Matching Items (166)
Description
In response to a national call within STEM to increase diversity within the sciences, there has been a growth in science education research aimed at increasing participation of underrepresented groups in science, such as women and ethnic/racial minorities. However, an underexplored underrepresented group in science are religious students. Though 82% of the United States population is religiously affiliated, only 52% of scientists are religious (Pew, 2009). Even further, only 32% of biologists are religious, with 25% identifying as Christian (Pew, 2009; Ecklund, 2007). One reason as to why Christian individuals are underrepresented in biology is because faculty may express biases that affect students' ability to persist in the field of biology. In this study, we explored how revealing a Christian student's religious identity on science graduate application would impact faculty's perception of the student during the biology graduate application process. We found that faculty were significantly more likely to perceive the student who revealed their religious identity to be less competent, hirable, likeable, and faculty would be less likely to mentor the student. Our study informs upon possible reasons as to why there is an underrepresentation of Christians in science. This further suggests that bias against Christians must be addressed in order to avoid real-world, negative treatment of Christians in science.
ContributorsTruong, Jasmine Maylee (Author) / Brownell, Sara (Thesis director) / Gaughan, Monica (Committee member) / Barnes, Liz (Committee member) / School of Life Sciences (Contributor) / W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Biomarkers are the cornerstone of modern-day medicine. They are defined as any biological substance in or outside the body that gives insight to the body's condition. Doctors and researchers can measure specific biomarkers to diagnose and treat patients, such as the concentration of hemoglobin Alc and its connection to diabetes. There are a variety of methods, or assays, to detect biomarkers, but the most common assay is enzyme-linked immunosorbent assay (ELISA). A new-generation assay termed mass spectrometric immunoassay (MSIA) can measure proteoforms, the different chemical variations of proteins, and their relative abundance. ELISA on the other hand measures the overall concentration of protein in the sample. Measuring each of the proteoforms of a protein is important because only one or two variations could be biologically significant and/or cause diseases. However, running MSIA is expensive. For this reason, an alternative plate-based MSIA technique was tested for its ability to detect the proteoforms of a protein called apolipoprotein C-III (ApoC-III). This technique combines the protein capturing procedure of ELISA to isolate the protein with detection in a mass spectrometer. A larger amount of ApoC-III present in the body indicates a considerable risk for coronary heart disease. The precision of the assay is determined on the coefficient of variation (CV). A CV value is the ratio of standard deviation in relation to the mean, represented as a percentage. The smaller the percentage, the less variation the assay has, and therefore the more ability it has to detect subtle changes in the biomarker. An accepted CV would be less than 10% for single-day tests (intra-day) and less than 15% for multi-day tests (inter-day). The plate-based MSIA was started by first coating a 96-well round bottom plate with 2.5 micrograms of ApoC-III antibody. Next, a series of steps were conducted: a buffer wash, then the sample incubation, followed by another buffer wash and two consecutive water washes. After the final wash, the wells were filled with a MALDI matrix, then spotted onto a gold plate to dry. The dry gold target was then placed into a MALDI-TOF mass spectrometer to produce mass spectra for each spot. The mass spectra were calibrated and the area underneath each of the four peaks representing the ApoC-III proteoforms was exported as an Excel file. The intra-day CV values were found by dividing the standard deviation by the average relative abundance of each peak. After repeating the same procedure for three more days, the inter-day CVs were found using the same method. After completing the experiment, the CV values were all within the acceptable guidelines. Therefore, the plate-based MSIA is a viable alternative for finding proteoforms than the more expensive MSIA tips. To further validate this, additional tests will need to be conducted with different proteins and number of samples to determine assay flexibility.
ContributorsTieu, Luc (Author) / Borges, Chad (Thesis director) / Nedelkov, Dobrin (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Brown adipose tissue (BAT) is thought to be important in combating obesity as it can expend energy in the form of heat, e.g. thermogenesis. The goal of this study was to study the effect of injected norepinephrine (NE) on the activation of BAT in rats that were fed a high fat diet (HFD). A dose of 0.25 mg/kg NE was used to elicit a temperature response that was measured using transponders inserted subcutaneously over the BAT and lower back and intraperitoneally to measure the core temperature. The results found that the thermic effect of the BAT increased after the transition from low fat diet to a high fat diet (LFD) yet, after prolonged exposure to the HFD, the effects resembled levels found with the LFD. This suggests that while a HFD may stimulate the effect of BAT, long term exposure may have adverse effects on BAT activity. This may be due to internal factors that will need to be examined further.
ContributorsSion, Paul William (Author) / Herman, Richard (Thesis director) / Borges, Chad (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Learning student names has been promoted as an inclusive classroom practice, but it is unknown whether students value having their names known by an instructor. We explored this question in the context of a high-enrollment active-learning undergraduate biology course. Using surveys and semistructured interviews, we investigated whether students perceived that instructors know their names, the importance of instructors knowing their names, and how instructors learned their names. We found that, while only 20% of students perceived their names were known in previous high-enrollment biology classes, 78% of students perceived that an instructor of this course knew their names. However, instructors only knew 53% of names, indicating that instructors do not have to know student names in order for students to perceive that their names are known. Using grounded theory, we identified nine reasons why students feel that having their names known is important. When we asked students how they perceived instructors learned their names, the most common response was instructor use of name tents during in-class discussion. These findings suggest that students can benefit from perceiving that instructors know their names and name tents could be a relatively easy way for students to think that instructors know their names. Academic self-concept is one's perception of his or her ability in an academic domain compared to other students. As college biology classrooms transition from lecturing to active learning, students interact more with each other and are likely comparing themselves more to students in the class. Student characteristics, such as gender and race/ethnicity, can impact the level of academic self-concept, however this has been unexplored in the context of undergraduate biology. In this study, we explored whether student characteristics can affect academic self-concept in the context of a college physiology course. Using a survey, students self-reported how smart they perceived themselves in the context of physiology compared to the whole class and compared to the student they worked most closely with in class. Using logistic regression, we found that males and native English speakers had significantly higher academic self-concept compared to the whole class compared with females and non-native English speakers, respectively. We also found that males and non-transfer students had significantly higher academic self-concept compared to the student they worked most closely with in class compared with females and transfer students, respectively. Using grounded theory, we identified ten distinct factors that influenced how students determined whether they are more or less smart than their groupmate. Finally, we found that students were more likely to report participating less than their groupmate if they had a lower academic self-concept. These findings suggest that student characteristics can influence students' academic self-concept, which in turn may influence their participation in small group discussion.
ContributorsKrieg, Anna Florence (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
It is well established that physical activity (PA) directly correlates with many health benefits, especially when active habits are formed during childhood and adolescence. PA practiced in adolescence has been seen to carry into adulthood, helping to combat a host of chronic diseases, such as obesity and diabetes. However, in recent years there has been a steady decline in PA among adolescents, followed by a resulting rise in sedentary behavior. Walking Intervention Through Texting for Adolescents, or WalkIT-A, was an 11.5-week intervention that built upon behavioral theory to provide an incentive-based, adaptive, physical activity intervention to inactive adolescents. The goal of this study was to investigate an intervention which combined walking with pointed behavior change strategies to incite a larger increase in PA. Using single-case, reversal (ABA) design, the study was aimed at shaping physical activity behavior in adolescents aged 12-17 through a mobile health intervention that paired adaptive goal setting with financial incentives to increase step count. The intervention was delivered using a semi-automated texting, mobile-Health (mHealth) platform, which incorporated FitBit tracking technology, adaptive goals, motivational messages, performance feedback, and points/incentives. It was hypothesized that during the adaptive intervention phase participants would increase both steps per day and active minutes compared to baseline values. Upon conclusion of the study, the three adolescent participants exhibited increased steps and active minutes during the intervention period compared to baseline and withdrawal phases. However, the specific trends identified suggest the need for future research to incorporate even stronger intervention components to overcome PA "drop-off" midway through the intervention, along with other external, environmental influencers. Despite this need, the use of adaptive goal setting combined with incentives can be an effective means to incite PA behavior change in adolescents.
ContributorsVan Bussum, Courtney Jessica (Author) / Adams, Marc (Thesis director) / Forzani, Erica (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor) / School of Nutrition and Health Promotion (Contributor)
Created2016-12
Description
Almost every form of cancer deregulates the expression and activity of anabolic glycosyltransferase (GT) enzymes, which incorporate particular monosaccharides in a donor acceptor as well as linkage- and anomer-specific manner to assemble complex and diverse glycans that significantly affect numerous cellular events, including tumorigenesis and metastasis. Because glycosylation is not template-driven, GT deregulation yields heterogeneous arrays of aberrant intact glycan products, some in undetectable quantities in clinical bio-fluids (e.g., blood plasma). Numerous glycan features (e.g., 6 sialylation, β-1,6-branching, and core fucosylation) stem from approximately 25 glycan “nodes:” unique linkage specific monosaccharides at particular glycan branch points that collectively confer distinguishing features upon glycan products. For each node, changes in normalized abundance (Figure 1) may serve as nearly 1:1 surrogate measure of activity for culpable GTs and may correlate with particular stages of carcinogenesis. Complementary to traditional top down glycomics, the novel bottom-up technique applied herein condenses each glycan node and feature into a single analytical signal, quantified by two GC-MS instruments: GCT (time-of-flight analyzer) and GCMSD (transmission quadrupole analyzers). Bottom-up analysis of stage 3 and 4 breast cancer cases revealed better overall precision for GCMSD yet comparable clinical performance of both GC MS instruments and identified two downregulated glycan nodes as excellent breast cancer biomarker candidates: t-Gal and 4,6-GlcNAc (ROC AUC ≈ 0.80, p < 0.05). Resulting from the activity of multiple GTs, t-Gal had the highest ROC AUC (0.88) and lowest ROC p‑value (0.001) among all analyzed nodes. Representing core-fucosylation, glycan node 4,6-GlcNAc is a nearly 1:1 molecular surrogate for the activity of α-(1,6)-fucosyltransferase—a potential target for cancer therapy. To validate these results, future projects can analyze larger sample sets, find correlations between breast cancer stage and changes in t-Gal and 4,6-GlcNAc levels, gauge the specificity of these nodes for breast cancer and their potential role in other cancer types, and develop clinical tests for reliable breast cancer diagnosis and treatment monitoring based on t-Gal and 4,6-GlcNAc.
ContributorsZaare, Sahba (Author) / Borges, Chad (Thesis director) / LaBaer, Joshua (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Aberrant glycosylation has been shown to be linked to specific cancers, and using this idea, it was proposed that the levels of glycans in the blood could predict stage I adenocarcinoma. To track this glycosylation, glycan were broken down into glycan nodes via methylation analysis. This analysis utilized information from N-, O-, and lipid linked glycans detected from gas chromatography-mass spectrometry. The resulting glycan node-ratios represent the initial quantitative data that were used in this experiment.
For this experiment, two Sets of 50 µl blood plasma samples were provided by NYU Medical School. These samples were then analyzed by Dr. Borges’s lab so that they contained normalized biomarker levels from patients with stage 1 adenocarcinoma and control patients with matched age, smoking status, and gender were examined. An ROC curve was constructed under individual and paired conditions and AUC calculated in Wolfram Mathematica 10.2. Methods such as increasing size of training set, using hard vs. soft margins, and processing biomarkers together and individually were used in order to increase the AUC. Using a soft margin for this particular data set was proved to be most useful compared to the initial set hard margin, raising the AUC from 0.6013 to 0.6585. In regards to which biomarkers yielded the better value, 6-Glc/6-Man and 3,6-Gal glycan node ratios had the best with 0.7687 AUC and a sensitivity of .7684 and specificity of .6051. While this is not enough accuracy to become a primary diagnostic tool for diagnosing stage I adenocarcinoma, the methods examined in the paper should be evaluated further. . By comparison, the current clinical standard blood test for prostate cancer that has an AUC of only 0.67.
For this experiment, two Sets of 50 µl blood plasma samples were provided by NYU Medical School. These samples were then analyzed by Dr. Borges’s lab so that they contained normalized biomarker levels from patients with stage 1 adenocarcinoma and control patients with matched age, smoking status, and gender were examined. An ROC curve was constructed under individual and paired conditions and AUC calculated in Wolfram Mathematica 10.2. Methods such as increasing size of training set, using hard vs. soft margins, and processing biomarkers together and individually were used in order to increase the AUC. Using a soft margin for this particular data set was proved to be most useful compared to the initial set hard margin, raising the AUC from 0.6013 to 0.6585. In regards to which biomarkers yielded the better value, 6-Glc/6-Man and 3,6-Gal glycan node ratios had the best with 0.7687 AUC and a sensitivity of .7684 and specificity of .6051. While this is not enough accuracy to become a primary diagnostic tool for diagnosing stage I adenocarcinoma, the methods examined in the paper should be evaluated further. . By comparison, the current clinical standard blood test for prostate cancer that has an AUC of only 0.67.
ContributorsDe Jesus, Celine Spicer (Author) / Taylor, Thomas (Thesis director) / Borges, Chad (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Course-Based Undergraduate Research Experiences, or CUREs have become an increasingly popular way to integrate research opportunities into the undergraduate biology curriculum. Unlike traditional cookbook labs which provide students with a set experimental design and known outcome, CUREs offer students the opportunity to participate in novel and interesting research that is of interest to the greater biology community. While CUREs have been championed as a way to provide more students with the opportunity to experience, it is unclear whether students benefit differently from participating in different CURE with different structural elements. In this study we focused in on one proposed element of a CURE, collaboration, to determine whether student's perception of this concept change over the course of a CURE and whether it differs among students enrolled in different CUREs. We analyzed pre and post open-ended surveys asking the question "Why might collaboration be important in science?" in two CUREs with different structures of collaboration. We also compared CURE student responses to the responses of senior honors thesis students who had been conducting authentic research. Five themes emerged in response to students' conceptions of collaboration. Comparing two CURE courses, we found that students' conceptions of collaboration were varied within each individual CURE, as well as what students were leaving with compared to the other CURE course. Looking at how student responses compared between 5 different themes, including "Different Perspectives", "Validate/Verify Results", "Compare Results", "Requires Different Expertise", and "Compare results", students appeared to be thinking about collaboration in distinct different ways by lack of continuity in the amount of students discussing each of these among the classes. In addition, we found that student responses in each of the CURE courses were not significantly different for any of the themes except "Different Expertise" compared to the graduating seniors. However, due to the small (n) that the graduating seniors group had, 22, compared to each of the CURE classes composing of 155 and 98 students, this comparison must be taken in a preliminary manner. Overall, students thought differently about collaboration between different CUREs. Still, a gap filling what it means to "collaborate", and whether the structures of CUREs are effective to portray collaboration are still necessary to fully elaborate on this paper's findings.
ContributorsWassef, Cyril Alexander (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Historically, Supreme Court interpretations of the Constitution of the United States have been significantly important, impacting the lives of every American. This honors thesis seeks to understand the ways in which the Constitution has been interpreted through the lens of political ideology. Using constitutional theory, I explain how the political ideologies of classical liberalism, conservatism, libertarianism, and progressive liberalism have played a role in the interpretations of the First, Second, and Fourth Amendments. I also examine how these ideological interpretations have changed from 1776 to 2017, dividing the history of the United States into four eras: the Founding Era, the Civil War Era, the New Deal Era, and the Modern Era. First, the First Amendment's clauses on religion are examined, where I focus on the separation between church and state as well as the concepts of "establishment" and "free exercise." The First Amendment transitions from classically liberal, to conservative, to progressively liberal and classically liberal, to progressively liberal and libertarian. Next, we look at the Second Amendment's notions of a "militia" and the "right to keep and bear arms." The Second Amendment's interpretations begin classically liberal, then change to classically liberal and progressively liberal, to progressively liberal, to conservative. Finally, the analysis on the Fourth Amendment's "unreasonable searches and seizures" as well as "warrants" lends evidence to ideological interpretations. The Fourth Amendment, like the other two, starts classically liberal for two eras, then becomes libertarian, and finally ends libertarian and conservative. The implications of each of these conclusions are then discussed, with emphasis on public opinion in society during the era in question, the ways in which the ideologies in each era seem to build upon one another, the ideologies of the justices who wrote the opinions, and the ideology of the court.
ContributorsSmith, Charlene Anne (Author) / Lennon, Tara (Thesis director) / Hudson, Jill (Committee member) / New College of Interdisciplinary Arts and Sciences (Contributor) / School of Criminology and Criminal Justice (Contributor) / School of Social and Behavioral Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Disturbances in the protein interactome often play a large role in cancer progression. Investigation of protein-protein interactions (PPI) can increase our understanding of cancer pathways and will disclose unknown targets involved in cancer disease biology. Although numerous methods are available to study protein interactions, most platforms suffer from drawbacks including high false positive rates, low throughput, and lack of quantification. Moreover, most methods are not compatible for use in a clinical setting. To address these limitations, we have developed a multiplexed, in-solution protein microarray (MISPA) platform with broad applications in proteomics. MISPA can be used to quantitatively profile PPIs and as a robust technology for early detection of cancers. This method utilizes unique DNA barcoding of individual proteins coupled with next generation sequencing to quantitatively assess interactions via barcode enrichment. We have tested the feasibility of this technology in the detection of patient immune responses to oropharyngeal carcinomas and in the discovery of novel PPIs in the B-cell receptor (BCR) pathway. To achieve this goal, 96 human papillomavirus (HPV) antigen genes were cloned into pJFT7-cHalo (99% success) and pJFT7-n3xFlag-Halo (100% success) expression vectors. These libraries were expressed via a cell-free in vitro transcription-translation system with 93% and 96% success, respectively. A small-scale study of patient serum interactions with barcoded HPV16 antigens was performed and a HPV proteome-wide study will follow using additional patient samples. In addition, 15 query proteins were cloned into pJFT7_nGST expression vectors, expressed, and purified with 93% success to probe a library of 100 BCR pathway proteins and detect novel PPIs.
ContributorsRinaldi, Capria Lakshmi (Author) / LaBaer, Joshua (Thesis director) / Mangone, Marco (Committee member) / Borges, Chad (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12