Chromatin marks govern mutation landscape of cancer at early stage of progression

Accumulation of somatic mutations over time leads to tissue abnormalities, such as cancer. Somatic mutation rates vary across the genome in a cell-type specific manner, depending on the types of mutation processes1–7. Although recent studies have identified several determinants relevant to the establishment of the cancer mutation landscape8–13, these studies have yet to propose the major time point at which these factors come into play during cancer progression. Here, we analyzed whole genome sequencing data from two different types of precancerous tissues, monoclonal B-cell lymphocytosis and Barrett’s esophagus, and their matching cancer types along with 423 epigenetic features from normal tissues to determine the critical time point when chromatin features contribute to the formation of the somatic mutation landscape. Our analyses revealed that a subset of cell-of-origin associated chromatin features can explain more than 80% of the regional mutation variance for both types of precancerous tissues, comparable to the variance explained level for the genomes of matching cancer types. In particular, major significant chromatin features explaining the mutation landscape of Barrett’s esophagus and esophageal adenocarcinoma were derived from stomach tissues, indicating that mutation landscape establishment occurs mostly after environment-mediated epigenetic changes during gastric metaplasia. Analyses of the genome of esophageal squamous cell carcinoma tissues demonstrated that the proposed time point for mutation landscape establishment of Barrett’s esophagus and esophageal adenocarcinoma were specific to the occurrence of cell-type shift. Thus, our data suggest that the major time point for the mutation landscape establishment dictated by chromatin features is early in the process of cancer progression, and epigenetic changes due to environmental conditions at early stages can dramatically impact the somatic mutation landscape of cancer.

Differential Environments Influence Initial Transplant Establishment Among Tree Species Produced in Five Container Sizes

Effects of two post-transplant environments were tested on trees grown in five nursery container sizes to determine differences in initial post-transplant growth. Vitex agnus-castus L., Acer rubrum L. var. drummondii (Hook. & Arn. ex Nutt.) Sarg., and Taxodium distichum (L.) Rich. grown in 3.5 L (#1), 11.7 L (#3), 23.3 L (#7), 97.8 L (#25), and 175.0 L (#45) containers were transplanted in early summer into field plots in College Station, Texas, and Starkville, Mississippi, U.S. Height, trunk diameter, and canopy width measurements were recorded after nursery production and the end of the first growing season to determine initial growth during landscape establishment. Growth of A. rubrum and T. distichum were significantly (P ≤ 0.05) affected by interactions among container sizes and environments, while V. agnus-castus did not demonstrate a difference between environments but were affected by container sizes. Across all species and locations, trees transplanted from smaller container sizes exhibited a greater percent change in growth than the larger container-size trees. Greater percent change in growth measures in the smaller container-size trees during the first growing season may indicate a more rapid establishment time compared to trees from larger containers. Where differential responses to environments occurred, predominantly the beneficial effects of smaller container sizes on post-transplant establishment were accentuated with more stressful establishment conditions.

Production and Landscape Establishment of Nursery Crops in Eastern Redcedar-Amended Substrates

Substrate material used for the purpose of growing ornamental plants in the Great Plains is generally shipped a significant distance, primarily from the Southeastern United States. Eastern redcedar (Juniperus virginiana; ERC) chips have been identified as a possible alternative to pine bark (PB) for nursery substrates. Landscape establishment of Ulmus parvifolia ‘Emer II’ (elm), Rosa ‘Radtkopink’ (rose), Ilex glabra ‘Compacta’ (holly), Miscanthus sinensis ‘Little Kitten’ (maiden grass), Gaillardia ×grandiflora (blanket flower), Sedum ‘Autumn Fire’ (sedum), Hosta ‘Sum and Substance’ (hosta), and Hemerocallis ‘Charles Johnston’ (daylily) plants were grown in three substrate mixes. Substrate mixes were composed of 80:20 PB:sand (PBS), 40:40:20 PB:ERC:sand (PBERCS) or 80:20 ERC:sand (ERCS) (by vol). The study was split into production and landscape phases. During the production phase, pH and EC were among the parameters measured. For both phases of the study, growth index (GI), SPAD, caliper and shoot- and root dry weight were measured. At the end of the production phase, differences in growth were observed in elm, holly, and maiden grass where substrates containing PB or a mixture of PB:ERC resulted in greater growth over a primarily ERC-based substrate. Sedum also exhibited growth differences, with plants growing larger in ERCS as a production substrate. At the conclusion of the landscape establishment phase, there were no observed differences in growth for tested species with the exception of holly and hosta which grew best if produced in PBS and/or PBERCS prior to transplanting based on shoot- and root dry weights as well as GI on most evaluation dates. The majority of species in this study overcame any growth shortages present at the end of production within the first growing season in the landscape. Therefore, ERC is a viable substrate option for producing and planting many nursery crops, though it is advisable for each nursery to evaluate their particular crops for production in alternative substrates.

Growth and Quality Response of Woody Shrubs to Nitrogen Fertilization Rates during Landscape Establishment in Florida

Despite inconsistent reports of nitrogen (N) fertilization response on growth of landscape-grown woody ornamentals, broad N fertilization recommendations exist in the literature. The objective of this research was to evaluate the growth and quality response of three landscape-grown woody shrub species to N fertilizer. Three ornamental shrub species, ‘Alba’ indian hawthorn (Raphiolepis indica), sweet viburnum (Viburnum odoratissimum), and ‘RADrazz’ (Knock Out™) rose (Rosa) were transplanted into field soils in central Florida (U.S. Department of Agriculture hardiness zone 9a). Controlled-release N fertilizer was applied at an annual N rate of 0, 2, 4, 6, and 12 lb/1000 ft2 for 100 weeks. Plant size index measurements, SPAD readings (a measure of greenness), and visual quality ratings were completed every month through 52 weeks after planting (WAP) and then every 3 months through 100 WAP. Plant tissue total Kjeldahl N (TKN) concentrations and shoot biomass were measured at 100 WAP. Results of regression analysis indicated little to no plant response (size index, biomass, SPAD) to N fertilizer rate. Shrub quality was acceptable for all species through 76 WAP regardless of the N fertilization rate. However, quality of rose and sweet viburnum fertilized with N at the low rates (<2 lb/1000 ft2) was less than acceptable (<3 out of 5) after 76 WAP. Results suggest that posttransplant applications of fertilizer may not increase plant growth, but that low-to-moderate levels of N fertilization (2 to 4 lb/1000 ft2 per year) may help plant maintain quality postestablishment.

Modern Industrial Zone Landscape Establishment of Industrial Behavior Orientation

Modern industrial zone landscape establishment is the idealized image form of high-tech industrial complex; landscape is one of the most important parts which involve industrial zone environment as well as practitioners working efficiency. We analyze industrial behavior caused by people and we discuss various industrial activities needs for the environment landscape, we put forward landscape establishment of industry-orientation.

Landscape Establishment of Woody Ornamentals Grown in Alternative Wood-Based Container Substrates

Due to concerns over future pine bark (PB) availability for container plant production, recent research has focused on evaluating suitable alternatives. For alternatives to be considered suitable substrate replacements, they must not only have desirable characteristics as a container substrate (e.g., adequate drainage, inert, pathogen free, etc.), but must also cause no negative fertility effects (e.g., nitrogen immobilization) following planting in the landscape. The study objective was to evaluate the landscape performance of three woody ornamentals grown in PB and in two alternative wood-based substrates, namely WholeTree (WT) and Clean Chip Residual (CCR). Crapemyrtle (Lagerstroemia indica × faurei ‘Acoma’), magnolia (Magnolia grandiflora ‘D.D. Blanchard’), and shumard oak (Quercus shumardii) were container grown in PB, WT, or CCR for an entire growing season prior to being planted into the landscape. Plants were grown in the landscape for two growing seasons. Data suggest that all species exhibited similar landscape performance when grown in WT or CCR compared to the PB standard. Therefore, the use of WT and CCR as alternative wood-based substrates for crapemyrtle, magnolia, and oak production may be acceptable from a landscape establishment standpoint.

Above-grade Planting with Organic Matter Improves Post-transplant Growth of Two Native Shrub Species

Planting shrubs above-grade with organic matter has shown potential for improving landscape establishment. To further investigate this technique, wax myrtle [Morella cerifera (syn. Myrica cerifera)] (3 gal) and mountain laurel (Kalmia latifolia ‘Olympic Wedding’) (5 gal) were planted on 30 Oct. 2006 (fall planting) and 12 Apr. 2007 (spring planting) in the ground in a shade house in Auburn, AL. At each planting date, plants of each species were assigned one of four treatments. Three of four treatments used a modified above-grade planting technique in which shrubs were planted such that the top 3 inches of the root ball remained above soil grade. Organic matter, either pine bark (PB), peat (PT), or cotton gin compost (CGC), was applied around the above-grade portion of the root ball, tapering down from the top of the root ball to the ground. In the fourth treatment, plants were planted at-grade with no organic matter (NOM). In general, both species had higher shoot dry weight (SDW) and root spread (RS) when planted in the fall than when planted in spring. Among all treatments, plants also typically had larger RS when planted above-grade with PB or PT. For easy-to-transplant species (such as wax myrtle) and especially for difficult-to-transplant species like mountain laurel, fall planting using this modified above-grade planting technique with PB or PT may improve post-transplant root growth and speed establishment in the first growing season.

Controlled-release Fertilizer Type and Rate Affect Landscape Establishment of Seven Herbaceous Perennials

Use of controlled-release fertilizers (CRF) has been recommended to the landscape service industry as a best management practice for establishing landscape plants. However, application practices vary considerably among professionals and recommendations are lacking for the appropriate type (tablet vs. granular), application rate, and timing of CRF to establish herbaceous perennials. In this study, cigar plant (Cuphea ignea), daylily (Hemerocallis ‘Stella de Oro’), gaura (Gaura lindheimeri ‘Siskiyou Pink’), lantana (Lantana camara ‘New Gold’), mexican heather (Cuphea hyssopifolia), purple coneflower (Echinacea purpurea), and rudbeckia (Rudbeckia fulgida ‘Goldsturm’) were fertilized with granular CRF (GF) 15N–3.9P–10K (8 to 9 month) at 0, 1, 2, or 4 lb/1000 ft2 nitrogen (N) at transplant (no fertilization, GF1, GF2, and GF4, respectively), a split application of GF with 1 lb/1000 ft2 N applied at transplant and 1 lb/1000 ft2 N applied 5-months later (GF2-split), or tablet CRF 16N–3.5P–10K (8 to 9 months) at two tablets per plant (7.5 g) at transplant (TF2). Plant size and visual quality (VQ) at 5 months after transplant (MAT) were improved by fertilization for all perennials except ‘Stella de Oro’ daylily. Compared to GF2, GF4 improved the growth of perennials of larger size and greater biomass production (i.e., cigar plant), but did not further improve their VQ. All perennials grown with TF2 had similar size and quality as those grown with GF2 at 5 MAT. At 15 MAT, no difference was found among fertilizer treatments for surviving perennials except cigar plant. Split application (GF2-split) did not improve overwinter survival or second-year plant growth and quality for most species when compared with GF2. On the basis of these results, we recommend applying two tablets (7.5 g) of 16N–3.5P–10K per plant at transplant to establish the perennials tested in this study.