Histogram Equalization Of 24-Bit Color Images In The Color-Difference (C-Y) Color Space

We describe a method of enhancing color images by applying histogram equalization to the saturation component in the color difference (C-Y) color space. When histogram equalization is applied to the saturation component of a 24-bit image, the transform often leads to red, green, and blue components that exceed the realizable RGB intensities. The histogram equalization algorithm presented reduces this problem by taking into account the relationship that exists between luminance and saturation and how the luminance value limits the range of possible saturations. This method also retains a more uniform distribution of color saturation once the components are transformed back into the RGB space. This is important for images that contain high-luminance, low-saturation features

Ab-initio calculations of the optical properties of the Si(113)3x2ADI surface

We investigated the stable silicon (113) surface with a 3x2ADI reconstruction by ab-initio methods. The ground state properties have been obtained using the density-functional theory. We present the dispersion of the electronic band structure, where the surface bands have been distinguished from the projected bulk bands by calculating their localization in the slab. The optical spectra, here the reflectance anisotropy (RAS), have been obtained within the independent particle random phase approximation. We identified surface features in the spectra tracing them back to the responsible electronic states and, studied their localization in the slab. A comparison with available experimental data for the band structure and the RAS shows a good agreement.Comment: 10 pages, 10 figure

Extensive stage-regulation of translation revealed by ribosome profiling of Trypanosoma brucei

Background Trypanosoma brucei subspecies infect humans and animals in sub-Saharan Africa. This early diverging eukaryote shows many novel features in basic biological processes, including the use of polycistronic transcription to generate all protein-coding mRNAs. Therefore we hypothesized that translational control provides a means to tune gene expression during parasite development in mammalian and fly hosts. Results We used ribosome profiling to examine genome-wide protein synthesis in animal-derived slender bloodstream forms and cultured procyclic (insect midgut) forms. About one-third of all CDSs showed statistically significant regulation of protein production between the two stages. Of these, more than two-thirds showed a change in translation efficiency, but few appeared to be controlled by this alone. Ribosomal proteins were translated poorly, especially in animal-derived parasites. A disproportionate number of metabolic enzymes were up-regulated at the mRNA level in procyclic forms, as were variant surface glycoproteins in bloodstream forms. Comparison with cultured bloodstream forms from another strain revealed stage-specific changes in gene expression that transcend strain and growth conditions. Genes with upstream ORFs had lower mean translation efficiency, but no evidence was found for involvement of uORFs in stage-regulation. Conclusions Ribosome profiling revealed that differences in the production of specific proteins in T. brucei bloodstream and procyclic forms are more extensive than predicted by analysis of mRNA abundance. While in vivo and in vitro derived bloodstream forms from different strains are more similar to one another than to procyclic forms, they showed many differences at both the mRNA and protein production level

Discovery of a natural product that binds to the mycobacterium tuberculosis protein Rv1466 using native mass spectrometry

Elucidation of the mechanism of action of compounds with cellular bioactivity is important for progressing compounds into future drug development. In recent years, phenotype-based drug discovery has become the dominant approach to drug discovery over target-based drug discovery, which relies on the knowledge of a specific drug target of a disease. Still, when targeting an infectious disease via a high throughput phenotypic assay it is highly advantageous to identifying the compound’s cellular activity. A fraction derived from the plant Polyalthia sp. showed activity against Mycobacterium tuberculosis at 62.5 µge/µL. A known compound, altholactone, was identified from this fraction that showed activity towards M. tuberculosis at an minimum inhibitory concentration (MIC) of 64 µM. Retrospective analysis of a target-based screen against a TB proteome panel using native mass spectrometry established that the active fraction was bound to the mycobacterial protein Rv1466 with an estimated pseudo-Kd of 42.0 ± 6.1 µM. Our findings established Rv1466 as the potential molecular target of altholactone, which is responsible for the observed in vivo toxicity towards M. tuberculosis

Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites

<p>Abstract</p> <p>Background</p> <p>The protozoan pathogens <it>Leishmania major</it>, <it>Trypanosoma brucei </it>and <it>Trypanosoma cruzi </it>(the Tritryps) are parasites that produce devastating human diseases. These organisms show very unusual mechanisms of gene expression, such as polycistronic transcription. We are interested in the study of tRNA genes, which are transcribed by RNA polymerase III (Pol III). To analyze the sequences and genomic organization of tRNA genes and other Pol III-transcribed genes, we have performed an <it>in silico </it>analysis of the Tritryps genome sequences.</p> <p>Results</p> <p>Our analysis indicated the presence of 83, 66 and 120 genes in <it>L. major, T. brucei </it>and <it>T. cruzi</it>, respectively. These numbers include several previously unannotated selenocysteine (Sec) tRNA genes. Most tRNA genes are organized into clusters of 2 to 10 genes that may contain other Pol III-transcribed genes. The distribution of genes in the <it>L. major </it>genome does not seem to be totally random, like in most organisms. While the majority of the tRNA clusters do not show synteny (conservation of gene order) between the Tritryps, a cluster of 13 Pol III genes that is highly syntenic was identified. We have determined consensus sequences for the putative promoter regions (Boxes A and B) of the Tritryps tRNA genes, and specific changes were found in tRNA-Sec genes. Analysis of transcription termination signals of the tRNAs (clusters of Ts) showed differences between <it>T. cruzi </it>and the other two species. We have also identified several tRNA isodecoder genes (having the same anticodon, but different sequences elsewhere in the tRNA body) in the Tritryps.</p> <p>Conclusion</p> <p>A low number of tRNA genes is present in Tritryps. The overall weak synteny that they show indicates a reduced importance of genome location of Pol III genes compared to protein-coding genes. The fact that some of the differences between isodecoder genes occur in the internal promoter elements suggests that differential control of the expression of some isoacceptor tRNA genes in Tritryps is possible. The special characteristics found in Boxes A and B from tRNA-Sec genes from Tritryps indicate that the mechanisms that regulate their transcription might be different from those of other tRNA genes.</p

NMR structure of an acyl-carrier protein from Borrelia burgdorferi

The high-resolution NMR structure of the acyl-carrier protein from the pathogen B. burgdorferi determined to a r.m.s. deviation of 0.4 Å over the protein backbone is reported. The NMR structure was determined using multidimensional NMR spectroscopy and consists of four α-helices and two 310-helices. Structural comparison reveals that this protein is highly similar to the acyl-carrier protein from A. aeolicus

Towards the Construction of Expressed Proteomes Using a Leishmania tarentolae Based Cell-Free Expression System

The adaptation of organisms to a parasitic life style is often accompanied by the emergence of novel biochemical pathways absent in free-living organisms. As a result, the genomes of specialized parasitic organisms often code for a large number (>50%) of proteins with no detectable homology or predictable function. Although understanding the biochemical properties of these proteins and their roles in parasite biogenesis is the next challenge of molecular parasitology, analysis tools developed for free-living organisms are often inadequate for this purpose. Here we attempt to solve some of these problems by developing a methodology for the rapid production of expressed proteomes in cell-free systems based on parasitic organisms. To do so we take advantage of Species Independent Translational Sequences (SITS), which can efficiently mediate translation initiation in any organism. Using these sequences we developed a single-tube in vitro translation system based on the parasitic protozoan Leishmania tarentolae. We demonstrate that the system can be primed directly with SITS containing templates constructed by overlap extension PCR. To test the systems we simultaneously amplified 31 of L. tarentolae's putative translation initiation factors and phosphatases directly from the genomic DNA and subjected them to expression, purification and activity analysis. All of the amplified products produced soluble recombinant proteins, and putative phosphatases could be purified to at least 50% purity in one step. We further compared the ability of L. tarentolae and E. coli based cell-free systems to express a set of mammalian, L. tarentolae and Plasmodium falciparum Rab GTPases in functional form. We demonstrate that the L. tarentolae cell-free system consistently produced higher quality proteins than E. coli-based system. The differences were particularly pronounced in the case of open reading frames derived from P. falciparum. The implications of these developments are discussed

Restenosis after excellent angiographic angioplasty result for chronic total coronary artery occlusion--Implications for newer percutaneous revascularization devices

The incidence of restenosis after coronary angioplasty for treatment of chronic total coronary occlusion is unacceptably high.1 The pathophysiology of restenosis after coronary angioplasty may be conceptually divided into an exuberant myointimal proliferation,2 and a residual partial obstruction that serves as a platform for atheroma regrowth and may potentiate that process by augmenting blood flow turbulence and platelet deposition. The techniques of atherectomy or laser ablation3 may lessen the likelihood of restenosis by minimizing the residual stenosis, although currently each may require supplemental balloon angioplasty to achieve this result. However, the effect of these techniques on later myointimal proliferation in human beings is largely unknown. The concept that intracoronary stenting4 may reduce restenosis is based largely on the supposition that, by forcing and maintaining the obstructive atheroma out of the normal arterial lumen, turbulence and hence platelet deposition would be reduced5 and a large amount of myointimal proliferation would be required to recreate an obstruction of physiologic consequence.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27757/1/0000150.pd

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology