Molecular Diagnostic Tests for Microsporidia

The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans

Chagas' disease and AIDS

Chagas' disease caused by Trypanosoma cruzi is an opportunistic infection in the setting of HIV/AIDS. Some individuals with HIV and chronic T. cruzi infection may experience a reactivation, which is most commonly manifested by meningoencephalitis. A reactivation myocarditis is the second most common manifestation. These presentations may be difficult to distinguish from toxoplasmosis in individuals with HIV/AIDS. The overlap of HIV and Trypanosoma cruzi infection occurs not only in endemic areas but also in non-endemic areas of North America and Europe where the diagnosis may be even more difficult. The pathological features, diagnosis and the role of cytokines in the pathogenesis of the disease are discussed

Gene expression in Leishmania is regulated predominantly by gene dosage

ABSTRACT Leishmania tropica, a unicellular eukaryotic parasite present in North and East Africa, the Middle East, and the Indian subcontinent, has been linked to large outbreaks of cutaneous leishmaniasis in displaced populations in Iraq, Jordan, and Syria. Here, we report the genome sequence of this pathogen and 7,863 identified protein-coding genes, and we show that the majority of clinical isolates possess high levels of allelic diversity, genetic admixture, heterozygosity, and extensive aneuploidy. By utilizing paired genome-wide high-throughput DNA sequencing (DNA-seq) with RNA-seq, we found that gene dosage, at the level of individual genes or chromosomal “somy” (a general term covering disomy, trisomy, tetrasomy, etc.), accounted for greater than 85% of total gene expression variation in genes with a 2-fold or greater change in expression. High gene copy number variation (CNV) among membrane-bound transporters, a class of proteins previously implicated in drug resistance, was found for the most highly differentially expressed genes. Our results suggest that gene dosage is an adaptive trait that confers phenotypic plasticity among natural Leishmania populations by rapid down- or upregulation of transporter proteins to limit the effects of environmental stresses, such as drug selection. IMPORTANCE Leishmania is a genus of unicellular eukaryotic parasites that is responsible for a spectrum of human diseases that range from cutaneous leishmaniasis (CL) and mucocutaneous leishmaniasis (MCL) to life-threatening visceral leishmaniasis (VL). Developmental and strain-specific gene expression is largely thought to be due to mRNA message stability or posttranscriptional regulatory networks for this species, whose genome is organized into polycistronic gene clusters in the absence of promoter-mediated regulation of transcription initiation of nuclear genes. Genetic hybridization has been demonstrated to yield dramatic structural genomic variation, but whether such changes in gene dosage impact gene expression has not been formally investigated. Here we show that the predominant mechanism determining transcript abundance differences (>85%) in Leishmania tropica is that of gene dosage at the level of individual genes or chromosomal somy

Classical trajectories in quantum transport at the band center of bipartite lattices with or without vacancies

Here we report on several anomalies in quantum transport at the band center of a bipartite lattice with vacancies that are surely due to its chiral symmetry, namely: no weak localization effect shows up, and, when leads have a single channel the transmission is either one or zero. We propose that these are a consequence of both the chiral symmetry and the large number of states at the band center. The probability amplitude associated to the eigenstate that gives unit transmission ressembles a classical trajectory both with or without vacancies. The large number of states allows to build up trajectories that elude the blocking vacancies explaining the absence of weak localization.Comment: 5 pages, 5 figure

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus <i>Pneumocystis jirovecii</i>.

Microbial pathogens commonly escape the human immune system by varying surface proteins. We investigated the mechanisms used for that purpose by &lt;i&gt;Pneumocystis jirovecii&lt;/i&gt; This uncultivable fungus is an obligate pulmonary pathogen that in immunocompromised individuals causes pneumonia, a major life-threatening infection. Long-read PacBio sequencing was used to assemble a core of subtelomeres of a single &lt;i&gt;P. jirovecii&lt;/i&gt; strain from a bronchoalveolar lavage fluid specimen from a single patient. A total of 113 genes encoding surface proteins were identified, including 28 pseudogenes. These genes formed a subtelomeric gene superfamily, which included five families encoding adhesive glycosylphosphatidylinositol (GPI)-anchored glycoproteins and one family encoding excreted glycoproteins. Numerical analyses suggested that diversification of the glycoproteins relies on mosaic genes created by ectopic recombination and occurs only within each family. DNA motifs suggested that all genes are expressed independently, except those of the family encoding the most abundant surface glycoproteins, which are subject to mutually exclusive expression. PCR analyses showed that exchange of the expressed gene of the latter family occurs frequently, possibly favored by the location of the genes proximal to the telomere because this allows concomitant telomere exchange. Our observations suggest that (i) the &lt;i&gt;P. jirovecii&lt;/i&gt; cell surface is made of a complex mixture of different surface proteins, with a majority of a single isoform of the most abundant glycoprotein, (ii) genetic mosaicism within each family ensures variation of the glycoproteins, and (iii) the strategy of the fungus consists of the continuous production of new subpopulations composed of cells that are antigenically different. &lt;b&gt;IMPORTANCE&lt;/b&gt; &lt;i&gt;Pneumocystis jirovecii&lt;/i&gt; is a fungus causing severe pneumonia in immunocompromised individuals. It is the second most frequent life-threatening invasive fungal infection. We have studied the mechanisms of antigenic variation used by this pathogen to escape the human immune system, a strategy commonly used by pathogenic microorganisms. Using a new DNA sequencing technology generating long reads, we could characterize the highly repetitive gene families encoding the proteins that are present on the cellular surface of this pest. These gene families are localized in the regions close to the ends of all chromosomes, the subtelomeres. Such chromosomal localization was found to favor genetic recombinations between members of each gene family and to allow diversification of these proteins continuously over time. This pathogen seems to use a strategy of antigenic variation consisting of the continuous production of new subpopulations composed of cells that are antigenically different. Such a strategy is unique among human pathogens

EPIC-DB: a proteomics database for studying Apicomplexan organisms

<p>Abstract</p> <p>Background</p> <p>High throughput proteomics experiments are useful for analyzing the protein expression of an organism, identifying the correct gene structure of a genome, or locating possible post-translational modifications within proteins. High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data.</p> <p>Description</p> <p>EPICDB is a publicly accessible, queryable, relational database that organizes and displays experimental, high throughput proteomics data for <it>Toxoplasma gondii </it>and <it>Cryptosporidium parvum</it>. Along with detailed information on mass spectrometry experiments, the database also provides antibody experimental results and analysis of functional annotations, comparative genomics, and aligned expressed sequence tag (EST) and genomic open reading frame (ORF) sequences. The database contains all available alternative gene datasets for each organism, which comprises a complete theoretical proteome for the respective organism, and all data is referenced to these sequences. The database is structured around clusters of protein sequences, which allows for the evaluation of redundancy, protein prediction discrepancies, and possible splice variants. The database can be expanded to include genomes of other organisms for which proteome-wide experimental data are available.</p> <p>Conclusion</p> <p>EPICDB is a comprehensive database of genome-wide <it>T. gondii </it>and <it>C. parvum </it>proteomics data and incorporates many features that allow for the analysis of the entire proteomes and/or annotation of specific protein sequences. EPICDB is complementary to other -genomics- databases of these organisms by offering complete mass spectrometry analysis on a comprehensive set of all available protein sequences.</p

Driving-Induced Symmetry Breaking in the Spin-Boson System

A symmetric dissipative two-state system is asymptotically completely delocalized independent of the initial state. We show that driving-induced localization at long times can take place when both the bias and tunneling coupling energy are harmonically modulated. Dynamical symmetry breaking on average occurs when the driving frequencies are odd multiples of some reference frequency. This effect is universal, as it is independent of the dissipative mechanism. Possible candidates for an experimental observation are flux tunneling in the variable barrier rf SQUID and magnetization tunneling in magnetic molecular clusters.Comment: 4 pages, 4 figures, to be published in PR

WR 110: A Single Wolf-Rayet Star With Corotating Interaction Regions In Its Wind?

A 30-day contiguous photometric run with the MOST satellite on the WN5-6b star WR 110 (HD 165688) reveals a fundamental periodicity of P = 4.08 +/- 0.55 days along with a number of harmonics at periods P/n, with n ~ 2,3,4,5 and 6, and a few other possible stray periodicities and/or stochastic variability on timescales longer than about a day. Spectroscopic RV studies fail to reveal any plausible companion with a period in this range. Therefore, we conjecture that the observed light-curve cusps of amplitude ~ 0.01 mag that recur at a 4.08 day timescale may arise in the inner parts, or at the base of, a corotating interaction region (CIR) seen in emission as it rotates around with the star at constant angular velocity. The hard X-ray component seen in WR 110 could then be a result of a high velocity component of the CIR shock interacting with the ambient wind at several stellar radii. Given that most hot, luminous stars showing CIRs have two CIR arms, it is possible that either the fundamental period is 8.2 days or, more likely in the case of WR 110, there is indeed a second weaker CIR arm for P = 4.08 days, that occurs ~ two thirds of a rotation period after the main CIR. If this interpretation is correct, WR 110 therefore joins the ranks with three other single WR stars, all WN, with confirmed CIR rotation periods (WR 1, WR 6, and WR 134), albeit with WR 110 having by far the lowest amplitude photometric modulation. This illustrates the power of being able to secure intense, continuous high-precision photometry from space-based platforms such as MOST. It also opens the door to revealing low-amplitude photometric variations in other WN stars, where previous attempts have failed. If all WN stars have CIRs at some level, this could be important for revealing sources of magnetism or pulsation in addition to rotation periods.Comment: 25 pages, 8 figures, 2 tables, accepted in Ap