Ulceroglandular Tularemia: A Typical Case of Relapse

Tularemia is an infectious disease that continues to occur sporadically and in epidemics in the United States. It is characterized as an acute febrile illness with constitutional symptoms associated with skin, glandular, respiratory, or gastrointestinal involvement. Tularemia usually can be treated effectively with streptomycin. Relapse most often occurs when patients are treated with bacteriostatic agents such as chloramphenicol or tetracycline. We present a case of ulceroglandular tularemia distinguished by its relapse after initial streptomycin/doxycycline therapy and subsequent slow response to additional streptomycin

Modeling ChIP Sequencing In Silico with Applications

ChIP sequencing (ChIP-seq) is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the observed statistical nature of this new type of high-throughput data. By linking sequence tags into clusters, we show that there are two components to the distribution of tag counts observed in a number of recent experiments: an initial power-law distribution and a subsequent long right tail. Then we develop in silico ChIP-seq, a computational method to simulate the experimental outcome by placing tags onto the genome according to particular assumed distributions for the actual binding sites and for the background genomic sequence. In contrast to current assumptions, our results show that both the background and the binding sites need to have a markedly nonuniform distribution in order to correctly model the observed ChIP-seq data, with, for instance, the background tag counts modeled by a gamma distribution. On the basis of these results, we extend an existing scoring approach by using a more realistic genomic-background model. This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion

Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters

The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G(2)/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence

Genome-Wide Occupancy of SREBP1 and Its Partners NFY and SP1 Reveals Novel Functional Roles and Combinatorial Regulation of Distinct Classes of Genes

The sterol regulatory element-binding protein (SREBP) family member SREBP1 is a critical transcriptional regulator of cholesterol and fatty acid metabolism and has been implicated in insulin resistance, diabetes, and other diet-related diseases. We globally identified the promoters occupied by SREBP1 and its binding partners NFY and SP1 in a human hepatocyte cell line using chromatin immunoprecipitation combined with genome tiling arrays (ChIP-chip). We find that SREBP1 occupies the promoters of 1,141 target genes involved in diverse biological pathways, including novel targets with roles in lipid metabolism and insulin signaling. We also identify a conserved SREBP1 DNA-binding motif in SREBP1 target promoters, and we demonstrate that many SREBP1 target genes are transcriptionally activated by treatment with insulin and glucose using gene expression microarrays. Finally, we show that SREBP1 cooperates extensively with NFY and SP1 throughout the genome and that unique combinations of these factors target distinct functional pathways. Our results provide insight into the regulatory circuitry in which SREBP1 and its network partners coordinate a complex transcriptional response in the liver with cues from the diet

Tilescope: online analysis pipeline for high-density tiling microarray data

Tilescope is a fully integrated and automated new data-processing pipeline for analyzing high-density tiling-array data

The influence of self-citation corrections on Egghe's g index

The g index was introduced by Leo Egghe as an improvement of Hirsch's index h for measuring the overall citation record of a set of articles. It better takes into account the highly skewed frequency distribution of citations than the h index. I propose to sharpen this g index by excluding the self-citations. I have worked out nine practical cases in physics and compare the h and g values with and without self-citations. As expected, the g index characterizes the data set better than the h index. The influence of the self-citations appears to be more significant for the g index than for the h index.Comment: 9 pages, 2 figures, submitted to Scientometric

Electrodynamic Dust Shield Technology for Thermal Radiators Used in Lunar Exploration

Two general types of thermal radiators are being considered for lunar missions: coated metallic surfaces and Second Surface Mirrors. Metallic surfaces are coated with a specially formulated white paint that withstands the space environment and adheres well to aluminium, the most common metal used in space hardware. AZ-93 White Thermal Control Paint, developed for the space program, is an electrically conductive inorganic coating that offers thermal control for spacecraft. It is currently in use on satellite surfaces (Fig 1). This paint withstands exposure to atomic oxygen, charged particle radiation, and vacuum ultraviolet radiation form 118 nm to 170 nm while reflecting 84 to 85% of the incident solar radiation and emitting 89-93% of the internal heat generated inside the spacecraft