Methods for Obtaining and Analyzing Whole Chloroplast Genome Sequences

During the past decade there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. Currently there are 43 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next five years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important recent developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circular amplification, cloning genomes into Fosmid or BAC vectors, and the development of an organellar annotation program (DOGMA). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms

Of Cholera and Commas: Science, Politics, and the Germ Theory Debates in Late Nineteenth-Century Britain

The Egyptian cholera epidemic of 1883-4 re-invigorated debates within the British and\ud international medical communities over the cause and transmission of the disease. Despite four major outbreaks of epidemic cholera in Britain alone prior to the Egyptian epidemic, the cause and treatment of cholera remained largely an enigma to British physicians. Dr. Robert Koch's\ud proposal of a germ theory, or micro-organism, cause of cholera, following his laboratory investigations of cholera in Egypt and India, provided new insight into the nature of the disease. Instead of a warm reception for his contributions to science, however, Koch's work encountered skepticism among many of Britain's leading physicians. This thesis uses articles published in Nature and The British Medical Journal during the 1883-4 epidemic as a lens through which to study the interplay between science and politics in the development and reception of germ theory in late nineteenth-century Britain. It examines the roots of a distinct British medical style in the\ud nineteenth century and how the practice of medicine led to a reading of the disease that\ud implicated environmental conditions in the cause and spread of cholera. Furthermore, the paper explores the political implications of Koch's germ theory and the antagonism this theory created to the empire's established commercial and public health policies. Finally, it illuminates the coincidence of medical and political objectives that informed the official British reaction to Koch's work

Infrared Spectroscopy with Multivariate Analysis Potentially Facilitates the Segregation of Different Types of Prostate Cell.

The prostate gland is conventionally divided into zones or regions. This morphology is of clinical significance as prostate cancer (CaP) occurs mainly in the peripheral zone (PZ). We obtained tissue sets consisting of paraffin-embedded blocks of cancer-free transition zone (TZ) and PZ and adjacent CaP from patients (n = 6) who had undergone radical retropubic prostatectomy; a seventh tissue set of snap-frozen PZ and TZ was obtained from a CaP-free gland removed after radical cystoprostatectomy. Paraffin-embedded tissue slices were sectioned (10-µm thick) and mounted on suitable windows to facilitate infrared (IR) spectra acquisition before being dewaxed and air dried; cryosections were dessicated on BaF2 windows. Spectra were collected employing synchrotron Fourier-transform infrared (FTIR) microspectroscopy in transmission mode or attenuated total reflection-FTIR (ATR) spectroscopy. Epithelial cell and stromal IR spectra were subjected to principal component analysis to determine whether wavenumber-absorbance relationships expressed as single points in "hyperspace" might on the basis of multivariate distance reveal biophysical differences between cells in situ in different tissue regions. After spectroscopic analysis, plotted clusters and their loadings curves highlighted marked variation in the spectral region containing DNA/RNA bands (1490–1000 cm–1). By interrogating the intrinsic dimensionality of IR spectra in this small cohort sample, we found that TZ epithelial cells appeared to align more closely with those of CaP while exhibiting marked structural differences compared to PZ epithelium. IR spectra of PZ stroma also suggested that these cells are structurally more different to CaP than those located in the TZ. Because the PZ exhibits a higher occurrence of CaP, other factors (e.g., hormone exposure) may modulate the growth kinetics of initiated epithelial cells in this region. The results of this pilot study surprisingly indicate that TZ epithelial cells are more likely to exhibit what may be a susceptibility-to-adenocarcinoma spectral signature. Thus, IR spectroscopy on its own may not be sufficient to identify premalignant prostate epithelial cells most likely to progress to CaP

Configuration Effects on Flow Dynamics and Convective Behavior in Large-Scale Solar Arrays

Effects of height and orientation within a model solar farm are studied with respect to heat transfer characteristics and flow mechanisms. Four configurations varying height and inclination were considered in a 4 × 10 unit, heated array. Temperature data compared panel surface convection, and Particle Image Velocimetry (PIV) captured corresponding velocity data. Array height increases produced greatest overall convection, promoting higher velocities and inducing sub-panel flow. Array reversal with respect to inflow captures high-momentum flow, increasing convective cooling on lower panel surfaces