Publications by authors named "David G Ackerman"

8 Publications

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Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain.

Cell 2019 09 5;179(1):268-281.e13. Epub 2019 Sep 5.

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA. Electronic address:

Neuronal cell types are the nodes of neural circuits that determine the flow of information within the brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of cell type and reveals how individual neurons route their output across the brain. Despite the importance of morphology, few projection neurons in the mouse brain have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the brain. We used this platform to reconstruct more than 1,000 projection neurons in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed neurons constitute more than 85 meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of projection neurons and suggest organizational principles of long-range connectivity.
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http://dx.doi.org/10.1016/j.cell.2019.07.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754285PMC
September 2019

Membrane Bending Moduli of Coexisting Liquid Phases Containing Transmembrane Peptide.

Biophys J 2018 05;114(9):2152-2164

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York. Electronic address:

A number of highly curved membranes in vivo, such as epithelial cell microvilli, have the relatively high sphingolipid content associated with "raft-like" composition. Given the much lower bending energy measured for bilayers with "nonraft" low sphingomyelin and low cholesterol content, observing high curvature for presumably more rigid compositions seems counterintuitive. To understand this behavior, we measured membrane rigidity by fluctuation analysis of giant unilamellar vesicles. We found that including a transmembrane helical GWALP peptide increases the membrane bending modulus of the liquid-disordered (Ld) phase. We observed this increase at both low-cholesterol fraction and higher, more physiological cholesterol fraction. We find that simplified, commonly used Ld and liquid-ordered (Lo) phases are not representative of those that coexist. When Ld and Lo phases coexist, GWALP peptide favors the Ld phase with a partition coefficient of 3-10 depending on mixture composition. In model membranes at high cholesterol fractions, Ld phases with GWALP have greater bending moduli than the Lo phase that would coexist.
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http://dx.doi.org/10.1016/j.bpj.2018.03.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961461PMC
May 2018

Line Tension Controls Liquid-Disordered + Liquid-Ordered Domain Size Transition in Lipid Bilayers.

Biophys J 2017 Apr;112(7):1431-1443

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York. Electronic address:

To better understand animal cell plasma membranes, we studied simplified models, namely four-component lipid bilayer mixtures. Here we describe the domain size transition in the region of coexisting liquid-disordered (Ld) + liquid-ordered (Lo) phases. This transition occurs abruptly in composition space with domains increasing in size by two orders of magnitude, from tens of nanometers to microns. We measured the line tension between coexisting Ld and Lo domains close to the domain size transition for a variety of lipid mixtures, finding that in every case the transition occurs at a line tension of ∼0.3 pN. A computational model incorporating line tension and dipole repulsion indicated that even small changes in line tension can result in domains growing in size by several orders of magnitude, consistent with experimental observations. We find that other properties of the coexisting Ld and Lo phases do not change significantly in the vicinity of the abrupt domain size transition.
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http://dx.doi.org/10.1016/j.bpj.2017.02.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390056PMC
April 2017

Effects of Transmembrane α-Helix Length and Concentration on Phase Behavior in Four-Component Lipid Mixtures: A Molecular Dynamics Study.

J Phys Chem B 2016 05 27;120(17):4064-77. Epub 2016 Apr 27.

Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States.

We used coarse-grained molecular dynamics simulations to examine the effects of transmembrane α-helical WALP peptides on the behavior of four-component lipid mixtures. These mixtures contain a high-melting temperature (high-Tm) lipid, a nanodomain-inducing low-Tm lipid, a macrodomain-inducing low-Tm lipid and cholesterol to model the outer leaflet of cell plasma membranes. In a series of simulations, we incrementally replace the nanodomain-inducing low-Tm lipid by the macrodomain-inducing low-Tm lipid and measure how lipid and phase properties are altered by the addition of WALPs of different length. Regardless of the ratio of the two low-Tm lipids, shorter WALPs increase domain size and all WALPs increase domain alignment between the two leaflets. These effects are smallest for the longest WALP tested, and increase with increasing WALP concentration. Thus, our simulations explain the experimental observation that WALPs induce macroscopic domains in otherwise nanodomain-forming lipid-only mixtures (unpublished). Since the cell plasma membrane contains a large fraction of transmembrane proteins, these findings link the behavior of lipid-only model membranes in vitro to phase behavior in vivo.
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http://dx.doi.org/10.1021/acs.jpcb.6b00611DOI Listing
May 2016

Lipid bilayers: clusters, domains and phases.

Essays Biochem 2015 ;57:33-42

Department of Molecular Biology and Genetics, Field of Biophysics, Cornell University, Ithaca, NY 14853, U.S.A.

In the present chapter we discuss the complex mixing behaviour of plasma membrane lipids. To do so, we first introduce the plasma membrane and membrane mixtures often used to model its complexity. We then discuss the nature of lipid phase behaviour in bilayers and the distinction between these phases and other manifestations of non-random mixing found in one-phase mixtures, such as clusters, micelles and microemulsions. Finally, we demonstrate the applicability of Gibbs phase diagrams to the study of increasingly complex model membrane systems, with a focus on phase coexistence, morphology and their implications for the cell plasma membrane.
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http://dx.doi.org/10.1042/bse0570033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377075PMC
October 2015

Multiscale modeling of four-component lipid mixtures: domain composition, size, alignment, and properties of the phase interface.

J Phys Chem B 2015 Mar 22;119(11):4240-50. Epub 2015 Jan 22.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States.

Simplified lipid mixtures are often used to model the complex behavior of the cell plasma membrane. Indeed, as few as four components-a high-melting lipid, a nandomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol)-can give rise to a wide range of domain sizes and patterns that are highly sensitive to lipid compositions. Although these systems are studied extensively with experiments, the molecular-level details governing their phase behavior are not yet known. We address this issue by using molecular dynamics simulations to analyze how phase separation evolves in a four-component system as it transitions from small domains to large domains. To do so, we fix concentrations of the high-melting lipid 16:0,16:0-phosphatidylcholine (DPPC) and chol, and incrementally replace the nanodomain-inducing low-melting lipid 16:0,18:2-PC (PUPC) by the macrodomain-inducing low-melting lipid 18:2,18:2-PC (DUPC). Coarse-grained simulations of this four-component system reveal that lipid demixing increases as the amount of DUPC increases. Additionally, we find that domain size and interleaflet alignment change sharply over a narrow range of replacement of PUPC by DUPC, indicating that intraleaflet and interleaflet behaviors are coupled. Corresponding united atom simulations show that only lipids within ∼2 nm of the phase interface are significantly perturbed regardless of domain composition or size. Thus, whereas the fraction of interface-perturbed lipids is negligible for large domains, it is significant for smaller ones. Together, these results reveal characteristic traits of bilayer thermodynamic behavior in four-component mixtures, and provide a baseline for investigation of the effects of proteins and other lipids on membrane phase properties.
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http://dx.doi.org/10.1021/jp511083zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377067PMC
March 2015

Limited perturbation of a DPPC bilayer by fluorescent lipid probes: a molecular dynamics study.

J Phys Chem B 2013 May 19;117(17):4844-52. Epub 2013 Apr 19.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States.

The properties of lipid bilayer nanometer-scale domains could be crucial for understanding cell membranes. Fluorescent probes are often used to study bilayers, yet their effects on host lipids are not well understood. We used molecular dynamics simulations to investigate perturbations in a fluid DPPC bilayer upon incorporation of three indocarbocyanine probes: DiI-C18:0, DiI-C18:2, or DiI-C12:0. We find a 10-12% decrease in chain order for DPPC in the solvation shell nearest the probe but smaller effects in subsequent shells, indicating that the probes significantly alter only their local environment. We also observe order perturbations of lipids directly across from the probe in the opposite leaflet. Additionally, the DPPC headgroup phosphorus-to-nitrogen vector of lipids nearest the probe exhibits preferential orientation pointing away from the DiI. We show that, while DiI probes perturb their local environment, they do not strongly influence the average properties of "nanoscopic" domains containing a few hundred lipids.
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http://dx.doi.org/10.1021/jp400289dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280801PMC
May 2013
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