The transcriptome of Toxoplasma gondii

BACKGROUND: Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. RESULTS: We have used serial analysis of gene expression (SAGE) to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags) representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. CONCLUSION: This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and expression levels of mRNAs in primary populations (Day-6 post-sporozoite infection) that occur prior to the onset of bradyzoite development that were uniquely shared with the virulent Type I-RH laboratory strain suggesting that development of RH may be arrested. By contrast, strains from Type II-Me49B7 and Type III-VEGmsj contain SAGE tags corresponding to bradyzoite genes, which suggests that priming of developmental expression likely plays a role in the greater capacity of these strains to complete bradyzoite development

Creating a honey bee consensus gene set

BACKGROUND: We wished to produce a single reference gene set for honey bee (Apis mellifera). Our motivation was twofold. First, we wished to obtain an improved set of gene models with increased coverage of known genes, while maintaining gene model quality. Second, we wished to provide a single official gene list that the research community could further utilize for consistent and comparable analyses and functional annotation. RESULTS: We created a consensus gene set for honey bee (Apis mellifera) using GLEAN, a new algorithm that uses latent class analysis to automatically combine disparate gene prediction evidence in the absence of known genes. The consensus gene models had increased representation of honey bee genes without sacrificing quality compared with any one of the input gene predictions. When compared with manually annotated gold standards, the consensus set of gene models was similar or superior in quality to each of the input sets. CONCLUSION: Most eukaryotic genome projects produce multiple gene sets because of the variety of gene prediction programs. Each of the gene prediction programs has strengths and weaknesses, and so the multiplicity of gene sets offers users a more comprehensive collection of genes to use than is available from a single program. On the other hand, the availability of multiple gene sets is also a cause for uncertainty among users as regards which set they should use. GLEAN proved to be an effective method to combine gene lists into a single reference set

Prophylactic Anticonvulsants in Intracerebral Hemorrhage

Background and Purpose Prophylactic anticonvulsants are routinely prescribed in the acute setting for intracerebral hemorrhage (ICH) patients, but some studies have reported an association with worse outcomes. We sought to characterize the prevalence and predictors of prophylactic anticonvulsant administration after ICH as well as guideline adherence. We also sought to determine whether prophylactic anticonvulsants were independently associated with poor outcome. Methods We performed a retrospective study of primary ICH in our two academic centers. We used a propensity matching approach to make treated and non-treated groups comparable. We conducted multiple logistic regression analysis to identify independent predictors of prophylactic anticonvulsant initiation and its association with poor outcome as measured by modified Rankin score. Results We identified 610 patients with primary ICH, of whom 98 were started on prophylactic anticonvulsants. Levetiracetam (97%) was most commonly prescribed. Age (OR 0.97, 95% CI 0.95–0.99, p < .001), lobar location (OR 2.94, 95% CI 1.76–4.91, p < .001), higher initial National Institutes of Health Stroke Scale (NIHSS) score (OR 2.31, 95% CI 1.40–3.79, p = .001), craniotomy (OR 3.06, 95% CI 1.51–6.20, p = .002), and prior ICH (OR 2.36, 95% CI 1.10–5.07, p = .028) were independently associated with prophylactic anticonvulsant initiation. Prophylactic anticonvulsant use was not associated with worse functional outcome [modified Rankin score (mRS) 4–6] at hospital discharge or with increased case-fatality. There was no difference in prescribing patterns after 2010 guideline publication. Discussion Levetiracetam was routinely prescribed following ICH and was not associated with worse outcomes. Future investigations should examine the effect of prophylactic levetiracetam on cost and neuropsychological outcomes as well as the role of continuous EEG in identifying subclinical seizures

Disparities and guideline adherence in drugs of abuse screening in intracerebral hemorrhage

OBJECTIVE: To characterize the pattern of urine drug screening in a cohort of intracerebral hemorrhage (ICH) patients at our academic centers. METHODS: We identified cases of primary ICH occurring from 2009 to 2011 in our academic centers. Demographic data, imaging characteristics, processes of care, and short-term outcomes were ascertained. We performed logistic regression to identify predictors for screening and evaluated preguideline and postguideline reiteration screening patterns. RESULTS: We identified 610 patients with primary ICH in 2009-2011; 379 (62.1%) were initially evaluated at an outside hospital. Overall, 142/610 (23.3%) patients were screened, with 21 positive for cocaine and 3 for amphetamine. Of patients <55 years of age, only 65/140 (46.4%) were screened. Black patients <55 years of age were screened more than nonblack patients <55 years of age (38/61 [62.3%] vs 27/79 [34.2%]; p = 0.0009). In the best multivariable model, age group (p = 0.0001), black race (p = 0.4529), first Glasgow Coma Scale score (p = 0.0492), current smoking (p < 0.0001), and age group × black race (p = 0.0097) were associated with screening. Guideline reiteration in 2010 did not improve the proportion <55 years of age who were screened: 42/74 (56.8%) were screened before and 23/66 (34.9%) after (p = 0.01). CONCLUSIONS: We found disparities in drugs of abuse (DOA) screening and suboptimal guideline adherence. Systematic efforts to improve screening for DOA are warranted. Improved identification of sympathomimetic exposure may improve etiologic classification and influence decision-making and prognosis counseling

A peculiar faint satellite in the remote outer halo of M31

We present Hubble Space Telescope imaging of a newly discovered faint stellar system, PAndAS-48, in the outskirts of the M31 halo. Our photometry reveals this object to be comprised of an ancient and very metal-poor stellar population with age ≳ 10 Gy

Exploring the nature and synchronicity of early cluster formation in the Large Magellanic Cloud - IV. Evidence for multiple populations in Hodge 11 and NGC 2210

We present a multiple population search in two old Large Magellanic Cloud (LMC) Globular clusters, Hodge 11 and NGC 2210. This work uses data from the Advanced Camera for Surveys and Wide Field Camera 3 on the Hubble Space Telescope from programme GO- 14164 in Cycle 23. Both of these clusters exhibit a broadened main sequence with the second population representing (20±~5) per cent forNGC2210 and (30±~5) per cent forHodge 11. In both clusters, the smaller population is redder than the primary population, suggesting CNO variations. Hodge 11 also displays a bluer second population in the horizontal branch, which is evidence for helium enhancement. However, even though NGC 2210 shows similarities to Hodge 11 in the main sequence, there does not appear to be a second population on NGC 2210's horizontal branch. This is the first photometric evidence that ancient LMC Globular clusters exhibit multiple stellar populations.Fil: Gilligan, Christina K.. Dartmouth College; Estados UnidosFil: Chaboyer, Brian. Dartmouth College; Estados UnidosFil: Cummings, Jeffrey D.. University Johns Hopkins; Estados UnidosFil: Mackey, Dougal. Australian National University. Research School of Astronomy & Astrophysics; AustraliaFil: Cohen, Roger E.. Space Telescope Science Institute; Estados UnidosFil: Geisler, Douglas. Universidad de La Serena; ChileFil: Grocholski, Aaron J.. University of Washington; Estados UnidosFil: Parisi, Maria Celeste. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; ArgentinaFil: Sarajedini, Ata. University of Florida; Estados UnidosFil: Ventura, Paolo. Osservatorio Astronomico Di Roma; ItaliaFil: Villanova, Sandro. Universidad de Concepción; ChileFil: Yang, Soung-Chul. Korea Astronomy And Space Science Institute; Corea del SurFil: Wagner-Kaiser, Rachel. University of Florida; Estados Unido

Exploring the nature and synchronicity of early cluster formation in the Large Magellanic Cloud - V. Multiple populations in ancient globular clusters

We examine four ancient LargeMagellanic Cloud (LMC) globular clusters (GCs) for evidence of multiple stellar populations using the Advanced Camera for Surveys andWide Field Camera 3 on the Hubble Space Telescope Programme GO-14164. NGC 1466, NGC 1841, and NGC 2257 all show evidence for a redder, secondary population along themain sequence. Reticulum does not showevidence for the presence of a redder population, but thisGChas the least number of stars and Monte Carlo simulations indicate that the sample of main-sequence stars is too small to robustly infer whether a redder population exists in this cluster. The second, redder, population of the other three clusters constitutes ∼ 30 - 40 per cent of the total population along the main sequence. This brings the total number of ancient LMC GCs with known split or broadened main sequences to five. However, unlike for Hodge 11 and NGC 2210 (see Gilligan et al. (2019)), none of the clusters shows evidence for multiple populations in the horizontal branch. We also do not find evidence of a second population along the red giant branch.Fil: Gilligan, Christina K.. Dartmouth College; Estados UnidosFil: Chaboyer, Brian. Dartmouth College; Estados UnidosFil: Cummings, Jeffrey D.. University Johns Hopkins; Estados UnidosFil: Mackey, Dougal. Australian National University; AustraliaFil: Cohen, Roger E.. Space Telescope Science Institute; Estados UnidosFil: Geisler, Douglas. Universidad de Concepción; ChileFil: Grocholski, Aaron J.. University of Florida; Estados UnidosFil: Parisi, Maria Celeste. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; ArgentinaFil: Sarajedini, Ata. University of Florida; Estados UnidosFil: Ventura, Paolo. Osservatorio Astronomico Di Roma; ItaliaFil: Villanova, Sandro. Universidad de Concepción; ChileFil: Yang, Soung-Chul. Korea Astronomy And Space Science Institute; Corea del SurFil: Wagner-Kaiser, Rachel. University of Florida; Estados Unido

Exploring the nature and synchronicity of early cluster formation in the Large Magellanic Cloud - III. Horizontal branch morphology

We leverage new high-quality data from Hubble Space Telescope program GO-14164 to explore the variation in horizontal branch morphology among globular clusters in the Large Magellanic Cloud (LMC). Our new observations lead to photometry with a precision commensurate with that available for the Galactic globular cluster population. Our analysis indicates that, once metallicity is accounted for, clusters in the LMC largely share similar horizontal branch morphologies regardless of their location within the system. Furthermore, the LMC clusters possess, on average, slightly redder morphologies than most of the inner halo Galactic population; we find, instead, that their characteristics tend to be more similar to those exhibited by clusters in the outer Galactic halo. Our results are consistent with previous studies, showing a correlation between horizontal branch morphology and age.DMis grateful for support from an Australian Research Council (ARC) Future Fellowship (FT160100206). DG gratefully acknowledges support from the Chilean BASAL Centro de Excelencia en Astrofisica y Tecnologıas Afines (CATA) grant PFB-06/2007

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM and an average map unit of ∼104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies