Letter from the Editor

Miami Engineering and Computing Review (MECR) is a student peer-review online journal focused on highlighting exceptional senior design teams and student accomplishments. Beginning in May 2012, MECR is the first student peer review journal produced by Miami Universities College of Engineering and Computing. MECR strives to strike a balance of conforming the senior design project papers into journalistic format while preserving both the differences among engineering disciplines and the reflective senior experience. To this end the articles include reflections written by senior design team members and the reference style has been adjusted to reflect modern footnote style. The editors for the 2012-13 papers consist of six senior engineers with the expectation of publishing in the fall of 2013. The goal was to include work from all departments. Hopefully MECR will continue to grow and highlight exceptional projects and students

Characterization of Ribeye Subunits in Zebrafish Hair Cells Reveals That Exogenous Ribeye B-Domain and CtBP1 Localize to the Basal Ends of Synaptic Ribbons

Synaptic ribbons are presynaptic structures formed by the self-association of RIBEYE–the main structural component of ribbon synapses. RIBEYE consists of two domains: a unique N-terminal A-domain and a C-terminal B-domain that is identical to the transcription co-repressor C-terminal binding protein 2 (CtBP2). Previous studies in cell lines have shown that RIBEYE A-domain alone is sufficient to form ribbon-like aggregates and that both A- and B- domains form homo-and heterotypic interactions. As these interactions are likely the basis for synaptic-ribbon assembly and structural plasticity, we wanted to examine how zebrafish Ribeye A- and B- domains interact with synaptic ribbons in vivo. To that end, we characterized the localization of exogenously expressed Ribeye A- and B- domains and the closely related protein, CtBP1, in the hair cells of transgenic zebrafish larvae. Unexpectedly, exogenously expressed Ribeye A-domain showed variable patterns of localization in hair cells; one zebrafish paralog of A-domain failed to self-associate or localize to synaptic ribbons, while the other self-assembled but sometimes failed to localize to synaptic ribbons. By contrast, Ribeye B-domain/CtBP2 was robustly localized to synaptic ribbons. Moreover, both exogenously expressed B-domain/CtBP2 and CtBP1 were preferentially localized to the basal end of ribbons adjacent to the postsynaptic density. Overexpression of B-domain/CtBP2 also appeared to affect synaptic-ribbon composition; endogenous levels of ribbon-localized Ribeye were significantly reduced as hair cells matured in B-domain/CtBP2 transgenic larvae compared to wild-type. These results reveal how exogenously expressed Ribeye domains interact with synaptic ribbons, and suggest a potential organization of elements within the ribbon body

Study of auxin responsive gene promoters in transient expression assays

Abstract only availableTransfection assays are an important tool for biochemists; the comparatively quick technique allows experimenters to see relative levels of expression of a particular gene in the presence or absence of a plant hormone and/or effector. Transfection assays can be used to study the promoter region of a gene to determine the importance of specific cis-regulatory elements in the control of gene expression. This is accomplished by fusing the promoter region with a reporter gene. A reporter gene allows the expression level of the promoter to be monitored by fluorescence or by other observable properties. Transfection can also be used to study growth substances and various cellular signaling pathways. This technique involves isolating protoplasts from cells such as carrot suspension cells. In order to use these suspension cells, the cell walls must be digested; thus the cells become protoplasts. The experimental DNA (effector and reporter genes) is then introduced into protoplasts by chemical methods. The protoplasts are incubated in the dark and the relative reporter gene activity is then read on a fluorometer. The goal of this project is to determine if two Aux/IAA genes are auxin inducible and what influence specific effectors have on their expression using carrot protoplasts to do transient transfection assays. We study auxin responsive gene promoters because many of them contain auxin responsive cis-regulatory elements designated as Auxin Response Elements (AuxREs), which contain the sequence TGTCTC. These promoters are regulated by at least two groups of transcription factors known as Auxin Response Factors (ARFs) and Aux/IAA proteins. One group of auxin inducible genes is Aux/IAA genes. We studied the Aux/IAA17 and Aux/IAA19 promoter regions by amplifying them through PCR and cloning them upstream of the ß-glucuronidase (GUS) reporter gene open reading frame (ORF). This reporter gene was used because the GUS activity can be detected through fluorescence. The GUS gene was terminated by a nopaline synthase (NOS) terminator cloned downstream of the GUS gene. The effectors used in these studies consisted of ARF proteins translated from ARF effector genes during the transfection process. Results showed that the Aux/IAA19 gene (which has 3 cis-regulatory AuxREs) was inducible by auxin. The ARF effectors influenced the expression of both Aux/IAA genes by positively or negatively regulating their expression. However, auxin was found to have no affect on Aux/IAA17 gene expression. This correlates with the fact that Aux/IAA17 has no AuxREs in its promoter region.Plant Genomics Internship @ M

Tidal Asymmetry Analysis of the Grand Bay, Ms Estuarine System and its Effects on Sediment Transport

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Unstructured Finite Element Mesh Decimation for Real Time Hurricane Storm Surge Forecasting

Motivation: Provide real time decision support Emergency mangers are interested in… When will the water rise? What height will it get? How long will it stay? Who will be impacted? Will mesh decimation give accurate results in order to predict forecasted water levels for storms in a faster time frame than is currently used by larger meshes

Development of a High-Resolution, Wind-Wave, Tide, and Hurricane Storm Surge Model for Southern Mississippi

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Hydrodynamic Assessment of Natural and Nature-Based Features for Escatawpa River and Grand Bay in the Northern Gulf of Mexico

This presentation showcases a hydrodynamic assessment of natural and nature-based features (NNBFs) for the Pascagoula River, the Escatawpa River and Grand Bay, located along the Mississippi coast of the northern Gulf of Mexico. Two separate NNBF projects are being considered to: (1) restore the historical footprint (ca. 1848) of Grand Batture Island for coastal protection purposes; and (2) reconnect the hydraulics between the Escatawpa River and Grand Bay for ecosystem services purposes. The intended coastal protection benefits of the first project include buffering agency to wave attack and attenuation of storm surge with the restored island. The intended ecosystem services benefits of the second project include replenishment of sediments to the salt marsh via increased hydroperiod (duration of tidal inundation) and availability for sediment accumulation. Astronomic tide and storm surge simulations are performed with the advanced circulation (ADCIRC) plus simulating waves nearshore (+SWAN) model to evaluate the hydrodynamic impact of the NNBF projects (Image). The simulated hydrodynamics are assessed firstly in terms of storm surge and waves for the open coast with and without the restoration of Grand Batture Island (Passeri et al., 2015), and secondly for tidal datums and inundation extent for the salt marsh with and without the hydraulic reconnection of the Escatawpa River with Grand Bay (Alizad et al., 2018). A key outcome from the analysis is the interconnectedness of the hydrodynamics within the system, where the implementation of the NNBFs results in local and non-local impacts. The numerical modeling approach with high-resolution feature definition at a system-wide scale affords such methodical evaluation of NNBFs for ecosystem restoration

Melding Wildlife Surveys to Improve Conservation Inference

Integrated models are a popular tool for analyzing species of conservation concern. Species of conservation concern are often monitored by multiple entities that generate several datasets. Individually, these datasets may be insufficient for guiding management due to low spatio-temporal resolution, biased sampling, or large observational uncertainty. Integrated models provide an approach for assimilating multiple datasets in a coherent framework that can compensate for these deficiencies. While conventional integrated models have been used to assimilate count data with surveys of survival, fecundity, and harvest, they can also assimilate ecological surveys that have differing spatio-temporal regions and observational uncertainties. Motivated by independent aerial and ground surveys of lesser prairie-chicken abundance, we developed an integrated modeling approach that assimilates density estimates derived from surveys with distinct sources of observational error into a joint framework that provides shared inference on spatio-temporal trends. For implementation, we model these data using a Bayesian Markov melding approach and apply several data augmentation strategies for efficient sampling. Our integrated model decreased uncertainty in annual density estimates, facilitated prediction at unsampled regions, and quantified the inferential cost associated with reduced survey effort.Comment: 22 pages; 5 figures, 1 table, submitted to Biometric