Mosaic VSGs in Trypanosoma brucei antigenic variation

Many parasites of mammals avoid elimination by varying their exposed antigens. African trypanosomes—deadly parasites of humans and livestock in tropical Africa—possess a comprehensive system of antigenic variation (AV). Trypanosoma brucei undergo frequent, stochastic changes to their variant surface glycoprotein (VSG) coats, and therefore a developing immune response will be only partially effective against the trypanosome population as some trypanosomes will have already switched to a different VSG coat. The source of VSG variability is an archive of ~2000, mostly pseudogenic, silent VSG genes, of which only one is expressed. VSG genes can also be segmentally recombined: ‘mosaic’ VSGs, constructed from more than one silent VSG donor, allow both the reparation of pseudogenes and potentially generation of additional VSG variability. The aim of this research was to investigate the patterns of segmental VSG gene conversion in T. brucei, and assess its contribution to AV. Multiple, longitudinal samples were taken from chronic infections to follow the course of AV, and VSG cDNA sequences were analysed, building a detailed portrait of VSG expression across infection. VSG variability during an infection was extensive, and segmental gene conversion was found to be a frequent occurrence from approximately week three. Two main patterns were found: (i) expressed VSGs readily acquired a 3’ end different from their silent copy, a pattern that probably represents the 3’ boundary of gene conversion occurring within the coding sequence; (ii) expressed VSGs often appeared in sets of related ‘mosaics’, whereby more than one donor gene had contributed to the putative epitope-encoding part of the VSG. To test whether varying donor contributions represents an additional source of antigenic variability available to trypanosomes, a set of five mosaic VSGs retrieved from a single infection was expressed in non-switching trypanosomes and used to raise antibody responses. Indirect immuno-fluorescence, complement-mediated lysis, and agglutination assays using both polyclonal and monoclonal antibodies showed that although 4/5 mosaics were cross-reactive, one variant was completely antigenically distinct. Segmental gene conversion was therefore found to be both prominent in chronic African trypanosome antigenic variation, and capable of bringing antigenic novelty to an infection, with important consequences for the dynamics of AV, and the nature of selection pressure on the silent VSG archive

Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

Horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. Conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. In some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to plasmid-borne genes. To investigate the evolutionary importance of alternative hosts to plasmid population dynamics in an ecologically relevant environment, we established simple soil microcosm communities comprising two species of common soil bacteria, Pseudomonas fluorescens and Pseudomonas putida, and a mercury resistance (Hg R) plasmid, pQBR57, both with and without positive selection [i.e., addition of Hg(II)]. In single-species populations, plasmid stability varied between species: although pQBR57 survived both with and without positive selection in P. fluorescens, it was lost or replaced by nontransferable Hg R captured to the chromosome in P. putida. A simple mathematical model suggests these differences were likely due to pQBR57's lower intraspecific conjugation rate in P. putida. By contrast, in two-species communities, both models and experiments show that interspecific conjugation from P. fluorescens allowed pQBR57 to persist in P. putida via source-sink transfer dynamics. Moreover, the replacement of pQBR57 by nontransferable chromosomal Hg R in P. putida was slowed in coculture. Interspecific transfer allows plasmid survival in host species unable to sustain the plasmid in monoculture, promoting community-wide access to the plasmid-borne accessory gene pool and thus potentiating future evolvability

Evaluation Research and Institutional Pressures: Challenges in Public-Nonprofit Contracting

This article examines the connection between program evaluation research and decision-making by public managers. Drawing on neo-institutional theory, a framework is presented for diagnosing the pressures and conditions that lead alternatively toward or away the rational use of evaluation research. Three cases of public-nonprofit contracting for the delivery of major programs are presented to clarify the way coercive, mimetic, and normative pressures interfere with a sound connection being made between research and implementation. The article concludes by considering how public managers can respond to the isomorphic pressures in their environment that make it hard to act on data relating to program performance.This publication is Hauser Center Working Paper No. 23. The Hauser Center Working Paper Series was launched during the summer of 2000. The Series enables the Hauser Center to share with a broad audience important works-in-progress written by Hauser Center scholars and researchers

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that large-amplitude RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps.Comment: 55 pages, 10 figure

Understanding the combined effects of multiple stressors : a new perspective on a longstanding challenge

This work was supported by the Office of Naval Research [grant numbers N000142012697, N000142112096]; and the Strategic Environmental Research and Development Program [grant numbers RC20-1097, RC20-7188, RC21-3091].Wildlife populations and their habitats are exposed to an expanding diversity and intensity of stressors caused by human activities, within the broader context of natural processes and increasing pressure from climate change. Estimating how these multiple stressors affect individuals, populations, and ecosystems is thus of growing importance. However, their combined effects often cannot be predicted reliably from the individual effects of each stressor, and we lack the mechanistic understanding and analytical tools to predict their joint outcomes. We review the science of multiple stressors and present a conceptual framework that captures and reconciles the variety of existing approaches for assessing combined effects. Specifically, we show that all approaches lie along a spectrum, reflecting increasing assumptions about the mechanisms that regulate the action of single stressors and their combined effects. An emphasis on mechanisms improves analytical precision and predictive power but could introduce bias if the underlying assumptions are incorrect. A purely empirical approach has less risk of bias but requires adequate data on the effects of the full range of anticipated combinations of stressor types and magnitudes. We illustrate how this spectrum can be formalised into specific analytical methods, using an example of North Atlantic right whales feeding on limited prey resources while simultaneously being affected by entanglement in fishing gear. In practice, case-specific management needs and data availability will guide the exploration of the stressor combinations of interest and the selection of a suitable trade-off between precision and bias. We argue that the primary goal for adaptive management should be to identify the most practical and effective ways to remove or reduce specific combinations of stressors, bringing the risk of adverse impacts on populations and ecosystems below acceptable thresholds.Publisher PDFPeer reviewe

Establishing Foundation Archives: A Reader and Guide to First Steps

This publication is an anthology of papers presented at a conference held at the Rockefeller Archive Center in January 1990, and sponsored by the Council on Foundations. This collaboration of the Archive Center and the Council provided a rare opponunity for foundations to learn both why preserving documents is imponant and how several foundations have approached finding a repository or setting up and managing an archives. Participants in the conference had the added privilege of conferring with experts and seeing an operating archive as they toured the Rockefeller Archive Center.Foundations are institutions that are shaping private initiatives for the public good, so documenting this aspect of American society falls uniquely under the stewardship of the organizations themselves. Foundation documents often provide the only surviving records of the important contributions of nonprofits and foundations to civic life. These records will help to inform future judgments and ensure that the history of the field is not lost. The publication of this volume was intended to make the information shared at the conference more widely available and to provide an entry point and a primer for foundations as they begin their records and archives journey

A Multi-City Comparison of Front and Backyard Differences in Plant Species Diversity and Nitrogen Cycling in Residential landscapes

We hypothesize that lower public visibility of residential backyards reduces households’ desire for social conformity, which alters residential land management and produces differences in ecological composition and function between front and backyards. Using lawn vegetation plots (7 cities) and soil cores (6 cities), we examine plant species richness and evenness and nitrogen cycling of lawns in Boston, Baltimore, Miami, Minneapolis-St. Paul, Phoenix, Los Angeles (LA), and Salt Lake City (SLC). Seven soil nitrogen measures were compared because different irrigation and fertilization practices may vary between front and backyards, which may alter nitrogen cycling in soils. In addition to lawn-only measurements, we collected and analyzed plant species richness for entire yards—cultivated (intentionally planted) and spontaneous (self-regenerating)—for front and backyards in just two cities: LA and SLC. Lawn plant species and soils were not different between front and backyards in our multi-city comparisons. However, entire-yard plant analyses in LA and SLC revealed that frontyards had significantly fewer species than backyards for both cultivated and spontaneous species. These results suggest that there is a need for a more rich and social-ecologically nuanced understanding of potential residential, household behaviors and their ecological consequences