Evaluating northern hardwood management using retrospective analysis and diameter distributions

Northern hardwood management was assessed throughout the state of Michigan using data collected on recently harvested stands in 2010 and 2011. Methods of forensic estimation of diameter at breast height were compared and an ideal, localized equation form was selected for use in reconstructing pre-harvest stand structures. Comparisons showed differences in predictive ability among available equation forms which led to substantial financial differences when used to estimate the value of removed timber. Management on all stands was then compared among state, private, and corporate landowners. Comparisons of harvest intensities against a liberal interpretation of a well-established management guideline showed that approximately one third of harvests were conducted in a manner which may imply that the guideline was followed. One third showed higher levels of removals than recommended, and one third of harvests were less intensive than recommended. Multiple management guidelines and postulated objectives were then synthesized into a novel system of harvest taxonomy, against which all harvests were compared. This further comparison showed approximately the same proportions of harvests, while distinguishing sanitation cuts and the future productive potential of harvests cut more intensely than suggested by guidelines. Stand structures are commonly represented using diameter distributions. Parametric and nonparametric techniques for describing diameter distributions were employed on pre-harvest and post-harvest data. A common polynomial regression procedure was found to be highly sensitive to the method of histogram construction which provides the data points for the regression. The discriminative ability of kernel density estimation was substantially different from that of the polynomial regression technique.

Systemic analysis of microarray data sets towards identifying genes regulating root development

Nitrogen and water are essential for plant growth and development. In this study, we designed experiments to produce gene expression data of poplar roots under nitrogen starvation and water deprivation conditions. We found low concentration of nitrogen led first to increased root elongation followed by lateral root proliferation and eventually increased root biomass. To identify genes regulating root growth and development under nitrogen starvation and water deprivation, we designed a series of data analysis procedures, through which, we have successfully identified biologically important genes. Differentially Expressed Genes (DEGs) analysis identified the genes that are differentially expressed under nitrogen starvation or drought. Protein domain enrichment analysis identified enriched themes (in same domains) that are highly interactive during the treatment. Gene Ontology (GO) enrichment analysis allowed us to identify biological process changed during nitrogen starvation. Based on the above analyses, we examined the local Gene Regulatory Network (GRN) and identified a number of transcription factors. After testing, one of them is a high hierarchically ranked transcription factor that affects root growth under nitrogen starvation. It is very tedious and time-consuming to analyze gene expression data. To avoid doing analysis manually, we attempt to automate a computational pipeline that now can be used for identification of DEGs and protein domain analysis in a single run. It is implemented in scripts of Perl and R.

Geospatial analysis of western juniper (Juniperus occidentalis) encroachment utilizing remotely sensed data

Utilizing remote sensing methods to assess landscape-scale ecological change are rapidly becoming a dominant force in the natural sciences. Powerful and robust non-parametric statistical methods are also actively being developed to compliment the unique characteristics of remotely sensed data. The focus of this research is to utilize these powerful, robust remote sensing and statistical approaches to shed light on woody plant encroachment into native grasslands--a troubling ecological phenomenon occurring throughout the world. Specifically, this research investigates western juniper encroachment within the sage-steppe ecosystem of the western USA. Western juniper trees are native to the intermountain west and are ecologically important by means of providing structural diversity and habitat for many species. However, after nearly 150 years of post-European settlement changes to this threatened ecosystem, natural ecological processes such as fire regimes no longer limit the range of western juniper to rocky refugia and other areas protected from short fire return intervals that are historically common to the region. Consequently, sage-steppe communities with high juniper densities exhibit negative impacts, such as reduced structural diversity, degraded wildlife habitat and ultimately the loss of biodiversity. Much of today's sage-steppe ecosystem is transitioning to juniper woodlands. Additionally, the majority of western juniper woodlands have not reached their full potential in both range and density. The first section of this research investigates the biophysical drivers responsible for juniper expansion patterns observed in the sage-steppe ecosystem. The second section is a comprehensive accuracy assessment of classification methods used to identify juniper tree cover from multispectral 1 m spatial resolution aerial imagery.