AJUR Volume 20 Issue 1 (June 2023)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 20 Issue 1 (June 2023) or https://doi.org/10.33697/ajur.2023.075

Links to individual manuscripts, abstracts, and keywords are provided below.

p.3. Divestment Movements over Environmental Issues: The Brazilian Amazon Case

Pedro Eymael


ABSTRACT: Devastating forest fires in Brazil’s Amazon rainforest, one of the most important biomes for Earth’s climate balance, have captured the world’s attention in 2019 and 2020. Foreign governments, non-governmental organizations, and institutional investors pressured Brazilian President Jair Bolsonaro to act and control the situation. Within this context, institutional investors threatened to divest from companies potentially linked to the wildfires and to sell government bonds, creating a divestment movement. Against this background, this article shows that Bolsonaro’s responses varied for each of the groups criticizing the handling of the environmental situation. It is argued that the Brazilian government adopted a more conciliatory tone and took more concrete actions when responding to institutional investors’ demands, compared to the responses for foreign governments and non-governmental organizations (NGOs). Based on fifteen in-depth interviews conducted in 2021 with professionals involved in this divestment case, the paper concludes that institutional investors played a key role in Bolsonaro’s winning coalition and electoral aspirations. Moreover, the shortage of financial capital due to the COVID-19 pandemic created further incentives for Bolsonaro to avoid conflicts with institutional investors. KEYWORDS: Divestment; Amazon Rainforest; Wildfires; Investors; Climate Change; Brazil; Politics

p.27. Using Coral Color to Indicate Coral Health in Five Caribbean Species

Gabriella Herrera, Alexandra M. Good, Alexander Hirota, Catherine Razal, Nicole Gaertner, Justin Sefcik, Jesse Gilbert, & Keisha D. Bahr


ABSTRACT: Coral reefs are one of the most biodiverse and productive ecosystems on Earth, and color has been shown to indicate coral health in Australian and Hawaiian reef systems. However, no standardized method exists to quantify coral health for Caribbean corals. Therefore, a health assessment card using coral color was developed for five species of Caribbean corals to monitor coral health non-invasively. To quantify coral health, individual corals of each species were photographed in a controlled environment to develop color profiles. Simultaneously, nondestructive measurements of “health” were quantified by measuring photosynthetic efficiency (Fv/Fm) using pulse amplitude modulation (PAM) fluorometry, which determines how efficiently the symbiotic algae provides energy to the coral host. The results of this work successfully corresponded photosynthetic efficiency to coral color for five dominant species of Caribbean corals to develop a Coral Health Assessment Card for Caribbean reefs. Implementing a standardized assessment of symbiont performance can assist in monitoring changes in coral health, which can consequently be implemented into long-term and widespread monitoring projects to track overall Caribbean reef health.
KEYWORDS: Photosynthetic Efficiency, Symbiodinium spp., Coral Bleaching, Pulse-amplitude Modulated Fluorometry, Health Assessment

p.37. Synthesis and Palladium-Catalyzed Cross-Coupling of an Alkyl-Substituted Alkenylboronic Acid Pinacol Ester with Aryl Bromides

Shoma Mukai & Nathan S. Werner


ABSTRACT: The palladium-catalyzed cross-coupling reaction of alkyl-substituted alkenylboron reagents with aryl halides is a versatile method to introduce a hydrophobic hydrocarbon chain onto organic compounds of interest. The application of the cross-coupling reaction is enabled by synthetic methods for the preparation of alkenylboron reagents. The geometrically pure, alkyl-substituted alkenylboron reagent, (E)-octenylboronic acid pinacol ester, was prepared by 9-BBN-catalyzed hydroboration reaction of 1-octene with pinacolborane in refluxing 1 M THF solution. This reagent was then evaluated in palladium-catalyzed cross-coupling reactions with aryl bromides. The highest yield of the (E)-1-phenyloctene was obtained when SPhos was used as the ligand, K2CO3 was used as the base, and DMF was used as the reaction solvent. Other electron-rich, electron-poor, sterically hindered, and heteroaromatic substrates produced the corresponding (E)-1-phenyloctene derivatives in moderate to good yield.
KEYWORDS: Organic synthesis; Aryl alkene synthesis; Palladium-catalyzed cross-coupling; Suzuki-Miyaura reaction; Stereocontrolled alkene preparation; Hydroboration; 9-Borobicyclo[3.3.1]nonane; Reaction optimization

p.47. Spawning Conditions Affect Clutch Probability and Size in Laboratory-Housed Zebrafish (Danio rerio)

Sydni Anderson, Elizabeth Sipes, Megan Franke, & Dena R. Hammond-Weinberger


ABSTRACT: Zebrafish are common experimental models used in biological studies that are bred and raised in laboratory settings. Published studies, anecdotal evidence, and industry practices are variable and offer conflicting suggestions on maximizing reproductive success, particularly regarding sex ratios and segregating males and females before spawning. This study identified conditions that promote maximum reproductive success (clutch probability and average clutch size) in zebrafish. Clutch probability was higher when females were seven to ten months old and bred in groups with equal sex ratios and an artificial spawning substrate in the winter or spring. Clutch size was significantly larger when females were seven to ten months old, outnumbered by males, and bred with an artificial spawning substrate. Optional spawning substrates (marbles and plants) improved reproductive success, whereas other parameters had no impact. These data support the implementation of simple steps that reliably maximize reproductive success of laboratory zebrafish.
KEYWORDS: Reproduction; Breeding; Seasonality; Behavior; Substrate; Sex Ratios; Captivity; Eggs

p.59. Color Saturation: Upper and Lower Percentage Histogram Manipulation

Kyra Obert , Maria Schudt , & Ian Bentley


ABSTRACT: There are various color correction techniques that can be applied to digital photographs to account for environmental lighting variations. This manuscript contains a proposed method for such color correction. The method involves saturating an image by a specified percentage of its pixels via upper and lower percentage histogram manipulation using the image’s RGB histograms. Variations of this new technique, the white balance (WB) correction method, and a multivariable fit are used to test its performance against common color correction techniques. The findings demonstrate that the upper and lower percentage histogram manipulation method is not only more applicable to photos because it doesn’t require calibration regions to be sampled but it is also more consistent in its correction of photos when there are substantial gray scale features (e.g. a black and white grid or text). Our motivation for testing these techniques is to find the most robust color correction technique that is broadly applicable (not requiring a color checker chart) and is consistent across different lighting.
KEYWORDS: Color Correction; Histogram Manipulation; Saturation; White Balance; Scientific Image Analysis; Color Comparisons; Euclidean Distance; Standard Deviation; Color Difference

p.77. Overexpression of MMACHC Prevents Craniofacial Phenotypes Caused by Knockdown of znf143b

Isaiah Perez, Nayeli G. Reyes-Nava, Briana E. Pinales, & Anita M. Quintana


ABSTRACT: ZNF143 is a sequence-specific DNA binding protein that regulates the expression of protein-coding genes and small RNA molecules. In humans, ZNF143 interacts with HCFC1, a transcriptional cofactor, to regulate the expression of downstream target genes, including MMACHC, which encodes an enzyme involved in cobalamin (cbl) metabolism. Mutations in HCFC1 or ZNF143 cause an inborn error of cobalamin metabolism characterized by abnormal cbl metabolism, intellectual disability, seizures, and mild to moderate craniofacial abnormalities. However, the mechanisms by which ZNF143 mutations cause individual phenotypes are not completely understood. Defects in metabolism and craniofacial development are hypothesized to occur because of decreased expression of MMACHC. But recent results have called into question this mechanism as the cause for craniofacial development. Therefore, in the present study, we implemented a loss of function analysis to begin to uncover the function of ZNF143 in craniofacial development using the developing zebrafish. The knockdown of znf143b, one zebrafish ortholog of ZNF143, caused craniofacial phenotypes of varied severity, which included a shortened and cleaved Meckel’s cartilage, partial loss of ceratobranchial arches, and a distorted ceratohyal. These phenotypes did not result from a defect in the number of total chondrocytes but were associated with a mild to moderate decrease in mmachc expression. Interestingly, expression of human MMACHC via endogenous transgene prevented the onset of craniofacial phenotypes associated with znf143b knockdown. Collectively, our data establishes that knockdown of znf143b causes craniofacial phenotypes that can be alleviated by increased expression of MMACHC.
KEYWORDS: ZNF143; MMACHC; Vertebrate abnormalities; Cobalamin; cblX-like syndrome; Chondrocytes; Neural crest cells; Hyosymplectic

AJUR Volume 19 Issue 4 (March 2023)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 19 Issue 4 (March 2023) or https://doi.org/10.33697/ajur.2023.069

Links to individual manuscripts, abstracts, and keywords are provided below.

p.3. Ethics of Artificial Intelligence in Society

Emma Johnson, Eloy Parrilla, & Austin Burg
ABSTRACT: Every day, artificial intelligence (AI) is becoming more prevalent as new technologies are presented to the public with the intent of integrating them into society. However, these systems are not perfect and are known to cause failures that impact a multitude of people. The purpose of this study is to explore how ethical guidelines are followed by AI when it is being designed and implemented in society. Three ethics theories, along with nine ethical principles of AI, and the Agent, Deed, Consequence (ADC) model were investigated to analyze failures involving AI. When a system fails to follow the models listed, a set of refined ethical principles are created. By analyzing the failures, an understanding of how similar incidents may be prevented was gained. Additionally, the importance of ethics being a part of AI programming was demonstrated, followed by recommendations for the future incorporation of ethics into AI. The term “failure” is specifically used throughout the paper because of the nature in which the events involving AI occur. The events are not necessarily “accidents” since the AI was intended to act in certain ways, but the events are also not “malfunctions” because the AI examples were not internally compromised. For these reasons, the much broader term “failure” is used. KEYWORDS: Ethics; Artificial Intelligence; Agent-Deed-Consequence (ADC) Model; Principles of Artificial Intelligence; Virtue Ethics; Deontology; Consequentialism; AI Systems

p.13. The By-Product of Ozone from Electrostatic Air Cleaners

Giovanni Cerrato & Nelson Fumo
ABSTRACT: Indoor Air Quality (IAQ) contributes to the health and comfort of people living and working indoors. Poor IAQ can be linked to indoor and outdoor sources of contaminants. One recent solution for improving IAQ is the use of Electrostatic (ES) Air Cleaning technology. An ES air cleaner can be installed in an heating, ventilation, and air conditioning system where it pre-filters large dust particles and shocks smaller particles into a collection tray. However, ES air cleaners have been known to give off ozone as a by-product, which is, itself, an air contaminant. Ozone is found outdoors as product of sunlight combining nitrogen oxides and volatile organic compounds generated from man-made pollution. Indoor ozone concentration will depend on the introduction of outdoor ozone indoors through natural ventilation, mechanical ventilation, and infiltration through the building’s envelope (in order of importance). Two different ES air cleaners, A and B, were installed in the air conditioning system of research House #2 of the TRANE Residential Heating and Cooling Research Lab at the University of Texas at Tyler. A series of ozone experiments were conducted, which included measuring the baseline ozone levels at the research houses with different levels of insulation, observing the increase in ozone due to the powering on of mechanical ventilation, and observing the increase in ozone due to the powering on of the installed ES air cleaners. The baseline ozone levels observed in research house #2, whose envelope is more tightly insulated, was found to be lower than in research house #1 whose envelope is less tightly insulated. With regards to mechanical ventilation, an increase in ozone levels were seen in addition to an even higher increase in ozone levels when the ES air cleaners were powered on in tandem. In terms of the single contribution of the ES air cleaners in raising indoor ozone levels, the data shows that although the ES air cleaners increased the ozone concentration in the house, the levels are not of concern as they were less than the FDA limit on indoor ozone generation. KEYWORDS: Indoor Air Quality; Ozone; Electrostatic Air Cleaner; Infiltration; Mechanical Ventilation; HVAC; Pollutant; Indoor Contaminant

p.31. Student Perceptions of Instructor-Student Rapport and Motivation In Hybrid Courses During COVID-19

Bianca S. Candelaria & Meredith L. Clements
ABSTRACT: The relationship between instructors and their students is essential for developing a classroom climate where students feel motivated to learn. The current study surveyed 658 undergraduate students to examine the relationship between instructor-student rapport and motivation in online and face-to-face classes during the COVID-19 pandemic. Results indicated (1) students experienced more rapport with their instructors during face-to-face classes compared to their online classes, (2) students perceived their motivation was greater during face-to-face classes than in online classes, and (3) there was a significant positive relationship between instructor-student rapport and student motivation in both online and face-to-face classes. This study’s findings lend further support to research that emphasizes the importance of creating a sense of community in online classes, where students feel connected to their instructors and, consequently, motivated to learn. KEYWORDS: Instructor-Student Rapport; Motivation; Hybrid Courses; COVID-19; Online Learning

p.41. “The Strong, Silent Type”: Analyzing the Portrayal of the Cost of Masculine Gender Performances in The Sopranos

Holly Taylor & Anna Curtis
ABSTRACT: Media portrayals of the “strong, silent type” reinforce the expectation that men should not demonstrate or even acknowledge their emotions. This trope, however, reflects more significant societal norms around masculine practices that can have profoundly negative impacts on individual men as well as those around them. Emotional compression (or modern stoicism) is fundamentally different from emotional repression. Emotional compression practices can allow men to process their feelings privately and then communicate their feelings clearly without the distortion of uncontrolled bursts of emotion. The treatment of mental health and masculinity in Season 5 of The Sopranos “holds up a mirror” to the costs of emotional repression for men as part of masculine gender performances. The show highlights, sometimes quite brutally, the costs of emotional repression to men and the people around them. In doing so, the content of the show implies that therapy could help men learn to face their feelings and alleviate their suffering as well as that of their families, though only if men are willing to face the feelings of vulnerability that come with having emotions. KEYWORDS: Stoicism; Alexithymia; Hegemonic masculinity; Emotional repression; Mental health; Gender performances

p.53. A Review of the Effect of Estrogen on Immune Efficacy in Zebrafish (Danio rerio) with Comparisons to Human and Murine Homologs

Michael S. Chembars & Lindsey C. Stevenson
ABSTRACT: A review was conducted on current research surrounding the effect of estrogen, and the estrogen receptor, on immune development. Estrogen can regulate many processes and genes throughout immune development, from modulating complement activation and regulating genes crucial for hematopoiesis, to elevating toll-like receptor gene expression. Estrogen has also been shown to have a pronounced effect on regulating certain cancers through inducing macrophage infiltration. It has also been demonstrated to play an important role in the regulation of microRNAs that are important for proper immune development. A greater understanding of this hormone’s effect gained through the zebrafish model can lead to the development of better practices to improve both human and ecological health. Contemporary reviews typically examine the effect of estrogen-like compounds (oftentimes referred to as estrogenic endocrine disrupting compounds) on a sequestered part of immune system development. A distinct lack of cohesion exists in combining contemporary and past reports of the effects of estrogen on various aspects of immune system development in zebrafish. This review serves to fill that gap in knowledge, and to provide a gateway for other researchers interested in this topic. KEYWORDS: Zebrafish; Immune development; Zebrafish immunology; Estrogen; Estrogen receptor; Autoimmunity; Altered signaling; Hematopoiesis

AJUR Volume 19 Issue 3 (December 2022)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 19 Issue 3 (December 2022) or https://doi.org/10.33697/ajur.2022.063

Links to individual manuscripts, abstracts, and keywords are provided below.

p.3. Comparison of Genotypic and Phenotypic Predictions for Heavy Metal Resistance in Salmonella enterica and Escherichia coli

Jeevan Rivera-Díaz, Haley Phillippi, Nyduta Mbogo, Erin M. Nawrocki, & Edward G. Dudley


ABSTRACT: Salmonella enterica and Escherichia coli are two pathogenic bacteria of worldwide importance that can infect the gastrointestinal tract. Contamination in the food supply chain is an area of concern. Animal feed may be supplemented with essential trace elements, which function as nutritional additives to promote growth & health and optimize production. Bacteria have acquired many metal resistance genes to adapt to the exposure of metals. In this study, our objectives were to evaluate in S. enterica and E. coli, the correlation between the resistance genotype and phenotype to certain heavy metals, and the ability of conjugative plasmids to transfer antimicrobial resistance genes (AMRGs) and heavy metal resistance genes (HMRGs). A total of 10 strains, five S. enterica and five E. coli, were used for this study. Minimal inhibitory concentrations (MICs) were determined for heavy metals: copper, silver, arsenic, and tellurite. The tested isolates showed resistance to copper (5/10; 50%), arsenic (7/10; 70%), and silver (9/10; 90%). Cohen’s Kappa statistics were used to analyze genotype to phenotype agreements. Among the 10 strains sampled, the accordance between geno- and phenotypic heavy metal resistance was fair for copper (kappa = 0.4), none to slight for arsenic (kappa = 0.19) and tellurite (kappa = 0), and no agreement for silver (kappa = -0.19). The transfer of HMRGs was determined in a conjugation experiment performed for all five Salmonella strains as donors using mixed broth cultures. Transconjugants were obtained only from the genotypically tellurite-resistant strain PSU-3260, which yielded a transfer frequency of 10⁻³ transconjugants per donor. In such strain, the tellurite-resistant genes reside on an IncHI2-type plasmid that shares high DNA sequence identity with known HMRG-disseminating Salmonella plasmids. Our results indicated no considerable correlation between the geno- and phenotypic resistance towards heavy metals in the sampled S. enterica and E. coli. The necessity of research in this area is supported by the lack of standardized protocols and MIC clinical breakpoints for heavy metals.

KEYWORDS: Heavy metal; resistance; Salmonella; E. coli; agriculture; genotype; phenotype; MIC

p.17. Preventing the Activation of a Stress Gene Response in Escherichia coli Using Acetate, Butyrate, and Propionate

Kaylee M. Weigel, Kathleen M Ruff-Schmidt, Birgit M. Prüß, & Danielle L J Condry


ABSTRACT: Regulation of microbial symbiosis in the human intestinal tract is imperative to maintain overall human health and prevent dysbiosis-related diseases, such as inflammatory bowel disease and obesity. Short-chain fatty acids (SCFA) in the intestine are produced by bacterial fermentation and aid in inflammation reduction, dietary fiber digestion, and metabolizing nutrients for the colon. SCFA, notably acetate, butyrate, and propionate, are starting to be used in clinical interventions for GI diseases. While acetate has been shown to mitigate a stress response in the proteome of Escherichia coli cells, little is known about the effects of butyrate and propionate on the same cells. This study aims to evaluate the effects that butyrate and propionate have on the activation of stress promoters in E. coli when induced with a known stressor. Three different strains of E. coli containing the pUCD615 plasmid were used, each with a different promoter fused to the structural genes of the lac operon on the plasmid. Each promoter detected a unique stress response: grpE’::lux fusion (heat shock), recA’::lux fusion (SOS response), and katG’::lux fusion (oxidative damage). Activation of these stress promoters by treatment groups resulted in the emission of bioluminescence which was quantified and compared across treatment groups. All three SCFAs at 25 mM added to cultures prior to stressing the bacteria caused significantly lower bioluminescence levels when compared to the stressed culture without prior addition of SCFA. This indicates that these SCFAs may reduce the stress response in E. coli.

KEYWORDS: Short-chain fatty acids; acetate; butyrate; propionate; Escherichia coli; stress response; Vibrio fischeri luxCDABE; grpE; katG; recA

p.27 Quantification of Microfibers from Marine Sediments from Three Locations in Southern California: An Exposed Beach (Ventura County), a Watershed (Los Angeles County), and an Enclosed Harbor (Orange County)

Adrianna Ebrahim & Mia LeClerc


ABSTRACT: Microfibers are small (<5 mm) fibers made of synthetic materials that are ubiquitous in the environment. The purpose of this observational study was to quantify the number of microfibers in marine sediments and determine which locations have the highest risk for this type of pollution. Sediment samples were taken from three locations in Southern California (Sycamore Watershed, Ventura State Beach Jetty, and Newport Beach Harbor) to determine which had the highest number of microfibers. It was hypothesized that microfibers would be found at each sample site and that the most microfibers would be found at Sycamore Watershed due to its proximity to a wastewater discharge point. The microfibers were separated from the sediment through a process of stratification and filtration and analyzed by a one-way ANOVA and Tukey’s test. Per sample, there was an average of 111.5 (土99.3, n=14) microfibers found per sample at Sycamore Watershed, 59 (土17.4, n=18) at Newport Beach Harbor, and 53 (土14.4, n=18) at Ventura State Beach Jetty. A total of 3,590 microfibers were found from all three sample sites. Analysis revealed that Sycamore Watershed had significantly more microfibers than any other site (p<.05). It is likely that Sycamore Watershed had the most microfibers because of its proximity to a sewage-sludge disposal site that contains the polluted water from our washing machines. In conclusion, microfibers are polluting the sediments in harbors, open coastlines, and watersheds in California, negatively affecting the ecosystems in these areas.

KEYWORDS: Microfiber; Microplastic; Macroplastic; Marine Pollution; Synthetic Materials; Wastewater Treatment Plants; Sediments; Watershed; Harbor; Jetty

p. 37. Stabilization of Cisplatin via Coordination of Ethylenediamine

Samantha L. Rea, Alexia Smith, Brooke Hornberger, Grace Fillmore, Jeremy Burkett, & Timothy Dwyer


ABSTRACT: While the chemotherapeutic cisplatin is used to treat a variety of cancers, metal toxicity and cisplatin resistance via genetic and epigenetic changes limits its use and calls for alternative therapies. To combat the observed toxicities and create a more stable compound, which avoids isomerization into a trans configuration, three cisplatin analogues including cispalladium, dichloro-(ethylenediamine)-platinum(II), and dichloro-(ethylenediamine)-palladium(II) were synthesized as potential cisplatin alternatives. Each compound was evaluated for cytotoxicity on SK-OV-3 cells against cisplatin. Synthesis of dichloro-(ethylenediamine)-platinum(II) yielded 20.5% of the theoretical yield, while dichloro-(ethylenediamine)-palladium(II) yielded 49.1%. Results from the cytotoxicity trial revealed that cispalladium was not effective against SK-OV-3 cells, and dichloro-(ethylenediamine)-palladium had minimal effects. The dichloro-(ethylenediamine)-platinum(II) was the most efficacious with an IC50 value of 0.77 µg/ml compared to the IC50 of 0.61 µg/ml for cisplatin. With a similar IC50 to cisplatin, these results suggest that dichloro-(ethylenediamine)-platinum(II) has the potential to serve as a cisplatin alternative for cancer patients who develop resistance following their clinical course of cisplatin. Future studies on the cytotoxicity of dichloro-(ethylenediamine)-platinum(II) to induce cell death on cisplatin-resistance cell lines are necessary to determine the ability of the compound to be utilized as a cisplatin alternative.

KEYWORDS: Cisplatin; Ovarian Cancer; SK-OV-3; Drug Resistance; Stability; Palladium; Ethylenediamine; Cispalladium; Dichloro-(ethylenediamine)-platinum(II); Dichloro-(ethylenediamine)-palladium(II)

p.47. Novel Interactors of the SH2 Domain of the Signaling Adaptors CRK and CRKL Identified in Neuro2A Cells

Caroline M. Dumas, Anna M. Schmoker, Shannon R. Bennett, Amara S. Chittenden, Chelsea B. Darwin, Helena K. Gaffney, Hannah L. Lewis, Eliana Moskovitz, Jonah T. Rehak, Anna A. Renzi, Claire E. Rothfelder, Adam J. Slamin, Megan E. Tammaro, Leigh M. Sweet, & Bryan A. Ballif*


ABSTRACT: CT10 regulator of kinase (CRK) and CRK-like (CRKL) form a family of signaling adaptor proteins that serve important roles in the regulation of fundamental cellular processes, including cell motility and proliferation, in a variety of cell types. The Src Homology 2 (SH2) domain of CRK and CRKL interacts with proteins containing phosphorylated tyrosine-X-X-proline (pYXXP) motifs, facilitating complex formation during signaling events. A handful of CRK/CRKL-SH2-specific interactors have been identified to date, although in silico analyses suggest that many additional interactors remain to be found. To identify CRK/CRKL-SH2 interactors with potential involvement in neuronal development, we conducted a mass spectrometry-based proteomics screen using a neuronal cell line (Neuro2A, or N2A). This resulted in the identification of 132 (6 known and 126 novel) YXXP-containing CRK/CRKL-SH2 interactors, of which 77 were stimulated to bind to the CRK/CRKL-SH2 domain following tyrosine phosphatase inhibition. Approximately half of the proteins identified were common interactors of both the CRK- and CRKL-SH2 domains. However, both CRK family member SH2 domains exhibited unique binding partners across experimental replicates. These findings reveal an abundance of novel neuronal CRK/CRKL-SH2 domain binding partners and suggest that CRK family SH2 domains possess undescribed docking preferences beyond the canonical pYXXP motif.

KEYWORDS: CRK; CRKL; SH2; LC-MS/MS; Proteomics; Neurodevelopment; Signal Transduction

SUPPLEMENT 1 (Figures)


AJUR Volume 19 Issue 2 (September 2022)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 19 Issue 2 (September 2022) or https://doi.org/10.33697/ajur.2022.058

Links to individual manuscripts, abstracts, and keywords are provided below.

p.3. Evaluating Driveway Cross Slopes and Social Equity in Cedar City, UT

Brock Anderson* & Jamie Spinney

Department of Geosciences, Southern Utah University, Cedar City, UT


Student: brock20anderson00@gmail.com*

Mentor: jamie.spinney@suu.edu


The Americans with Disabilities Act (ADA) is the most comprehensive law governing accessibility, and it requires local governments to develop transition plans to become compliant. Among the key ADA requirements is a continuous unobstructed pedestrian circulation network that consists of a sidewalk that has a cross slope of no more than two degrees. The primary objective of this research was to evaluate whether driveway cross slopes in Cedar City were ADA compliant, so a digital level was used to measure a random sample of driveway cross slopes. A secondary objective was to determine whether there is evidence of social inequities in Cedar City’s pedestrian environment. The estimated value of each residential property (a proxy for income) was retrieved from Zillow® to evaluate the statistical relationship between incomes and driveway cross slopes. The results of this study indicate that there was no widespread evidence of social inequities. However, most driveway cross slopes (78.8 percent) were not ADA compliant and, thus, require retrofitting that should incorporate more widespread use of sidewalk buffer strips. The results also highlight priority areas for sidewalk improvements and can be used to inform a transition plan for sidewalk enhancements and funding.


Social Equity; ADA; Sidewalks; Advocacy Planning; Driveway Cross Slope; Walkability

p.11. Conversations About Mental Health and Well-being During the COVID-19 Pandemic: Why and How Restaurant Employees Talk With Each Other and Managers

Anamaria Tepordei* & Kirsten Foot

Department of Communication, University of Washington, Seattle, WA


Student: anamaria.tepordei@outlook.com*
Mentor: kfoot@uw.edu

Restaurant employees in the United States have experienced unprecedented challenges to their mental health and well-being (MHW) during the COVID-19 pandemic, yet little is known about communication regarding MHW in the restaurant industry. Drawing on health, organizational, and interpersonal communication concepts, this exploratory, survey-based study probed whether, how, and why or why not restaurant employees in western Washington State conversed about MHW with one another and their managers during the winter of 2021. Key findings include that there are many reasons why some restaurant employees do not engage in conversations about MHW with other members of the workplace. However, when such conversations do occur, they are typically mutual, positive, and relationally-oriented—more so among coworkers than between employees and managers. Additionally, both coworkers and managers are sources of social support and resource exchange during these conversations, although the evidence is stronger among coworkers. Our findings contribute to the extant literature on mental health communication in the workplace and demonstrate the merit in more closely examining superior-subordinate and coworker communication about personal and sensitive topics, like MHW. Comparative analysis of employees’ MHW-related communication with coworkers versus managers revealed both similarities and differences that carry implications for managerial practice and future research.

Mental Health and Well-being (MHW); Disclosure; Superior-subordinate Communication; Peer Coworker; Social Exchange; Social Support; Interpersonal Communication Motives (ICM), Restaurant Employees

p. 33. Differential Expression of Hub Genes and Activation of p53 by Anti-cancer Compound Curaxin CBL0137

Tanvi Patel*, Rochelle Ratner, & Niharika Nath

Department of Biological & Chemical Sciences, New York Institute of Technology, New York, NY


Students: tpatel60@nyit.edu*, rratne02@nyit.edu

Mentor: nnath@nyit.edu


Cancer is a global concern and there is a need for effective drugs. CBL0137 is a small water-soluble molecule and a new second-generation compound in the family of curaxins with potential anti-cancer activity. Curaxins in general, including CBL0137 intercalate into DNA, and act by targeting the histone chaperone ‘facilitates chromatin transcription’ (FACT) complex and have the potential to treat tumors by reducing the growth of cancer cells which is shown in a variety of cell lines and animal models. CBL0137 is found to activate the tumor suppressor gene p53. However, the mechanism of p53 activation is poorly understood. Utilizing bioinformatics analysis on available datasets of CBL0137 treated cancer cells of glioma, cervical and multiple myeloma, differentially expressed genes (DEGs) that may lead to the activation of p53 were examined. Three GEO datasets of cells treated with various concentrations of CBL0137 were analyzed, namely HSJD-DIPG007 (GSE153441), MM1.S (GSE117611) and HeLa S3 (GSE117611). The DEGs were identified based on p-values less than 0.05, logFC values greater than 1 and less than -1 and analyzed using GEO2R, Enrichr, and STRING, and data visualization was performed on Tableau. Compared to the controls, a total of 229, 1425, and 1005 genes were upregulated while 368, 2322, and 1673 genes were downregulated for HSJD-DIPG007, MM1.S and HeLa S3 datasets, respectively. Further collective analysis revealed a total of 38 common DEGs among the three datasets. Using Enrichr and STRING on these 38 DEGs, seven hub genes were obtained, SKP2, RGS16, CSRP2, CENPA, HJURP, DTL, and HEXIM1 with these possible mechanisms:  inhibition of AKT phosphorylation by upregulated genes RGS16 and CSRP2, p300-mediated acetylation of p53 via SKP2, inhibition of MDM2 by DTL downregulation and HEXIM1 upregulation, and inhibition of AURKB via CENPA and HJURP downregulation. This study analyzed the three datasets and highlighted how these identified hub genes may play a role in leading to p53 activation by CBL0137.


Curaxin; CBL0137; Differentially Expressed Genes; Cancer; p53; Glioblastoma; Cervical; Myeloma

p. 43. Cemetery Analysis of Whitewater, WI

David H. Nehlsen

Department of Political Science and Philosophy at the University of Green Bay, WI


Students: nehldh03@uchicago.edu*

Mentor: weinscha@uwgb.edu


Procedures and customs surrounding funerals, burial, and grave marking vary widely by time period, location, culture, and religion, among many other factors. This project investigated the gravestone customs of cemeteries in Southern Wisconsin, USA. Utilizing a dataset of 500 gravestone samples collected from cemeteries in Whitewater, WI, the aim of this project was to objectively measure how people choose to remember their dead and how these practices have evolved over the years. Because of the decline in American religiosity in recent decades, the expectation of this project was to see the usage of religious symbols decline. Based upon this analysis, this does not appear to be the case. Practices such as the recording of one’s name and year of birth/death have remained constant; however, other customs of remembrance, such as the use of religious symbols and the recording of one’s date of marriage, have shifted dramatically over the years, reflecting the evolution of society and culture.


Cemetery; Symbols; Funeral; Thanatology; Death; Demography; Monuments; History

AJUR Volume 19 Issue 1 (June 2022)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 19 Issue 1 (June 2022) or https://doi.org/10.33697/ajur.2022.053

Links to individual manuscripts, abstracts, and keywords are provided below.

p.3 Myrica cerifera, a Medicinal Plant of the Lumbee Tribe, has Antibacterial and Nematicidal Properties

Ashley Edwards, Kazhmiri Deberry, Hannah Mariani, Darian H. Taylor, Nicholas J. Cochran, Ana C. Barrios Sosa, Andrea Regan Scott, R. Thomas Williamson, Cornelia Tirla, Conner Sandefur, & Courtney Carroll Alexander


ABSTRACT: Currently threatening the world of medicine is a growing number of antibiotic-resistant diseases. More specifically, bacteria and nematodes have gained resistance to many of the world’s leading antibiotics and nematicides, respectively, making infections more difficult to treat. Subsequently, these parasitic organisms are able to continue damaging crops and other living organisms like humans without strong interference. To help people and the environment, the development of new and novel antibiotics is vital. Previous research suggests that phytochemicals are a potential solution that will not only help inhibit bacterial growth but also reduce nematode survival. We hypothesized that Myrica cerifera, a plant often used by the Lumbee tribe to treat illness, possesses antibacterial and nematicidal properties. To answer our hypothesis, we began by collecting plant specimens to extract material for biological assays and to subsequently isolate and elucidate the structures of active components. The extract was evaluated for antibacterial properties with an agar diffusion assay and then nematicidal properties using Caenorhabditis elegans. M. cerifera extract was added onto an agar lawn at various doses, and the nematodes’ lifespans were scored. The findings of this study show that extracts of this plant, more commonly referred to as ‘wax myrtle’, do significantly decrease the lifespan of C. elegans and increase the zone of inhibition for Staphylococcus epidermidis and Staphylococcus aureus. In addition, two compounds were isolated and characterized through chemical extraction, chromatographic separation, and spectroscopic analysis. These compounds could potentially be used to treat bacterial and nematode infections.

KEYWORDS: Antibacterial; Antimicrobial; Caenorhabditis elegans; Plant extract; Myrica cerifera; Nematicidal; NMR; Phytochemical

Supplemental Data for https://doi.org/10.33697/ajur.2022.054

p.13 State Adoption of Cryptocurrency: a Case Study Analysis of Iran, Russia, and Venezuela

Rose Mahdavieh


ABSTRACT: The emergence of digital currency is becoming prevalent in the age of globalization – specifically, cryptocurrencies, a subset of digital currency that encompass revolutionary technology. This study postulates that certain governments are more prone to adopting cryptocurrencies, especially those seeking to eschew international sanctions and protect corrupt practices. Three comparative case studies focus on countries (Iran, Russia, and Venezuela) that share attributes that result in adopting what has been called “native cryptocurrencies”: corruption, GDP level, economic volatility, and Western sanctions.

KEYWORDS: Cryptocurrency; Blockchain; Political Science; Law; Foreign Sanctions; Government; Iran; Russia; Venezuela

p23. Salinity Affects Wound Healing in Wild Common Bottlenose Dolphins (Tursiops truncatus)

Brianna Hurst & Dara N. Orbach


ABSTRACT: Dolphins are often individually identified by unique naturally-acquired markings. Identification becomes difficult when markings heal, or new scars appear. As salt accelerates wound healing in many organisms, the diminishment of scars on common bottlenose dolphins (Tursiops truncatus) residing in varying natural salinities was determined. South Texas contains the only hypersaline lagoon in the USA, located adjacent to hyposaline waters, with genetically distinct populations of dolphins in the two environments. Photographs of dolphin dorsal fins were collected, and scar stability over time was determined and compared by measuring changes in the relative lengths and surfaces of scars. All scars on dolphins in the hypersaline lagoon completely diminished between three to six years, while scars on dolphins in the hyposaline bay ranged in the amount of fading between three to six years. Data from this case study indicate that high salinity may increase the healing speed of wounds on common bottlenose dolphins compared to low salinity, although a larger sample size is needed for robust statistical comparison. Scar diminishment is an important consideration in determining the temporal reliability of photo identification.

KEYWORDS: Bottlenose dolphin; Corpus Christi Bay; healing; hypersaline; Laguna Madre; photo-identification; salinity; scar

p.31 Validation of Accelerometer-Based Estimations of Energy Expenditure During High-Intensity Interval Training

Nicholas Remillard, Marisa Mulvey, Gregory Petrucci Jr, & John R Sirard


ABSTRACT: Accelerometers are used to assess free-living physical activity (PA) and energy expenditure (EE). Energy expenditure estimation algorithms have been calibrated using steady-state exercise. However, most free-living PA is not steady-state. Objective: The purpose of this study was to discern the differences between criterion-measured and accelerometer-estimated EE (kCals) during a non-steady-state High-Intensity Interval Training (HIIT) session. Methods: Recreationally active adults (N=29, 18-30 years) completed one of two HIIT protocols. Each participant wore ActiGraph GT3X+ accelerometers on the right hip and non-dominant wrist while EE was measured using portable indirect calorimetry. Data analysis was conducted using custom R scripts and bias [95% CIs] to determine significant differences between indirect calorimetry and EE estimates using previously developed algorithms. Results: All accelerometer algorithms underestimated EE during recovery intervals (range; -4.31 to -6.55 kCals) and overestimated EE during work intervals (0.57 to 5.70 kcals). Over the whole HIIT session, only the Hildebrand wrist method was not significantly different from the criterion measured EE. Conclusion: Current ActiGraph EE estimations based on steady-state activities underestimate EE during recovery periods of treadmill HIIT sessions. Future studies should investigate accelerometer signals immediately after high-intensity bouts to more accurately predict EE of the subsequent recovery period.

KEYWORDS: ActiGraph; Accelerometer; HIIT; Indirect calorimetry; EPOC; Energy expenditure; Non-steady state; Calories

AJUR Volume 18 Issue 4 (March 2022)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 18 Issue 4 (March 2022) or https://doi.org/10.33697/ajur.2022.050

Links to individual manuscripts, abstracts, and keywords are provided below.

p.3. The Effects of the NBA COVID Bubble on the NBA Playoffs: A Case Study for Home-Court Advantage
Michael Price & Jun Yan
ABSTRACT: The 2020 NBA playoffs were played inside of a bubble at Disney World because of the COVID-19 pandemic. This meant that there were no fans in attendance, games were played on neutral courts and no traveling for teams. In theory, these conditions should remove home-court advantage from the games. This setting generated discussion and concern, as analysts and fans debated the possible effects it may have on the outcome of games. Home-court advantage has historically played an influential role in NBA playoff series outcomes. The 2020 playoffs provided a unique opportunity to study the effects of the bubble and home-court advantage by comparing the 2020 season with the seasons in the past. While many factors contribute to the outcome of games, points scored is the deciding factor of who wins. Thus, scoring is the primary focus of this study. The specific measures of interest are team scoring totals and team shooting percentage on two-pointers, three-pointers, and free throws. Comparing these measures for home teams and away teams in 2020 vs. 2017-2019 shows that the 2020 playoffs favored away teams more than usual, particularly with two-point shooting and total scoring.
KEYWORDS: NBA; NBA Covid; NBA Bubble; Homecourt Advantage

p.15. Internalizing Symptoms in Children Exposed to Adversity: Examining Associations with Resilience, Social Support, and Community Cohesion
Rachel Stobbe, Taylor Napier, Debra Bartelli, & Kathryn H. Howell
ABSTRACT: Exposure to adverse childhood experiences (ACEs) contributes to increased rates of psychopathology in youth. Specific environmental factors have been linked to improved functioning following adversity, but few studies have taken a social-ecological approach to examine how resilience, social support, and community cohesion may be associated with internalizing problems (i.e., anxiety, depression) in young children. The current study included 49 children between the ages of 8 and 13 (Mage = 10.43, SD = 1.57; 55.1% male; 95.8% Black or African American) who were recruited from four community programs in the Midsouth, United States that serve families experiencing adversity. Regarding income, 77.3% of youth’s caregivers reported an annual household income under $15,000. Almost all children reported experiencing at least one ACE (92.6%). Two linear regression models were run to assess how resilience, social support, and community cohesion were related to youth’s depression and anxiety symptoms while controlling for ACEs and family income. The model examining depression was significant, (F (5, 48) = 4.16, p < .01, R2 = .33) with fewer reported ACEs (β = 1.55, p < .02) and higher resilience (β = -.73, p = .01) associated with lower depressive symptoms. The model assessing anxiety was not significant. Results indicate that personal resilience may be a key target for intervention in children exposed to ACEs as efforts to strengthen individual resources (e.g., self-efficacy, emotion regulation skills) could be linked to reduced psychopathology.
KEYWORDS: Adverse Childhood Experiences; Social Ecology; Resilience; Social Support; Community Cohesion; Internalizing Symptoms; Anxiety; Depression

AJUR Volume 18 Issue 3 (December 2021)

Click on this link to download the full high-definition interactive pdf for AJUR Volume 18 Issue 3 (December 2021)

Links to individual manuscripts, abstracts, and keywords are provided below.

p. 3. An Optimal Control Experiment for an SEIRS Epidemiological Model
Tanner Snyder & Ryan Nierman
Department of Mathematics and Computer Science, Madonna University, Livonia, MI
ABSTRACT: This work studies an optimal control model for a discrete-time Susceptible/Exposed/Infective/Removed/Susceptible (SEIRS) deterministic epidemiological model with a finite time horizon and changing population. The model presented converts a continuous SEIRS model that would typically be solved using differential equations into a discrete model that can be solved using dynamic programming. The discrete approach more closely resembles real life situations, as the number of individuals in a population, the rate of vaccination to be applied, and the time steps are all discrete values. The model utilizes a previously developed algorithm and applies it to the presented SEIRS model. To demonstrate the applicability of the algorithm, a series of numerical results are presented for various parameter values.
KEYWORDS: Control; Cost; Discrete; Disease; Epidemiology; Minimization; Modeling; Optimality; SEIRS; Vaccination

p. 15. Factors Associated with Surgery Among South Asian American and Non-Hispanic White Women with Breast Cancer
Lydia Lo & Jaya M. Satagopan
Department of Industrial and Systems Engineering, School of Engineering, Rutgers University,New Brunswick, NJ
Department of Biostatistics and Epidemiology & Center for South Asian Quantitative Health and Education, School of Public Health, Rutgers University, New Brunswick, NJ
ABSTRACT: South Asian American (SA) women are diagnosed with more aggressive breast cancer than non-Hispanic White (NHW) women. Understanding the factors associated with the types of surgery received by these women sheds light on disease management in these culturally distinct populations. We used data on age at diagnosis, stage, grade, estrogen and progesterone receptors, and surgery from 4,590 SA and 429,030 NHW breast cancer cases in the Surveillance, Epidemiology and End Results (SEER) program. We used logistic regression with surgery as the binary outcome (subcutaneous, total, or radical mastectomy (STRM) versus partial mastectomy, no, unknown or other (PNUM)) and included additive effects of all the variables and interactions of age, stage, grade, and estrogen and progesterone receptors with race/ethnicity. Type I error of 5% was used to assess statistical significance of the effects. SA were significantly more likely than NHW cases to receive STRM relative to PNUM surgery among women diagnosed at or after age 50 years and having localized stage disease (Odds Ratio (OR) = 1.27, 95% Confidence Interval (CI) = 1.06 – 1.52). Further, SA were significantly less likely than NHW cases to receive STRM relative to PNUM surgery among those diagnosed before age 50 years and having regional or distant stage disease (OR = 0.75, 95% CI = 0.59 – 0.95 for age at diagnosis < 40 years; OR = 0.77, 95% CI = 0.62 – 0.95 for age at diagnosis 40-49 years). The type of surgery received by SA and NHW women differ according to age at diagnosis and disease stage. 
KEYWORDS: Breast Cancer; Surgery; Cancer Health Equity; Disease Characteristics; South Asian American; Non-Hispanic White; Logistic Regression; Interaction

p. 25. The Effect of Perceived Uncertainty on Competitive Behavior
Duncan James Drewry & Zachary Reese
Weinberg Institute for Cognitive Science, University of Michigan, Ann Arbor, MI
Department of Psychology, University of Michigan, Ann Arbor, MI
ABSTRACT: How do people behave in the face of uncertainty? Some studies suggest that even when they are unaware of how others will behave, people default to cooperative behavior; however, other research suggests that uncertainty leads to more competitive behavior. Little research has examined how individual differences moderate such behavioral decisions. This study proposes that a stable (dispositional) sense of justice may, ironically, lead to more competitive behavior. Specifically, people who score highly in belief in a just world, system justification, and religiosity, and low in ambiguity tolerance may be more inclined to compete rather than cooperate because they believe people who experience positive outcomes deserve those outcomes regardless of the means taken to achieve them. Across two studies, participants (N = 288) engaged in a prisoner’s dilemma game — a task where they must choose to compete or cooperate — and completed the aforementioned individual difference measures. Results show that people tended to cooperate, but those high in system justification and belief in a just world were more likely to compete. In other words, people with a strong sense of cosmic justice were likely to exhibit competitive behavior under uncertain conditions.
KEYWORDS: Ambiguity Tolerance; Competition; Cooperation; Just World Beliefs; Prisoner’s Dilemma; Prosocial Behavior; Religiosity; System Justification; Uncertainty

Volume 12, Issue 1, August 2014

Volume 12 Issue 1 August 2014 interactive pdf


Design Techniques for the DNA Cubic-Lattice

Tyler Hotte and Miranda LaRocque

A Student Approach to a Mathematical Simulation of a Racing Electric Vehicle

Fernando Daniel León-Cázares and Daniel Xoconostle-Luna

Proteomic Study of Ribosomal Proteins from Escherichia coli, Saccharomyces cerevisiae, Bos taurus, Gallus gallus, and Oncorhynchus tshawytscha: Application in a Teaching Laboratory Setting

Yoshihiro Miura, Eric Yeager, James A. MacKenzie, and Kestutis Bendinskas

A Cellular Automaton Model for Traffic Flow -Investigating the Effect of Turning

Tracy Finner and Matthew A. Beauregard

On Deflection of Potentially Dangerous Asteroids

Josh Fixelle and Mikhail Kagan


August 2014 articles (full details and links):


Design Techniques for the DNA Cubic-Lattice


Tyler Hotte and Miranda LaRocque

Saint Michael’s College, One Winooski Park, Colchester, VT 05439 USA

Link to PDF  Link to Supplemental Information

Abstract: We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for self-assembling cubic lattices.  Our objective is a mathematical design strategy that can be expanded systematically to any size cubic lattice.  This design consists of threading a scaffolding strand of DNA through the lattice that is secured in place by short staple strands of DNA.  We first add augmenting edges to the cubic lattice to enable a single scaffolding strand threading.   We then thread the scaffolding strand through the augmented cube in a way that minimizes the number of different vertex configurations in the structure.

Key Words: Watson-Crick, DNA Self-Assembly, Origami folding, Cubic Lattice, Scaffolding Strand, Threading, Staple Strands

Student Authors’ Bios: Miranda LaRocque graduated from Saint Michael’s College with a BS degree in Mathematics in May 2014. She is currently working as an Actuarial Systems Analyst at National Life Group, a life insurance company in Montpelier, Vermont.
Tyler Hotte graduated from the Saint Michael’s College and the University of Vermont in May 2014 with a BS degree in Mechanical Engineering (minor in math). He is currently living in Burlington, VT and works as a Timber Framer for Vermont Frames in Starksboro, VT.

Press Summary: DNA nanostructures are nanoscale structures made of self-assembling DNA, which can be used for biomolecular computing, targeted drug delivery, and biosensors. We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for a cubic lattice. Our methods involve a single scaffolding strand of DNA and short staple strands of DNA that secure the scaffolding strand into the shape of a cubic lattice. Our objective was a mathematical design strategy that could be expanded systematically for self-assembly of any size cubic lattice.


A Student Approach to a Mathematical Simulation of a Racing Electric Vehicle


Fernando Daniel León-Cázares and Daniel Xoconostle-Luna

Instituto Tecnológico y de Estudios Superiores de Monterrey Campus Estado de México

Link to PDF

Abstract: A program was developed using the software Mathematica to simulate the dynamical behavior of an electric racing car, an electrathon. In conjunction with experimental data it is focused to allow the Borregos-CEM Racing Team decide which settings have to be adjusted in order to increase the velocity of the racing car while decreasing its energy consumption, i.e. the current demanded to the batteries.

Keywords: Model, electric, racing, vehicle, dynamic, simulation, Electrathon

Student Authors’ Bios: Fernando León-Cázares is a senior student in the area of mechanical engineering in Instituto Tecnológico y de Estudios Superiores de Monterrey Campus Estado de México. He was the Electrathon Borregos CEM Racing’s captain for two years and he has participated in a research group in the same institute dealing with the mathematical modeling of a plasma nitriding process. Daniel Xoconostle-Luna is a mechatronics engineering student who began to work full time in 2013.

Press Summary: An Electrathon is a custom built electric vehicle, similar in appearance to a Go-Kart but powered by an electric motor. We developed a mathematical model to simulate the performance of such vehicle under different conditions so that it is possible to predict its velocity, acceleration and energy consumption at any point of any specific track. This allows for the optimization of different parameters of the vehicle to build the best Electrathon possible.


Proteomic Study of Ribosomal Proteins from Escherichia coli, Saccharomyces cerevisiae, Bos taurus, Gallus gallus, and Oncorhynchus tshawytscha: Application in a Teaching Laboratory Setting


Yoshihiro Miura1,2, Eric Yeager2, James A. MacKenzie2, Kestutis Bendinskas1*

1Department of Chemistry and 2Department of Biological Sciences, SUNY-Oswego

Link to PDF  Link to Supplemental Information

Abstract: Ribosomes are central to protein synthesis and our understanding of ribosomes has advanced antibiotics research. The proteomic study of ribosomes presented here utilizes a combination of differential centrifugation and matrix assisted laser desorption/ionization – time of flight mass spectrometry (MALDI-TOF MS) to analyze ribosomes from various species in a teaching laboratory setting. Five biologically varied species were used: Escherichia coli (bacteria), Saccharomyces cerevisiae (yeast), Bos taurus (cow), Gallus gallus (chicken), and Oncorhynchus tshawytscha (Chinook salmon). Samples were lysed, ribosomes were isolated via ultracentrifugation using a discontinuous sucrose gradient and the individual protein subunits were separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis. Tryptic digest and MALDI-TOF MS were then conducted on fifteen bands excised from the gel, and the mass spectra of both the whole protein sample and peptides were analyzed. Five out of these fifteen bands were positively identified as various ribosomal proteins, with two uncertain identifications. Additionally, three of the five positively identified proteins that travelled the same distance on the gel were determined to be orthologous. Finally, a class of 14 Biochemistry II students utilized these protocols, identified 3 ribosomal proteins and provided their evaluations of the ultracentrifugation-proteomics teaching laboratory.

Key Words: Proteomics, MALDI-TOF MS, ultracentrifugation, ribosomes, teaching laboratory

Student Authors’ Bios: Yoshihiro Miura graduated from SUNY Oswego in December 2012 with a BS in Biochemistry and Biology. He chose to get his D.P.T. degree at Columbia University, NYC, New York.

Eric Yeager graduated from the State University of New York (SUNY) at Oswego in May, 2010 with a BS degree in Zoology (minor in Chemistry). He is currently living in Ithaca, NY, while attending the New York State College of Veterinary Medicine at Cornell University pursuing his Doctorate in Veterinary Medicine (DVM).

Press Summary: Ribosomes are central to protein synthesis and our understanding of ribosomes has advanced antibiotics research. We purified ribosomes and then ribosomal proteins and identified some of those proteins in five species: bacteria, yeast, salmon, chicken, and cow. We taught these advanced techniques to a class of biochemistry students. We suggest that other biochemists could use our protocols for teaching ultracentrifugation and proteomics in their teaching laboratories.


A Cellular Automaton Model for Traffic Flow -Investigating the Effect of Turning


Tracy Finner1 & Matthew A. Beauregard2

1 Department of Mathematics, University of Arizona, AZ

2 Department of Mathematics, Baylor University, Waco, TX

Link to PDF 

Abstract: A cellular automaton model is proposed, modeling vehicular traffic flow on a two dimensional lattice in which the vehicles turn at an intersection with a given probability. It is shown that the introduction of turning reduces the long-term average velocity, and can be predicted by a power law depending on the probability of a vehicle turning and the density of cars. The reduction in speed decreases rapidly once the light cycle length surpasses a certain threshold, the value of which can be predicted from the observed power law.

Keywords: cellular automaton, traffic flow, traffic light strategy, turning, dynamical systems, power law

Student Authors’ Bios:

Tracy Finner worked on this project during her senior year (2010-2011) at the University of Arizona. She finished her M.Sc. in industrial engineering in the spring of 2014. She is now an Industrial Engineer at Raytheon.

Press Summary: “Traffic flow models are central to urban planners and developers.  In this paper, a traffic flow model is proposed that models the interaction between individual vehicles and subsequent driver behavior to the traffic light system.  The model is then used to develop empirical evidence for a statistical correlation between the density of vehicles, frequency of turning vehicles, and the timing of the traffic signal.”


On Deflection of Potentially Dangerous Asteroids


Josh Fixelle and Mikhail Kagan

Department of Science and Engineering, The Pennsylvania State University, Abington, 1600 Woodland Road, Abington, PA 19116, USA

Link to PDF 

Abstract: As has been widely discussed recently, our planet may become a target for asteroids. We consider several scenarios proposed to prevent asteroid collisions with Earth. The asteroid 99942 Apophis is considered as a typical representative. Among others, the recent “gravitational tractor” scenario is discussed. For a simplistic toy-model we obtain estimates for both the mass of the tractor and the amount of fuel required to tow a potentially dangerous asteroid off-course so as to avoid a collision with the Earth. In addition, we analyze two more scenarios titled “sling-shot” and “bumping”, and comment on their relative efficiency compared to the ‘towing” scenario. Based on the analysis, the bumping scenario looks most promising.

KeyWords: Near-Earh Objects, 99942 Apophis, Asteroid Deflection, Gravitational Tractor, “Bumping” Scenario, “Sling-shot” Scenario

Student Authors’ Bios: Joshua Fixelle graduated from the Pennsylvania State University in December, 2013 with BS degrees in Astronomy & Astrophysics and Engineering Science & Mechanics (minors in Mathematics and Physics). He is currently living in Evanston, IL, while attending Northwestern University pursuing his Doctorate in Astrophysics (PhD).

Press Summary: As has been widely discussed recently, our planet may become a target for asteroids (the asteroid 99942 Apophis is considered as a typical representative). We considered several scenarios proposed to prevent asteroid collisions with Earth, including the “gravitational tractor”, “sling-shot”, and “bumping” scenarios. We analyzed and compared the scenarios in regards to their relative efficiency compared to the “gravitational tractor”, and concluded that the bumping scenario looks most promising.