skip to main content

Search for: All records

Creators/Authors contains: "Johnson, D."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Hussain, A. ; Tarman T. (Ed.)
  2. Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature that distinguishes the two types of bacteria. The transpeptidase activity of sortases make them an important tool in protein engineering applications, e.g., in sortase-mediated ligations or sortagging. However, due to relatively low catalytic efficiency, there are ongoing efforts to create better sortase variants for these uses. Here, we use bioinformatics tools, principal component analysis and ancestral sequence reconstruction, in combination with protein biochemistry, to analyze natural sequence variation in these enzymes. Principal component analysis on the sortase superfamily distinguishes previously described classes and identifies regions of relatively high sequence variation in structurally-conserved loops within each sortase family, including those near the active site. Using ancestral sequence reconstruction, we determined sequences of ancestral Staphylococcus and Streptococcus Class A sortase proteins. Enzyme assays revealed that the ancestral Streptococcus enzyme is relatively active and shares similar sequence variation with other Class A Streptococcus sortases. Taken together, we highlight how natural sequence variation can be utilized to investigate this important protein family, arguing that these and similar techniques may be used to discover or design sortases with increased catalytic efficiency and/or selectivity for sortase-mediated ligation experiments. 
    more » « less
  3. Consumer-mediated movement can couple food webs in distinct habitats and facilitate energy flow between them. In New England saltmarshes, mummichogs (Fundulus heteroclitus) connect the vegetated marsh and creek food webs by opportunistically foraging on the invertebrate communities of the marsh surface when access is permitted by tidal flooding and marsh-edge geomorphology. Via their movements, mummichog represent a critical food web node, as they can potentially transport energy from the marsh surface food web to creek food web and exert top-down control on the communities of the vegetated marsh surface. Here, I use gut content analysis, calorimetric analysis, and field surveys to demonstrate that access to the marsh surface (afforded by marsh-edge geomorphology) impacts the trophic relay of marsh production to creek food webs. Fish populations in creeks with greater connectivity had a higher total biomass of terrestrial invertebrates in their guts. However, bomb calorimetry showed no difference in the average caloric content of mummichog individuals from creeks with different creek edge geomorphology. Access also did not impact mummichog distribution across the marsh platform and exhibited no evidence of top-down control on their invertebrate prey. Thus, mummichogs function as initial nodes in the trophic relay, unidirectionally moving energy from the vegetated marsh to the creek food web. Reduced marsh surface access via altered marsh-edge geomorphology results in a 50 % to 66 % reduction in total energy available to aquatic predators via this route. Estuarine systems are intimately connected to coastal and offshore systems via consumer mediated flows of energy; thus, disruptions to the trophic relay from the marsh surface at the tidal creek scale can have far reaching impacts on secondary productivity in multiple disparate systems and must be accounted for in considerations of impacts to future food-web function. 
    more » « less
  4. null (Ed.)
  5. Presentation by OSC Sys Admins at the ACM SIGHPC SYSPROS Symposium held in conjunction with the PEARC19 conference 
    more » « less
  6. null (Ed.)
    Abstract Context Most protected areas are managed based on objectives related to scientific ecological knowledge of species and ecosystems. However, a core principle of sustainability science is that understanding and including local ecological knowledge, perceptions of ecosystem service provision and landscape vulnerability will improve sustainability and resilience of social-ecological systems. Here, we take up these assumptions in the context of protected areas to provide insight on the effectiveness of nature protection goals, particularly in highly human-influenced landscapes. Objectives We examined how residents’ ecological knowledge systems, comprised of both local and scientific, mediated the relationship between their characteristics and a set of variables that represented perceptions of ecosystem services, landscape change, human-nature relationships, and impacts. Methods We administered a face-to-face survey to local residents in the Sierra de Guadarrama protected areas, Spain. We used bi- and multi-variate analysis, including partial least squares path modeling to test our hypotheses. Results Ecological knowledge systems were highly correlated and were instrumental in predicting perceptions of water-related ecosystem services, landscape change, increasing outdoors activities, and human-nature relationships. Engagement with nature, socio-demographics, trip characteristics, and a rural–urban gradient explained a high degree of variation in ecological knowledge. Bundles of perceived ecosystem services and impacts, in relation to ecological knowledge, emerged as social representation on how residents relate to, understand, and perceive landscapes. Conclusions Our findings provide insight into the interactions between ecological knowledge systems and their role in shaping perceptions of local communities about protected areas. These results are expected to inform protected area management and landscape sustainability. 
    more » « less
  7. Project update from the Open OnDemand User Group meeting held at the PEARC 19 conference 
    more » « less
  8. This paper reports on the first phase of research on a scholarship program VTAB (Vertical Transfers’ Access to the Baccalaureate) funded by a five-year grant from the National Science Foundation (NSF) that focuses on students who transfer at the 3rd year level from 2-year schools to the engineering and engineering technology BS programs at our university [1]. The goals of the program are: (i) to expand and diversify the engineering/technology workforce of the future, (ii) to develop linkages and articulations with 2-year schools and their S-STEM programs, (iii) to recruit, retain, and graduate 78 low-income students, and place them in industry or graduate schools, (iv) to generate knowledge about the program elements that can help other universities, and (v) to serve as a model for other universities to provide vertical transfer students access to the baccalaureate degree. 
    more » « less