Jamie A Davies

Jamie A Davies
The University of Edinburgh | UoE · Centre for Integrative Physiology

MA, PhD

About

299
Publications
77,891
Reads
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17,520
Citations
Introduction
My main interest is in biological self-organization. The lab investigates how this operates in normal development, models it in computers and synthetic biological constructs, and uses self-organizing processes for tissue engineering. The lab also hosts two major databases, www.gudmap.org (urogenital development) and the IUPHAR/BPS www.guidetopharmacology.org database of drugs and receptors. I am also involved in public engagement (books, broadcasts etc).
Additional affiliations
April 1995 - present
The University of Edinburgh
Position
  • Professor of Experimental Anatomy
April 1995 - present
The University of Edinburgh
Position
  • Professor of Experiomental Anatomy
Description
  • Teaching undergraduate medicine and science, and post-graduate science and technology. I run various experiments in new teaching techniques, and and a Principal Fellow of the Higher Education Academy
April 1991 - March 1995
The University of Manchester
Position
  • PostDoc Position
Description
  • Cancer Research Campaign Postdoctoral Research Fellow working on cell adhesion in organogenesis.
Education
October 1986 - September 1989
University of Cambridge
Field of study
  • Developmetal Neurobiology
October 1983 - May 1986
University of Cambridge
Field of study
  • Natural Sciences

Publications

Publications (299)
Article
Full-text available
There is intense worldwide effort in generating kidney organoids from pluripotent stem cells, for research, for disease modelling and, perhaps, for making transplantable organs. Organoids generated from pluripotent stem cells (PSC) possess accurate micro-anatomy, but they lack higher-organization. This is a problem, especially for transplantation,...
Article
Full-text available
Kidney explant cultures are an important tool to gain insights into developmental processes, insights that can be used to develop strategies for engineering kidneys from stem cells. However, explants are not connected to a perfused vascular system. This limits their survival and limits physiological studies, for example of blood filtration, the mai...
Article
Full-text available
Advances in regenerative medicine have led to the construction of many types of organoids, which reproduce important aspects of endogenous organs but may be limited or disorganised in nature. While their usefulness for restoring function remains unclear, they have undoubted usefulness in research, diagnostics and toxicology. In toxicology, there is...
Article
Full-text available
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; www.guidetopharmacology.org) is an open-access, expert-curated database of molecular interactions between ligands and their targets. We describe expansion in content over nine database releases made during the last two years, which has focussed on three main areas of infection. The COVID-19 pandemic con...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targe...
Article
Current techniques for making renal organoids generate tissues that show function when transplanted into a host, but they have no ureter through which urine can drain. There are at least 4 possible strategies for adding a ureter: connecting to ta host ureter; inducing an engineered kidney to make a ureter; making a stem-cell derived ureter; and rep...
Article
Background: There is intense interest in replacing kidneys from stem cells. It is now possible to produce, from embryonic or induced pluripotent stem cells, kidney organoids that represent immature kidneys and display some physiologic functions. However, current techniques have not yet resulted in renal tissue with a ureter, which would be needed...
Chapter
Optogenetic approaches facilitate the study of signaling and metabolic pathways in animal cell systems. In the past 10 years, a plethora of light-regulated switches for the targeted control over the induction of gene expression, subcellular localization of proteins, membrane receptor activity, and other cellular processes have been developed and su...
Article
Full-text available
The development of natural tissues, organs and bodies depends on mechanisms of patterning and of morphogenesis, typically (but not invariably) in that order, and often several times at different final scales. Using synthetic biology to engineer patterning and morphogenesis will both enhance our basic understanding of how development works, and prov...
Article
Full-text available
In this review, we identify opportunities for drug discovery in the treatment of COVID‐19 and in so doing, provide a rational roadmap whereby pharmacology and pharmacologists can mitigate against the global pandemic. We assess the scope for targetting key host and viral targets in the mid‐term, by first screening these targets against drugs already...
Article
Full-text available
Given the critical role that the immune system plays in a multitude of diseases, having a clear understanding of the pharmacology of the immune system is crucial to new drug discovery and development. Here we describe the IUPHAR Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb), which connects expert‐curated pharmacology with key immunological concepts and...
Article
Full-text available
We describe a system that automatically generates from a curated database a collection of short conventional publications—citation summaries—that describe the contents of various components of the database. The purpose of these summaries is to ensure that the contributors to the database receive appropriate credit through the currently used measure...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
We focus on three strategies for renal regenerative medicine; administering cells to replace damaged tissue, promoting endogenous regeneration, and growing stem cell-derived organs. Mouse kidney regeneration can be promoted by stem cells injected into the circulation which do not become new kidney tissue but seem to secrete regeneration-promoting h...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www....
Article
Full-text available
The IUPHAR/BPS Guide to PHARMACOLOGY (www.guidetopharmacology.org) is an open-access, expert-curated database of molecular interactions between ligands and their targets. We describe significant updates made over the seven releases during the last two years. The database is notably enhanced through the continued linking of relevant pharmacology wit...
Article
Full-text available
A major feature of twenty-first century medical research is the development of therapeutic strategies that use 'biologics' (large molecules, usually engineered proteins) and living cells instead of, or as well as, the small molecules that were the basis of pharmacology in earlier eras. The high power of these techniques can bring correspondingly hi...
Article
Full-text available
We apply an information‐theoretic measure to anatomical models of the Edinburgh Mouse Atlas Project. Our goal is to quantify the anatomical complexity of the embryo and to understand how this quantity changes as the organism develops through time. Our measure, Structural Entropy, takes into account the geometrical character of the intermingling of...
Article
Full-text available
The path taken by the loop of Henle, from renal cortex to medulla and back, is critical to the ability of the kidney to concentrate urine and recover water. Unlike most developing tubules, which navigate as blind‐ended cylinders, the loop of Henle extends as a sharply bent loop, the apex of which leads the double tubes behind it in a ‘V’ shape. Her...
Article
Full-text available
The origins and functions of kidney macrophages in the adult have been explored, but their roles during development remain largely unknown. Here we characterise macrophage arrival, localisation, heterogeneity, and functions during kidney organogenesis. Using genetic approaches to ablate macrophages, we identify a role for macrophages in nephron pro...
Article
Full-text available
Authors often assert that a key feature of 21st-century synthetic biology is its use of an ‘engineering approach’; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey...
Chapter
Some aspects of renal physiology, in particular transport across tubular epithelia, are highly relevant to pharmacokinetics and to drug toxicity. The use of animals to model human renal physiology is limited, but human-derived renal organoids offer an alternative, relevant system in culture. Here, we explain how the activity of specific transport s...
Article
Full-text available
The database itself is at http://www.guidetoimmunopharmacology.org/immuno/index.jsp
Article
Full-text available
Optogenetic switches are emerging molecular tools for studying cellular processes as they offer higher spatiotemporal and quantitative precision than classical, chemical-based switches. Light-controllable gene expression systems designed to upregulate protein expression levels meanwhile show performances superior to their chemical-based counterpart...
Article
Methods for making specific modifications to the genomes of living cells are powerful research tools. Two methods currently dominate, CRISPR and Cre recombinase. CRISPR has the advantage that it can act on unmodified target genes; Cre has the advantage of being available in drug-inducible versions, allowing temporal control, but it requires enginee...
Article
Full-text available
A major challenge in synthetic biology, particularly for mammalian systems, is the inclusion of adequate external control for the synthetic system activities. Control at the transcriptional level can be achieved by adaptation of bacterial repressor–operator systems (e.g., TetR), but altering the activity of a protein by controlling transcription is...
Article
Full-text available
Connecting chemistry to pharmacology has been an objective of Guide to PHARMACOLOGY (GtoPdb) and its precursor the International Union of Basic and Clinical Pharmacology Database (IUPHAR-DB) since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical struc...
Article
Full-text available
We present path entropy, an information-theoretic measure that captures the notion of patterning due to phase separation in organic tissues. Recent work has demonstrated, both in silico and in vitro, that phase separation in epithelia can arise simply from the forces at play between cells with differing mechanical properties. These qualitative resu...
Book
Organoids and mini-organs combines contributions from leading practitioners who work under the editorial control of an acclaimed researcher who also served for eight years as Editor-in-Chief of the journal Organogenesis, the first journal on this topic. The book begins with an introduction, but then delves into chapters that present advice on how t...
Chapter
Techniques for producing organoids have advanced rapidly over the last few years, and methods are now available to make primitive organoids, at least, to represent a large variety of many organs and tissues. Applying this technology to practical problems will depend on our overcoming three main technical challenges: the ability to make organoids re...
Chapter
Development of the permanent mammalian kidney, the metanephros, relies on complex reciprocal interactions between two nephrogenic cell populations; the branching ureteric bud and the metanephrogenic mesenchyme. Exploiting these interactions in vitro using murine renal progenitor cells allows the formation of self-organizing organoids of differing l...
Chapter
Organoids are three-dimensional assemblies that contain multiple cell types, arranged similarly to the cells in a specific tissue, at least at the micro-scale; mini-organs add to this micro-realism a realistic macro-scale anatomy as well. Researchers have been producing organoids for at least 60 years, initially to explore basic mechanisms of devel...
Article
The mesonephros of mammals is a transient renal structure that contributes to various aspects of mammalian fetal development including the male reproductive system, hematopoietic stem cells and vascular endothelial cells. The mesonephros develops from the intermediate mesoderm and forms tubules that are segmented in a similar way to the nephrons of...
Article
Full-text available
The IUPHAR/BPS Guide to PHARMACOLOGY is an expert‐curated, open‐access database of information on drug targets and the substances that act on them. This unit describes the procedures for searching and downloading ligand‐target binding data and for finding detailed annotations and the most relevant literature. The database includes concise overviews...
Article
Here, we present a detailed protocol on setting up embryonic renal organ cultures using a culture method that we have optimised for anatomical maturation and imaging. Our culture method places kidney rudiments on glass in a thin film of medium, which results in very flat cultures with all tubules in the same image plane. For reasons not yet underst...
Preprint
Full-text available
Connecting chemistry to pharmacology (c2p) has been an objective of GtoPdb and its precursor IUPHAR-DB since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents and the protein targets in the assays (D-A-R...
Preprint
Connecting chemistry to pharmacology (c2p) has been an objective of GtoPdb and its precursor IUPHAR-DB since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents and the protein targets in the assays (D-A-R...
Article
Background: The term druggable genome was coined in 2002 for the estimate of 10% of the human proteome likely to bind small molecules with lead-like chemical properties and sufficient binding affinity for activity modulation. A number of databases now provide protein target lists based largely on chemistry-to-protein mappings extracted from the lit...
Article
Introduction: The pharmacological literature and patents connect compound structures to their bioactivity. However, entombing these relationships among millions of PDFs is seriously problematic. The situation is ameliorated by resources that extract data relationships the authors put in to their PDFs back out into structured database records. The I...
Article
Background: NC-IUPHAR has the primary objective of issuing guidelines for the nomenclature and classification of receptors and ion channels, as well as all the targets of current/future prescription medicines. NC-IUPHAR has addressed many important questions, issues and controversies in pharmacology, and has overseen the development and expert-driv...
Article
Introduction: GtoPdb has been traditionally focused on the pharmacology associated with non-infectious diseases [1]. However, in October of 2017 we initiated a collaboration with Medicines for Malaria Venture (MMV) in Geneva, where we have been piloting the curation of antimalarial compounds and Plasmodium targets for approved drugs and the global...
Article
Background: The IUPHAR/BPS Guide to PHARMACOLOGY database (GtoPdb) is an open access, expert-curated, online database of human drug targets and their ligands. It provides succinct overviews, key references and recommended experimental ligands for 2,800 targets and related proteins organised into families. The database includes 9,000 ligand molecule...
Preprint
p>A major challenge in synthetic biology, particularly for mammalian systems, is inclusion of adequate external control for the synthetic system activities. Control at the transcriptional level can be achieved by adaptation of bacterial repressor-operator systems (e.g. TetR), but altering the activity of a protein by controlling transcription is in...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 is the third in this series of biennial publications. This version provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmac...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
Full-text available
The Concise Guide to PHARMACOLOGY 2017/18 provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand...
Article
In this issue of Cell Stem Cell, Taguchi and Nishinakamura (2017) describe a carefully optimized method for making a branch-competent ureteric bud, a tissue fundamental to kidney development, from mouse embryonic stem cells and human induced pluripotent stem cells. The work illuminates embryology and has important implications for making more reali...