The Baryon Content of Cosmic Structures

We make an inventory of the baryonic and gravitating mass in structures ranging from the smallest galaxies to rich clusters of galaxies. We find that the fraction of baryons converted to stars reaches a maximum between M500 = 1E12 and 1E13 Msun, suggesting that star formation is most efficient in bright galaxies in groups. The fraction of baryons detected in all forms deviates monotonically from the cosmic baryon fraction as a function of mass. On the largest scales of clusters, most of the expected baryons are detected, while in the smallest dwarf galaxies, fewer than 1% are detected. Where these missing baryons reside is unclear.Comment: ApJ Letters, in pres

Kinematic and Photometric Evidence for a Bar in NGC 2683

We present optical long-slit and SparsePak Integral Field Unit emission line spectroscopy along with optical broadband and near IR images of the edge-on spiral galaxy NGC 2683. We find a multi-valued, figure-of-eight velocity structure in the inner 45 arcsec of the long-slit spectrum and twisted isovelocity contours in the velocity field. We also find, regardless of wavelength, that the galaxy isophotes are boxy. We argue that taken together, these kinematic and photometric features are evidence for the presence of a bar in NGC 2683. We use our data to constrain the orientation and strength of the bar.Comment: Accepted for publication in AJ; 10 pages, 8 figure

Heterogeneity and organization of the ribosomal RNA genes of Cucurbita maxima

Thirty-six clones were recovered from Cucurbita maxima genomic DNA which had been enriched for rDNA and cleaved at the unique repeat unit Hin d III site. Twenty-nine of these, which contain complete rDNA units, were compared to a standard whose intergenic spacer (IGS) nucleotide sequence has been determined. Twenty-one are identical in length and restriction site pattern. Eight which differ from the standard in length do so because of addition or deletion of varying numbers of IGS subrepetitive units of two different classes, with four of the length variants being different in both of these classes. Seven clones were isolated which contain incomplete repeat units, six of which are composites of rDNA and non-rDNA material. They have been cleaved at the unique rDNA Hin d III site at one end and at a non-rDNA Hin d III site at the other. We consider it most likely that these are derived from the termini of repeat unit tandem arrays, although other explanations are possible. Twelve individual plants of two different cultivars were examined for heterogeneity of IGS length distribution. They all appear to be identical in this regard.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43423/1/11103_2004_Article_BF00019390.pd

Pathogen Proteins Eliciting Antibodies Do Not Share Epitopes with Host Proteins: A Bioinformatics Approach

The best way to prevent diseases caused by pathogens is by the use of vaccines. The advent of genomics enables genome-wide searches of new vaccine candidates, called reverse vaccinology. The most common strategy to apply reverse vaccinology is by designing subunit recombinant vaccines, which usually generate an humoral immune response due to B-cell epitopes in proteins. A major problem for this strategy is the identification of protective immunogenic proteins from the surfome of the pathogen. Epitope mimicry may lead to auto-immune phenomena related to several human diseases. A sequence-based computational analysis has been carried out applying the BLASTP algorithm. Therefore, two huge databases have been created, one with the most complete and current linear B-cell epitopes, and the other one with the surface-protein sequences of the main human respiratory bacterial pathogens. We found that none of the 7353 linear B-cell epitopes analysed shares any sequence identity region with human proteins capable of generating antibodies, and that only 1% of the 2175 exposed proteins analysed contain a stretch of shared sequence with the human proteome. These findings suggest the existence of a mechanism to avoid autoimmunity. We also propose a strategy for corroborating or warning about the viability of a protein linear B-cell epitope as a putative vaccine candidate in a reverse vaccinology study; so, epitopes without any sequence identity with human proteins should be very good vaccine candidates, and the other way around

Detection of single base differences using biotinylated nucleotides with very long linker arms.

A simple primer extension method for detecting nucleotide differences is based on the substitution of mobility-shifting analogs for natural nucleotides (1). This technique can detect any single-base difference that might occur including previously unknown mutations or polymorphisms. Two technical limitations of the original procedure have now been addressed. First, switching to Thermococcus litoralis DNA polymerase has eliminated variability believed to be due to the addition of an extra, non-templated base to the 3' end of DNA by Taq DNA polymerase. Second, with the analogs used in the original study, the mobility shift induced by a single base change can usually be resolved only in DNA segments 200 nt or smaller. This size limitation has been overcome by synthesizing biotinylated nucleotides with extraordinarily long linker arms (36 atom backbone). Using these new analogs and conventional sequencing gels (0.4 mm thick), mutations in the human beta-hexosaminidase alpha and CYP2D6 genes have been detected in DNA segments up to 300 nt in length. By using very thin (0.15 mm) gels, single-base polymorphisms in the human APOE gene have been detected in 500-nt segments