Resources, mortality, and disease ecology: Importance of positive feedbacks between host growth rate and pathogen dynamics

This is an Accepted Manuscript of an article published by Taylor & Francis in Israel Journal of Ecology and Evolution in 2015, available online: http://www.tandfonline.com/10.1080/15659801.2015.1035508.Resource theory and metabolic scaling theory suggest that the dynamics of a pathogen within a host should strongly depend upon the rate of host cell metabolism. Once an infection occurs, key ecological interactions occur on or within the host organism that determine whether the pathogen dies out, persists as a chronic infection, or grows to densities that lead to host death. We hypothesize that, in general, conditions favoring rapid host growth rates should amplify the replication and proliferation of both fungal and viral pathogens. If a host population experiences an increase in mortality, to persist it must have a higher growth rate, per host, often reflecting greater resource availability per capita. We hypothesize that this could indirectly foster the pathogen, which also benefits from increased within-host resource turnover. We first bring together in a short review a number of key prior studies which illustrate resource effects on viral and fungal pathogen dynamics. We then report new results from a semi-continuous cell culture experiment with SHIV, demonstrating that higher mortality rates indeed can promote viral proliferation. We develop a simple model that illustrates dynamical consequences of these resource effects, including interesting effects such as alternative stable states and oscillatory dynamics. Our paper contributes to a growing body of literature at the interface of ecology and infectious disease epidemiology, emphasizing that host abundances alone do not drive community dynamics: the physiological state and resource content of infected hosts also strongly influence host-pathogen interactions

The X-ray Remnant of SN1987A

We present high resolution Chandra observations of the remnant of SN1987A in the Large Magellanic Cloud. The high angular resolution of the Chandra X-ray Observatory (CXO) permits us to resolve the X-ray remnant. We find that the remnant is shell-like in morphology, with X-ray peaks associated with some of the optical hot spots seen in HST images. The X-ray light curve has departed from the linear flux increase observed by ROSAT, with a 0.5-2.0 keV luminosity of 1.5 x 10^35 erg/s in January 2000. We set an upper limit of 2.3 x 10^34 ergs/s on the luminosity of any embedded central source (0.5 - 2 keV). We also present a high resolution spectrum, showing that the X-ray emission is thermal in origin and is dominated by highly ionized species of O, Ne, Mg, and Si.Comment: 16 pages, 3 figures, Accepted for publication in ApJ Letter

ASCA Observations of the Supernova Remnant IC 443: Thermal Structure and Detection of Overionized Plasma

We present the results of X-ray spatial and spectral studies of the ``mixed-morphology'' supernova remnant IC 443 using ASCA. IC 443 has a center-filled image in X-ray band, contrasting with the shell-like appearance in radio and optical bands. The overall X-ray emission is thermal, not from a synchrotron nebula. ASCA observed IC 443 three times, covering the whole remnant. From the image analysis, we found that the softness-ratio map reveals a shell-like structure. At the same time, its spectra require two (1.0 keV and 0.2 keV) plasma components; the emission of the 0.2 keV plasma is stronger in the region near the shell than the center. These results can be explained by a simple model that IC 443 has a hot (1.0 keV) interior surrounded by a cool (0.2 keV) outer shell. From the emission measures, we infer that the 0.2 keV plasma is denser than the 1.0 keV plasma, suggesting pressure equilibrium between the two. In addition, we found that the ionization temperature of sulfur, obtained from H-like K$\alpha$ to He-like K$\alpha$ intensity ratio, is 1.5 keV, significantly higher than the gas temperature of 1.0 keV suggested from the continuum spectrum. The same can be concluded for silicon. Neither an additional, hotter plasma component nor a multi-temperature plasma successfully accounts for this ratio, and we conclude that the 1.0 keV plasma is overionized. This is the first time that overionized gas has been detected in a SNR. For the gas to become overionized in the absence of a photoionizing flux, it must cool faster than the ions recombine. Thermal conduction from the 1.0 keV plasma to the 0.2 keV one could cause the 1.0 keV plasma to become overionized, which is plausible within an old (3$\times10^4$ yr) SNR.Comment: 11 pages, 15 figures, 2 tables, accepted for publication in The Astrophysical Journa

Targeted Assembly of Short Sequence Reads

As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants, by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled strin-gently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming ge-nomic mutations, polymorphism, fusion and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly

Antigen depot is not required for alum adjuvanticity

Alum adjuvants have been in continuous clinical use for more than 80 yr. While the prevailing theory has been that depot formation and the associated slow release of antigen and/or inflammation are responsible for alum enhancement of antigen presentation and subsequent T- and B-cell responses, this has never been formally proven. To examine antigen persistence, we used the chimeric fluorescent protein EαGFP, which allows assessment of antigen presentation in situ, using the Y-Ae antibody. We demonstrate that alum and/or CpG adjuvants induced similar uptake of antigen, and in all cases, GFP signal did not persist beyond 24 h in draining lymph node antigen-presenting cells. Antigen presentation was first detectable on B cells within 6–12 h of antigen administration, followed by conventional dendritic cells (DCs) at 12–24 h, then finally plasmacytoid DCs at 48 h or later. Again, alum and/or CpG adjuvants did not have an effect on the magnitude or sequence of this response; furthermore, they induced similar antigen-specific T-cell activation in vivo. Notably, removal of the injection site and associated alum depot, as early as 2 h after administration, had no appreciable effect on antigen-specific T- and B-cell responses. This study clearly rules out a role for depot formation in alum adjuvant activity

COVID’s Lasting Impact on Georgia Libraries

Special Article Call: This spring marks three years since the onset of the COVID-19 pandemic. Looking back, what have been the pandemic\u27s lasting impacts on your work or your library? What have you or your library learned or how have you changed

Physical Structure and Nature of Supernova Remnants in M101

Supernova remnant (SNR) candidates in the giant spiral galaxy M101 have been previously identified from ground-based H-alpha and [SII] images. We have used archival Hubble Space Telescope (HST) H-alpha and broad-band images as well as stellar photometry of 55 SNR candidates to examine their physical structure, interstellar environment, and underlying stellar population. We have also obtained high-dispersion echelle spectra to search for shocked high-velocity gas in 18 SNR candidates, and identified X-ray counterparts to SNR candidates using data from archival observations made by the Chandra X-ray Observatory. Twenty-one of these 55 SNR candidates studied have X-ray counterparts, although one of them is a known ultra-luminous X-ray source. The multi-wavelength information has been used to assess the nature of each SNR candidate. We find that within this limited sample, ~16% are likely remnants of Type Ia SNe and ~45% are remnants of core-collapse SNe. In addition, about ~36% are large candidates which we suggest are either superbubbles or OB/HII complexes. Existing radio observations are not sensitive enough to detect the non-thermal emission from these SNR candidates. Several radio sources are coincident with X-ray sources, but they are associated with either giant HII regions in M101 or background galaxies. The archival HST H-alpha images do not cover the entire galaxy and thus prevents a complete study of M101. Furthermore, the lack of HST [SII] images precludes searches for small SNR candidates which could not be identified by ground-based observations. Such high-resolution images are needed in order to obtain a complete census of SNRs in M101 for a comprehensive investigation of the distribution, population, and rates of SNe in this galaxy.Comment: 37 pages, 4 Tables, 7 Figures, accepted for publication in the Astronomical Journa