Using Flow Cytometry to Analyze Cryptococcus Infection of Macrophages.

Flow cytometry is a powerful analytical technique, which is increasingly being used to study the interaction between host cells and intracellular pathogens. Flow cytometry is capable of measuring a greater number of infected cells within a sample compared to alternative techniques such as fluorescence microscopy. This means that robust quantification of rare events during infection is possible. Our lab and others have developed flow cytometry methods to study interactions between host cells and intracellular pathogens, such as Cryptococcus neoformans, to quantify phagocytosis, intracellular replication, and non-lytic expulsion or "vomocytosis" from the phagosome. Herein we describe these methods and how they can be applied to the study of C. neoformans as well as other similar intracellular pathogens

Using Flow Cytometry to Analyze Cryptococcus Infection of Macrophages.

Flow cytometry is a powerful analytical technique, which is increasingly being used to study the interaction between host cells and intracellular pathogens. Flow cytometry is capable of measuring a greater number of infected cells within a sample compared to alternative techniques such as fluorescence microscopy. This means that robust quantification of rare events during infection is possible. Our lab and others have developed flow cytometry methods to study interactions between host cells and intracellular pathogens, such as Cryptococcus neoformans, to quantify phagocytosis, intracellular replication, and non-lytic expulsion or "vomocytosis" from the phagosome. Herein we describe these methods and how they can be applied to the study of C. neoformans as well as other similar intracellular pathogens

Daytime lidar measurements of tidal winds in the mesospheric sodium layer at Urbana, Illinois

For more than 15 years lidar systems have been used to study the chemistry and dynamics of the mesospheric sodium layer. Because the layer is an excellent tracer of atmospheric wave motions, sodium lidar has proven to be particularly useful for studying the influence of gravity waves and tides on mesospheric dynamics. These waves, which originate in the troposphere and stratosphere, propagate through the mesosphere and dissipate their energy near the mesopause making important contributions to the momentum and turbulence budget in this region of the atmosphere. Recently, the sodium lidar was modified for daytime operation so that wave phenomena and chemical effects could be monitored throughout the complete diurnal cycle. The results of continuous 24 hour lidar observations of the sodium layer structure are presented alond with measurement of the semidiurnal tidal winds

Groundwater faunas as indicators of groundwater quality: the South Platte River system

February 1989.Bibliography: pages 33-39

Highly accelerated simulations of glassy dynamics using GPUs: caveats on limited floating-point precision

Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD) simulations for system sizes ranging up to about 1 million particles. Particular emphasis is put on the numerical long-time stability in terms of energy and momentum conservation, and caveats on limited floating-point precision are issued. Strict energy conservation over 10^8 MD steps is obtained by double-single emulation of the floating-point arithmetic in accuracy-critical parts of the algorithm. For the slow dynamics of a supercooled binary Lennard-Jones mixture, we demonstrate that the use of single-floating point precision may result in quantitatively and even physically wrong results. For simulations of a Lennard-Jones fluid, the described implementation shows speedup factors of up to 80 compared to a serial implementation for the CPU, and a single GPU was found to compare with a parallelised MD simulation using 64 distributed cores.Comment: 12 pages, 7 figures, to appear in Comp. Phys. Comm., HALMD package licensed under the GPL, see http://research.colberg.org/projects/halm

Witness and Worship in Pluralistic America

American society in the twenty- first century poses a myriad of challenges for the church as it seeks to be an effective witness to the Gospel of Jesus Christ. Among these challenges is an increasingly pluralistic cultural and religious context.https://scholar.csl.edu/ebooks/1040/thumbnail.jp

Automated Analysis of Cryptococcal Macrophage Parasitism Using GFP-Tagged Cryptococci

The human fungal pathogens Cryptococcus neoformans and C. gattii cause life-threatening infections of the central nervous system. One of the major characteristics of cryptococcal disease is the ability of the pathogen to parasitise upon phagocytic immune effector cells, a phenomenon that correlates strongly with virulence in rodent models of infection. Despite the importance of phagocyte/Cryptococcus interactions to disease progression, current methods for assaying virulence in the acrophage system are both time consuming and low throughput. Here, we introduce the first stable and fully characterised GFP–expressing derivatives of two widely used cryptococcal strains: C. neoformans serotype A type strain H99 and C. gattii serotype B type strain R265. Both strains show unaltered responses to environmental and host stress conditions and no deficiency in virulence in the macrophage model system. In addition, we report the development of a method to effectively and rapidly investigate macrophage parasitism by flow cytometry, a technique that preserves the accuracy of current approaches but offers a four-fold improvement in speed

Vertical Structure and Color of Jovian Latitudinal Cloud Bands during the Juno Era

The identity of the coloring agent(s) in Jupiter's atmosphere and the exact structure of Jupiter's uppermost cloud deck are yet to be conclusively understood. The Cr\`{e}me Br\^ul\'ee model of Jupiter's tropospheric clouds, originally proposed by Baines et al. (2014) and expanded upon by Sromovsky et al. (2017) and Baines et al. (2019), presumes that the chromophore measured by Carlson et al. (2016) is the singular coloring agent in Jupiter's troposphere. In this work, we test the validity of the Cr\`{e}me Br\^ul\'ee model of Jupiter's uppermost cloud deck using spectra measured during the Juno spacecraft's 5$^{\mathrm{th}}$ perijove pass in March 2017. These data were obtained as part of an international ground-based observing campaign in support of the Juno mission using the NMSU Acousto-optic Imaging Camera (NAIC) at the 3.5-m telescope at Apache Point Observatory in Sunspot, NM. We find that the Cr\`{e}me Br\^ul\'ee model cloud layering scheme can reproduce Jupiter's visible spectrum both with the Carlson et al. (2016) chromophore and with modifications to its imaginary index of refraction spectrum. While the Cr\`{e}me Br\^ul\'ee model provides reasonable results for regions of Jupiter's cloud bands such as the North Equatorial Belt and Equatorial Zone, we find that it is not a safe assumption for unique weather events, such as the 2016-2017 Southern Equatorial Belt outbreak that was captured by our measurements.Comment: 38 pages, 21 figures; Accepted for publication in AAS Planetary Science Journa

A Sensitive High-Throughput Assay for Evaluating Host-Pathogen Interactions in Cryptococcus neoformans Infection

Background: Cryptococcus neoformans causes serious disease in immunocompromised individuals, leading to over 600,000 deaths per year worldwide. Part of this impact is due to the organism’s ability to thwart what should be the mammalian hosts ’ first line of defense against cryptococcal infection: internalization by macrophages. Even when C. neoformans is engulfed by host phagocytes, it can survive and replicate within them rather than being destroyed; this ability is central in cryptococcal virulence. It is therefore critical to elucidate the interactions of this facultative intracellular pathogen with phagocytic cells of its mammalian host. Methodology/Principal Findings: To accurately assess initial interactions between human phagocytic cells and fungi, we have developed a method using high-throughput microscopy to efficiently distinguish adherent and engulfed cryptococci and quantitate each population. This method offers significant advantages over currently available means of assaying hostfungal cell interactions, and remains statistically robust when implemented in an automated fashion appropriate for screening. It was used to demonstrate the sensitivity of human phagocytes to subtle changes in the cryptococcal capsule, a major virulence factor of this pathogen. Conclusions/Significance: Our high-throughput method for characterizing interactions between C. neoformans and mammalian phagocytic cells offers a powerful tool for elucidating the relationship between these cell types durin

Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others