Biology subjects

Elmer, J.

Publications and source records attributed to Elmer, J..

3 recordsLinked to original sources

bioRxiv2018

An algorithm for automated, noninvasive detection of cortical spreading depolarizations based on EEG simulations

We present a novel signal processing algorithm for automated, noninvasive detection of Cortical Spreading Depolarizations (CSDs) using electroencephalography (EEG) signals and validate the algorithm on simulated EEG signals. CSDs are waves of neurochemical changes that suppress neuronal activity as they propagate across the brains cortical surface. CSDs are believed to mediate secondary brain damage after brain trauma and cerebrovascular diseases like stroke. We address key challenges in detecting CSDs from EEG signals: (i) decay of high spatial frequencies as they travel from the cortical surface to the scalp surface; and (ii) presence of sulci and gyri, which makes it difficult to track the CSD waves as they travel across the cortex. Our algorithm detects and tracks \"wavefronts\" of the CSD wave, and stitches together data across space and time to decide on the presence of a CSD wave. To test our algorithm, we provide different models and complex patterns of CSD waves, including different widths of CSD suppressions, and use these models to simulate scalp EEG signals using head models of 4 subjects from the OASIS dataset. Our results suggest that the average width of suppression that a low-density EEG grid of 40 electrodes can detect is 1.1 cm, which includes a vast majority of CSD suppressions, but not all. A higher density EEG grid having 340 electrodes can detect complex CSD patterns as thin as 0.43 cm (less than minimum widths reported in prior works), among which single-gyrus propagation is the hardest to detect because of its small suppression area.

bioengineering↗

bioRxiv2018

Small Molecule Inhibition of the Innate Immune Response Increases Transgene Expression

Foreign molecules like plasmid DNA trigger a complex and potent innate immune response comprised of highly redundant signal transduction cascades that result in the activation of transcription factors and the production of inflammatory cytokines. Unfortunately, this defense mechanism can hinder gene therapy by inhibiting transgene expression. The goal of this study was to increase transgene expression by inhibiting key components of the innate immune response ({beta}-catenin, NF-{kappa}B/AP1, TBK1, TLR9, and p38 MAPK) with small molecule inhibitors (iCRT-14, curcumin, BX-795, E6446, and VX-702 respectively). The effects of each drug on transgene (luciferase) expression, inflammatory cytokine (IL-6) levels, and cell viability were quantified in prostate (PC3), breast (MCF-7), and murine bladder (MB49) cancer cell lines. The {beta}-catenin inhibitor iCRT-14 (1 M) provided the highest enhancement of 35.5 {+/-} 19-fold in MCF-7 cells, while the other inhibitors increased transgene expression at a more modest level (2-9 fold). The optimal concentrations of iCRT-14, curcumin, and VX-702 showed no significant effect on cell proliferation; however, optimal concentrations of BX-795 and E6446 did significantly reduce cell proliferation. Nonetheless, inhibition of the innate immune response by iCRT-14 and curcumin was confirmed by a concomitant decrease in IL-6 production in PC3 cells. These results demonstrate that these inhibitors can improve gene therapy by preventing an inflammatory innate immune response.

bioengineering↗

bioRxiv2018

Enhancement of Transgene Expression by NF-Y and CTCF

If a transgene is effectively delivered to a cell, its expression may still be limited by epigenetic mechanisms that silence the transgene. Indeed, once the transgene reaches the nucleus, it may be bound by histone proteins and condensed into heterochromatin or associated with repressor proteins that block transcription. In this study, we sought to enhance transgene expression by adding binding motifs for several different epigenetic enzymes either upstream or downstream of two promoters (CMV and EF1). Screening these plasmids revealed that luciferase expression was enhanced 10-fold by the addition of a CCAAT box just upstream of the EF1 promoter to recruit nuclear transcription factor Y (NF-Y), while inserting a CCCTC-binding factor (CTCF) motif downstream of the EF1 promoter enhanced expression 14-fold (14.03 {+/-} 6.54). ChIP assays confirmed that NF-Y and CTCF bound to the motifs that were added to each plasmid, but the presence of NF-Y and CTCF did not significantly affect the levels of histone acetylation (H3K9ac). Overall, these result show that transgene expression from the EF1 promoter can be significantly increased with motifs that recruit NF-Y or CTCF.

bioengineering↗