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"Reed, Samuel"
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If I could tell you just one thing-- : encounters with remarkable people and their most valuable advice
\"[S]ome of the world's most remarkable people share their most valuable pieces of wisdom\"--Amazon.com.
Book
Simultaneous DNA amplification and detection using a pH-sensing semiconductor system
A semiconductor chip, coupled to an ion-sensitive field effect transistor (ISFET) pH sensor, can amplify and quantitate DNA in real time without dyes, cameras and external heating devices.
We developed an integrated chip for real-time amplification and detection of nucleic acid using pH-sensing complementary metal-oxide semiconductor (CMOS) technology. Here we show an amplification-coupled detection method for directly measuring released hydrogen ions during nucleotide incorporation rather than relying on indirect measurements such as fluorescent dyes. This is a label-free, non-optical, real-time method for detecting and quantifying target sequences by monitoring pH signatures of native amplification chemistries. The chip has ion-sensitive field effect transistor (ISFET) sensors, temperature sensors, resistive heating, signal processing and control circuitry all integrated to create a full system-on-chip platform. We evaluated the platform using two amplification strategies: PCR and isothermal amplification. Using this platform, we genotyped and discriminated unique single-nucleotide polymorphism (SNP) variants of the cytochrome P450 family from crude human saliva. We anticipate this semiconductor technology will enable the creation of devices for cost-effective, portable and scalable real-time nucleic acid analysis.
Journal Article
Linked disturbance in the temperate forest
Despite the large body of theory concerning multiple disturbances, relatively few attempts have been made to test the theoretical assumptions of how and if disturbances interact. Of particular importance is whether disturbance events are linked, as this can influence the probability and intensity of ecological change. Disturbances are linked when one disturbance event increases or decreases the likelihood or extent of another. To this end, we used two long-term, multi-disturbance experiments in northern Wisconsin to determine whether earthworm invasion is linked to canopy gap creation and white-tailed deer browsing. These three disturbances are common and influential within North American temperate forests, making any interactions among them particularly important to understand. We expected both deer and canopy gaps to favor invasive earthworms, particularly species that live close to or on the soil surface. However, we found only partial support of our hypotheses, as both deer exclosures and canopy gaps decreased earthworms in each experiment. Further, earthworm density increased the most over time in areas far from the gap center and in areas with deer present. Deer exclosures primarily decreased Aporrectodea and Lumbricus species, while gaps decreased Dendrobaena and Lumbricus species. Our findings show that earthworm invasion is linked to deer presence and gap-creating disturbances, which provides new insight in multiple disturbance theory, above ground–below ground dynamics, and temperate forest management.
Journal Article
Let the Young Gs Lead the Way
In this issue’s In Dialogue, our featured contributors reflect on challenges and opportunities of media literacy relating to digital technologies, particularly in current times of division. These pieces discuss the experiences of English educators, researchers, and students, and offer frameworks for how people might teach and learn about digital and media literacies in this era. We begin with a dialogic piece between Samuel A. Reed III and his former student Anthony Rivera, reflecting real ways educators and students individually and collaboratively learn and grow in these times of simultaneous connective possibilities and divisive realities. Megan Boler continues the conversation by highlighting ways digital manipulations—of data, emotions, and more—necessitate a pedagogy of discomfort to directly and meaningfully unpack experiences in and with digital media. We end with a call by Antero Garcia to turn toward the analog and the local to intervene as justice-oriented literacy educators, as the digital further complicates oppressions and inequities.
Journal Article
Transdisciplinary academic-NGO collaborations for the resilience of food, energy, and water: a case study on the INFEWS-ER experience in post-disaster Puerto Rico
The communities of Puerto Rico are highly vulnerable to climate change as the archipelago has experienced a multitude of compounding crises and extreme weather events in recent years. To address these issues, the research, analysis, and design of grand challenge solutions for disaster-prone regions like Puerto Rico can utilize collaborative transdisciplinary efforts. Local non-governmental and community-based organizations have a pivotal role in the reconstruction processes and the building of community and environmental resilience in underserved communities. This paper contributes an empirical case study of an online transdisciplinary collaboration between a group of academics and a Puerto Rican non-governmental organization, Caras con Causa. From participant observation, it includes a document analysis of meeting notes with cohort members who were involved in a collaborative National Science Foundation Project, The INFEWS-ER: A Virtual Resource Center Enabling Graduate Innovations at the Nexus of Food, Energy, and Water Systems, with Caras con Causa between October 2020 and April 2021. Caras con Causa focuses on uplifting Puerto Ricans by creating and administering environmental, educational, economic, and community programs, highlighting disaster relief and resilience to help Puerto Rican food, energy, and water systems. Eight key discussion themes emerged from the document analysis: team organization, collaboration with Caras con Causa, deliverables, team contributions, context understanding, participation outcomes, technology setup, and lessons learned. We analyze each of the emerging themes to explain how academics may use transdisciplinary skill sets in addition to standard disciplinary-based approaches or techniques to enhance the institutional capacity of a non-governmental organization doing community resilience work to benefit local food, energy, and water systems. While the learned lessons in this non-governmental organization-academic collaboration may be context-specific, we provide insights that may be generalizable to collaborations in comparable transdisciplinary settings.
Journal Article
Recommendations for developing, documenting, and distributing data products derived from NEON data
The National Ecological Observatory Network (NEON) provides over 180 distinct data products from 81 sites (47 terrestrial and 34 freshwater aquatic sites) within the United States and Puerto Rico. These data products include both field and remote sensing data collected using standardized protocols and sampling schema, with centralized quality assurance and quality control (QA/QC) provided by NEON staff. Such breadth of data creates opportunities for the research community to extend basic and applied research while also extending the impact and reach of NEON data through the creation of derived data products—higher level data products derived by the user community from NEON data. Derived data products are curated, documented, reproducibly‐generated datasets created by applying various processing steps to one or more lower level data products—including interpolation, extrapolation, integration, statistical analysis, modeling, or transformations. Derived data products directly benefit the research community and increase the impact of NEON data by broadening the size and diversity of the user base, decreasing the time and effort needed for working with NEON data, providing primary research foci through the development via the derivation process, and helping users address multidisciplinary questions. Creating derived data products also promotes personal career advancement to those involved through publications, citations, and future grant proposals. However, the creation of derived data products is a nontrivial task. Here we provide an overview of the process of creating derived data products while outlining the advantages, challenges, and major considerations.
Journal Article
Miscibility gap alloys with a ceramic matrix for thermal energy storage
New miscibility gap alloys with a ceramic matrix have been explored in the ZrO
2
–Al, AlN–Al, AlN-(Al–Si), Al
2
O
3
–Al and MgO–Al systems with a view to creating oxidation-resistant macroscopically solid, phase change-enhanced, thermal energy storage materials. Materials were manufactured by mixing the components, pressing and firing at 700 °C under argon. Oxidation tests at 700 °C in air for up to 72 h showed a mix of responses. Despite favourable thermodynamic properties of some published Ellingham diagrams, samples in the ZrO
2
–Al system underwent a strong exchange reaction, which did not result in a useful material. In the AlN–Al, AlN–(Al–Si) systems, viable MGA-type materials with encapsulated Al particles providing latent heat storage within a solid matrix were formed. There was no degradation of the materials after 24 h of oxidation testing; however, severe oxidation of the Al or Al–Si was observed after 72 h. The Al
2
O
3
–Al and MgO–Al systems not only formed a viable ceramic matrix material after firing, but also showed no signs of Al oxidation after 72 h in air at 700 °C. These results open up a promising new series of thermal energy storage materials, some of which appear to have very good oxidation resistance under the test conditions.
Journal Article
Characterization of Specific Aptamer Interactions With NGAL
Aptamers, short oligonucleotide molecules, are renowned for their high specificity and affinity toward target molecules, providing valuable opportunities for targeted molecular interactions. This study focuses on elucidating the binding dynamics between aptamers and neutrophil gelatinase-associated lipocalin (NGAL), a protein of clinical interest, employing a comprehensive experimental approach. Analyses were primarily conducted on three aptamers, 37NGAL1A (2’FY-RNA), 56NGAL3A (2’FY-RNA) and 75NGAL10A (DNA), to determine their binding sites and affinities with NGAL.It was hypothesized that specific positively charged amino acid residues on NGAL are crucial for binding to the negatively charged phosphate backbone of the aptamers. Site-directed mutagenesis confirmed that mutations in these residues significantly reduced the binding signal for all examined aptamers, with notable differences between the aptamers identified. These results indicated that 37NGAL1A and 75NGAL10A may bind through different residues and could target distinct epitopes on the NGAL protein. Nuclear magnetic resonance (NMR) analysis provided a deeper visualization and understanding of the interaction sites and complementing theoretical predictions. By using the NMR results, the 75NGAL10A aptamer was found to interact through a variety of residues surrounding the brim of the calyx of NGAL, with a possibility to interact with the calyx itself. Employing both the NMR results and the mutation binding results, the 37NGAL1A aptamer was found to interact through residues opposite the DNA aptamer, indicating the two aptamers do not share an epitope on the NGAL protein. Direct binding competition studies were conducted, which also suggested no competition between the 37NGAL1A and 75NGAL10A aptamer.This study’s findings demonstrate the crucial roles of specific residues in aptamer binding and direct competition assays confirm that the aptamers interact with NGAL through different mechanisms. These insights not only advance the understanding of aptamer-protein dynamics but also have significant implications for the development of aptamer-based diagnostics and therapeutics, tailored for enhanced specificity and efficacy.
Dissertation
Multiple Disturbances and the Turbulent Forest
I have always been drawn to change, whether I liked it or not. As a kid, I was obsessed with dinosaurs and their extinction, all while having to move constantly as a Navy brat. As an adult, I am devoted to understanding how and why systems change, likely inspired by the unending change of my childhood. However, as I matured, I realized that change is almost never spurred by a single event, but rather a multitude of shocks to the system. This dissertation focuses on the complexity of multiple ecological disturbances and highlights their importance in the world. Using several multi-disturbance experiments, I explore a wide variety of disturbance interactions in the temperate deciduous forest. The first chapter of this dissertation focuses on how deer and canopy gaps influence invasive earthworms, shedding new light on how aboveground events can change belowground communities. The second chapter builds upon the first and tests how combined deer and canopy gaps influence understory regeneration over 15 years, with some reference to invasive earthworms. Lastly, the third chapter explores how combined fire, deer, and canopy gaps change the seed bank over 13 years. Each of the aforementioned disturbances are common and influential in eastern forests, although they are not often studied together. In each chapter we find that community responses vary depending on the disturbances in question. This dissertation is meant to highlight how little we know about the many ways in which multiple disturbances change ecosystems and how critical it is that we start to study these complex drivers of change, particularly as the climate warms and disturbances become more frequent on the landscape.
Dissertation
Implementing Extended Tasks: Developing Perseverance
Encouraging students to persevere in problem solving can be accomplished using extended tasks where students solve a problem over an extended time. This article presents a structure for use of extended tasks and examples of student thinking that can emerge through such tasks. Considerations for implementation are provided.
Journal Article