Distribution Changes, Genetic Population Structure, and a Novel Environmental DNA (eDNA) Detection Method for Darters (Subgenus Nothonotus) in the Upper Ohio River Watershed

In the upper Ohio River watershed three species of small-bodied benthic fish the Bluebreast Darter, Etheostoma (Nothonotus) camurum (Cope), the Tippecanoe Darter, Etheostoma (Nothonotus) tippecanoe Jordan and Evermann, and the Spotted Darter, Etheostoma (Nothonotus) maculatum Kirtland previously existed in disjunct distributions due to poor water quality and habitat degradation. Signs of recovery indicated that these species were moving from areas of refugia into the deeper mainstem waters of the Allegheny and Ohio rivers and expanding their distributions. To provide information for the proper conservation management of these species this dissertation was divided into three stages: 1) distribution records were updated by performing State-mandated electrified-benthic trawling and compiling as many historic and contemporary records as possible, 2) the genetic diversity and genetic population structure of E. camurum was assessed using six polymorphic microsatellite loci, and 3) environmental DNA (eDNA) methods with species detection from water samples via fragment analysis were developed to assist current survey methods which are costly, time consuming, and may be harmful to the fish. The surveys and compilation of data showed that E. camurum and E. tippecanoe are utilizing deeper habitat (than previously reported) in the tailwaters of the navigational lock and dam system, and have nearly continuous distributions from the upper Allegheny River downstream into the Ohio River. Etheostoma maculatum showed a less robust expansion and a more limited use of the tailwater habitat. The genetic assessment of E. camurum indicated high genetic diversity within their populations with no evident signs of isolation or inbreeding. The genetic population structure of E. camurum was weak indicating that the navigational lock and dam system was not strongly influencing gene flow between the populations. In addition, there were signs of a newly advancing population. With eDNA methodologies, a protocol was developed that successfully detected E. tippecanoe eDNA from water samples taken from the Allegheny and Kiskiminetas rivers and Deer Creek in Harmarville, PA. A second set of PCR primers were developed that have the potential to detect all three focal species using eDNA from water samples

NGO Outreach for Early Recovery: Strategies for Improved Coordination and Implementation of the Early Recovery Approach

The Cluster Working Group on Early Recovery (CWGER) is the United Nations global Working Group tasked to integrate Early Recovery into the international humanitarian architecture. As part of their outreach campaign, the CWGER commissioned a report to analyze the extent to which selected humanitarian INGOs integrated aspects of the Early Recovery approach during the 2010 flood response in Pakistan. The CWGER requested an analysis of INGO programs, with explicit interest regarding the planning, coordinating and transition processes each INGO applied during the relief phase of the response. In addition, the CWGER wanted to know the extent to which the selected INGOs integrated elements of the Early Recovery approach into their planning and coordination processes. The CWGER hopes to use the information provided in this report to learn how best to engage and collaborate with INGOs before and during humanitarian crises. Furthermore, the CWGER hopes to use the recommendations included in this report to determine what feasible measures it can or should take to support the selected INGOs in their efforts to integrate Early Recovery in their programs before and during a crisis

Engineering Skeletal Muscle for Histological and Functional Regeneration Following Volumetric Muscle Loss

Tissue engineered skeletal muscle has great potential to successfully treat volumetric muscle loss (VML), a condition with no ideal clinical treatment option. A broad range of engineered muscle constructs have been evaluated in preclinical models of VML with a few cases of clinical use as well. Despite improvements to muscle function following treatment, histological regeneration of the muscle tissue has varied broadly with the method of treatment. In addition, few studies have attempted to restore the damaged connection between muscle and nerve and robust neuromuscular regeneration following VML injury has yet to be achieved. To enable functional and histological muscle regeneration post-VML, a broad range of factors must be considered including a biomimetic and biocompatible scaffold design, selection of a translatable cell source, and modification of the regenerating environment to promote neuromuscular regeneration. The objective of this thesis was to develop a translatable engineered muscle construct with the ability to promote neuromuscular regeneration of murine VML defects. This body of work describes a multistep approach towards the fulfillment of the above objective. First, an electrospun fibrin scaffold was developed that mimics the native stiffness and alignment of skeletal muscle and when combined with mouse myoblasts, enables the formation of an implantable skeletal muscle construct and robust muscle regeneration post-VML. The next two chapters describe the myogenic potential of two translatable cell sources on electrospun scaffolds: adipose derived stem cells (ASCs) and human pluripotent stem cells (hPSCs). While ASCs resulted in limited in vitro myogenesis on electrospun fibers and provided a minimal regenerative benefit, hPSC-derived myoblasts purified for a Pax7 myogenic subpopulation demonstrated robust in vitro myogenesis in 3D constructs. While the regenerative potential of hPSC-derived myoblast constructs in muscle defects was limited, the results are a promising step towards the use of these cells to treat VML. Lastly, engineered muscle constructs were pre-treated to promote acetylcholine receptor (AChR) clustering and neuromuscular regeneration through the delivery of agrin, a heparan sulfate proteoglycan, by either chemically tethering agrin to the scaffold or providing it in solution. Following implantation in VML defects for four weeks, the agrin pre-treated muscle constructs resulted in increased neuromuscular junctions, regenerating myofibers, vascular infiltration, neural infiltration, and nuclear yes-associated protein within the defect region. In addition, sustained local agrin delivery by the tethered agrin constructs resulted in higher densities of neurofilament and regenerating myofibers than soluble agrin constructs. This investigation revealed the remarkable potential of agrin-modified engineered muscle constructs for neuromuscular regeneration post-VML. Taken together, these findings have significant implications for the development of tissue engineered skeletal muscle and enabling the functional and histological regeneration of skeletal muscle following VML

A highly reproducible rotenone model of Parkinson's disease

Producción CientíficaThe systemic rotenone model of Parkinson's disease (PD) accurately replicates many aspects of the pathology of human PD and has provided insights into the pathogenesis of PD. The major limitation of the rotenone model has been its variability, both in terms of the percentage of animals that develop a clear-cut nigrostriatal lesion and the extent of that lesion. The goal here was to develop an improved and highly reproducible rotenone model of PD. In these studies, male Lewis rats in three age groups (3, 7 or 12-14 months) were administered rotenone (2.75 or 3.0 mg/kg/day) in a specialized vehicle by daily intraperitoneal injection. All rotenone-treated animals developed bradykinesia, postural instability, and/or rigidity, which were reversed by apomorphine, consistent with a lesion of the nigrostriatal dopamine system. Animals were sacrificed when the PD phenotype became debilitating. Rotenone treatment caused a 45% loss of tyrosine hydroxylase-positive substantia nigra neurons and a commensurate loss of striatal dopamine. Additionally, in rotenone-treated animals, alpha-synuclein and poly-ubiquitin positive aggregates were observed in dopamine neurons of the substantia nigra. In summary, this version of the rotenone model is highly reproducible and may provide an excellent tool to test new neuroprotective strategies

Field Deployed Ni-Amended Sediments Shows Varying Effects in Two Central MIchigan Streams

Most research on Ni contaminated sediments has occurred under laboratory conditions, which can lead to exposure to formulated water that is not representative of environmentally relevant conditions. For example, laboratory conditions don’t accurately represent natural fluctuations in temperature, light, or flow. The purpose of our study was to 1) assess the bioavailability and toxicity of Ni contaminated sediments to stream macroinvertebrate communities under in situ conditions and 2) compare these effects across two similar streams in close proximity of each other. Sediments were removed from two, second order streams in central Michigan (Black Creek (BC) and Little Molasses (LM)) that were similar in hardness, pH, dissolved oxygen (DO), dissolved organic carbon (DOC), and alkalinity. The sediments were directly spiked with Ni at two treatment levels, low nickel (210 mg/kg dry weight) and high nickel (1889 mg/kg dry weight), equilibrated for 10 days, and re-deployed in macroinvertebrate colonization baskets within the respective streams. Sediment geochemistry (e.g. AVS, SEMNi, total Ni, total Fe, and total Mn) and water quality measurements (e.g. hardness, alkalinity, pH, and dissolved organic carbon (DOC)) were determined at deployment and three successive sampling periods (14, 28, and 56 days post-deployment). In situ chambers with Hyallela azteca were used to conduct 96-h acute toxicity tests at day 0 and 14. In addition, we deployed a microbial decomposition test from day 0 to 14 to assess Ni effect on the microbial community. We found varying responses to Ni treatments in each stream. The 96-h acute toxicity tests only showed significant toxicity in the sediment-water interface exposure at day 0 for BC. Both Ni treatments adversely impacted the microbial community in BC, but not in LM. The benthic community recolonization response was limited with only the family Gammaridae showing a response to Ni treatment in both streams on day 14. Stepwise stream-dependent regression of the measured variables showed that the SEMNi/AVS model of potential toxicity significantly predicted Gammaridae abundance in BC, but not LM. BC showed a trend of toxicity from Ni-amended sediments with increased mortality to H. azteca (acute exposure), the microbial community, and Gammaridae.Master of ScienceNatural Resources and EnvironmentUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/99546/1/Honick_Thesis_2013.pd

STRUCTURE-DEPENDENT PHOTODYNAMICS IN PHOTOSWITCHABLE AND SUPRAMOLECULAR MATERIALS

Understanding how molecular structure impacts non-adiabatic transitions that underlie E/Z photoisomerization and 6pi photocyclization is crucial for improving the responses and efficiencies of molecular photoswitches. We previously identified a diarylethene (DAE) structure that exclusively enables cis to trans isomerization, but with low yields (only 5%). The work presented here utilizes ultrafast spectroscopy to elucidate the isomerization pathway and identifies several factors contributing to quantum yield losses, including the presence of non-reactive conformers that are simultaneously excited as well as photophysical losses that occur during the relaxation that follows excitation of a reactive conformer. An investigation of a novel series of photo-cyclizing DAE photo- switches with structurally varied core-bridge groups is also discussed. This effort examined how properties (e.g. rigidity, aromaticity) of a core structural motif impacts cycloreversion dynamics. The key result from this work is that rigid-core switches experience less structural relaxation, with excited-state surfaces characterized by shallower potential minima and relatively smaller energetic barriers to transition states or conical intersections when compared to counterparts with flexible core motifs. These rigid-core switches thus demonstrate faster cycloreversion while quantum yields are not impacted. The second part of this thesis focuses on supramolecular systems comprised of peptide-functionalized organic semiconductors that undergo pH-triggered assembly in aqueous environments to form self-assembled 1-D nanomaterials primarily through hydrogen bonding interactions and with electronic coupling strengths that are sensitive to the peptide sequence. Fluence-dependent singlet-annihilation measurements reveal correlation between exciton diffusion and the degree of coupling permitted by the specific peptide-sequence employed. Thus, diffusion rates of excitons may be synthetically tuned. This work is complemented by a discussion of the novel electron-transfer reaction that occurs between photoexcited acenes and peptidic PDI. Following selective excitation of a donor, peptidic PDI serves as an electron acceptor and forms stable anions and dianions at high pH. When reduced PDIs encounter each other, formation of pi-dimer dianions with distinct absorption characteristics are observed. This may be driven by the stabilization gained by forming “pancake bonds”. The formation of these species is inhibited for PDIs with larger/hydrophobic peptides that prevent the close orbital overlap necessary for pi-dimer interactions

It\u27s Exhausting : Reconciling a Prisoner\u27s Right to Meaningful Remedies for Constitutional Remedies for Constitutional Violations With the Need for Agency Autonomy

This Comment will address the inadequacy and injustice of the PLRA, specifically the “proper exhaustion” rule as expressed in Woodford v. Ngo. “Proper exhaustion” means that “a prisoner must complete the administrative review process in accordance with applicable procedural rules, including deadlines, as a precondition to bringing suit in federal court.” Failure to adhere to even the slightest procedural requirement is sufficient to warrant procedural default, i.e., a dismissal regardless of the merits of the underlying claim. The PLRA seeks to achieve laudable ends, but the means by which it does so leave much to be desired

Data Curation Toolbox: Empowering FAIR Data Sharing via Science Gateways

<p>A paradigm shift in open science is occurring as national funding agencies for scientific research are requiring that researchers guarantee to publish their data in repositories in accordance with the FAIR Principles. Thus, effective data sharing among repositories has become a critical concern for multiple stakeholder groups: scientists sharing data, data curators organizing and coordinating datasets, technologists crafting repository tools (including infrastructure, network, security, graphics, and more), and end users consuming the data. To balance the needs and goals presented by the other stakeholder groups, data curators must be strategic in their role to successfully integrate data and metadata files from various sources and organize them for sharing via science gateways. <br><br>Data curators ensure that data submissions to repositories adhere to the FAIR Principles, addressing issues that can arise from data or metadata. For instance, curators often encounter a lack of database fields that would allow benchmarking queries and reports to be created. There may also be problems with the data itself, such as incorrect formatting, missing data, duplicate values, etc. Data ingest workflows should be carefully designed to take these types of issues into consideration so they are rectified (or at least minimized) and not exacerbated. The complexity of ingesting datasets requires planning to preserve both data accuracy and incorporation of FAIR standards. <br><br>Since data curators serve as a connection between technologists and scientists, they are uniquely positioned to offer insight on how to help digital repositories maintain FAIR and open standards. This poster presents a "data curation toolbox," useful tools and tactics that data curators can employ in their professional practice. This toolbox is generalized to allow for reproducibility by curators working on other gateways as well as empowering scientists to perform curation on their own projects.</p&gt