Databases in SenseLab for the genomics, proteomics, and function of olfactory receptors

Bitter Taste and Olfactory Receptors: Beyond Chemical Sensing in the Tongue and the Nose

Abstract

The Up-and-Coming-Scientist section of the current issue of the Journal of Membrane Biology features the invited essay by Dr. Mercedes Alfonso-Prieto, Assistant Professor at the Forschungszentrum Jülich (FZJ), Germany, and the Heinrich-Heine University Düsseldorf, Vogt Institute for Brain Research. Dr. Alfonso-Prieto completed her doctoral degree in chemistry at the Barcelona Science Park, Spain, in 2009, pursued post-doctoral research in computational molecular sciences at Temple University, USA, and then, as a Marie Curie post-doctoral fellow at the University of Barcelona, worked on computations of enzyme reactions and modeling of photoswitchable ligands targeting neuronal receptors. In 2016, she joined the Institute for Advanced Science and the Institute for Computational Biomedicine at the FZJ, where she pursues research on modeling and simulation of chemical senses. The invited essay by Dr. Alfonso-Prieto discusses state-of-the-art modeling of molecular receptors involved in chemical sensing – the senses of taste and smell. These receptors, and computational methods to study them, are the focus of Dr. Alfonso-Prieto’s research. Recently, Dr. Alfonso-Prieto and colleagues have presented a new methodology to predict ligand binding poses for GPCRs, and extensive computations that deciphered the ligand selectivity determinants of bitter taste receptors. These developments inform our current understanding of how taste occurs at the molecular level.

Graphic Abstract

Using a community-engaged health informatics approach to develop a web analytics research platform for sharing data with community stakeholders

Marginalized communities are rarely included in the planning of research relevant to their own health or have access to research data. We implemented a community-based participatory research approach in developing a new health informatics system, WARP (Web Analytics Research Platform), to enable stakeholders to access and analyze research data. We leveraged data from a cohort study of 751 patients in the Transitions Clinic Network (TCN), a network of clinical programs serving patients with a history of incarceration. WARP holds de-identified, patient data, streamlines data processing (i.e. transformation, archival, and partitioning), and has a web analytic tool for users to perform statistical analyses. We used feedback from focus groups of patients with a history of incarceration and workshops with TCN research teams, including patients, community health workers and policymakers, to develop WARP. Our approach advances mechanisms to engage stakeholders in research. Future work will evaluate its effect on community-engagement in research.

ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions

We present here an exploration of the evolution of three well-established, web-based resources dedicated to the dissemination of information related to olfactory receptors (ORs) and their functional ligands, odorants. These resources are: the Olfactory Receptor Database (ORDB), the Human Olfactory Data Explorer (HORDE) and ODORactor. ORDB is a repository of genomic and proteomic information related to ORs and other chemosensory receptors, such as taste and pheromone receptors. Three companion databases closely integrated with ORDB are OdorDB, ORModelDB and OdorMapDB; these resources are part of the SenseLab suite of databases (http://senselab.med.yale.edu). HORDE (http://genome.weizmann.ac.il/horde/) is a semi-automatically populated database of the OR repertoires of human and several mammals. ODORactor (http://mdl.shsmu.edu.cn/ODORactor/) provides information related to OR-odorant interactions from the perspective of the odorant. All three resources are connected to each other via web-links.

Database URL: http://senselab.med.yale.edu; http://genome.weizmann.ac.il/horde/; http://mdl.shsmu.edu.cn/ODORactor/