Publications by category
Journal articles
Castro I, Richards DM, Metz J, Costello JL, Passmore JB, Schrader TA, Gouveia A, Ribeiro D, Schrader M (2018). A role for MIRO1 in motility and membrane dynamics of peroxisomes.
Traffic Full text.
Richards DM, Endres RG (2017). How cells engulf: a review of theoretical approaches to phagocytosis.
Reports on Progress in Physics,
80(12), 126601-126601.
Full text.
Richards DM, Endres RG (2016). Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis.
Proceedings of the National Academy of Sciences of USAAbstract:
Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis
Phagocytosis and receptor-mediated endocytosis are vitally important particle uptake mechanisms in many cell types, ranging from single-cell organisms to immune cells. In both processes, engulfment by the cell depends critically on both particle shape and orientation. However, most previous theoretical work has focused only on spherical particles and hence disregards the wide-ranging particle shapes occurring in nature, such as those of bacteria. Here, by implementing a simple model in one and two dimensions, we compare and contrast receptor-mediated endocytosis and phagocytosis for a range of biologically relevant shapes, including spheres, ellipsoids, capped cylinders, and hourglasses. We find a whole range of different engulfment behaviors with some ellipsoids engulfing faster than spheres, and that phagocytosis is able to engulf a greater range of target shapes than other types of endocytosis. Further, the 2D model can explain why some nonspherical particles engulf fastest (not at all) when presented to the membrane tip-first (lying flat). Our work reveals how some bacteria may avoid being internalized simply because of their shape, and suggests shapes for optimal drug delivery.
Abstract.
Full text.
Micali G, Aquino G, Richards DM, Endres RG (2015). Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation. PLOS Computational Biology, 11(6), e1004222-e1004222.
Richards DM, Saunders TE (2015). Spatiotemporal Analysis of Different Mechanisms for Interpreting Morphogen Gradients. Biophysical Journal, 108(8), 2061-2073.
Richards DM, Endres RG (2014). The Mechanism of Phagocytosis: Two Stages of Engulfment. Biophysical Journal, 107(7), 1542-1553.
Richards D, Berry S, Howard M (2013). Illustrations of Mathematical Modeling in Biology: Epigenetics, Meiosis, and an Outlook. Cold Spring Harbor Symposia on Quantitative Biology, 77(0), 175-181.
Richards DM, Hempel AM, Flärdh K, Buttner MJ, Howard M (2012). Mechanistic basis of branch-site selection in filamentous bacteria.
PLoS Computational Biology,
8(3).
Abstract:
Mechanistic basis of branch-site selection in filamentous bacteria
Many filamentous organisms, such as fungi, grow by tip-extension and by forming new branches behind the tips. A similar growth mode occurs in filamentous bacteria, including the genus Streptomyces, although here our mechanistic understanding has been very limited. The Streptomyces protein DivIVA is a critical determinant of hyphal growth and localizes in foci at hyphal tips and sites of future branch development. However, how such foci form was previously unknown. Here, we show experimentally that DivIVA focus-formation involves a novel mechanism in which new DivIVA foci break off from existing tip-foci, bypassing the need for initial nucleation or de novo branch-site selection. We develop a mathematical model for DivIVA-dependent growth and branching, involving DivIVA focus-formation by tip-focus splitting, focus growth, and the initiation of new branches at a critical focus size. We quantitatively fit our model to the experimentally-measured tip-to-branch and branch-to-branch length distributions. The model predicts a particular bimodal tip-to-branch distribution results from tip-focus splitting, a prediction we confirm experimentally. Our work provides mechanistic understanding of a novel mode of hyphal growth regulation that may be widely employed. © 2012 Richards et al.
Abstract.
Richards DM, Greer E, Martin AC, Moore G, Shaw PJ, Howard M (2012). Quantitative Dynamics of Telomere Bouquet Formation. PLoS Computational Biology, 8(12), e1002812-e1002812.
Flärdh K, Richards DM, Hempel AM, Howard M, Buttner MJ (2012). Regulation of apical growth and hyphal branching in Streptomyces. Current Opinion in Microbiology, 15(6), 737-743.
Hempel AM, Cantlay S, Molle V, Wang S-B, Naldrett MJ, Parker JL, Richards DM, Jung Y-G, Buttner MJ, Flardh K, et al (2012). The Ser/Thr protein kinase AfsK regulates polar growth and hyphal branching in the filamentous bacteria Streptomyces. Proceedings of the National Academy of Sciences, 109(35), E2371-E2379.
Richards DM (2008). The one-loop five-graviton amplitude and the effective action. Journal of High Energy Physics, 2008(10), 042-042.
Richards DM (2008). The one-loopH2R3andH2(∇H)2Rterms in the effective action. Journal of High Energy Physics, 2008(10), 043-043.
Publications by year
2018
Castro I, Richards DM, Metz J, Costello JL, Passmore JB, Schrader TA, Gouveia A, Ribeiro D, Schrader M (2018). A role for MIRO1 in motility and membrane dynamics of peroxisomes.
Traffic Full text.
2017
Richards DM, Endres RG (2017). How cells engulf: a review of theoretical approaches to phagocytosis.
Reports on Progress in Physics,
80(12), 126601-126601.
Full text.
2016
Richards DM, Endres RG (2016). Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis.
Proceedings of the National Academy of Sciences of USAAbstract:
Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis
Phagocytosis and receptor-mediated endocytosis are vitally important particle uptake mechanisms in many cell types, ranging from single-cell organisms to immune cells. In both processes, engulfment by the cell depends critically on both particle shape and orientation. However, most previous theoretical work has focused only on spherical particles and hence disregards the wide-ranging particle shapes occurring in nature, such as those of bacteria. Here, by implementing a simple model in one and two dimensions, we compare and contrast receptor-mediated endocytosis and phagocytosis for a range of biologically relevant shapes, including spheres, ellipsoids, capped cylinders, and hourglasses. We find a whole range of different engulfment behaviors with some ellipsoids engulfing faster than spheres, and that phagocytosis is able to engulf a greater range of target shapes than other types of endocytosis. Further, the 2D model can explain why some nonspherical particles engulf fastest (not at all) when presented to the membrane tip-first (lying flat). Our work reveals how some bacteria may avoid being internalized simply because of their shape, and suggests shapes for optimal drug delivery.
Abstract.
Full text.
2015
Micali G, Aquino G, Richards DM, Endres RG (2015). Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation. PLOS Computational Biology, 11(6), e1004222-e1004222.
Richards DM, Saunders TE (2015). Spatiotemporal Analysis of Different Mechanisms for Interpreting Morphogen Gradients. Biophysical Journal, 108(8), 2061-2073.
2014
Richards DM, Endres RG (2014). The Mechanism of Phagocytosis: Two Stages of Engulfment. Biophysical Journal, 107(7), 1542-1553.
2013
Richards D, Berry S, Howard M (2013). Illustrations of Mathematical Modeling in Biology: Epigenetics, Meiosis, and an Outlook. Cold Spring Harbor Symposia on Quantitative Biology, 77(0), 175-181.
2012
Richards DM, Hempel AM, Flärdh K, Buttner MJ, Howard M (2012). Mechanistic basis of branch-site selection in filamentous bacteria.
PLoS Computational Biology,
8(3).
Abstract:
Mechanistic basis of branch-site selection in filamentous bacteria
Many filamentous organisms, such as fungi, grow by tip-extension and by forming new branches behind the tips. A similar growth mode occurs in filamentous bacteria, including the genus Streptomyces, although here our mechanistic understanding has been very limited. The Streptomyces protein DivIVA is a critical determinant of hyphal growth and localizes in foci at hyphal tips and sites of future branch development. However, how such foci form was previously unknown. Here, we show experimentally that DivIVA focus-formation involves a novel mechanism in which new DivIVA foci break off from existing tip-foci, bypassing the need for initial nucleation or de novo branch-site selection. We develop a mathematical model for DivIVA-dependent growth and branching, involving DivIVA focus-formation by tip-focus splitting, focus growth, and the initiation of new branches at a critical focus size. We quantitatively fit our model to the experimentally-measured tip-to-branch and branch-to-branch length distributions. The model predicts a particular bimodal tip-to-branch distribution results from tip-focus splitting, a prediction we confirm experimentally. Our work provides mechanistic understanding of a novel mode of hyphal growth regulation that may be widely employed. © 2012 Richards et al.
Abstract.
Richards DM, Greer E, Martin AC, Moore G, Shaw PJ, Howard M (2012). Quantitative Dynamics of Telomere Bouquet Formation. PLoS Computational Biology, 8(12), e1002812-e1002812.
Flärdh K, Richards DM, Hempel AM, Howard M, Buttner MJ (2012). Regulation of apical growth and hyphal branching in Streptomyces. Current Opinion in Microbiology, 15(6), 737-743.
Hempel AM, Cantlay S, Molle V, Wang S-B, Naldrett MJ, Parker JL, Richards DM, Jung Y-G, Buttner MJ, Flardh K, et al (2012). The Ser/Thr protein kinase AfsK regulates polar growth and hyphal branching in the filamentous bacteria Streptomyces. Proceedings of the National Academy of Sciences, 109(35), E2371-E2379.
2008
Richards DM (2008). The one-loop five-graviton amplitude and the effective action. Journal of High Energy Physics, 2008(10), 042-042.
Richards DM (2008). The one-loopH2R3andH2(∇H)2Rterms in the effective action. Journal of High Energy Physics, 2008(10), 043-043.
