designed, that utilize judicious combinations of labeled varieties of two substrates (sucrose and glutamine), to maximize the statistical quality of the evaluated fluxes.;The identity of four intense peaks observed in the 2-D [13C, 1H] spectra of protein isolated from soybean embryos, was investigated. These peaks were identified as levulinic acid and 5-hydroxymethyl furfural, and were degradation products of glycosylating sugars associated with soybean embryo protein. A 2-D NMR study was conducted on them, and it was shown that the metabolic information in the degradation products can be used toward metabolic flux or pathway analysis.;In addition, the elemental make-up and composition of the biomass of C. roseus hairy roots (crucial toward flux analysis) is reported. 89.2% (+/-9.7%) of the biomass was accounted for.*;*This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Adobe Acrobat

Environmental impact of organic agriculture in temperate regions

Can organic agriculture elaborate a scientifically based, resource-efficien and agroecological approach to low-input farm management? This review examines the literature from temperate regions, with a particular emphasison Canadian and USstudies that relate to environmental and ecological impacts of organic agriculture with respect to (i )soil organic matter storage, (ii) soil quality/soil health, (iii) nutrient loading and risks of off-farm nutrient and agrochemical losses, (iv) biodiversity and (v) energy use and global warming potential. The context and implications of semi-arid conditions and low soil P levels, common to many organic farms in North America, and wide spread adoption of genetically engineered crops in conventional production, is also considered. The consensus of the data available to date indicates the distinctiveness of cropping, flora and habitat diversity, soil management regime, nutrient intensity and use efficiency and energy, and pesticide use in organic farming confer important environmental and ecological benefits. These include maintenance of soil organic matter and added return of carbon to soil, improved soil health, reduced off-farm nitrogen and phosphorus losses, enhanced vegetative and wildlife (bird) biological diversity, extended some times to other taxa depending on landscape context, improved support for pollinators and pollination and reduced energy use and improved energy efficiency. The continued evolution of organic agriculture to a more outcomes-based, agroe cological production system will require an expanded multi-disciplinary research effort, linked ideally to support from consumers and policy-makers on the basis of renewed under-standing of its potential contribution to global environmental sustainability