Benthic diatom assemblages as indicators of water quality in the Everglades and three tropical karstic wetlands

Limestone-based (karstic) freshwater wetlands of the Everglades, Belize, Mexico, and Jamaica are distinctive in having a high biomass of CaCO3-rich periphyton mats. Diatoms are common components of these mats and show predictable responses to environmental variation, making them good candidates for assessing nutrient enrichment in these naturally ultraoligotrophic wetlands. However, aside from in the Everglades of southern Florida, very little research has been done to document the diatoms and their environmental preferences in karstic Caribbean wetlands, which are increasingly threatened by eutrophication. We identified diatoms in periphyton mats collected during wet and dry periods from the Everglades and similar freshwater karstic wetlands in Belize, Mexico, and Jamaica. We compared diatom assemblage composition and diversity among locations and periods, and the effect of the limiting nutrient, P, on species composition among locations. We used periphyton-mat total P (TP) as a metric of availability. A total of 176 diatom species in 45 genera were recorded from the 4 locations. Twenty-three of these species, including 9 that are considered indicative of Everglades diatom flora, were found in all 4 locations. In Everglades and Caribbean sites, we identified assemblages and indicator species associated with low and high periphyton-mat TP and calculated TP optima and tolerances for each indicator species. TP optima and tolerances of indicator species differed between the Everglades and the Caribbean, but weighted averaging models predicted periphyton-mat TP concentrations from diatom assemblages at Everglades (R2  =  0.56) and Caribbean (R2  =  0.85) locations. These results show that diatoms can be effective indicators of water quality in karstic wetlands of the Caribbean, but application of regionally generated transfer functions to distant sites provides less reliable estimates than locally developed functions.

Seizure detection in subdural recordings using nonlinear decision functions

This dissertation proposed a new approach to seizure detection in intracranial EEG recordings using nonlinear decision functions. It implemented well-established features that were designed to deal with complex signals such as brain recordings, and proposed a 2-D domain of analysis. Since the features considered assume both the time and frequency domains, the analysis was carried out both temporally and as a function of different frequency ranges in order to ascertain those measures that were most suitable for seizure detection. In retrospect, this study established a generalized approach to seizure detection that works across several features and across patients. ^ Clinical experiments involved 8 patients with intractable seizures that were evaluated for potential surgical interventions. A total of 35 iEEG data files collected were used in a training phase to ascertain the reliability of the formulated features. The remaining 69 iEEG data files were then used in the testing phase. ^ The testing phase revealed that the correlation sum is the feature that performed best across all patients with a sensitivity of 92% and an accuracy of 99%. The second best feature was the gamma power with a sensitivity of 92% and an accuracy of 96%. In the frequency domain, all of the 5 other spectral bands considered, revealed mixed results in terms of low sensitivity in some frequency bands and low accuracy in other frequency bands, which is expected given that the dominant frequencies in iEEG are those of the gamma band. In the time domain, other features which included mobility, complexity, and activity, all performed very well with an average a sensitivity of 80.3% and an accuracy of 95%. ^ The computational requirement needed for these nonlinear decision functions to be generated in the training phase was extremely long. It was determined that when the duration dimension was rescaled, the results improved and the convergence rates of the nonlinear decision functions were reduced dramatically by more than a 100 fold. Through this rescaling, the sensitivity of the correlation sum improved to 100% and the sensitivity of the gamma power to 97%, which meant that there were even less false negatives and false positives detected. ^

Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions

Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA both in vivo and in vitro. This phenomenon has been explained by a “twin-supercoiled-domain” model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In E. coli cells, transcription-induced topological change of chromosomal DNA is expected to actively remodel chromosomal structure and greatly influence DNA transactions such as transcription, DNA replication, and recombination. In this study, an IPTG-inducible, two-plasmid system was established to study transcription-coupled DNA supercoiling (TCDS) in E. coli topA strains. By performing topology assays, biological studies, and RT-PCR experiments, TCDS in E. coli topA strains was found to be dependent on promoter strength. Expression of a membrane-insertion protein was not needed for strong promoters, although co-transcriptional synthesis of a polypeptide may be required. More importantly, it was demonstrated that the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. These phenomenon can be explained by the “twin-supercoiled-domain” model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA. Additionally, in order to explore whether TCDS is able to greatly influence a coupled DNA transaction, such as activating a divergently-coupled promoter, an in vivo system was set up to study TCDS and its effects on the supercoiling-sensitive leu-500 promoter. The leu-500 mutation is a single A-to-G point mutation in the -10 region of the promoter controlling the leu operon, and the AT to GC mutation is expected to increase the energy barrier for the formation of a functional transcription open complex. Using luciferase assays and RT-PCR experiments, it was demonstrated that transient TCDS, “confined” within promoter regions, is responsible for activation of the coupled transcription initiation of the leu-500 promoter. Taken together, these results demonstrate that transcription is a major chromosomal remodeling force in E. coli cells.