Online social media as a social-ecological systems research tool: Facebook and two rural Alaskan communities

Thesis (M.A.) University of Alaska Fairbanks, 2013The earth has transitioned into the anthropocene, which is defined by complex environmental change linked to human behavior and requires new tools of analysis in order to understand shifting social-ecological system (SES) dynamics. In this work, I explore taking advantage of widespread online social media participation to develop the tools for doing so. Spatially grounded public exchanges on Facebook are examined with three goals in mind: 1) examine the types of SES content being passed through this communication medium, 2) compare community observations to relevant scientific observations, and 3) define a flexible and reproducible research method for integrating these communications signals into a wide range of SES studies. Facebook activity from two communities in northwest Alaska was studied. Communication patterns were assessed combining content and network analysis methodology. My results indicate that signals are passed through this mode of communication directly addressing the SES topics of subsistence, food security, and human-weather interactions. Data from instrumentally based weather observations are qualitatively aligned with posting frequency and content. A context and community-based research method is defined that uses staged deductive/inductive content analysis, in conjunction with network analysis, to identify emergent local SES relationships.General introduction -- Chapter 1: Placing the study within the context of ongoing academic research -- Chapter 2: Identifying SES in community-based social media networks -- Chapter 3: Exploring Facebook activity in relation to instrumental observations -- General conclusion

Networks of change: extending Alaska-based communication networks to meet the challenges of the anthropocene

Thesis (Ph.D.) University of Alaska Fairbanks, 2017The Anthropocene is a contested term. As I conceptualize it throughout this dissertation, the Anthropocene is defined by an increased coupling of social and environmental systems at the global scale such that the by-products of human processes dominate the global stratigraphic record. Additionally, I connect the term to a worldview that sees this increased coupling as an existential threat to humanity's ability to sustain life on the planet. Awareness that the planet-wide scale of this coupling is fundamentally a new element in earth history is implicit in both understandings. How individuals and communities are impacted by this change varies greatly depending on a host of locally specific cross-scale factors. The range of scales (physical and social) that must be negotiated to manage these impacts places novel demands on the communication networks that shape human agency. Concern for how these demands are being met, and whose interests are being served in doing so, are the primary motivation for my research. My work is grounded in the communication-oriented theoretical traditions of media ecology and the more recent social-ecological system conceptualizations promoted in the study of resilience. I combine these ideas through a mixed methodology of digital ethnography and social network analysis to explore the communication dynamics of four Alaska-based social-ecological systems. The first two examples capture communication networks that formed in response to singular, rapid change environmental events (a coastal storm and river flood). The latter two map communication networks that have formed in response to more diffuse, slower acting environmental changes (a regional webinar series and an international arctic change conference). In each example, individuals or organizations enter and exit the mapped network(s) as they engage in the issue and specific communication channel being observed. Under these parameters a cyclic pattern of network expansion and contraction is identified. Expansion events are heavily influenced by established relationships retained during previous contraction periods. Many organizational outreach efforts are focused on triggering and participating in expansion events, however my observations highlight the role of legacy networks in system change. I suggest that for organizations interested in fostering sustainable socialecological relationships in the Anthropocene, strategic intervention may best be accomplished through careful consideration of how communicative relationships are maintained immediately following and in between expansion events. In the final sections of my dissertation I present a process template to support organizations interested in doing so. I include a complete set of learning activities to facilitate organizational use as well as examples of how the Alaska Native Knowledge Network is currently applying the process to meet their unique organizational needs

Genre Mash-Up: When Two Worldviews Collide, the Genre Conventions from Each Undergo a Syncretistic Re-emergence

The current study proposes to trace the process by which genre features get preserved, modified, or discarded when a politically-sensitive topic draws on both scientific and indigenous knowledge. Initially a network analysis is included to demonstrate the extent to which literature exists that draws on either scientific or indigenous knowledge resources as relating to Arctic climate change; that macrostructural analysis demonstrates that while both exist, there are few linkages in citation between the literatures. The authors then look at the negotiation processes involved in trying to bring more indigenous elements into the scientific literature. This was done by studying the full sets of article submission, all reviewer comments, and revised articles. The focus is on an invited article for The International Panel on Climate Change, which had responded to feedback from previous iterations of their annual report by including a specific chapter dedicated to the perspectives of the tribes that live in the Arctic region, a region that is experiencing more rapid climate change than other parts of the globe. The authorship of that chapter was assigned to a group of researchers, primarily housed at University of Alaska– Fairbanks, that includes Alaskan Native researchers (Inupiat and Athabaskan) and an assortment of biologists, ecologists, marine chemists, etc. The chapter has gone through three iterations with reviewers, and additionally the correspondences between the chapter authors were considered. For comparison, an article in the social science disciplines was also considered, with strikingly similar reviewer comments. These compared cases illustrate the themes used to protect/enforce the genre conventions of the scientific article, and thus serve to perpetuate the separations visible in the network data

Population Inventory, Threat Assessment, And Anticipated Effects Of Global Climate Change On An Endemic, Cliff Habitat Specialist, Aliciella Penstemonoides (Polemoniaceae)

The ongoing biodiversity crisis necessitates assessment of rare and endemic taxa so that we can recognize how global climate change influences species distributions and understand when local extirpations may amount to global extinctions. Vertical cliffs provide a unique ecosystem for highly adapted species to avoid competition. Cliff-dwelling species incur strong selective pressures that lead to regional restrictions and narrow distributions. Aliciella penstemonoides (M.E. Jones) J.M. Porter (Black Canyon Gilia) is a cliff habitat specialist in the Polemoniaceae (Phlox) family and is restricted to vertical cliff habitats above stream and river drainages of the Upper Gunnison River Basin and Headwaters of the Rio Grande in southwest-central Colorado, USA. Field research in 2016 located 14 populations of A. penstemonoides and identified over 2,000 individuals, indicating that this species is locally abundant yet regionally rare. I employed distance sampling line transect methods in combination with rock climbing techniques to document population density and threats across five populations. MaxEnt software modeled the current extent of suitable habitat and predicted suitable habitat under projected climate scenarios for 2050. Models had excellent accuracy according to evaluation statistics and indicate a loss of 70 - 99% of suitable habitat by 2050. I screened microsatellite markers developed for a distant relative (Ipomopsis aggregata) for cross-species applicability in A. penstemonoides. Four microsatellites showed amplification of targeted loci and indicate genetic conservatism within the Loeselieae tribe and Polemoniaceae family. Further research is needed to complete an assessment of intraspecific genetic diversity. A. penstemonoides is confined to narrowly distributed habitats across a relatively large range, yet retains the ability to occupy a wide array of microhabitats and morphologies within an occupied cliff face. Morphological diversity may be accompanied by genetic or thermotolerance diversity, and may provide a means for adaptation and survival in future climates. Populations are often separated by expanses of unsuitable habitat and appear to have adapted to local rock surface variability. Future research may use A. penstemonoides as a model species to test how fragmented populations of a narrowly restricted species respond to a rapidly changing climate

Monitoring Biosensor Activity in Living Cells with Fluorescence Lifetime Imaging Microscopy

Live-cell microscopy is now routinely used to monitor the activities of the genetically encoded biosensor proteins that are designed to directly measure specific cell signaling events inside cells, tissues, or organisms. Most fluorescent biosensor proteins rely on Förster resonance energy transfer (FRET) to report conformational changes in the protein that occur in response to signaling events, and this is commonly measured with intensity-based ratiometric imaging methods. An alternative method for monitoring the activities of the FRET-based biosensor proteins is fluorescence lifetime imaging microscopy (FLIM). FLIM measurements are made in the time domain, and are not affected by factors that commonly limit intensity measurements. In this review, we describe the use of the digital frequency domain (FD) FLIM method for the analysis of FRET signals. We illustrate the methods necessary for the calibration of the FD FLIM system, and demonstrate the analysis of data obtained from cells expressing “FRET standard” fusion proteins. We then use the FLIM-FRET approach to monitor the changes in activities of two different biosensor proteins in specific regions of single living cells. Importantly, the factors required for the accurate determination and reproducibility of lifetime measurements are described in detail

Breathing Easy: Lung Health and Associated Conditions in the Day Care Setting

Introduction: Air pollutants are associated with many health risks. Children in the day care environment are uniquely suscept-ible to lung damage, infection, systemic illness & pollutant triggered hypersensitivity reactions. The latest public report by the CDC reports Vermont’s (VT) asthma rate is the high-est in the country at 11.1%. This project compared VT’s day care regulations regarding specific environmental factors linked with health risks to regulations in six surrounding New England states. We sought to assess whether VT’s regulations adequately protect children in day carehttps://scholarworks.uvm.edu/comphp_gallery/1064/thumbnail.jp

Emergence of Epizootic Ulcerative Syndrome in Native Fish of the Murray-Darling River System, Australia: Hosts, Distribution and Possible Vectors

Epizootic ulcerative syndrome (EUS) is a fish disease of international significance and reportable to the Office International des Epizootics. In June 2010, bony herring Nematalosa erebi, golden perch Macquaria ambigua, Murray cod Maccullochella peelii and spangled perch Leiopotherapon unicolor with severe ulcers were sampled from the Murray-Darling River System (MDRS) between Bourke and Brewarrina, New South Wales Australia. Histopathology and polymerase chain reaction identified the fungus-like oomycete Aphanomyces invadans, the causative agent of EUS. Apart from one previous record in N. erebi, EUS has been recorded in the wild only from coastal drainages in Australia. This study is the first published account of A. invadans in the wild fish populations of the MDRS, and is the first confirmed record of EUS in M. ambigua, M. peelii and L. unicolor. Ulcerated carp Cyprinus carpio collected at the time of the same epizootic were not found to be infected by EUS, supporting previous accounts of resistance against the disease by this species. The lack of previous clinical evidence, the large number of new hosts (n = 3), the geographic extent (200 km) of this epizootic, the severity of ulceration and apparent high pathogenicity suggest a relatively recent invasion by A. invadans. The epizootic and associated environmental factors are documented and discussed within the context of possible vectors for its entry into the MDRS and recommendations regarding continued surveillance, research and biosecurity are made

Increasing the resilience of plant immunity to a warming climate

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) was reduced at the higher growth temperature. The altered GDAC formation in vivo is linked to impaired recruitment of GBPL3 and SA-associated Mediator subunits to the promoters of CBP60g and SARD1, which encode master immune transcription factors. Unlike many other SA signalling components, including the SA receptor and biosynthetic genes, optimized CBP60g expression was sufficient to broadly restore SA production, basal immunity and effector-triggered immunity at the elevated growth temperature without significant growth trade-offs. CBP60g family transcription factors are widely conserved in plants. These results have implications for safeguarding the plant immune system as well as understanding the concept of the plant–pathogen–environment disease triangle and the emergence of new disease epidemics in a warming climate

The Human Phenotype Ontology in 2017.

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology