Solute channels of the outer membrane: from bacteria to chloroplasts

Chloroplasts, unique organelles of plants, originated from endosymbiosis of an ancestor of today's cyanobacteria with a mitochondria-containing host cell. It is assumed that the outer envelope membrane, which delimits the chloroplast from the surrounding cytosol, was thus inherited from its Gram-negative bacterial ancestor. This plastid-specific membrane is thus equipped with elements of prokaryotic and eukaryotic origin. In particular, the membrane-intrinsic outer envelope proteins (OEPs) form solute channels with properties reminiscent of porins and channels in the bacterial outer membrane. OEP channels are characterised by distinct specificities for metabolites and a quite peculiar expression pattern in specialised plant organs and plastids, thus disproving the assumption that the outer envelope is a non-specific molecular sieve. The same is true for the outer membrane of Gram-negative bacteria, which functions as a permeability barrier in addition to the cytoplasmic membrane, and embeds different classes of channel pores. The channels of these prokaryotic prototype proteins, ranging from unspecific porins to specific channels to ligand-gated receptors, are exclusively built of P-barrels. Although most of the OEP channels are formed by P-strands as well, phylogeny based on sequence homology alone is not feasible. Thus, the comparison of structural and functional properties of chloroplast outer envelope and bacterial outer membrane channels is required to pinpoint the ancestral OEP `portrait gallery'

Lensing by Lyman Limit Systems: Determining the Mass to Gas Ratio

We present a new method to determine the total mass-to-neutral gas ratio in Lyman-limits systems. The method exploits the relation between the neutral hydrogen column density and the magnification of background sources due to the weak gravitational lensing that these systems induce. Because weak lensing does not provide a direct measure of mass, one must use this relation in a statistical sense to solve for the average mass-to-gas ratio and its distribution. We use a detailed mock catalog of quasars (sources) and Lyman-limit systems (lenses) to demonstrate the applicability of this approach through our ability to recover the parameter. This mock catalog also allows us to check for systematics in the method and to sketch its limitations. For a universal constant mass-to-gas ratio and a sample of N quasars, we obtain an unbiased estimate of its value with 95% confidence limits (independent of its actual value) of +/- 140 {10^5/N)^0.5.Comment: 20 pages, 11 figures submitted to Ap

Reducing Disparities by way of a Cancer Disparities Research Training Program

Background: For minority populations, there is a continuing disparity in the burden of death and illness from cancer. Research to address this disparity should be conducted by investigators who can best understand and address the needs of culturally diverse communities. However, minorities are under-represented in health-related research. The goal of this project was to develop and evaluate an approach to motivating and preparing master’s degree students for careers dedicated to cancer disparities research. Method: A Cancer Disparities Research Training Program (CDRTP) was initiated in 2010. The program consists of coursework, practicum experiences, and research opportunities. Assessment of the curriculum is based on monitoring achievement of evaluation indicators and includes a quantitative assessment and qualitative approach. Results: In its first three years, the program graduated 20 trainees, all of whom were minorities (18 African Americans and two Asians). When asked about career goals, two-thirds of the trainees indicated interest in pursuing careers in research on cancer prevention and control. The trainees expressed high satisfaction with the courses, instructor, materials, and curriculum. Although trainees had suggestions about course details, evaluations overall were positive. Across focus groups, three recurrent themes emerged regarding activities to enhance the student experience: having a wider variety of topics, more guest speakers, and field trips. Conclusion: The CDRTP was intended to recruit students – primarily African Americans – into research on prevention and control of cancer disparities. Although final evaluation of the program’s overall outcome will not be available for several years, a preliminary evaluation indicates the program is being successful

Cosmological Implications of Lyman-Break Galaxy Clustering

We review our analysis of the clustering properties of ``Lyman-break'' galaxies (LBGs) at redshift z~3, previously discussed in Wechsler et al (1998). We examine the likelihood of spikes found by Steidel et al (1998) in the redshift distribution of LBGs, within a suite of models for the evolution of structure in the Universe. Using high-resolution dissipationless N-body simulations, we analyze deep pencil-beam surveys from these models in the same way that they are actually observed, identifying LBGs with the most massive dark matter halos. We find that all the models (with SCDM as a marginal exception) have a substantial probability of producing spikes similar to those observed, because the massive halos are much more clumped than the underlying matter -- i.e., they are biased. Therefore, the likelihood of such a spike is not a good discriminator among these models. The LBG correlation functions are less steep than galaxies today (gamma~1.4), but show similar or slightly longer correlation lengths. We have extened this analysis and include a preliminary comparison to the new data presented in Adelberger et al (1998). We also discuss work in progress, in which we use semi-analytic models to identify Lyman-break galaxies within dark-matter halos.Comment: 4 pages, 2 figures, Latex, uses aipproc.sty; to appear in the proceedings of the 9th Annual October Maryland Astrophysics Conference, "After the Dark Ages: When the Galaxies Were Young (the Universe at 2<z<5)

On the harmonic measure of stable processes

Using three hypergeometric identities, we evaluate the harmonic measure of a finite interval and of its complementary for a strictly stable real L{\'e}vy process. This gives a simple and unified proof of several results in the literature, old and recent. We also provide a full description of the corresponding Green functions. As a by-product, we compute the hitting probabilities of points and describe the non-negative harmonic functions for the stable process killed outside a finite interval

Do Gamma-Ray Burst Sources Repeat?

The demonstration of repeated gamma-ray bursts from an individual source would severely constrain burst source models. Recent reports (Quashnock and Lamb 1993; Wang and Lingenfelter 1993) of evidence for repetition in the first BATSE burst catalog have generated renewed interest in this issue. Here, we analyze the angular distribution of 585 bursts of the second BATSE catalog (Meegan et al. 1994). We search for evidence of burst recurrence using the nearest and farthest neighbor statistic and the two-point angular correlation function. We find the data to be consistent with the hypothesis that burst sources do not repeat; however, a repeater fraction of up to about 20% of the observed bursts cannot be excluded.Comment: ApJ Letters, in press, 13 pages, including three embedded figures. uuencoded Unix-compressed PostScrip

Caenorhabditis elegans Operons Contain a Higher Proportion of Genes with Multiple Transcripts and Use 3′ Splice Sites Differentially

RNA splicing generates multiple transcript isoforms from a single gene and enhances the complexity of eukaryotic gene expression. In some eukaryotes, operon exists as an ancient regulatory mechanism of gene expression that requires strict positional and regulatory relationships among its genes. It remains unknown whether operonic genes generate transcript isoforms in a similar manner as non-operonic genes do, the expression of which is less likely limited by their positions and relationships with surrounding genes. We analyzed the number of transcript isoforms of Caenorhabditis elegans operonic genes and found that C. elegans operons contain a much higher proportion of genes with multiple transcript isoforms than non-operonic genes do. For genes that express multiple transcript isoforms, there is no apparent difference between the number of isoforms in operonic and non-operonic genes. C. elegans operonic genes also have a different preference of the 20 most common 3′ splice sites compared to non-operonic genes. Our analyses suggest that C. elegans operons enhance expression complexity by increasing the proportion of genes that express multiple transcript isoforms and maintain splicing efficiency by differential use of common 3′ splice sites