Evaluation of Autonomously Measured Alkalinity, pH, and pCO2 Variability on a Coral Reef

Currently, our understanding of alkalinity (AT) variability in highly dynamic environments such as coral reefs is limited by the dearth of AT measurements. In order to better characterize these environments, high temporal resolution AT data are needed. This work employed the newly developed Submersible Autonomous Moored Instrument for Alkalinity (SAMI-alk), a fully autonomous in situ AT analyzer, to study seawater AT variability. The main goals of this research were to evaluate the utility of combining the SAMI-alk data with currently available in situ measurements of pH and partial pressure of carbon dioxide (pCO2) to characterize the inorganic carbon cycle, and to measure AT variability and determine what drives it on a coral reef. Autonomous AT and pH sensors (SAMI-alk and SAMI-pH) were deployed along with existing pCO2 (MAPCO2) and pH (SeaFET) sensors in Kanoehe Bay, HI from June 4 – 21, 2013. The results show that the pH – AT combination can provide important information about autonomously measured in situ data quality, and that it can be used to fully characterize the inorganic CO2 system in seawater. The SAMI-alk data were also used to examine AT variability and thereby calcification rates on coral reefs in Kaneohe Bay. AT varied by more than 100 µmol kg-1 on a diel basis due to CaCO3 production and dissolution. Dissolved inorganic carbon (DIC), calculated from the pH – AT sensor pair, varied by more than 200 µmol kg-1, due primarily to biological metabolism on the reef. Reef calcification and metabolism dramatically alter the seawater chemistry from the open ocean source water and drive the large diel changes in all measured inorganic carbon parameters (i.e. aragonite saturation state (Ωarag), pH, pCO2, AT, DIC). This data set demonstrates the value of a high-quality in situ AT analyzer in a coral reef environment; making it possible to determine combined CO2 system variability with unprecedented temporal resolution. These data show that NEC can be consistently sustained (net CaCO3 production) until a threshold level of net respiration (NEP) is reached, around -50 (mmol m-2 h-1), which corresponds to an AT : DIC ratio of about 1:1

Comprehensive financial plan for Tyler and Maria Bedo

A comprehensive financial plan developed from the case study of Tyler and Mia Bedo

Investigating physiological collaborations between a lower termite and its symbionts

This project was completed in an effort to better understand the contributions of symbiotic microbes to the biology of Reticulitermes flavipes, the eastern subterranean termite. Lower-termites, like R. flavipes, house symbionts from all three domains of life within their hindgut paunch. This intimate association is reflected in nearly every aspect of termite biology. Here, I investigate these physiological collaborations as they relate to digestion and immunity. My efforts focused on 1) quantifying the role of bacteria in wood digestion within the termite gut, 2) evaluating the role of symbionts in protection against pathogens, and 3) identifying gene products that bacterial symbionts contribute to naïve and pathogen-challenged termites. Bioassays coupled with in vitro enzyme assays, gene expression analysis, and symbiont population estimations show that termites with reduced gut fauna have less lignocellulolytic potential. Using a suite of antimicrobial compounds, bacterial contributions (direct or indirect) to wood digestion were calculated on average at ∼23-50%. Apart from digestive potential, termite gut symbionts were also implicated in pathogen-resistance. Defaunated workers were 2-3X more susceptible to fungal infections and had significantly altered the expression of endogenous, immune-associated genes in response to challenge with the bacterial entomopathogen, Serratia marcescens. Using recombinant enzymes, in vitro assays, and bioassays, two protist-derived glycosyl hydrolase family 7 (GHF7) enzymes showed promise as a potential mechanism for symbiont-derived, anti-fungal defense in R. flavipes. These signatures of symbiont- mediated immunity/protection were further explored using RNAseq to capture a snapshot of the termite holobiont transcriptional response following pathogen challenge. This strategy served as a means of pinpointing critical taxa and physiological roles of microbes in this system by taking a global, metatranscriptomic approach. Differential expression analysis identified a bacterially-encoded amidohydrolase that may be important for anti-fungal defense. Overall, this project has significantly expanded our perspective on the importance of microbes in termite physiology as a whole. With examples from digestion and immunity, this research lays the groundwork for future explorations of termite-symbiota collaborations including, but not limited to, the collaborations described herein. Together, these results highlight the importance of a holistic “systems biology” approach to understanding termite biology from the perspective of the termite’s intimate associations with microbes. Assessing termite and microbe responses in isolation (as independent systems) may not provide an accurate account of the collaborative nature of this relationship. Additionally, my findings emphasize the importance of considering both organismal (termite and microbe) and sub-organismal (cellular and molecular) level processes when investigating physiology, symbiosis, and the link between them

The Germ of Death Itself: A Study of Tuberculosis and Community Education in Ghana

Background: Tuberculosis remains a significant threat to global public health, despite advancements in treatment and detection in recent decades. Treatment regimens are unpleasant and time-consuming, particularly when the disease-causing strain is partially or completely drug-resistant. Approximately one-third of the global population is currently infected with tuberculosis, but the majority of these cases are dormant and non-contagious. These dormant cases are more difficult to diagnose, but if the immune system is compromised, as in the case of HIV/AIDS, the individual will transition to an active and contagious case of tuberculosis. Resistant strains are increasing around the world, making treatment of a potential future drug-resistant tuberculosis pandemic all the more difficult. Purpose: The purpose of this study is to examine the relationship between trends in tuberculosis prevalence, and community education regarding the nature of the disease. This study analyzes data collected in the West African nation of Ghana, which is considered to have a high-burden tuberculosis and HIV/AIDS epidemic. The study period is between 2008 and 2014, and examines the relationship between accuracy of tuberculosis education and trends in tuberculosis prevalence, over that time period. Methods: This secondary data analysis used data from the Ghana Demographic and Health Survey, performed by the United States Agency for International Development. SPSS statistical software was used to relate tuberculosis prevalence numbers to correctness of tuberculosis-related responses in the Ashanti, Eastern and Northern regions of Ghana. Results: Data analysis indicates limited improvement in correctness of tuberculosis-related education in the three districts, between 2008 and 2014. Ordinal regression indicates a weak or negligible difference in correctness of responses between the three districts under study. Conclusion: While the DHS survey data is extensive, only a small proportion of the survey questions are related to tuberculosis knowledge. In addition, the data did not support a strong relationship between community levels of education, and tuberculosis prevalence trends

A Comparison of Turkish Students in Istanbul and Syracuse: Using Three-Day Food Records, Surveys, and PhotoVoice to Evaluate Changes in Dietary Habits with Acculturation and Plan an Appropriate Nutrition Intervention

The immigrant population of the United States is growing rapidly, so the health status of immigrant populations is an important public health issue. When it comes to nutrition, research has shown that immigration to the United States is often associated with an increased risk of chronic diseases, in particular, those related to dietary changes that include lower fruit and vegetable consumption and higher fat intake (Satia et al., 2002). “Dietary acculturation” is the term used to describe the changing dietary patterns of immigrants, but in this research it is used in relation to the changing dietary habits of international students coming to the United States (Satia, 2010). Nutrition professionals can use dietary acculturation research to help specific groups have a more positive and healthy acculturation experience. In these cases, understanding the culture from which people come, and how their habits change in the United States, is crucial for successful client-counselor relationships. Since less attention is often given to smaller populations, their acculturation experiences of such people are largely undocumented. This project focuses specifically on Turkish students who have come to Syracuse University, in the United States, and how their dietary habits compare to their peers in Istanbul, Turkey. The students are not immigrants; however, the changes in their dietary habits are useful to study because they are preliminary changes that could set the framework for how their dietary habits might change if they were to immigrate. There are four key components to this project. First, I actively engaged in a process of seeking out activities to increase my own cultural competency: “recognizing and reforming one’s attitudes, beliefs, skills, values, and levels of awareness to provide culturally appropriate, respectful, and relevant care and education” (Goody, 2010). Second, I collected dietary and food cultural data from Turkish students in both Istanbul and Syracuse for comparison. Third, I organized a nutrition education intervention to encourage healthy dietary acculturation for Turkish students at Syracuse University. Finally, there is this report which documents my complete transition from knowing very little about Turkish culture to being able to work closely with Turkish students to improve their dietary habits. It displays how nutrition professionals with very little background knowledge on any culture can expose themselves to the culture and actively learn about it to improve their cultural competency, learn about acculturation issues, and plan an appropriate intervention. It also displays the importance of working with minority groups who would otherwise be lost on a large campus. It is hoped to be an example for other students and nutrition professionals, who with their own cultural interests and target populations, are trying to best meet the needs of their clients’

Improving Forecasts Of Winter Storm Tracks Using A Local Ensemble

Winter storms can affect millions of people, with impacts such as disruptions to transportation, hazards to human health, reduction in retail sales, and structural damage. Blizzard forecasts for Alberta Clippers can be a particular challenge in the Northern Plains, as these systems typically depart from the Canadian Rockies, intensify, and impact the Northern Plains all within 24 hours. The purpose of this study is to determine whether probabilistic forecasts derived from a local physics-based ensemble can improve specific aspects of winter storm forecasts for three Alberta Clipper cases. Verification is performed on the ensemble members and ensemble mean with a focus on quantifying uncertainty in the storm track, two-meter winds, and precipitation using the MERRA and NOHRSC SNODAS datasets. This study finds that addition improvements are needed to proceed with operational use of the ensemble blizzard products, but the use of a proxy for blizzard conditions yields promising results

PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward since they may need multiple processing tasks and iterations. Furthermore, parameter and performance studies are common approaches used to characterize a simulation, often requiring traversal of a large parameter space. High-performance computers offer practical resources at the expense of users handling the setup, submission, and management of jobs. This work presents the design of PaPaS, a portable, lightweight, and generic workflow framework for conducting parallel parameter and performance studies. Workflows are defined using parameter files based on keyword-value pairs syntax, thus removing from the user the overhead of creating complex scripts to manage the workflow. A parameter set consists of any combination of environment variables, files, partial file contents, and command line arguments. PaPaS is being developed in Python 3 with support for distributed parallelization using SSH, batch systems, and C++ MPI. The PaPaS framework will run as user processes, and can be used in single/multi-node and multi-tenant computing systems. An example simulation using the BehaviorSpace tool from NetLogo and a matrix multiply using OpenMP are presented as parameter and performance studies, respectively. The results demonstrate that the PaPaS framework offers a simple method for defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions.

Background: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations. Termites are one of the best studied systems for physiological collaborations between host and symbiota however, most work in lower termites (those with bacterial and protist symbionts) focuses on the eukaryotic members of this symbiotic consortium. Here we present a metatranscriptomic analysis which provides novel insights into bacterial contributions to the holobiont of the eastern subterranean termite, Reticulitermes flavipes, in the presence and absence of a fungal pathogen. Results: Using a customized ribodepletion strategy, a metatranscriptome assembly was obtained representing the host termite as well as bacterial and protist symbiota. Sequence data provide new insights into biosynthesis, catabolism, and transport of major organic molecules and ions by the gut consortium, and corroborate previous findings suggesting that bacteria play direct roles in nitrogen fixation, amino acid biosynthesis, and lignocellulose digestion. With regard to fungal pathogen challenge, a total of 563 differentially expressed candidate host and symbiont contigs were identified (162 up- and 401 downregulated; α/FDR = 0.05) including an upregulated bacterial amidohydrolase. Conclusions: This study presents the most complete bacterial metatranscriptome from a lower termite and provides a framework on which to build a more complete model of termite-symbiont interactions including, but not limited to, digestion and pathogen defense. © 2016 The Author(s)

Human Milk Retains Important Immunologic Properties After Defatting

BackgroundIn neonatal chylothorax, thoracic lymphatic drainage is ineffective. The resultant effusions often require drainage, leading to a loss of immune components. Affected infants can be managed with formula or defatted human milk feedings low in long‐chain triglycerides to decrease lymph production. We hypothesized that there is no significant difference in the immunological profile or antibacterial effect of full‐fat and defatted human milk.MethodsMilk from lactating mothers was divided into 1 aliquot that was defatted via centrifugation with the full‐fat aliquot as control. Macronutrient content was analyzed with mid‐infrared spectroscopy. Flow cytometry was used to measure immune cell populations. Lactoferrin, lysozyme, immunoglobulin (Ig)A, and IgG values were determined using enzyme‐linked immunosorbent assay. The antibacterial properties were determined by inoculating paired full‐fat and defatted milk samples with Escherichia coli or Streptococcus pneumoniae bacteria and performing colony counts.ResultsCompared with full‐fat milk, defatted milk demonstrated decreased total energy and fat and increased carbohydrate concentrations. Defatted milk demonstrated a significant decrease in all immune cell populations. There was no difference in IgA, IgG, lysozyme, or lactoferrin concentrations. Both aliquots demonstrated equivalent growth inhibition of E. coli and S. pneumoniae.ConclusionsUnexpectedly, defatted human milk contained significantly less leukocytes than full‐fat milk. IgA, IgG, lysozyme, and lactoferrin concentrations were preserved. The ability of defatted milk to inhibit bacterial growth was unaffected, suggesting that the antibacterial benefits of human milk remain after the defatting process. Further investigation regarding the clinical effect of leukocyte loss in defatted milk is warranted.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156146/3/jpen1722-supl-0001.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156146/2/jpen1722_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156146/1/jpen1722.pd