Novel methodology for assessing phytoplankton response to pCO2 enrichment in fresh and saltwater

Atmospheric CO2 emissions are on the rise and are expected to reach 780 parts per million by the year 2100. Research investigating the impacts of increasing CO2 is a relatively new field and the response of phytoplankton communities is largely unknown, especially in coastal and freshwater ecosystems where no CO2 manipulation studies have completed. The present study attempts to encourage uniformity in methods utilized in CO2 perturbation studies and identifies changes in phytoplankton abundance in freshwater (James River) and coastal ocean (Atlantic, Cape Hatteras) sites. A novel bubbling method to manipulate pCO2 was compared with the classic method of acid addition in conjunction with laboratory and in situ experiments. The novel and classic methods were equally effective at manipulating carbonate chemistry to predicted levels. However, the laboratory experiment saw greater variation in both pCO2 levels and chlorophyll-a concentrations throughout the four-day incubation period. The results from the present study encourage use of the novel methodology in combination with in situ experimental setup to assess changes in phytoplankton communities as a result of pCO2 enrichment. This pairing will allow greater replication of small volume incubations without introducing new abiotic conditions such as temperature and light. Additionally this study found no significant treatment effect on phytoplankton communities in either freshwater James River or coastal Atlantic

Predicting the effectiveness of hepatitis C virus neutralizing antibodies by bioinformatic analysis of conserved epitope residues using public sequence data

Hepatitis C virus (HCV) is a global health issue. Although direct-acting antivirals are available to target HCV, there is currently no vaccine. The diversity of the virus is a major obstacle to HCV vaccine development. One approach toward a vaccine is to utilize a strategy to elicit broadly neutralizing antibodies (bNAbs) that target highly-conserved epitopes. The conserved epitopes of bNAbs have been mapped almost exclusively to the E2 glycoprotein. In this study, we have used HCV-GLUE, a bioinformatics resource for HCV sequence data, to investigate the major epitopes targeted by well-characterized bNAbs. Here, we analyze the level of conservation of each epitope by genotype and subtype and consider the most promising bNAbs identified to date for further study as potential vaccine leads. For the most conserved epitopes, we also identify the most prevalent sequence variants in the circulating HCV population. We examine the distribution of E2 sequence data from across the globe and highlight regions with no coverage. Genotype 1 is the most prevalent genotype worldwide, but in many regions, it is not the dominant genotype. We find that the sequence conservation data is very encouraging; several bNAbs have a high level of conservation across all genotypes suggesting that it may be unnecessary to tailor vaccines according to the geographical distribution of genotypes

Notch1 and Notch2 Receptors Regulate Human and Mouse Gastric Epithelial Cell Homeostasis.

The gastric epithelium undergoes constant turnover that is maintained by a population of gastric stem cells. Gastric stem cells are under the regulation of multiple signaling pathways to promote proper epithelial homeostasis. Previous studies have shown that the Notch signaling pathway plays a crucial role in regulating epithelial differentiated cell fate, stem cell function, and epithelial cell proliferation in the stomach. My thesis work has focused on identifying the mechanisms by which Notch signaling regulates gastric epithelial cell homeostasis. I identified NOTCH1 and NOTCH2 as the key receptors contributing to the regulation of gastric epithelial cells by Notch. Using inhibitory antibodies targeting NOTCH1 and NOTCH2, I observed a marked reduction in proliferation of both corpus and antral epithelial cells that mimicked the reduced proliferation observed with global Notch inhibition. Inhibition of NOTCH1 or NOTCH2 signaling led to an intermediate reduction in proliferation in both regions of the glandular stomach. In the antrum, inhibition of both receptors resulted in a general increase in expression of markers of differentiated cells, including enteroendocrine, surface mucous, and deep mucous cells. Inhibition of both receptors also led to increased secretory granules in antral cells and expression of secretory products from other regions of the gastrointestinal tract, including the corpus and intestine. To investigate if Notch signaling is intrinsic to the epithelium, I refined the conditions for gastric organoid establishment from mouse and human antrum and corpus tissue. In mouse and human antral and corpus organoids, inhibition of NOTCH1 and NOTCH2 resulted in a reduction of organoid growth similar to that seen with global Notch inhibition. In corpus organoids, inhibition of either NOTCH1 or NOTCH2 resulted in an intermediate disruption of organoid growth. However, in antral organoids, inhibition of NOTCH1 mimicked growth similar to that seen with global inhibition, suggesting that NOTCH1 may play a more significant role in antral organoid growth than NOTCH2. In summary, my thesis work has expanded the understanding of the role of Notch in gastric epithelial homeostasis. I have illustrated an important role for the NOTCH1 and NOTCH2 receptors in regulating gastric epithelial proliferation and differentiation in vivo and in vitro.PhDMolecular and Integrative PhysiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120753/1/gcbutler_2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/120753/2/gcbutler_1.pd

Remote learning for the beginning band trumpet student

Master of MusicSchool of Music, Theatre, and DancePhillip PayneIn this report, I will use video recordings as teaching demonstrations to assist beginning band trumpet students with the basic skills required to begin their journey in band. Through examples and demonstration, students will be afforded the opportunity to have a one-on-one lesson that will mold them in the areas of instrument care, proper posture and breathing techniques, and creating and developing their first sounds. The access to these video demonstrations affords the student the ability to repeat lessons and reference back to them as needed for mastery. Through this program, I have developed in self-evaluation as well as flexibility of an ever-changing learning environment. Remote learning is becoming more of necessity in education. Creating a video library with video demonstrations is not only something that will function in a remote learning environment; it will also allow students to begin development as they transition from elementary school to middle school. I have learned that developing a comprehensive approach to teaching partnered with a hands-on approach will have the most success for students. Videos can be re-evaluated and designed to accommodate what a “one size fits all” approach will not handle. Assessment for these videos can be utilized through video recordings of students demonstrating the tasks each video teaches as well as using zoom in a live time evaluation of the student. These methods of instruction have shown me that students do not always have to be directly in front of you to learn. Having remote access can still benefit the student’s ability to learn

The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes

Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe are a useful source of information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci. We identified a total of 179 CVe sequences, most of which have not been reported previously. We show that these CVe loci reflect at least 19 distinct germline integration events. We determine the structure of CVe loci, identifying some that show evidence of potential functionalization. We also identify orthologous copies of CVe in snakes, fish, birds, and mammals, allowing us to add new calibrations to the timeline of circovirus evolution. Finally, we observed that some ancient CVe group robustly with contemporary circoviruses in phylogenies, with all sequences within these groups being derived from the same host class or order, implying a hitherto underappreciated stability in circovirus-host relationships. The openly available dataset constructed in this investigation provides new insights into circovirus evolution, and can be used to facilitate further studies of circoviruses and CVe

The association of state per capita income and military service deaths in the Vietnam and Iraq wars

<p>Abstract</p> <p>Background</p> <p>In the United States, social burdens including war casualties are often distributed unequally across groups of individuals, communities, and states. The purpose of this report was to examine the association between war deaths and per capita income in the 50 states and District of Columbia during the Vietnam and Iraq wars.</p> <p>Methods</p> <p>The numbers of deaths by the home state of record for each conflict were obtained from Department of Defense records on the Internet as were key variables including age at death, gender, race, branch of service, rank, circumstances of death, home state of record and the ratio of wounded to dead. In addition, we obtained state per capita income and state population for the relevant times.</p> <p>Results</p> <p>Characteristics of decedents in the 2 conflicts were very similar with young, white enlisted men accounting for the majority of deaths. However, in the Iraq war, women accounted for a 2.4% of casualties. Also of note was the higher ratio of wounded to dead in Iraq. At the level of the state, the correlation between the ratio of deaths per 100,000 and per capita income was -0.51 (p < 0.0001) for Vietnam and -0.52 for Iraq (p < 0.0001). In both eras, states with lower per capita income tended to have higher ratios of deaths per population.</p> <p>Conclusion</p> <p>For military service members serving in the Vietnam and Iraq conflicts, there were many more women who died in the latter war. Whether war deaths resulted in lower per capita income cannot be determined from these cross sectional data; we simply note a strong association between per capita income and war casualty rates for both wars.</p

Structuring Thought: Concepts, Computational Syntax, and Cognitive Explanation

The topic of this dissertation is what thought must be like in order for the laws and generalizations of psychology to be true. I address a number of contemporary problems in the philosophy of mind concerning the nature and structure of concepts and the ontological status of mental content. Drawing on empirical work in psychology, I develop a number of new conceptual tools for theorizing about concepts, including a counterpart model of concepts\u27 role in linguistic communication, and a deflationary theory of concepts\u27 formal features. I also suggest some new answers to old problems, arguing, for example, that content realism is not hostage to a naturalized semantics. This dissertation can, as a whole, be read as a sympathetic re-evaluation of the language of thought hypothesis (LOT). LOT claims that thoughts are sentences in a mental language of computation, and are composed of meaningful, atomic symbols—concepts—which are individuated entirely by their formal features. Each chapter either defends various components of LOT from recent criticism, or fills in gaps in the theory. I begin the dissertation by introducing the language of thought project, and motivating and explaining each of its central components. In chapter 2, I discuss a recent competitor to atomism—neo-empiricism—and argue that it fails to meet several key desiderata on theories of concepts, and defend atomism from similar charges. In chapter 3, I argue against a view common to both philosophy and psychology: that concepts must be shareable. If true, atomism is in jeopardy. I find shareability to be unmotivated, and suggest an alternative counterpart model of concepts that does a better job of explaining the things shareability was supposed to explain. Chapter 4 takes up the question of what formal features are and how mental symbols are individuated. I develop a reductive account, arguing that formal features are certain sorts of physical properties and symbol types are sets of these properties. I turn to the topic of content in chapter 5, and defend a very strong version of content realism against recent criticism