The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.
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http://dx.doi.org/10.1152/physiolgenomics.00040.2005 | DOI Listing |
BMC Med Genomics
January 2025
School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, 430065, Hubei, China.
Background: Drug and protein targets affect the physiological functions and metabolic effects of the body through bonding reactions, and accurate prediction of drug-protein target interactions is crucial for drug development. In order to shorten the drug development cycle and reduce costs, machine learning methods are gradually playing an important role in the field of drug-target interactions.
Results: Compared with other methods, regression-based drug target affinity is more representative of the binding ability.
Cardiovasc Diabetol
January 2025
Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Background: Diabetic myocardial disorder (DbMD, evidenced by abnormal echocardiography or cardiac biomarkers) is a form of stage B heart failure (SBHF) at high risk for progression to overt HF. SBHF is defined by abnormal LV morphology and function and/or abnormal cardiac biomarker concentrations.
Objective: To compare the evolution of four DbMD groups based on biomarkers alone, systolic and diastolic dysfunction alone, or their combination.
Genes Brain Behav
February 2025
Laboratory of Addiction Genetics, Department of Pharmaceutical Sciences and Center for Drug Discovery, Northeastern University, Boston, Massachusetts, USA.
Opioid use disorder is heritable, yet its genetic etiology is largely unknown. C57BL/6J and C57BL/6NJ mouse substrains exhibit phenotypic diversity in the context of limited genetic diversity which together can facilitate genetic discovery. Here, we found C57BL/6NJ mice were less sensitive to oxycodone (OXY)-induced locomotor activation versus C57BL/6J mice in a conditioned place preference paradigm.
View Article and Find Full Text PDFBMC Biol
January 2025
Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Diepenbeek, Belgium.
Background: Stress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness.
View Article and Find Full Text PDFBiophys Rep (N Y)
January 2025
UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA,; Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA,; Department of Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA,; California Nano Systems Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA,; Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
Membrane potential (MP) changes can provide a simple readout of bacterial functional and metabolic state or stress levels. While several optical methods exist for measuring fast changes in MP in excitable cells, there is a dearth of such methods for absolute and precise measurements of steady-state membrane potentials (MPs) in bacterial cells. Conventional electrode-based methods for the measurement of MP are not suitable for calibrating optical methods in small bacterial cells.
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