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- Creators: School of Life Sciences
- Creators: Hurlbut, Ben
- Creators: Tieu, Lienna
- Status: Published
Description
The phytoplankton communities in the open oceans are dominated by picophytoplankton (0.7-2µm) and nanophytoplankton (3-5µm). Studying the community dynamics of these phytoplankton is important to learn about their role in the carbon cycle and food web of the oceans. Dilution experiments were used, along with microscopy and molecular techniques, to determine abundance, biomass and phytoplankton growth and grazing rates in the oligotrophic Sargasso Sea (western North Atlantic subtropical gyre) around the Bermuda Atlantic Time Series Station (BATS) in the summer of 2012. With low biomass and chlorophyll a, the Sargasso Sea appears to be unproductive at first glance, but I found that pico- and nanophytoplankton have high instantaneous growth rates that are balanced by the high grazing rates of microzooplankton.
Mesoscale eddies are important features in the Sargasso Sea that can increase or decrease the available nutrients in the euphotic zone. Two different mesoscale eddies were sampled: an anti-cyclonic eddy and the BATS station which was located at the edge of a cyclonic eddy. The results indicated that BATS had overall higher instantaneous growth (µ between 0.1 d-1 and 3.7 d-1) and grazing rates on pico- and nanophytoplankton, as well as diatoms, compared to the anti-cyclonic eddy (µ between 0.2 d-1 and 3 d-1). I also determined taxon-specific rates using quantitative polymerase chain reaction (qPCR) for the order Mamiellales, one of the smallest representatives of the abundant prasinophytes. This method yielded surprisingly high growth (9.7 d-1 ) and grazing rates (-8.2 d-1) at 80m for BATS. The euphotic zone (~100m) integrated biomass of all phytoplankton did not vary significantly between BATS (379 mg C m-2) and the anti-cyclonic eddy (408 mg C m-2) and the net growth rates at both locations were very close to zero for most of the groups. Although the biomass and net growth rates did not vary greatly between the two locations, the high instantaneous growth and grazing rates of pico- and nano-eukaryotic phytoplankton indicate an increase in the rate of the marine microbial food web, or microbial loop, compared to the anti-cyclonic eddy. This could have been due to the input of new nutrients in the edge of the cyclonic eddy at BATS. Thus, my study suggests that mesoscale variability is of considerable importance for the dynamics of the phytoplankton community and their role in the microbial loop. Much can be learned when using DNA based taxon-specific rates, especially to understand the relative importance and contribution of specific taxa.
More taxon-specific molecular studies will have to be carried out to quantify specific rates of more phytoplankton groups, which will supply a more complete knowledge of phytoplankton community dynamics in the Sargasso Sea. This will increase our understanding of the role of specific groups to the biological carbon dynamics in the euphotic zone into the deep ocean.
Mesoscale eddies are important features in the Sargasso Sea that can increase or decrease the available nutrients in the euphotic zone. Two different mesoscale eddies were sampled: an anti-cyclonic eddy and the BATS station which was located at the edge of a cyclonic eddy. The results indicated that BATS had overall higher instantaneous growth (µ between 0.1 d-1 and 3.7 d-1) and grazing rates on pico- and nanophytoplankton, as well as diatoms, compared to the anti-cyclonic eddy (µ between 0.2 d-1 and 3 d-1). I also determined taxon-specific rates using quantitative polymerase chain reaction (qPCR) for the order Mamiellales, one of the smallest representatives of the abundant prasinophytes. This method yielded surprisingly high growth (9.7 d-1 ) and grazing rates (-8.2 d-1) at 80m for BATS. The euphotic zone (~100m) integrated biomass of all phytoplankton did not vary significantly between BATS (379 mg C m-2) and the anti-cyclonic eddy (408 mg C m-2) and the net growth rates at both locations were very close to zero for most of the groups. Although the biomass and net growth rates did not vary greatly between the two locations, the high instantaneous growth and grazing rates of pico- and nano-eukaryotic phytoplankton indicate an increase in the rate of the marine microbial food web, or microbial loop, compared to the anti-cyclonic eddy. This could have been due to the input of new nutrients in the edge of the cyclonic eddy at BATS. Thus, my study suggests that mesoscale variability is of considerable importance for the dynamics of the phytoplankton community and their role in the microbial loop. Much can be learned when using DNA based taxon-specific rates, especially to understand the relative importance and contribution of specific taxa.
More taxon-specific molecular studies will have to be carried out to quantify specific rates of more phytoplankton groups, which will supply a more complete knowledge of phytoplankton community dynamics in the Sargasso Sea. This will increase our understanding of the role of specific groups to the biological carbon dynamics in the euphotic zone into the deep ocean.
ContributorsHamill, Demetra Scott (Author) / Neuer, Susanne (Thesis director) / Elser, Jim (Committee member) / De Martini, Francesca (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
Pathway analysis helps researchers gain insight into the biology behind gene expression-based data. By applying this data to known biological pathways, we can learn about mutations or other changes in cellular function, such as those seen in cancer. There are many tools that can be used to analyze pathways; however, it can be difficult to find and learn about the which tool is optimal for use in a certain experiment. This thesis aims to comprehensively review four tools, Cytoscape, PaxtoolsR, PathOlogist, and Reactome, and their role in pathway analysis. This is done by applying a known microarray data set to each tool and testing their different functions. The functions of these programs will then be analyzed to determine their roles in learning about biology and assisting new researchers with their experiments. It was found that each tools holds a very unique and important role in pathway analysis. Visualization pathways have the role of exploring individual pathways and interpreting genomic results. Quantification pathways use statistical tests to determine pathway significance. Together one can find pathways of interest and then explore areas of interest.
ContributorsRehling, Thomas Evan (Author) / Buetow, Kenneth (Thesis director) / Wilson, Melissa (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Malignant Pleural Mesothelioma is a type of lung cancer usually discovered at an advanced stage at which point there is no cure. Six primary MPM cell lines were used to conduct in vitro research to make conclusions about specific gene mutations associated with Mesothelioma. DNA exome sequencing, a time efficient and inexpensive technique, was used for identifying specific DNA mutations. Computational analysis of exome sequencing data was used to make conclusions about copy number variation among common MPM genes. Results show a CDKN2A gene heterozygous deletion in Meso24 cell line. This data is validated by a previous CRISPR-Cas9 outgrowth screen for Meso24 where the knocked-out gene caused increased Meso24 growth.
ContributorsKrdi, Ghena (Author) / Plaisier, Christopher (Thesis director) / Wilson, Melissa (Committee member) / School of Life Sciences (Contributor) / Hugh Downs School of Human Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The world of podcasting has exploded in popularity in recent years. This medium is being used in education as well as in the public sector to share ideas, news, and stories. This paper reviews the research behind podcast success as a news form and in the educational sector and the implications of these findings for the future. Podcast listeners tend to listen to podcasts for entertainment and, notably, to diversify their time while completing other tasks. New ways to directly stream media from portable devices and advances in the internet have helped bolster the popularity of this media form. Podcasting proved to be successful in higher education as students tended to perform better when given access to podcasts. However, they were only successful when using podcasts as classroom adjuncts. This implies that educational podcasts must be produced differently than ones intended for the public. By reviewing the neuroscience behind language, emotion and memory, it was found that narrative formats that also evoked emotions had a positive ability in enhancing the listeners learning and memory. Keeping this in mind, the developed podcast aimed to bridge educational material to the general public by utilizing narrative as a vessel in which to deliver complex information about medicine, science and neuroscience. The accessibility and virtually non-existent barriers to the podcasting world offer a breadth of knowledge and opinions that have numerous factors of social influence. The impact of podcasting on the modern world deserves more research in sociology and psychology as it continues to grow in popularity.
ContributorsCharbel, Milad (Author) / Sirven, Joseph (Thesis director) / Reddy, Swapna (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Herpes simplex virus 2 (HSV-2) is one of the most common sexually transmitted infections (STI), affecting over 267 million women worldwide. HSV-2 causes a chronic, latent infection that increases the risk for acquisition with other STI, including HIV. Currently, there is no vaccine against HSV-2 and novel anti-viral treatments are needed. IL-36γ is a newly characterized cytokine that has been shown to play a role in inflammation and be upregulated in response to microbial infection and tissue damage. We have shown that IL-36γ is expressed in the female reproductive tract (FRT) and is upregulated by HSV-2 infection in vitro and in vivo. IL-36γ in turn induces production of proinflammatory cytokines and chemokines in human vaginal epithelial cells (VEC) that can aid in immune cell recruitment. We hypothesize that IL-36γ is a key regulator of mucosal inflammation in the FRT and functions to limit HSV-2 infection. We have demonstrated that IL-36γ treatment prior to infection protects against HSV-2 replication, disease severity, and promotes survival in a lethal mouse model. Thus, the objective of this study is to understand the mechanisms whereby IL-36γ inhibits HSV-2 replication. To understand the impact of IL-36γ on the HSV-2 lifecycle, we pretreated VEC with IL-36γ and evaluated viral titer during virus attachment and entry, replication, and cell-to-cell spread by plaque assay. Pretreatment with IL-36γ 4h prior to infection did not significantly reduce viral titers in VEC monolayers relative to untreated groups. This suggesting that IL-36γ may play a more significant role in immune cell recruitment during HSV-2 infection. To test this, FRT tissue samples from HSV-2 infected IL-36γ -/- and WT mice were analyzed by histochemistry to characterize immune cell recruitment. No clear pattern was determined for tissue samples in which cell clusters were observed and cell type within recruited clusters was unable to be identified at the current magnification. As these projects continue, the data will aid in elucidating the mechanism and level to which IL-36γ impacts HSV-2 infection in human VEC and FRT models.
ContributorsAlexander, Thessaly E (Author) / Herbst-Kralovetz, Melissa (Thesis director) / Capco, David (Committee member) / Hogue, Ian (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The inherent risk in testing drugs has been hotly debated since the government first started regulating the drug industry in the early 1900s. Who can assume the risks associated with trying new pharmaceuticals is unclear when looked at through society's lens. In the mid twentieth century, the US Food and Drug Administration (FDA) published several guidance documents encouraging researchers to exclude women from early clinical drug research. The motivation to publish those documents and the subsequent guidance documents in which the FDA and other regulatory offices established their standpoints on women in drug research may have been connected to current events at the time. The problem of whether women should be involved in drug research is a question of who can assume risk and who is responsible for disseminating what specific kinds of information. The problem tends to be framed as one that juxtaposes the health of women and fetuses and sets their health as in opposition. That opposition, coupled with the inherent uncertainty in testing drugs, provides for a complex set of issues surrounding consent and access to information.
ContributorsMeek, Caroline Jane (Author) / Maienschein, Jane (Thesis director) / Brian, Jennifer (Committee member) / School of Life Sciences (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The concept of “good” research is concrete in terms of technique, but complex in theory. As technology advances, the complexity of problems we must solve also grows. Research is facing an ethical dilemma—which projects, applied or basic, should be funded. Research is no longer an isolated sector in society, and the decisions made inside of the laboratory are affecting the general public more directly than ever before. While there is no correct answer to what the future of research should be, it is clear that good research can no longer be only defined by the current classification system, which is rooted in antiquated, yet ingrained, social status distinctions.
Differences between basic and applied research were explored through a wet-lab case study. Vaccinia virus (VACV) infections are a prime model of the competition between a virus and its host. VACV contains a gene that is highly evasive of the host immune system, gene E3L. The protein encoded by E3L is E3, which contains two highly conserved regions, a C-terminus, and a N-terminus. While the C-terminus is well-understood, the mechanism by which the N-terminus grants IFN resistance was previously unknown. This project demonstrated that the N-terminus prevents the initiation of programmed necrosis through host-encoded cellular proteins RIP3 and DAI. These findings provide insight into the function of the N-terminus of E3, as well as the unique functions of induced programmed necrosis.
This project was an example of “basic” research. However, it highlights the interconnectivity of basic and applied research and the danger in isolating both projects and perspectives. It points to the difficult decisions that must be made in science, and the need for a better research classification system that considers what makes science “good” outside of antiquated social class ideologies that have shaped science since ancient Greece. While there are no easy answers to determine what makes research “good,” thinking critically about the types of research projects that will be pursued, and the effects that research has on both science and society, will raise awareness, initiate new conversations, and encourage more dialogue about science in the 21st century.
Differences between basic and applied research were explored through a wet-lab case study. Vaccinia virus (VACV) infections are a prime model of the competition between a virus and its host. VACV contains a gene that is highly evasive of the host immune system, gene E3L. The protein encoded by E3L is E3, which contains two highly conserved regions, a C-terminus, and a N-terminus. While the C-terminus is well-understood, the mechanism by which the N-terminus grants IFN resistance was previously unknown. This project demonstrated that the N-terminus prevents the initiation of programmed necrosis through host-encoded cellular proteins RIP3 and DAI. These findings provide insight into the function of the N-terminus of E3, as well as the unique functions of induced programmed necrosis.
This project was an example of “basic” research. However, it highlights the interconnectivity of basic and applied research and the danger in isolating both projects and perspectives. It points to the difficult decisions that must be made in science, and the need for a better research classification system that considers what makes science “good” outside of antiquated social class ideologies that have shaped science since ancient Greece. While there are no easy answers to determine what makes research “good,” thinking critically about the types of research projects that will be pursued, and the effects that research has on both science and society, will raise awareness, initiate new conversations, and encourage more dialogue about science in the 21st century.
ContributorsSnyder, Caroline Jane (Author) / Jacobs, Bertram (Thesis director) / Hurlbut, Ben (Committee member) / Mateusz, Szczerba (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Autism Spectrum Disorder (ASD) is a lifelong neurodevelopmental disorder that is becoming increasingly common. Autism does not yet have a known etiology, nor a definitive diagnostic test, thus making diagnosis a difficult and rarely uniform task. Currently, ASD is behaviorally diagnosed based on criteria defined by the American Psychiatric Association in the Diagnostic and Statistical Manual of Mental Disorders (DSM). Recently, a change was made in the criteria from more lenient criteria in DSM-IV-TR, to more narrow criteria laid out by the DSM-V, which supersedes the DSM-IV-TR. This drastic change raised many questions and debates about which set of criteria are better. The more lenient criteria offers a more inclusive diagnosis giving greater access to therapies; while the narrow diagnostic criteria excludes some individuals, creating a more uniform diagnosis that's easier to use in research. This thesis analyzes the change in diagnostic criteria from the DSM-IV-TR to the DSM-V and the effects of these changes on the practices of diagnosis. In addition, it explores the implications of this change for the families of children with autism and for those involved in autism research, examining their respective opinions and interests pertaining to narrow verses broad diagnostic criteria. Building on this analysis, the thesis offers recommendations about diagnostic criteria should be set. It argues that the wellbeing of patients takes priority over the interests of researchers, and thus diagnosis should be done in a way that offers the best prognosis for all children who suffer from autistic symptoms.
ContributorsBremer, Michelle Nichole (Author) / Hurlbut, Ben (Thesis director) / Robert, Jason (Committee member) / Brian, Jennifer (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
In the face of the world's most pressing sustainability challenges, such as climate change, ecosystem degradation, and loss of biodiversity, the following questions must be explored: Why are these situation occurring? How can we understand their complexity? How can we research these challenges to mitigate negative outcomes? This thesis investigates the relationships between people and nature through coupled human and natural systems, or CHANS, and argues for a transdisciplinary research approach for sustainability science. The following questions and topics are discussed: 1. The Complexity of Sustainability and Implications for Traditional Research Approaches 2. Coupled Human and Natural Systems Research 3. What is Transdisciplinary Research, and How Does it Relate to the Living With Locusts Team's Coupled Human and Natural Systems Research? This thesis uses the case of a team researching international locust plagues to argue for this approach. The team's project is titled "Living With Locusts" and is directed by Arianne Cease of Arizona State University's School of Sustainability.
ContributorsLantz, Kayna Mishelle (Author) / Cease, Arianne (Thesis director) / Campbell, Jacob (Committee member) / School of Sustainability (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
This project aimed to identify barriers to participation and develop strategies to increase the accessibility of a diabetes prevention program in the Latino community. Surveys were administered to past participants of a randomized control trial at a community event where study results were shared. The top concerns expressed by respondents were related to the use of personal information. Primary barriers to participation included work/school commitments and transportation issues. Strategies to increase accessibility included providing flexible class times, having bilingual research staff, and using multiple forms of community outreach such as flyers, health events, phone calls, texts, and social media. Expanding community partners was also identified as a primary strategy for increasing program reach. Researchers should focus on addressing confidentiality concerns, providing financial compensation for attendance, flexible scheduling, and utilizing diverse outreach methods to enhance access to diabetes prevention programs in the Latino community
ContributorsHouck, Kassidy (Author) / Shaibi, Gabriel (Thesis director) / Williams, Allison (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2023-05