The Cure: Making a game of gene selection for breast cancer survival prediction

Motivation: Molecular signatures for predicting breast cancer prognosis could greatly improve care through personalization of treatment. Computational analyses of genome-wide expression datasets have identified such signatures, but these signatures leave much to be desired in terms of accuracy, reproducibility and biological interpretability. Methods that take advantage of structured prior knowledge (e.g. protein interaction networks) show promise in helping to define better signatures but most knowledge remains unstructured. Crowdsourcing via scientific discovery games is an emerging methodology that has the potential to tap into human intelligence at scales and in modes previously unheard of. Here, we developed and evaluated a game called The Cure on the task of gene selection for breast cancer survival prediction. Our central hypothesis was that knowledge linking expression patterns of specific genes to breast cancer outcomes could be captured from game players. We envisioned capturing knowledge both from the players prior experience and from their ability to interpret text related to candidate genes presented to them in the context of the game. Results: Between its launch in Sept. 2012 and Sept. 2013, The Cure attracted more than 1,000 registered players who collectively played nearly 10,000 games. Gene sets assembled through aggregation of the collected data clearly demonstrated the accumulation of relevant expert knowledge. In terms of predictive accuracy, these gene sets provided comparable performance to gene sets generated using other methods including those used in commercial tests. The Cure is available at http://genegames.org/cure

Seroprevalence of Toxoplasma gondii among stray cats using different serological techniques in Erbil City: Kurdistan Region/Iraq

Background: The causative agent of toxoplasmosis is Toxoplasma gondii which is an intracellular protozoan. Felines including cats are the only definitive hosts for T. gondii and they play a significant role in spreading the oocysts in the environment. It has been estimated that T. gondii infects about one-third of the human population. This study was performed to estimate the seroprevalence rate of Anti-T. gondii IgG Abs in 100 strays by using different serological techniques.Methods: Hundred stray cats of both sexes (50 males and 50 females) from different ages (one month to 48 months) were hunted by trap cage and shooting tranquilizer gun in Erbil city and used for detecting T. gondii antibodies.Results: The seroprevalence rates obtained were: 22%, 20% and 11% by MAT, ELISA and LAT respectively. Male cats showed higher seroprevalence than females (13% versus7%). According to the agreement between MAT titers and ELISA IgG (cutoff ELISA≥1) in stray cat’s sera, the percent of positive results in ELISA (cutoff≥1) method were exactly matched with the MAT titer (≥1:50) while the overall agreement and negative percent agreement were elevated by increasing MAT titers and the positive percent agreement was stable in all titers. The overall agreement results were 96% and 100% for MAT titers ≥1:25 and ≥1:50, respectively and negative percent agreement results were 97.4% and 100% for MAT titers ≥1:25 and ≥1:50 respectively.Conclusions: Exactly matched between MAT technique titer (≥1:50) and ELISA technique. Index (cutoff≥1). Therefore, MAT could be used for detecting IgG Abs of Toxoplasma gondii instead of ELISA technique

Population structure of <i>Toxoplasma gondii</i> in Argentina

The protozoan Toxoplasma gondii is worldwide distributed showing a particular population structure that may differ among continents and countries. The aim of this study was to analyze the T. gondii population structure in Argentina and compare it with genotyping information from other South American countries. For the analysis, 39 samples from Argentina (isolates from the provinces of Buenos Aires, Misiones, Entre Ríos and San Luis) were genotyped using 10 multilocus PCR-RFLP markers including SAG1, SAG2 (5′-3′SAG2, alt. SAG2), SAG3, BTUB, GRA6, C22-8, C29-2, L358, PK1, and Apico. The T. gondii DNA samples were obtained from domestics animals (chickens n = 20; cats n = 3; pigs n = 2; goat n = 1; rabbit n = 1), humans (n = 6), zoo animals (n = 5) and a rat (n = 1). Phylogenetic relationship of these Argentinean isolates together with representative reference genotypes was determined by phylogenetic network analysis. Thirty-seven Argentinean samples belonged to 21 genotypes and two samples were genotyped at 8 of the 10 loci and considered incomplete characterized. Among these 37 typed samples, five genotypes were not previously reported. The majority of the samples grouped with the Type III (ToxoDB PCR-RFLP genotype #2) lineage. The clonal Type II (ToxoDB genotypes #1 and #3) was also identified. Our results suggest a unique population structure with combination of unique genotypes and the common Type II and Type III lineages in Argentina. Nevertheless, different regions showed distinctive pattern of genotypes, revealing a higher variability in Northern provinces.Facultad de Ciencias Veterinaria

Population structure of <i>Toxoplasma gondii</i> in Argentina

The protozoan Toxoplasma gondii is worldwide distributed showing a particular population structure that may differ among continents and countries. The aim of this study was to analyze the T. gondii population structure in Argentina and compare it with genotyping information from other South American countries. For the analysis, 39 samples from Argentina (isolates from the provinces of Buenos Aires, Misiones, Entre Ríos and San Luis) were genotyped using 10 multilocus PCR-RFLP markers including SAG1, SAG2 (5′-3′SAG2, alt. SAG2), SAG3, BTUB, GRA6, C22-8, C29-2, L358, PK1, and Apico. The T. gondii DNA samples were obtained from domestics animals (chickens n = 20; cats n = 3; pigs n = 2; goat n = 1; rabbit n = 1), humans (n = 6), zoo animals (n = 5) and a rat (n = 1). Phylogenetic relationship of these Argentinean isolates together with representative reference genotypes was determined by phylogenetic network analysis. Thirty-seven Argentinean samples belonged to 21 genotypes and two samples were genotyped at 8 of the 10 loci and considered incomplete characterized. Among these 37 typed samples, five genotypes were not previously reported. The majority of the samples grouped with the Type III (ToxoDB PCR-RFLP genotype #2) lineage. The clonal Type II (ToxoDB genotypes #1 and #3) was also identified. Our results suggest a unique population structure with combination of unique genotypes and the common Type II and Type III lineages in Argentina. Nevertheless, different regions showed distinctive pattern of genotypes, revealing a higher variability in Northern provinces.Facultad de Ciencias Veterinaria

A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior

Glyoxalase 1 (Glo1) has been implicated in anxiety-like behavior in mice and in multiple psychiatric diseases in humans. We used mouse Affymetrix exon arrays to detect copy number variants (CNV) among inbred mouse strains and thereby identified a approximately 475 kb tandem duplication on chromosome 17 that includes Glo1 (30,174,390-30,651,226 Mb; mouse genome build 36). We developed a PCR-based strategy and used it to detect this duplication in 23 of 71 inbred strains tested, and in various outbred and wild-caught mice. Presence of the duplication is associated with a cis-acting expression QTL for Glo1 (LOD>30) in BXD recombinant inbred strains. However, evidence for an eQTL for Glo1 was not obtained when we analyzed single SNPs or 3-SNP haplotypes in a panel of 27 inbred strains. We conclude that association analysis in the inbred strain panel failed to detect an eQTL because the duplication was present on multiple highly divergent haplotypes. Furthermore, we suggest that non-allelic homologous recombination has led to multiple reversions to the non-duplicated state among inbred strains. We show associations between multiple duplication-containing haplotypes, Glo1 expression and anxiety-like behavior in both inbred strain panels and outbred CD-1 mice. Our findings provide a molecular basis for differential expression of Glo1 and further implicate Glo1 in anxiety-like behavior. More broadly, these results identify problems with commonly employed tests for association in inbred strains when CNVs are present. Finally, these data provide an example of biologically significant phenotypic variability in model organisms that can be attributed to CNVs.These studies were funded by MH070933, MH79103 and MH020065

Changes in the proteomic profiles of mouse brain after infection with cyst-forming Toxoplasma gondii

Background Toxoplasma gondii is an opportunistic pathogenic protozoan parasite, which infects approximately one third of the human population worldwide, causing opportunistic zoonotic toxoplasmosis. The predilection of T. gondii for the central nervous system (CNS) causes behavioral disorders and fatal necrotizing encephalitis and thus constitutes a major threat especially to AIDS patients. Methods In the present study, we explored the proteomic profiles of brain tissues of the specific pathogen-free (SPF) Kunming mice at 7 d, 14 d and 21 d after infection with cysts of the Toxoplasma gondii Prugniaud (PRU) strain (Genotype II), by two-dimensional gel electrophoresis (2-DE) combined with MALDI-TOF/TOF tandem mass spectrometry (MS/MS). Results A total of 60 differentially expressed protein spots were selected. Fifty-six spots were successfully identified, which corresponded to 45 proteins of the mouse. Functional analysis using a Gene Ontology database showed that these proteins were mainly involved in metabolism, cell structure, signal transduction and immune responses, and will be beneficial for the understanding of molecular mechanisms of T. gondii pathogenesis. Conclusions This study identified some mouse brain proteins involved in the response with cyst-forming T. gondii PRU strain. These results provided an insight into the responsive relationship between T. gondii and the host brain tissues, which will shed light on our understanding of the mechanisms of pathogenesis in toxoplasmic encephalitis, and facilitate the discovery of new methods of diagnosis, prevention, control and treatment of toxoplasmic encephalopathy

Genetic characterization of \u3cem\u3eToxoplasma gondii\u3c/em\u3e from pigs from different localities in China by PCR-RFLP

Background Toxoplasma gondii is a widely prevalent protozoan parasite that causes serious toxoplasmosis in humans and animals. The present study aimed to determine the genetic diversity of T. gondii isolates from pigs in Jiangxi, Sichuan, Guangdong Provinces and Chongqing Municipality in China using multilocous polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. Methods A total of 38 DNA samples were extracted from hilar lymph nodes of pigs with suspected toxoplasmosis, and were detected for the presence of T. gondii by semi-nested PCR of B1 gene. The positive DNA samples were typed at 11 genetic markers, including 10 nuclear loci, namely, SAG1, 5′-SAG2 and 3′-SAG2, alternative SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and an apicoplast locus Apico. Results Twenty-five of the 38 DNA samples were T. gondii B1 gene positive. Complete genotyping data for all loci could be obtained for 17 of the 25 samples. Two genotypes were revealed (ToxoDB PCR-RFLP genotypes #9 and #3). Sixteen samples belong to genotype #9 which is the major lineage in mainland China and one sample belongs to genotype #3 which is Type II variant. Conclusions To our knowledge, this is the first report of genetic typing of T. gondii isolates from pigs in Jiangxi, Sichuan Province and Chongqing Municipality, and the first report of ToxoDB #3 T. gondii from pigs in China. These results have implications for the prevention and control of foodborne toxoplasmosis in humans