Characterizing ancient chemoclines through the use of pigment biomarkers and sedimentary stable isotope signatures

This dissertation focuses on identifying and qualifying chemocline dynamics, namely depth and stability, in stratified aquatic systems through the use of sedimentary pigments and the stable carbon and nitrogen isotopes of organic matter. The central aim of the research comprising this volume is to identify how chemocline fluctuations are expressed in the pigment and stable isotope signatures of aquatic sediments, and how those fluctuations may have impacted nutrient cycling in past intervals of marine anoxia and mass extinction. In order to help gauge how the depth of the chemocline may affect specific pigment signatures and concentrations in sediments, I first investigated how pigment distributions changed in microbialites over a shallow depth gradient. The immobile nature and relative stability of the environment surrounding the microbialites allowed for the investigation of how depth, and by extension changing light regime, can affect microbial community structure and the production of light harvesting vs. photoprotective pigments. It was found that the concentration of the photoprotective pigment scytonemin and its abundance relative to that of chlorophyll a decrease logarithmically with depth, consistent with the function of scytonemin as a UV screening pigment. As well, the increase in the concentration of chlorophyll a, b and the photosynthetic accessory carotenoids fucoxanthin and β-carotene with depth are consistent with lower irradiance at depth. The distribution and relative abundance of photosynthetic and light shielding pigments therefore, may provide a means for determining the relative water depth/incident radiation levels of ancient microbialites in which pigments or their derivatives are preserved. As well, it provides a modern proof of concept for utilizing changing pigment concentrations and ratios in an aquatic system to reconstruct past changes in light regime, or the depth of the locus of primary production. The next phase of this research was then to investigate how pigment and stable isotope signatures varied in a modern stratified system during periods of know chemocline fluctuations. For this, I turned to the sediments of Lake Kivu, East Africa, a deep meromictic lake that has experienced large scale mixing events and chemocline destabilizations in the past. Within the studied core, sediments deposited coevally with mixing events exhibited distinct pigment, and carbon and nitrogen stable isotopic signatures (δ13Corg and δ15Nbulk respectively) compared to surrounding background sediments. The δ13Corg and δ15Nbulk values displayed sharp negative excursions at the base of the high TOC sapropel layers that are associated with the mixing events. These negative excursions provide evidence for the greater influence of 13C-depleted dissolved inorganic carbon and 15N-depleted ammonium derived from below the chemocline. Additionally, ratios of zeaxanthin:chlorophyllone (photoprotective and photosynthetic pigments respectively) display enormous fluctuations and spikes in the studied interval, with the sapropel layers hosting the highest values. This coupled with the presence of bacteriochlorophyll derivatives is further evidence for the breakdown of permanent stratification and shallowing of the chemocline during sapropel deposition. This study provides a mechanistic link to the strongly depleted δ15Nbulk values in the black shales of Mesozoic OAEs, and other anoxic basins of the past and can bolster predictions on the effects of future warming and deoxygenation on nutrient cycling in the modern ocean. Additionally, it provides a set of stable isotope and pigment signatures that can be used to characterize chemocline dynamics in ancient sedimentary sequences. The final phase of this body of work characterizes chemocline dynamics in a more ancient sedimentary system, namely, the black shales from the Appalachian and Illinois basins, associated with the Late Devonian Frasnian-Famennian biotic crisis. The Frasnian-Famennian biotic crisis marked by two distinct intervals known as the Lower and Upper Kellwasser Events that in many locations are associated with deposition of organic-rich shales. Black shales from the Illinois and Appalachian basins, including the Kellwasser Events, are 15N-depleted and have significantly lower δ15Nbulk than interbedded grey shales, a trend consistent with many instances of black shale deposition in the Phanerozoic. Organic carbon isotopes exhibit the broad, positive excursions (~+3.5 ‰ from background) that are typical of the KWEs globally. Superimposed over these positive excursions in δ13Corg are sharp decreases within the black shale beds. The pattern of δ15Nbulk and δ13Corg values suggests that, similar to Lake Kivu, the depth/stability of the chemocline and the degree of water-column stratification exert a primary control on both δ15Nbulk and δ13Corg during black shale deposition. In the context of the Frasnian-Famennian biotic crisis, the oscillating redox state and changing temperatures would have likely placed extreme stress on organisms within the marine environment of the Appalachian and Illinois basins, and may potentially have been a contributing factor to diversity loss over this time period

Sclerostin antibody improves skeletal parameters in a Brtl/+ mouse model of osteogenesis imperfecta

Osteogenesis imperfecta (OI) is a genetic bone dysplasia characterized by osteopenia and easy susceptibility to fracture. Symptoms are most prominent during childhood. Although antiresorptive bisphosphonates have been widely used to treat pediatric OI, controlled trials show improved vertebral parameters but equivocal effects on long‐bone fracture rates. New treatments for OI are needed to increase bone mass throughout the skeleton. Sclerostin antibody (Scl‐Ab) therapy is potently anabolic in the skeleton by stimulating osteoblasts via the canonical wnt signaling pathway, and may be beneficial for treating OI. In this study, Scl‐Ab therapy was investigated in mice heterozygous for a typical OI‐causing Gly→Cys substitution in col1a1 . Two weeks of Scl‐Ab successfully stimulated osteoblast bone formation in a knock‐in model for moderately severe OI (Brtl/+) and in WT mice, leading to improved bone mass and reduced long‐bone fragility. Image‐guided nanoindentation revealed no alteration in local tissue mineralization dynamics with Scl‐Ab. These results contrast with previous findings of antiresorptive efficacy in OI both in mechanism and potency of effects on fragility. In conclusion, short‐term Scl‐Ab was successfully anabolic in osteoblasts harboring a typical OI‐causing collagen mutation and represents a potential new therapy to improve bone mass and reduce fractures in pediatric OI. © 2013 American Society for Bone and Mineral ResearchPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95242/1/1717_ftp.pd

Advancing qualitative rare disease research methodology: a comparison of virtual and in-person focus group formats

Background: Rare disease research is hampered in part by the fact that patients are geographically dispersed. Rare disease patient communities are recognized for their use of the internet to learn about their condition and find peer-to-peer support. As such, web-based technologies offer promise for overcoming geographic barriers in rare disease research for many. Qualitative focus groups (FGs) are a widely used methodology used to understand patients and parents/families ‘lived experience’ and unmet needs is important to improve care for rare diseases. It is unclear if web-enabled (virtual) FGs are comparable to traditional in-person approaches. We conducted in-person (n = 3) and virtual (n = 3) FGs with rare disease patients to determine if virtual FGs produce similar results in-person FGs. Results: Three in-person (n = 33 participants) and three virtual (n = 25 participants) FGs were conducted examining attitudes and beliefs regarding genetic testing and family communication of risk. Participants included 30 males, 18 females, and 10 parents/guardians. Two independent investigators identified excerpts (meaningful sections of text) and coded themes/sub-themes using a codebook. Inter-coder agreement across identified excerpts (n = 530) in both FG formats was 844/875 (96.5%). Two additional investigators reviewed coded excerpts and did not identify additional themes/sub-themes—supporting data saturation across FG formats. Virtual FGs accounted for 303/530 (57.2%) of total excerpts and 957/1721 (55.7%) of all identified themes/sub-themes. Formats were similar in terms of overall number of excerpts (101 ± 7.8 vs. 75.7 ± 18.8, p = 0.26) and themes/sub-themes (319 ± 6.1 vs. 254.7 ± 103.6, p = 0.34) between virtual and in-person FGs. However, virtual FGs had significantly more coded excerpts specifically relating to sensitive/intimate topics including ‘attitudes and beliefs’ (n = 320 vs. n = 235, p < 0.001), ‘information and support’ (n = 184 vs. n = 99, p < 0.001), and ‘family communication’ (n = 208 vs. n = 114, p < 0.001). Conclusions: Virtual FGs yielded similar numbers of coded excerpts compared to traditional in-person FGs. Virtual FGs appear to support the relative anonymity of participants, resulting in richer discussion of highly sensitive, intimate topics. Findings support the validity and methodologic rigor of using web-enabled technologies for conducting FGs in rare diseases

Paradigm shift in public administration: Implications for teaching in professional training programs

10.1111/j.1540-6210.2009.02085.xPublic Administration Review69SUPPL.

Pharmacological and SAR analysis of the LINS01 compounds at the human histamine H1, H2 and H3 receptors

Histamine is a transmitter that activates the four receptors H1R to H4R. The H3R is found in the nervous system as an auto and heteroreceptor, and controls the release of neurotransmitters, making it a potential drug target for neuropsychiatric conditions. We have previously reported that the 1?(2,3?dihydro?1?benzofuran?2?yl)methylpiperazines (LINS01 compounds) have selectivity for the H3R over the H4R. Here we describe their pharmacological properties at the human H1R, H2R in parallel with the H3R, thus providing a full analysis of these compounds as histamine receptor ligands through reporter gene assays. Eight of the nine LINS01 compounds inhibited H3R?induced histamine responses but no inhibition of H2R?induced responses were seen. Three compounds were weakly able to inhibit H1R?induced responses. No agonist responses were seen to any of the compounds at any receptor. SAR analysis shows that the N?methyl group improves H3R affinity whilst the N?phenyl group is detrimental. The methoxy derivative, LINS01009, had the highest affinity

The Benefits and Burdens of Pediatric Palliative Care and End-of-Life Research: A Systematic Review

Objective: The aim of this study is to report the benefits and burdens of palliative research participation on children, siblings, parents, clinicians, and researchers. Background: Pediatric palliative care requires research to mature the science and improve interventions. A tension exists between the desire to enhance palliative and end-of-life care for children and their families and the need to protect these potentially vulnerable populations from untoward burdens. Methods: Systematic review followed PRISMA guidelines with prepared protocol registered as PROSPERO #CRD42018087304. MEDLINE, CINAHL, PsycINFO, EMBASE, Scopus, and The Cochrane Library were searched (2000–2017). English-language studies depicting the benefits or burdens of palliative care or end-of-life research participation on either pediatric patients and/or their family members, clinicians, or study teams were eligible for inclusion. Study quality was appraised using the Mixed Methods Appraisal Tool (MMAT). Results: Twenty-four studies met final inclusion criteria. The benefit or burden of palliative care research participation was reported for the child in 6 papers; siblings in 2; parents in 19; clinicians in 3; and researchers in 5 papers. Benefits were more heavily emphasized by patients and family members, whereas burdens were more prominently emphasized by researchers and clinicians. No paper utilized a validated benefit/burden scale. Discussion: The lack of published exploration into the benefits and burdens of those asked to take part in pediatric palliative care research and those conducting the research is striking. There is a need for implementation of a validated benefit/burden instrument or interview measure as part of pediatric palliative and end-of-life research design and reporting

Near-infrared fluorescent probe traces bisphosphonate delivery and retention in vivo

Bisphosphonate use has expanded beyond traditional applications to include treatment of a variety of low-bone-mass conditions. Complications associated with long-term bisphosphonate treatment have been noted, generating a critical need for information describing the local bisphosphonate-cell interactions responsible for these observations. This study demonstrates that a fluorescent bisphosphonate analogue, far-red fluorescent pamidronate (FRFP), is an accurate biomarker of bisphosphonate deposition and retention in vivo and can be used to monitor site-specific local drug concentration. In vitro, FRFP is competitively inhibited from the surface of homogenized rat cortical bone by traditional bisphosphonates. In vivo, FRFP delivery to the skeleton is rapid, with fluorescence linearly correlated with bone surface area. Limb fluorescence increases linearly with injected dose of FRFP; injected FRFP does not interfere with binding of standard bisphosphonates at the doses used in this study. Long-term FRFP retention studies demonstrated that FRFP fluorescence decreases in conditions of normal bone turnover, whereas fluorescence was retained in conditions of reduced bone turnover, demonstrating preservation of local FRFP concentration. In the mandible, FRFP localized to the alveolar bone and bone surrounding the periodontal ligament and molar roots, consistent with findings of osteonecrosis of the jaw. These findings support a role for FRFP as an effective in vivo marker for bisphosphonate site-specific deposition, turnover, and long-term retention in the skeleton. © 2010 American Society for Bone and Mineral ResearchPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77952/1/66_ftp.pd

Identification of Novel Human WW Domain-containing Proteins by Cloning of Ligand Targets

A recently described protein module consisting of 35-40 semiconserved residues, termed the WW domain, has been identified in a number of diverse proteins including dystrophin and Yes-associated protein (YAP). Two putative ligands of YAP, termed WBP-1 and WBP-2, have been found previously to contain several short peptide regions consisting of PPPPY residues (PY motif) that mediate binding to the WW domain of YAP. Although the function(s) of the WW domain remain to be elucidated, these observations strongly support a role for the WW domain in protein-protein interactions. Here we report the isolation of three novel human cDNAs encoding a total of nine WW domains, using a newly developed approach termed COLT (cloning of ligand targets), in which the rapid cloning of modular protein domains is accomplished by screening cDNA expression libraries with specific peptide ligands. Two of the new genes identified appear to be members of a family of proteins, including Rsp5 and Nedd-4, which have ubiquitin-protein ligase activity. In addition, we demonstrate that peptides corresponding to PY and PY-like motifs present in several known signaling or regulatory proteins, including RasGAP, AP-2, p53BP-2 (p53-binding protein-2), interleukin-6 receptor-alpha, chloride channel CLCN5, and epithelial sodium channel ENaC, can selectively bind to certain of these novel WW domains