Monte Carlo Simulation of a Knudsen Effusion Mass Spectrometer Sampling System

Knudsen flow is easily simulated with a Monte Carlo method. In this study we develop a Visual Basic for Excel (VBA) code to simulate the molecular beam from a vaporizing solid. The system at NASA Glenn uses the restricted collimation method of Chatillon and colleagues, which consists of two apertures between the effusion cell and the ionizer. The diameter of the first aperture is smaller than the diameter of the effusion cell orifice, so the ionizer effectively only sees inside the effusion cell. The code is able to calculate the transmission coefficient through the cell orifice, through the cell orifice and the first aperture, and through the cell orifice and first and second aperatures. Calculated transmission coefficients through the cell orifice are compared to tabulated values to validate the code. Then transmission coefficients are calculated through the cell orifice and both apertures to the ionizer. This allows the geometry (aperture spacing and diameters) of the sampling system the sampling system to be optimized. Calculated transmission factors are also compared to literature values calculated via an analytic method

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

Monte Carlo simulation of a Knudsen effusion mass spectrometer sampling system

RATIONALE: Knudsen effusion mass spectrometry (KEMS) shows improved performance with the restricted collimation method of Chatillon and colleagues, which consists of two apertures between the Knudsen cell orifice and the ionizer. These apertures define the shape and position of the molecular beam independently of the sample and effusion orifice and as a result reduce background and improve sampling from the Knudsen cell.Modeling of the molecular beam in restricted collimation allows optimization of the apertures’ diameters and spacing. METHODS:Knudsen flow is easily simulated with a Monte Carlo method. In this study a Visual Basic for Excel (VBA) code is developed to simulate the molecular beam originating from a vaporizing condensed phase in a Knudsen cell and passing through the cell orifice and the two apertures. RESULTS: The code is able to calculate the transmission coefficient through the cell orifice, through the cell orifice and the first aperture, and through the cell orifice and first and second apertures. Also calculated are the angular distributions of the effusate density emerging from the cell and average number of collisions with the orifice walls. CONCLUSIONS: This code allows the geometry (aperture spacing and diameters) of the sampling system to be optimized for maximum transmission. The calculated effusate distributions and low average number of orifice wall collisions illustrated the advantages of restricted collimation. Calculated transmission factors are also compared to literature values calculated via the analytical method of Chatillon and colleagues

Transcriptional repression by ApiAP2 factors is central to chronic toxoplasmosis

Tachyzoite to bradyzoite development in Toxoplasma is marked by major changes in gene expression resulting in a parasite that expresses a new repertoire of surface antigens hidden inside a modified parasitophorous vacuole called the tissue cyst. The factors that control this important life cycle transition are not well understood. Here we describe an important transcriptional repressor mechanism controlling bradyzoite differentiation that operates in the tachyzoite stage. The ApiAP2 factor, AP2IV-4, is a nuclear factor dynamically expressed in late S phase through mitosis/cytokinesis of the tachyzoite cell cycle. Remarkably, deletion of the AP2IV-4 locus resulted in the expression of a subset of bradyzoite-specific proteins in replicating tachyzoites that included tissue cyst wall components BPK1, MCP4, CST1 and the surface antigen SRS9. In the murine animal model, the mis-timing of bradyzoite antigens in tachyzoites lacking AP2IV-4 caused a potent inflammatory monocyte immune response that effectively eliminated this parasite and prevented tissue cyst formation in mouse brain tissue. Altogether, these results indicate that suppression of bradyzoite antigens by AP2IV-4 during acute infection is required for Toxoplasma to successfully establish a chronic infection in the immune-competent host

Toxoplasma gondii AP2IX-4 Regulates Gene Expression during Bradyzoite Development

Toxoplasma gondii is a protozoan parasite of great importance to human and animal health. In the host, this obligate intracellular parasite persists as a tissue cyst that is imperceptible to the immune response and unaffected by current therapies. The tissue cysts facilitate transmission through predation and give rise to chronic cycles of toxoplasmosis in immunocompromised patients. Transcriptional changes accompany conversion of the rapidly replicating tachyzoites into the encysted bradyzoites, and yet the mechanisms underlying these alterations in gene expression are not well defined. Here we show that AP2IX-4 is a nuclear protein exclusively expressed in tachyzoites and bradyzoites undergoing division. Knockout of AP2IX-4 had no discernible effect on tachyzoite replication but resulted in a reduced frequency of tissue cyst formation following alkaline stress induction-a defect that is reversible by complementation. AP2IX-4 has a complex role in regulating bradyzoite gene expression, as the levels of many bradyzoite mRNAs dramatically increased beyond those seen under conditions of normal stress induction in AP2IX-4 knockout parasites exposed to alkaline media. The loss of AP2IX-4 also resulted in a modest virulence defect and reduced cyst burden in chronically infected mice, which was reversed by complementation. These findings illustrate that the transcriptional mechanisms responsible for tissue cyst development operate across the intermediate life cycle from the dividing tachyzoite to the dormant bradyzoite. IMPORTANCEToxoplasma gondii is a single-celled parasite that persists in its host as a transmissible tissue cyst. How the parasite converts from its replicative form to the bradyzoites housed in tissue cysts is not well understood, but the process clearly involves changes in gene expression. Here we report that parasites lacking a cell cycle-regulated transcription factor called AP2IX-4 display reduced frequencies of tissue cyst formation in culture and in a mouse model of infection. Parasites missing AP2IX-4 lose the ability to regulate bradyzoite genes during tissue cyst development. Expressed in developing bradyzoites still undergoing division, AP2IX-4 may serve as a useful marker in the study of transitional forms of the parasite

ISG15 connects autophagy and IFN-γ-dependent control of Toxoplasma gondii infection in human cells

The intracellular protozoan parasit

Hyperboloidal slices for the wave equation of Kerr-Schild metrics and numerical applications

We present new results from two open source codes, using finite differencing and pseudo-spectral methods for the wave equations in (3+1) dimensions. We use a hyperboloidal transformation which allows direct access to null infinity and simplifies the control over characteristic speeds on Kerr-Schild backgrounds. We show that this method is ideal for attaching hyperboloidal slices or for adapting the numerical resolution in certain spacetime regions. As an example application, we study late-time Kerr tails of sub-dominant modes and obtain new insight into the splitting of decay rates. The involved conformal wave equation is freed of formally singular terms whose numerical evaluation might be problematically close to future null infinity.Comment: 15 pages, 12 figure

Triton Haze Analogs: The Role of Carbon Monoxide in Haze Formation

Triton is the largest moon of the Neptune system and possesses a thin nitrogen atmosphere with trace amounts of carbon monoxide and methane, making it of similar composition to that of the dwarf planet Pluto. Like Pluto and Saturn\u27s moon Titan, Triton has a haze layer thought to be composed of organics formed through photochemistry. Here, we perform atmospheric chamber experiments of 0.5% CO and 0.2% CH4 in N2 at 90 K and 1 mbar to generate Triton haze analogs. We then characterize the physical and chemical properties of these particles. We measure their production rate, their bulk composition with combustion analysis, their molecular composition with very high resolution mass spectrometry, and their transmission and reflectance from the optical to the near-infrared with Fourier Transform Infrared (FTIR) Spectroscopy. We compare these properties to existing measurements of Triton\u27s tenuous atmosphere and surface, as well as contextualize these results in view of all the small, hazy, nitrogen-rich worlds of our solar system. We find that carbon monoxide present at greater mixing ratios than methane in the atmosphere can lead to significantly oxygen- and nitrogen-rich haze materials. These Triton haze analogs have clear observable signatures in their near-infrared spectra, which may help us differentiate the mechanisms behind haze formation processes across diverse solar system bodies

Testing gravitational-wave searches with numerical relativity waveforms: Results from the first Numerical INJection Analysis (NINJA) project

The Numerical INJection Analysis (NINJA) project is a collaborative effort between members of the numerical relativity and gravitational-wave data analysis communities. The purpose of NINJA is to study the sensitivity of existing gravitational-wave search algorithms using numerically generated waveforms and to foster closer collaboration between the numerical relativity and data analysis communities. We describe the results of the first NINJA analysis which focused on gravitational waveforms from binary black hole coalescence. Ten numerical relativity groups contributed numerical data which were used to generate a set of gravitational-wave signals. These signals were injected into a simulated data set, designed to mimic the response of the Initial LIGO and Virgo gravitational-wave detectors. Nine groups analysed this data using search and parameter-estimation pipelines. Matched filter algorithms, un-modelled-burst searches and Bayesian parameter-estimation and model-selection algorithms were applied to the data. We report the efficiency of these search methods in detecting the numerical waveforms and measuring their parameters. We describe preliminary comparisons between the different search methods and suggest improvements for future NINJA analyses.Comment: 56 pages, 25 figures; various clarifications; accepted to CQ