AJUR Volume 13 Issue 4 (December 2016)

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Click on the link below to download the full high-definition interactive pdf for
AJUR Volume 13 Issue 4 (December 2016)

https://doi.org/10.33697/ajur.2016.029

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

p. 5 Green Chemistry: Comparison of Ionic Liquid vs Conventional Solvent for
Indole Alkylation

https://doi.org/10.33697/ajur.2016.030

Jonathan G. Redrico & John L. Krstenansky
ABSTRACT
A comparison of the effectiveness of two synthetic methods was done for a green chemistry method using an ionic liquid-based solvent relative to a conventional method using organic solvents for the N-alkylation of indole. The green method used potassium hydroxide in the ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate, followed by addition of the alkyl halide. The conventional method used sodium hydride in dimethylformamide. Possible advantages of the green method would be the use of a non-volatile solvent, the possibility of recycling the solvent, and the use of a less reactive base. However, its reaction yield was lower than for the conventional method, the reagent expense was higher, and recycling and reuse of the ionic solvent require considerable amounts of conventional solvent to clean it up sufficiently for reuse. On a laboratory scale, the ionic liquid method yielded neither a “green” nor an efficiency advantage. It is possible that with optimization on an industrial scale involving solvent reclamation that the green method could realize its promise.
KEYWORDS
Green Chemistry; Sustainable Chemistry; Ionic Liquids; N-alkylation; Indole; Solvent Recycling; Organic Chemistry; 1-Butyl-3-methylimidazolium Tetrafluoroborate; Synthesis

p. 11 Use of the Bruker AXS SMART BREEZE™ System for Macromolecular
X-ray Data Collection

https://doi.org/10.33697/ajur.2016.031

Christiana Standler, G. Blake Overson, Cody A. Black, Guizella A. Rocabado,
& Bruce R. Howard
ABSTRACT
The Bruker AXS SMART BREEZE™ system is a single-crystal X-ray diffractometer designed to collect data from crystals of small organic or inorganic compounds. It is typically equipped with a Molybdenum-anode sealed tube to facilitate data collection from small unit cells. We recently acquired this system, but chose to have it installed with a copper-anode sealed tube with the hope of using it to collect data from larger unit cells such as those found in crystals of proteins or other macromolecules. This is the first and only BREEZE™ system installed by Bruker AXS with a copper-anode to date. Here we show that this system is capable of efficiently collecting quality X-ray diffraction data from crystals of the enzymes lysozyme and xylanase. This capability to collect diffraction data from both macromolecular and small-molecule crystals greatly expands the scope of undergraduate research projects that can be addressed using this instrument.
KEYWORDS
X-ray; Diffraction; Crystallography; Diffractometer; Protein; Enzyme; Crystal; Structure

p. 21 Ebola Impact and Quarantine in a Network Model

https://doi.org/10.33697/ajur.2016.032

Anca Radulescu & Joanna Herron
ABSTRACT
Much effort has been directed towards using mathematical models to understand and predict contagious disease, in particular Ebola outbreaks. Classical SIR (susceptible-infected-recovered) compartmental models capture well the dynamics of the outbreak in certain communities, and accurately describe the differences between them based on a variety of parameters. However, repeated resurgence of Ebola contagions suggests that there are components of the global disease dynamics that we don’t yet fully understand and can’t effectively control. In order to understand the dynamics of a more widespread contagion, we placed SIR models within the framework of dynamic networks, with the communities at risk of contracting the virus acting as nonlinear systems, coupled based on a connectivity graph. We study how the effects of the disease (measured as the outbreak impact and duration) change with respect to local parameters, but also with changes in both short-range and long-range connectivity patterns in the graph. We discuss the implications of optimizing both these measures in increasingly realistic models of coupled communities.
KEYWORDS
Epidemic Spread; Network Dynamics; Network Connectivity; Coupled Differential Equations; Compartmental Model; Information Transfer; Outbreak Impact; Outbreak Duration

p. 37 Analysis of Vortex Pool-and-Chute Fishway

https://doi.org/10.33697/ajur.2016.033

Mathew Nyberg, Brian Draeger, Brian Weekly, Eileen Cashman, & Michael Love
ABSTRACT
Fishways are constructed in riverine habitats where structures such as culverts, dams, and flood channels have negatively impacted flow conditions suitable for the movement of native and migratory fish species. These auxiliary channels are engineered to resist gravitational force with frictional force, resulting in sustained depth and reduced velocity over a range of design flow rates. The Chézy hydraulic resistance coefficient accounts for such forces and provides a metric useful for determining the effectiveness of a fishway to alter flow conditions prohibitive to the passage of fish. The objective of this analysis was to use a scale model of an innovative vortex pool-and-chute fishway, that operates with both plunging and streaming flow simultaneously, designed by Michael Love and Associates, to determine the Chézy resistance coefficients over a range of flow rates under controlled hydraulic conditions. Using dimensional analysis to ensure proper scaling allowed laboratory measurements of the model to be translated into a real-world prototype design. The conceptual prototype fishway is a 144-foot-long by 30-foot-wide channel with an 8% slope. A 1:15 scale model was constructed to evaluate the design at prototype equivalent flow rates between 58 and 283 cubic feet per second (cfs). Chézy coefficients were estimated by two different calculation methods; the streaming flow method and the streaming and plunging flow method. Coefficients ranging between 22.3 and 39.2 ft1/2/s were determined by the streaming flow calculation method, whereas the streaming and plunging flow calculation method yielded estimates from 18.9 to 25.0 ft1/2/s at corresponding flow rates. For flows that were exclusively plunging, values of 32.2 to 41.9 ft1/2/s were found. In general, Chézy coefficient estimates were observed to decrease with increasing discharge and values were found to be comparable to those calculated for fishways implemented at similar slopes. The preliminary model fishway results indicated that implementation of a prototype fishway could effectively alter flows for adequate fish passage under the given conditions.
KEYWORDS
Hydraulics; Fish Passage; Fishway; Chézy Coefficient; Geometric Scaling; Froude Scaling; Streaming Flow; Plunging Flow; Dimensional Analysis; Similitude

p. 59 Dynamic Visualization of Time-Based Changes to Data Generated by
Reddit.com: The Real Time Conversation Project

https://doi.org/10.33697/ajur.2016.034

Daniel Wang, Andy Luse, & Jim Burkman
ABSTRACT
With the increased amount of data generated by social networking sites there is also increased difficulty in the analysis of this data, including time-based changes, which can provide unique insights in social network analysis. Information visualization is a vital tool in assisting social scientists with analysis of large quantities of data; however, the gathering, formatting, and visualizing of time-related data from social networking sites still remains an obstacle. This research explores the process of gathering time-based data in real time and using dynamic visualization techniques to visualize and analyze time-based changes in data generated by discussions on the social networking site Reddit. The outcome culminates in our deliverable, the Real Time Conversation Project.
KEYWORDS
Visualization; Network Analysis; Social Network; Reddit; Gephi

p. 69 Effects similar to anxiolysis in an organic extract of Stypopodium zonale on an anxiety-related behavior in Drosophila melanogaster

https://doi.org/10.33697/ajur.2016.035

Keysh Mejías, Grisel Robles, Zulmari Martínez, Anamaris Torres, Lee Algarín, Genesis López, & Ricardo Chiesa
ABSTRACT
Nature has a great diversity of organisms whose bioactive compounds may potentially be studied. When it comes to aquatic life we find that algae are organisms that are well suited for screening and identification of bioactive compounds due to their widespread distribution in both salt and freshwater. Our hypothesis is that a crude organic extract of the brown algae Stypopodium zonale can decrease anxiety-related behaviors in Drosophila melanogaster. Stypopodium zonale was collected in the south coast of Puerto Rico and the potential anxiolytic-like effects of the extract were studied in an anxiogenic-like behavioral paradigm in Drosophila melanogaster. This behavior is called centrophobia and is measured using an Open Field Arena (OFA). Validation of the paradigm gave the expected results as reported in the literature, in which Drosophila exhibits a phobia (avoidance) of remaining in the center of the OFA, which corresponds to a behavior with anxiety components. The organic extract was dissolved with dimethyl sulfoxide (DMSO). Toxicity tests were performed both for DMSO and the crude organic extract, and neither showed positive results. To perform the behavioral trials, 1 mL of the crude extract and 4 mL of water were mixed with 1.8 g of Drosophila food. The final concentration of the crude extract in the food was 5.4 mg/mL. The adult flies were grown in a tube with the extract until a considerable quantity of larvae was observed, and then the adults were removed. These new larvae, once turned into adult flies, were used for the behavioral trials. The behavior of control flies (food without extract) and experimental flies (extract containing food) was recorded with a video camera and the results of the centrophobic behavior were analyzed and compared using quantitative criteria. Both the control and experimental trials were performed in triplicate. The results show that flies grown in food containing the crude extract present a significant reduction in centrophobia compared with control flies. In conclusion, our results suggest that the organic crude extract from Stypopodium zonale has anxiolytic-like effects in a Drosophila melanogaster model with anxiety components. We are currently performing Nuclear Magnetic Resonance (NMR) studies on the crude extracts to identify the most abundant secondary metabolites. Future experiments should include the administration of the crude extracts (or fractions of the most abundant secondary metabolites) to a vertebrate model in to test the effect in a behavior with anxiety components. We are also in the process of developing a preliminary model of possible mechanisms of action of the crude organic extract in the reduction of centrophobia.
KEYWORDS
Anxiety; Algae; Drosophila melanogaster; Open Field Arena; Organic extracts; Centrophobia; Stypopodium zonale