Real-Time Music Following in Score Sheet Images via Multi-Resolution Prediction

The task of real-time alignment between a music performance and the corresponding score (sheet music), also known as score following, poses a challenging multi-modal machine learning problem. Training a system that can solve this task robustly with live audio and real sheet music (i.e., scans or score images) requires precise ground truth alignments between audio and note-coordinate positions in the score sheet images. However, these kinds of annotations are difficult and costly to obtain, which is why research in this area mainly utilizes synthetic audio and sheet images to train and evaluate score following systems. In this work, we propose a method that does not solely rely on note alignments but is additionally capable of leveraging data with annotations of lower granularity, such as bar or score system alignments. This allows us to use a large collection of real-world piano performance recordings coarsely aligned to scanned score sheet images and, as a consequence, improve over current state-of-the-art approaches.

DeepSNP: An End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data

Clinical decision-making in cancer and other diseases relies on timely and cost-effective genome-wide testing. Classical bioinformatic algorithms, such as Rawcopy, can support genomic analysis by calling genomic breakpoints and copy-number variations (CNVs), but often require manual data curation, which is error prone, time-consuming, and thus substantially increasing costs of genomic testing and hampering timely delivery of test results to the treating physician. We aimed to investigate whether deep learning algorithms can be used to learn from genome-wide single-nucleotide polymorphism array (SNPa) data and improve state-of-the-art algorithms. We developed, applied, and validated a novel deep neural network (DNN), DeepSNP. A manually curated data set of 50 SNPa analyses was used as truth-set. We show that DeepSNP can learn from SNPa data and classify the presence or absence of genomic breakpoints within large genomic windows with high precision and recall. DeepSNP was compared with well-known neural network models as well as with Rawcopy. Moreover, the use of a localization unit indicates the ability to pinpoint genomic breakpoints despite their exact location not being provided while training. DeepSNP results demonstrate the potential of DNN architectures to learn from genomic SNPa data and encourage further adaptation for CNV detection in SNPa and other genomic data types.

Genotypic Characterization of Cryptosporidium Species in Humans and Peri-Domestic Animals in Ekiti and Oyo States, Nigeria

Cryptosporidiosis is one of the leading causes of diarrhea in humans and several other vertebrate species. Because surveys of Cryptosporidium genotypes from animals and humans living in the same region are rare, our understanding of the importance of zoonotic transmission in the epidemiology of cryptosporidiosis remains superficial. PCR was used to amplify a portion of the Cryptosporidium 18S small subunit ribosomal RNA gene from fecal DNA from humans and livestock living in Ekiti and Oyo states, Nigeria. PCR-positive samples were further analyzed using PCR targeting the heat-shock protein HSP-70, the actin, and the sporozoite glycoprotein gene gp60. A questionnaire was used to collect demographic information. Sixteen of 187 samples collected were Cryptosporidium 18S PCR positive. Of these, 5 samples originating from HIV-positive patients, 5 from otherwise healthy children, 2 from chickens, 3 from goats, and 1 from a dog were positive for at least 1 marker. Sequencing of the 18S rRNA amplicons revealed the presence of Cryptosporidium parvum in 2 HIV positive patients and in a child; the actin sequence confirmed the presence of this species. Two samples of HIV-positive patients amplified Cryptosporidium hominis 18S rRNA, one of them confirmed by the HSP-70, actin, and gp60 sequences. Cryptosporidium meleagridis was found in another HIV patient, while C. hominis was detected in 3 children (of which 2 were confirmed by gp60). Cryptosporidium muris was found in 1 child. In birds, we found C. meleagridis and, significantly, C. parvum, whereas we detected C. parvum and C. muris in 1 goat each. The only dog sampled was positive for Cryptosporidium canis. We conclude that, in the environment we surveyed, humans and animals are a potential part of the same transmission cycle. Measures to prevent zoonotic transmission should therefore be considered to reduce the prevalence of cryptosporidiosis.

Getting Closer to the Essence of Music

This text offers a personal and very subjective view on the current situation of Music Information Research (MIR). Motivated by the desire to build systems with a somewhat deeper understanding of music than the ones we currently have, I try to sketch a number of challenges for the next decade of MIR research, grouped around six simple truths about music that are probably generally agreed on but often ignored in everyday research.

Trichomonad Gastritis in Rhesus Macaques (Macaca mulatta) Infected with Simian Immunodeficiency Virus

In a retrospective study, 51 cases of gastritis (14%) were identified from among 341 necropsies performed on simian immunodeficiency virus (SlV)-infected rhesus macaques ( Macaca mulatta) at the New England Primate Research Center from 1993 to 2001. Protozoa were seen in the stomach of 13 monkeys (25%) with gastritis. Two histopathologic manifestations of gastritis were observed: seven cases of lymphoplasmacytic gastritis with trichomonad trophozoites within lumens of gastric glands and four cases of necrosuppurative gastritis containing intralesional periodic acid-Schiff-positive protozoa; two cases of gastritis had morphologic features of both types of gastritis. In instances of necrosuppurative and combined lymphoplasmacytic and necrosuppurative gastritis, protozoa were 4-35 μm in diameter and round to tear-shaped. Because of the unusual morphology of the protozoa in these latter cases, transmission electron microscopy and polymerase chain reaction (PCR) were used to further identify these organisms. The protozoa were definitively identified as Tritrichomonas in all cases on the basis of ultrastructural characteristics (flagella and undulating membranes) and amplification of a 347-bp product of the 5.8S ribosomal RNA gene of Tritrichomonas foetus, Tritrichomonas suis and Tritrichomonas mobilensis by PCR using DNA extracted from stomach tissue. On the basis of these observations, we conclude that Tritrichomonas can be a significant cofactor in the development of necrosup-purative gastritis in SIV-infected rhesus macaques.

Genomics and population biology of Cryptosporidium species

We describe recent advances in the genomics and population biology of Cryptosporidium parvum and C. hominis, the causative agents of cryptosporidiosis in humans and animals. Many basic aspects of the biology of Cryptosporidium species remain to be investigated and effective drugs to control cryptosporidiosis are not available. Sequencing and annotation of the genome of C. parvum and C. hominis has uncovered unique features of the metabolism of these species. The recently sequenced genome of the gastric species C. muris is providing new insights into the evolution of the genus. Cryptosporidian sequence information has facilitated the identification of polymorphic genetic markers. Genotyping of oocysts excreted by human and animal hosts using such markers has revealed many new species and genotypes, and is leading to a better understanding of the epidemiology of cryptosporidiosis.

Exploring the music similarity space on the web

This article comprehensively addresses the problem of similarity measurement between music artists via text-based features extracted from Web pages. To this end, we present a thorough evaluation of different term-weighting strategies, normalization methods, aggregation functions, and similarity measurement techniques. In large-scale genre classification experiments carried out on real-world artist collections, we analyze several thousand combinations of settings/parameters that influence the similarity calculation process, and investigate in which way they impact the quality of the similarity estimates. Accurate similarity measures for music are vital for many applications, such as automated playlist generation, music recommender systems, music information systems, or intelligent user interfaces to access music collections by means beyond text-based browsing. Therefore, by exhaustively analyzing the potential of text-based features derived from artist-related Web pages, this article constitutes an important contribution to context-based music information research.

YQX Plays Chopin

The article is about AI research in the context of a complex artistic behavior: expressive music performance. A computer program is presented that learns to play piano with 'expression' and that even won an international computer piano performance contest. A superficial analysis of an expressive performance generated by the system seems to suggest creative musical abilities. After a critical discussion of the processes underlying this behavior, we abandon the question of whether the system is really creative, and turn to the true motivation that drives this research: to use AI methods to investigate and better understand music performance as a human creative behavior. A number of recent and current results from our research are briefly presented that indicate that machines can give us interesting insights into such a complex creative behavior, even if they may not be creative themselves.

Cryptosporidium parvum DNA replication in cell-free culture

The lack of robust methods for culturing Cryptosporidium parasites remains a major challenge and is hampering efforts to screen for anti-cryptosporidial drugs. In existing culture methods, monolayers of mammalian epithelial cells are inoculated with oocysts. The system supports an initial phase of asexual proliferation of the parasite. For reasons that are not clear, development rapidly declines within 2-3 days. The unexpected report of Cryptosporidium parvum culture in the absence of host cells, and the failure of others to reproduce the method, prompted us to apply quantitative PCR to measure changes in C. parvum DNA levels in cell-free cultures, and parasite-specific antibodies to identify different life cycle stages. Based on this approach, which has not been applied previously to analyze C. parvum growth in cell-free culture, we found that the concentration of C. parvum DNA increased by about 5-fold over 5 days of culture. Immuno-labeling of cultured organisms revealed morphologically distinct stages, only some of which reacted with Cryptosporidium-specific monoclonal antibodies. These observations are indicative of a modest proliferation of C. parvum in cell-free culture.

Adaptation of Cryptosporidium oocysts to different excystation conditions

Within the genus Cryptosporidium 2 lineages have evolved, one adapted to the acid environment of the stomach and abomasum, the other comprising parasites that multiply in the small intestine. We tested whether the release of sporozoites from oocysts, a process known as excystation, is triggered by conditions which mimic the site of infection. Specifically, we exposed oocysts from gastric and intestinal Cryptosporidium species to acid conditions or to a neutral solution of taurocholic acid, at 37 degrees C. We found that oocysts from the gastric species C. muris and C. andersoni excysted in both conditions, whereas the intestinal species C. parvum and C. hominis did not respond to acid. When the effect of temperature alone was tested on C. muris and C. parvum, only oocysts from the former species excysted in significant numbers. Oocysts from intestinal species did not respond to temperature alone, nor to acidity. These observations are consistent with the need of gastric species to rapidly excyst and release the sporozoites upon ingestion, and indicate that Cryptosporidium oocysts have evolved to maximize delivery of sporozoites to the region of the gastro-intestinal tract where the parasite multiplies.

Host-shaped segregation of the Cryptosporidium parvum multilocus genotype repertoire

Cattle are among the major reservoirs of Cryptosporidium parvum in nature. However, the relative contribution of C. parvum oocysts originating from cattle to human disease burden is difficult to assess, as various transmission pathways -- including the human to human route -- can co-occur. In this study, multilocus genotype richness of representative samples of human and bovine C. parvum are compared statistically using analytical rarefaction and non-parametric taxonomic richness estimators. Results suggest that in the time and space frames underlying the analysed data, humans were infected with significantly wider spectra of C. parvum genotypes than cattle, and consequently, a significant fraction of human infections may not have originated from the regional bovine reservoirs. This study provides statistical support to the emerging idea of the existence of distinct anthroponotic C. parvum cycles that do not involve cattle.

Preferential infection of dividing cells by Cryptosporidium parvum

In spite of its limitations, the culture of Cryptosporidium parvum in monolayers of epithelial cells is a suitable model to study the interaction of this protozoan parasite with the host cell, to assay oocyst infectivity, and to screen drugs for anti-cryptosporidial activity. For unknown reasons, growth of Cryptosporidium in culture is limited in time and generally does not lead to the production of significant numbers of oocysts. In monolayers infected with high doses of oocysts, we observed that many cells remain uninfected, suggesting that some cells are less susceptible to the infection. Since C. parvum and the related species C. hominis lack many essential biosynthetic pathways, we tested whether the dependence of the parasite on host cell metabolites may favour the infection of cells in mitosis. The proportion of monolayer cells in stationary (G0/G1) phase and in mitosis (S/G2/M) was determined and the prevalence of infected cells in each subpopulation was quantified. Although C. parvum infects and develops in dividing and stationary cells, a significant preference for cells in S/G2/M phase was observed. Consistent with previous observations showing that C. parvum induces apoptosis in cell monolayers, infection was accompanied by a significant increase in the proportion of mitotic cells.

Genetic analysis of a Cryptosporidium parvum human genotype 1 isolate passaged through different host species

Cryptosporidium parvum TU502, a genotype 1 isolate of human origin, was passaged through three different mammalian hosts, including humans, pigs, and calves. It was confirmed to be genotype 1 by PCR-restriction fragment length polymorphism analysis of the Cryptosporidium oocyst wall protein gene, direct sequencing of PCR fragments of the small subunit rRNA and beta-tubulin genes, and microsatellite analysis. This isolate was shown to be genetically stable when passaged through the three mammalian species, with no evidence of the emergence of new subpopulations as observed by a genotype-specific PCR assay. TU502 oocysts from different sources failed to infect gamma interferon knockout mice, a characteristic of genotype 1 isolates. The genotypic and phenotypic characterization of TU502 is significant since it is the isolate selected to sequence the genome of C. parvum genotype 1 and is currently used in several research projects including human volunteer studies.

Genotyping Cryptosporidium parvum by single-strand conformation polymorphism analysis of ribosomal and heat shock gene regions

Polymerase chain reaction (PCR)-coupled single-strand conformation polymorphism (SSCP) approaches utilizing nuclear DNA regions of the small subunit (SSU) of ribosomal RNA and heat shock protein 70 gene (HSP70) were established for genotyping Cryptosporidium parvum. The regions were amplified (individually or in a multiplex reaction) by PCR from DNA extracted from oocysts from ruminant or human hosts, then denatured and subjected to electrophoresis in a mutation detection enhancement (nondenaturing) gel matrix. Single-strand profiles produced in SSCP allowed the unequivocal identification/differentiation of the two common (human, 1 and cattle, 2) genotypes of C. parvum and the direct display of sequence variability within some samples, reflecting population variation. As these are considered among the most closely related genotypes (based on SSU and HSP70 sequence data), these findings and other preliminary results for C. felis (from cat) C. serpentis (from snake) and C. baileyi (from bird) indicate that the SSCP approaches established could be employed to identify any of the currently recognised genotypes and species of Cryptosporidium.

Host cell apoptosis impairs Cryptosporidium parvum development in vitro

The absence of a self-sustaining in vitro propagation method for Cryptosporidium parvum is a major obstacle for research on this parasite. Conventional cell monolayers are unsuitable for long-term parasite propagation because the level of infection decreases over time and few oocysts, if any, are produced. The interaction between parasite and host cell was studied to identify factors limiting parasite development in vitro. Loss of substrate adherence and death of parasitized host cells was observed in 2 epithelial cell lines. Nuclear morphology, DNA laddering, annexin V binding, and terminal deoxytransferase-mediated dUTP nick end labeling indicated that host cell death occurred by apoptosis. At 6 hr postinfection, only a minority of infected cells remained in the monolayer, and few survived the initial phase of parasite development without losing adherence. Treatment of infected monolayers with caspase inhibitors drastically reduced cell detachment but failed to increase the number of parasites in monolayers. In contrast, cell cultures grown on laminin-coated plates showed a higher proportion of infected cells. These observations indicate that cell detachment and apoptosis in C. parvum-infected cell culture negatively affect parasite survival in vitro.

Extensive polymorphism in Cryptosporidium parvum identified by multilocus microsatellite analysis

Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.

Animal propagation and genomic survey of a genotype 1 isolate of Cryptosporidium parvum

Human cryptosporidiosis is attributed to two major Cryptosporidium parvum genotypes of which type 1 appears to be the predominant. Most laboratory investigations however are performed using genotype 2 isolates, the only type which readily infects laboratory animals. So far type 1 has only been identified in humans and primates. A type 1 isolate, obtained from an individual with HIV and cryptosporidiosis, was successfully adapted to propagate in gnotobiotic piglets. Genotypic characterization of oocyst DNA from this isolate using multiple restriction fragment length polymorphisms, a genotype-specific PCR marker, and direct sequence analysis of two polymorphic loci confirmed that this isolate, designated NEMC1, is indeed type 1. No changes in the genetic profile were identified during multiple passages in piglets. In contrast, the time period between infection and onset of fecal oocyst shedding, an indicator of adaptation, decreased with increasing number of passages. Consistent with other type 1 isolates, NEMC1 failed to infect mice. A preliminary survey of the NEMC1 genome covering approximately 2% of the genome and encompassing 200 kb of unique sequence showed an average similarity of approximately 95% between type 1 and 2 sequences. Twenty-four percent of the NEMC1 sequences were homologous to previously determined genotype 2 C. parvum sequences. To our knowledge, this is the first successful serial propagation of genotype 1 in animals, which should facilitate characterization of the unique features of this human pathogen.

Constitutive expression of small subunit ribosomal RNA transcripts in Cryptosporidium parvum oocysts and intracellular stages

As in other apicomplexan protozoa, the ribosomal genes of Cryptosporidium parvum are present in small number and dispersed on several chromosomes. Two types of ribosomal small subunit genes have been identified in bovine isolates by sequencing and sequence-specific polymerase chain reaction. Using denaturing gradient gel electrophoresis, ribosomal gene expression was investigated in C. parvum oocysts and intracellular stages grown in tissue culture. In a calf-propageted C. parvum isolate, extra and intracellular stages expressed 2 types of transcripts. This observation contrasts with the differential expression of rRNA, genes in malaria species. Analysis of ribosomal gene expression in oocysts of a different genotype indicates that some C. parvum isolates express only l type of small subunit ribosomal RNA. These observations highlight fundamental differences in ribosomal gene expression among apicomplexan protozoa and within the species C. parvum and support the view that differential expression in malaria is an adaptation to a dixeneous life cycle.

beta-tubulin mRNA as a marker of Cryptosporidium parvum oocyst viability

Determining the viability of waterborne Cryptosporidium parvum oocysts remains a technical challenge. rRNA and mRNA were evaluated in a reverse transcription (RT)-PCR assay as potential markers of oocyst viability. The rationale for this approach is the rapid turnover and postmortem decay of cellular RNA. The beta-tubulin mRNA and an anonymous mRNA transcript were chosen as potential markers because they are the only mRNA species in C. parvum known to possess introns. This feature facilitated the distinction between genuine RT-PCR products and PCR products originating from copurifying DNA. Prolonged incubation at room temperature of initially viable oocysts resulted in a gradual decrease in mRNA levels, which correlated with the loss of oocyst infectivity to neonatal mice. In contrast, oocysts stored at 4 degrees C for over 39 weeks maintained their infectivity and displayed no decrease in the level of beta-tubulin RT-PCR product. The postmortem decay of two mRNA species demonstrates that RT-PCR analysis can provide information on the viability of C. parvum oocysts. The methodological similarity between PCR detection and RT-PCR viability analysis could facilitate the development of a combined detection and viability assay.

Transmission and serial propagation of Enterocytozoon bieneusi from humans and Rhesus macaques in gnotobiotic piglets

For over a decade Enterocytozoon bieneusi infections in people with AIDS have been linked with chronic diarrhea and wasting. The slow scientific progress in treating these infections is attributed to the inability of investigators to cultivate the parasite, which has also precluded evaluation of effective therapies. We report here successful serial transmissions of E. bieneusi from patients with AIDS and from macaques with AIDS to immunosuppressed gnotobiotic piglets. One infected piglet was still excreting spores at necropsy 50 days after an oral challenge. Spores in feces were detected microscopically by trichrome stain and by PCR and within enterocytes by in situ hybridization and immunohistochemistry. E. bieneusi infection induced no symptoms. The development of an animal model for E. bieneusi will open up new opportunities for investigating this parasite.

Sequence polymorphism in the beta-tubulin gene reveals heterogeneous and variable population structures in Cryptosporidium parvum

Restriction fragment length polymorphism (RFLP) analysis of isolates of Cryptosporidium parvum has revealed two subgroups, termed H and C. The limited resolution of the RFLP method precludes an in-depth study of the genetic structure of C. parvum populations. Published C. parvum restriction polymorphisms lie within protein-coding regions known to be more homogeneous than noncoding sequences. To better assess the degrees of heterogeneity between and within C. parvum isolates, sequence polymorphism in the beta-tubulin intron, the only C. parvum intron described to date, was investigated. In contrast to the two genotypes distinguished by multilocus RFLP, several alleles were detected by sequence and RFLP analysis of the beta-tubulin intron and adjacent exon 2. Isolates carrying different beta-tubulin alleles were found. Significantly, one of the beta-tubulin alleles present in two geographically unrelated isolates combined features of C- and H-type isolates, suggesting that it might have arisen from a recombination event. A comparison of multiple samples of a calf-propagated laboratory isolate showed that the ratio of different beta-tubulin alleles fluctuated during serial passage.

Multilocus genotypic analysis of Cryptosporidium parvum isolates from different hosts and geographical origins

The genetic analysis of oocysts recovered from the stools of humans and animals infected with Cryptosporidium parvum has consistently shown the existence of two distinct genotypes. One of the genotypes is found exclusively in some human infections, whereas the other genotype is found in human as well as in animal infections. On the basis of these observations and the results of published epidemiological studies with single polymorphic markers, the existence of two separate transmission cycles has been postulated, one exclusively anthroponotic and the other involving both animals and humans. To test this hypothesis, C. parvum isolates of different geographic and host origins were analyzed by using unlinked genetic polymorphisms. A total of 28 isolates originating from Europe, North and South America, and Australia were examined. Isolates clustered into two groups, one comprising both human and animal isolates and the other comprising isolates only of human origin. The absence of recombinant genotypes is consistent with two reproductively isolated populations within the species C. parvum.

Genotypic and phenotypic characterization of Cryptosporidium parvum isolates from people with AIDS

Genotypic analysis of Cryptosporidium parvum has demonstrated the presence of two subgroups within the species, whereas biochemical and antigenic characterization have shown more heterogeneity. The clinical relevance of these observations is unknown. C. parvum isolates from people with AIDS were studied with respect to parasite genotypes and virulence in cell monolayers and laboratory animals. Ten of 13 oocyst samples had a characteristic human-associated (H) genotype; 3 had a genotype typical of calf-excreted oocysts (C). Virulence in cell culture was mildly or markedly lower in the 5 isolates tested (4 H and 1 C) compared with the GCH1 reference isolate. H isolates did not infect newborn ICR mice, whereas 1 of the 2 C isolates tested did. These findings reinforce the concept of C. parvum genetic subgroupings that correlate to some extent with infectivity and suggest that additional heterogeneity is present within the subgroups.

A study of Cryptosporidium parvum genotypes and population structure

Genetic evidence for the occurrence of two Cryptosporidium parvum subgroups is presented. This evidence is based on restriction fragment length polymorphism analysis of several independent loci. Sequence analysis of the beta-tubulin intron revealed additional polymorphism. The stability of the genetic profiles following passage of C. parvum isolates between different hosts was investigated.

Paromomycin and geneticin inhibit intracellular Cryptosporidium parvum without trafficking through the host cell cytoplasm: implications for drug delivery

Cryptosporidium parvum, which causes intractable diarrhea and lethal wasting in people with AIDS, occupies an unusual intracellular but extracytoplasmic niche. No reliable therapy for cryptosporidiosis exists, though the aminoglycoside paromomycin is somewhat effective. We report that paromomycin and the related compound geneticin manifest their major in vitro anti-C. parvum activity against intracellular parasites via a mechanism that does not require drug trafficking through the host cell cytoplasm. We used both normal and transformed aminoglycoside-resistant Caco-2 or MDBK cells in these studies. Timed-exposure experiments demonstrated that these drugs inhibit intracellular but not extracellular parasites. Apical but not basolateral exposure of infected cells to these drugs led to very significant parasite inhibition, indicating an apical topological restriction of action. We estimated intracytoplasmic concentrations of paromomycin, using an intracellular bacterial killing assay, and found that C. parvum infection did not lead to increased paromomycin concentrations compared to those in uninfected cells. Global [3H]paromomycin uptake by Caco-2 cells was approximately 200-fold higher than the estimated intracytoplasmic paromomycin concentration, suggestive of host cell vesicular uptake and concentration (as has been reported with other cell lines). However, preinfection exposure of Caco-2 cells to paromomycin did not result in subsequent inhibition of parasite development, indicating that if exogenous paromomycin enters the infected host cell vesicular compartment, it does not effectively communicate with the parasite. Thus, the apical membranes overlying the parasite and parasitophorous vacuole may be the unsuspected major route of entry for paromomycin and may be of importance in the design and discovery of novel drug therapies for the otherwise untreatable C. parvum.

Genetic heterogeneity and PCR detection of Cryptosporidium parvum

A variety of methods have been applied to the study of genotypic and phenotypic polymorphism in Cryptosporidium parvum. Results from these studies have consistently shown the existence of different genotypes and phenotypes within the species. A long-term goal of this work is the identification of markers for virulence in humans and animals and the elucidation of transmission cycles of C. parvum. Achievement of these goals will depend on the identification of highly polymorphic loci. Of particular interest are polymorphisms amenable to typing by polymerase chain reaction (PCR), as C. parvum cannot be expanded in vitro. Fingerprinting of isolates by restriction of PCR fragments or allele-specific PCR has given promising results. As originally observed by isoenzyme analysis, genetic fingerprinting has confirmed the occurrence in humans of unique C. parvum genotypes which are not found among calf isolates. This observation remains to be reconciled with the cross-infectivity of C. parvum to ruminant and nonruminant hosts and the important role that bovines play in the epidemiology of C. parvum and human cryptosporidiosis. Although PCR detection of C. parvum DNA from individual oocysts has been reported, the sensitivity of PCR detection when working with environmental or fecal samples is significantly reduced. Therefore, PCR is currently not used for routine diagnosis or environmental monitoring for C. parvum. Inhibitors present in environmental samples, mainly in water and soil, which can negatively affect PCR recoveries, have been identified, and several methods have been proposed to circumvent these problems. The further refinement of detection and genetic fingerprinting protocols will provide essential tools for indentifying environmental sources of oocysts and elucidating transmission cycles.

A new restriction fragment length polymorphism from Cryptosporidium parvum identifies genetically heterogeneous parasite populations and genotypic changes following transmission from bovine to human hosts

Length and restriction site polymorphism within a 2.8-kb threonine-rich open reading frame from Cryptosporidium parvum was identified and used to determine the genotypes of isolates from calves and humans. In agreement with observations of other genetic loci, all calf isolates were identical at this locus. In contrast, human isolates showed two profiles, one found exclusively in humans and one a superposition of both profiles, which were indicative of heterogeneous parasite populations. PCR fingerprints were consistent with a change in the genetic profile of C. parvum isolates following transmission from bovine to human hosts.

Parameters affecting polymerase chain reaction detection of waterborne Cryptosporidium parvum oocysts

Cryptosporidium parvum is an enteric protozoan parasite of medical and veterinary importance. Dissemination of environmentally resistant oocysts in surface water plays an important role in the epidemiology of cryptospridiosis. Although the polymerase chain reaction (PCR) is a well-established technique and is widely used for detecting microorganisms, it is not routinely applied for monitoring waterborne C. parvum. In order to facilitate the application of PCR to the detection of waterborne C. parvum oocysts, a comparison of published PCR protocols was undertaken and different sample-preparation methods tested. The sensitivity of a one-step PCR method, consisting of 40 temperature cycles, was 10 purified oocysts or fewer than 100 oocysts spiked in raw lake water. The detection limit of two primer pairs, one targeting the ribosomal small subunit and another specific for a C. parvum sequence of unknown function, was approximately ten-fold lower than achieved with a primer pair targeting an oocyst shell protein gene. Three cycles of freezing/thawing were sufficient to expose oocyst DNA and resulted in higher sensitivity than proteinase K digestion, sonication or electroporation. Inhibition of PCR by surface water from different local sources was entirely associated with the soluble fraction of lake water. Membrane filtration was evaluated in bench-scale experiments as a means of removing lake water inhibitors and improving the detection limit of PCR. Using gel and membrane filtration, the molecular size of inhibitory solutes from lake water was estimated to less than 27 kDa.

Development and application of genetic probes for detection of Enterocytozoon bieneusi in formalin-fixed stools and in intestinal biopsy specimens from infected patients

The microsporidium Enterocytozoon bieneusi is closely linked to wasting and diarrhea in a high proportion of individuals with AIDS. However, its relative contribution to disease is uncertain because diagnosis until recently depended on procedures involving endoscopy. A sensitive PCR technique which amplifies a fragment of the small-subunit rRNA gene of E. bieneusi from formalin-fixed stool samples was developed. Of 80 formalin-fixed stool samples collected from 74 Zimbabweans and 6 U.S. patients who were human immunodeficiency virus positive, 50% tested positive for E. bieneusi by PCR, whereas 24% tested positive for E. bieneusi by light microscopy of trichrome-stained fecal smears. In addition, we describe an in situ hybridization technique which detected and identified E. bieneusi as the causative agent in all six intestinal biopsy specimens tested. Both the PCR and in situ hybridization procedures are sensitive diagnostic tools which will complement currently available techniques and enable the differentiation of E. bieneusi from other microsporidia to be made.

Transmission and establishment of a persistent infection of Enterocytozoon bieneusi, derived from a human with AIDS, in simian immunodeficiency virus-infected rhesus monkeys

Enterocytozoon bieneusi is closely linked with chronic diarrhea and wasting in AIDS. Although reported >10 years ago, little is known about the infection and the disease it induces in humans. Duodenal E. bieneusi spores from an AIDS patient were orally transmitted to 2 simian immunodeficiency virus-infected rhesus monkeys. Both animals began shedding spores within a week of inoculation, as confirmed by microscopy and polymerase chain reaction, and continued until euthanatized 7 and 8 months later. E. bieneusi infection in the gut was sparse, either because of moderate numbers of circulating CD4 cells or because monkeys are less susceptible than humans to this infection. This is apparently the first documented transmission of E. bieneusi infection between hosts.

Water-borne Cryptosporidium: A perspective from the USA

In the USA, Cryptosporidium parvum has attracted considerable interest due to recent outbreaks of cryptosporidiosis attributed to water supplies contaminated with oocysts. Because of its unprecedented magnitude, the outbreak which occurred in Milwaukee in April 1993 was widely publicized and studied. Information collected during this and other recent outbreaks is being evaluated by regulatory agencies and the water industry with the aim of designing cost-effective measures that will reduce the risk of future water-borne outbreaks, as discussed here by Giovanni Widmer, Margaretha Carraway and Saul Tzipori.

Identification of genetic heterogeneity in the Cryptosporidium parvum ribosomal repeat

Oocysts of the protozoan parasite Cryptosporidium parvum are found in most surface waters and can contaminate municipal water supplies, as demonstrated by recent outbreaks of cryptosporidiosis. A method capable of fingerprinting C. parvum isolates from the environment would facilitate the study of epidemiology and transmission cycles and aid in the implementation of preventive measures to reduce water contamination by oocytes. In this study, we report polymorphism in C. parvum isolates on the basis of analysis of random amplified polymorphic DNA and nucleotide sequences in a region of the 18S rRNA and the internal transcribed spacer 1. Isolate-specific primers for these two regions were designed, and PCR tests capable of discriminating between isolates were developed. In both PCR assays, the five C. parvum isolates analyzed segregated into two subgroups. One group consisted of isolates that originated directly from human patients, and the other group had various host origins and had been propagated in laboratory animals. These results demonstrate the feasibility of distinguishing C. parvum isolates by sequence-specific PCR tests.

Leishmania RNA virus 1-mediated cap-independent translation

Recently, a group of related Leishmania RNA viruses (Leishmania RNA virus 1 [LRV1]) has been isolated from Leishmania guyanensis and L. brasiliensis. These viruses persist in the cytoplasm and contain double-stranded RNA genomes. Miniexon sequences are absent from the 5' end of the viral RNA, and the 5' end of the viral RNA lacks a cap structure, suggesting that LRV1 has evolved a cap-independent mechanism of translation. Cap-independent translation of picornavirus genomic RNA requires a cis element, within the 5' untranslated region (UTR), referred to as an internal ribosome entry site (IRES). In order to find out if the 5' UTR of LRV1 possessed IRES activity, we modified a Leishmania expression vector, pX63NEO-GUS, so that it would produce a dicistronic transcript in which the neomycin phosphotransferase gene was separated from the downstream beta-glucuronidase (GUS) gene by the LRV1 5' UTR. High levels of GUS activity were detected in L. major stably transformed with this plasmid. Elimination of the first 120 nucleotides of the viral 5' UTR lowered GUS activity 10-fold. Furthermore, when the entire 5' UTR was eliminated, GUS activity was undetectable. These results, together with the absence of trans-spliced GUS transcripts, are consistent with the hypothesis that the 5' UTR of LRV1 functions as an IRES element. The ability to couple expression of genes via an IRES element should prove useful in genetic experiments with Leishmania spp.

Suppression of Leishmania RNA virus replication by capsid protein overexpression

Some strains of the protozoan parasite genus Leishmania are persistently infected with single-segmented double-stranded RNA viruses, which are termed LRV. The function of these cytoplasmic viruses is unknown. In order to address the question of whether LRV affects the parasite's phenotype, pairs of isogenic LRV(+)-LRV- lines are required. Since the persistent nature of these viruses precludes de novo infection of virus-negative strains, LRV(+)-LRV- strains were transformed with a Leishmania expression vector expressing the LRV capsid protein with the aim of determining if LRV- promastigotes support capsid assembly and if LRV replication is affected by excess capsid protein. I found that in LRV- promastigotes, capsid protein was capable of self-assembly into virus-like capsids and that capsid overexpression in a naturally infected LRV+ line resulted in a progressive reduction in LRV copy number. Clonal lines derived from an LRV+ capsid overexpressor had no detectable levels of LRV. These results demonstrate that LRV replication can be inhibited and that a significant reduction of viral copy number has no effect on the parasite's viability in liquid medium.

Phylogenetic analysis of Leishmania RNA virus and Leishmania suggests ancient virus-parasite association

Some strains of the protozoan parasite Leishmania belonging to the new world species guyanensis and braziliensis are infected with persistent, single-segmented, non-enveloped dsRNA viruses termed LRV1. A single old world strain classified as L. major was recently found to harbor a similar virus, designated LRV2-1. The genomic nucleotide sequences of two LRV1 types (1-1 and 1-4) isolated from two L. guyanensis strains have been determined and found to be highly conserved. In contrast, LRV1-specific cDNA probes derived from the conserved genomic 5' region failed to recognize LRV2 RNA on Northern blots, suggesting a greater degree of divergence between LRV1 and LRV2 than among LRV1 types. This observation suggests a long-term association and coevolution of LRV within each parasite strain. We tested this concept by comparing nucleotide sequences of seven LRV types and PCR fingerprints of the parasite strains from which these viruses were derived. In support of the idea of virus-parasite co-evolution, we find that genetic distances between LRV types mirror the heterogeneity between parasite fingerprints and are clustered according to the geographical origin of the strains. In agreement with the postulated common origin of persistent dsRNA viruses of protozoa and fungi, we conclude that the infection of Leishmania with LRV pre-dates the divergence of Leishmania into different lineages.

Evaluation of an animal model system for cryptosporidiosis: therapeutic efficacy of paromomycin and hyperimmune bovine colostrum-immunoglobulin

Several immunodeficient rodent models currently exist in which persistent, largely asymptomatic, Cryptosporidium parvum infections can be established. Piglets, in contrast, develop a self-limiting diarrheal illness. We have consequently developed an animal model system in which scid mice were used to screen drugs for inhibitory activity against C. parvum, after which the drugs' therapeutic potential was evaluated with piglets. Paromomycin and hyperimmune bovine colostrum-immunoglobulin were selected to evaluate this system. C. paravum infections in suckling scid mice tended to be associated with villus surfaces, while in weaned and in older scid mice infections were more commonly localized in abscessed crypts. Rates of oocyst shedding in suckling scid mice were 50 to 200 times higher than in weaned mice and therefore made suckling mice a considerably more sensitive model for drug testing. Paromomycin given in high doses over 9 to 10 days was not toxic to either scid mice (3,000 mg/kg of body weight per day) or piglets (500 mg/kg/day). Paromomycin treatment was very effective against villus surface infections in suckling mice and considerably less effective against infections in inaccessible sites such as abscessed crypts and stomach pits seen in weaned and adult scid mice. The therapeutic efficacy of paromomycin in piglets depended on the severity of the diarrheal illness. Mild to moderate diarrhea and infection were cleared after paromomycin treatment of piglets infected with one C. parvum isolate. However, paromomycin had no impact on severely affected piglets infected with a second isolate, presumably because of a rapid transit time through the gut. In contrast to paromomycin hyperimmune bovine colostrum-immunoglobulin treatment reduced the rate of C. parvum infection moderately in scid mice and only slightly in piglets, again probably because of a rapid transit time through the gut and inactivation in the stomach. It was also clear that the impact of effective drugs against C. parvum can be detected within 5 days after the onset of treatment in either model.

Complete sequence of Leishmania RNA virus 1-4 and identification of conserved sequences

In order to understand the coding strategies and identify potential cis-acting sequences in Leishmania RNA virus 1 (LRV1), a complete cDNA sequence was obtained for LRV1-4 and compared to the sequence reported for LRV1-1. The results show that the 5' end of LRV1 is conserved at the nucleotide level while open reading frames (ORFs) 2 and 3 are conserved at the amino acid level. A simple translation initiation consensus sequence is conserved at the 5' end of ORF2 but absent from ORF3, consistent with a possibility that ORF3 is expressed as a gag-pol fusion protein. Comparison of secondary structure predictions obtained for both isolates identified nucleotide sequences capable of forming conserved stem-loops at the virus termini and in the putative frameshift region between ORF2 and ORF3. Although direct evidence is lacking, the appearance of compensatory nucleotide substitutions suggests that the structures may form in vivo. Possible functions for the conserved structures are discussed.