A Semiquantitative Analysis of the Chorda Tympani Taste Pathway in the Rat Brain with the 2-deoxyglucose Method

This thesis is based on a semiquantitative analysis of four nuclear relay centers [nucleus tractus solitarius (NTS), parabrachial nucleus (PBN), ventroposteromedial nucleus (VPM), gustatory neocortex (GNC)] in the chorda tympani nerve pathway. Metabolic changes were examined by the 2-deoxyglucose method in which one chorda tympani nerve was chemically stimulated and its contralateral side lesioned. Coronal sections of four taste centers were prepared for autoradiography and Nissl staining. Densities of the autoradiograms were determined by means of a video based image processor. Relative differences in the optical density ratios of the stimulated versus lesioned nuclear grey matter areas to white matter areas indicate an effect of the stimulation on the uptake of the radioactive glucose analog. Greater 2-deoxyglucose uptake on the intact side reflects increased cellular functional activity which was noted in the first (NTS) and possibly the second (PBN) levels of the chorda tympani pathway. The highest brain levels showed no significant changes in glucose metabolism. The 2-deoxyglucose method was verified in this study by several criteria and the neuroanatomy of the chorda tympani is discussed. Also, improvements for the study of the taste pathway using the 2-deoxyglucose method are suggested. Metabolic increases in some taste nuclei support the thesis that the chorda tympani projection pathway as reported in previous literature can be demonstrated and analyzed semiquantitatively using the 2-deoxyglucose method

Expanded encyclopaedias of DNA elements in the human and mouse genomes

All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.© The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article