Project description:Understanding neurological disorders necessitates systems-level approaches that integrate multimodal data, but progress has been hindered by limited sample availability, and the absence of combined electrophysiological and molecular data from live patients. Here, we demonstrate that stereo electroencephalography (sEEG)—stereologically-implanted electrodes routinely used for monitoring epilepsy—enables the integration of RNA sequencing and epigenome maps with in vivo recordings and brain imaging. Here we report a method MoPEDE (Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes) that enables this by recovering extensive protein-coding transcripts and DNA methylation profiles from explanted depth electrodes containing matched electrophysical and radiological data, hence allowing for high-resolution reconstructions of brain structure and function in patients. Our proof-of-concept study shows that epilepsies of different etiologies have distinct molecular landscapes and identifies transcripts correlating with neurophysiological signals, including immediate early genes, inflammation markers, and axon guidance molecules. Additionally, we identify DNA methylation profiles indicative of transcriptionally permissive or restrictive chromatin states. While gene expression gradients corresponded with the assigned epileptogenicity index, we found outlier molecular fingerprints in some electrodes, potentially indicating seizure spread or generation zones not detected during clinical assessments. These findings validate that RNA profiles and genome-wide epigenetic data from explanted sEEGs offer high-resolution surrogate molecular landscapes of brain activity. This revolutionary approach has the potential to enhance diagnostic decisions and deepen our understanding of epileptogenic processes.
Project description:Understanding neurological disorders necessitates systems-level approaches that integrate multimodal data, but progress has been hindered by limited sample availability, and the absence of combined electrophysiological and molecular data from live patients. Here, we demonstrate that stereo electroencephalography (sEEG)—stereologically-implanted electrodes routinely used for monitoring epilepsy—enables the integration of RNA sequencing and epigenome maps with in vivo recordings and brain imaging. Here we report a method MoPEDE (Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes) that enables this by recovering extensive protein-coding transcripts and DNA methylation profiles from explanted depth electrodes containing matched electrophysical and radiological data, hence allowing for high-resolution reconstructions of brain structure and function in patients. Our proof-of-concept study shows that epilepsies of different etiologies have distinct molecular landscapes and identifies transcripts correlating with neurophysiological signals, including immediate early genes, inflammation markers, and axon guidance molecules. Additionally, we identify DNA methylation profiles indicative of transcriptionally permissive or restrictive chromatin states. While gene expression gradients corresponded with the assigned epileptogenicity index, we found outlier molecular fingerprints in some electrodes, potentially indicating seizure spread or generation zones not detected during clinical assessments. These findings validate that RNA profiles and genome-wide epigenetic data from explanted sEEGs offer high-resolution surrogate molecular landscapes of brain activity. This revolutionary approach has the potential to enhance diagnostic decisions and deepen our understanding of epileptogenic processes.
Project description:In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar
Project description:ntracranial electroencephalography (EEG) is commonly used to study epileptogenesis and epilepsy in experimental models. Chronic gliosis and neurodegeneration at the injury site are known to be associated with surgically implanted electrodes in both humans and experimental models. Currently, however, there are no reports on the impact of intracerebral electrodes on proteins in the hippocampus and proinflammatory cytokines in the cerebral cortex and plasma in experimental models. We used an unbiased, label-free proteomics approach to identify the altered proteins in the hippocampus, and multiplex assay for cytokines in the cerebral cortex and plasma of C57BL/6J mice following bilateral surgical implantation of electrodes into the cerebral hemispheres.
Project description:Desulfovibrio ferrophilus IS5 was incubated on indium-tin oxide (ITO) electrodes poised at −0.4 V and −0.5 V (versus standard hydrogen electrode) in H-type reactors for 10 days. Total RNA was extracted from cells after incubation, and RNA fragments were purified and transcribed into cDNA. cDNA was sequenced by NovaSeq 6000 System.