Multimedia
Filter :
Publication date
Article type
Subject
Single-Cell Studies of Phage λ: Hidden Treasures Under Occam's Rug: Video 7
A video from the 2016 review by Ido Golding "Single-Cell Studies of Phage λ: Hidden Treasures Under Occam’s Rug" from the Annual Review of Virology.
Shown: Spatiotemporal dynamics of phage (red) and bacterial (green) genome loci inside the infected Escherichia coli cell during the lysogenic pathway (see Figure 2b ). The phage genome is labeled using mCherry-ParB. In the same cell the bacterial attB site is detected using an orthogonal ParB system and a GFP. For more information see Tal et al. 2014 PNAS 111:7308–12. Video courtesy of Louis McLane and Samuel Skinner; Golding lab (unpublished).
Single-Cell Studies of Phage λ: Hidden Treasures Under Occam's Rug: Video 8
A video from the 2016 review by Ido Golding "Single-Cell Studies of Phage λ: Hidden Treasures Under Occam’s Rug" from the Annual Review of Virology.
Shown: Spatiotemporal dynamics of the phage genome inside the cell during the lytic pathway. At t = 0 min the cell is infected by a gpD-YFP-labeled phage (green). At t = 5 min a SeqA-ECFP focus corresponding to the injected phage DNA appears. Later this focus is converted to two foci corresponding to two hemimethylated phage DNAs. The cell eventually lyses (not shown). Video reproduced from Shao et al. 2015 Biophys. J. 108:2048–60 with permission from Elsevier.
More than Meets the Eye: Hidden Structures in the Proteome: Video 1
A video from the 2016 review by Hal Wasserman and Erica Ollmann Saphire "More than Meets the Eye: Hidden Structures in the Proteome" from the Annual Review of Virology.
Shown: Morphs modeling how the VP40 dimer might transition to the matrix-assembling linear hexamer (this video) and the RNA-binding octameric ring (Video 2). In each of these videos N-terminal domains are blue and C-terminal domains are orange. In this video construction of the hexamer form the dimer it is modeled that three VP40 dimers gather at the membrane surface. It is hypothesized that an electrostatic interaction with lipid head groups triggers conformational rearrangement and assembly of the hexamer. Note that in the crystal structure of this hexamer (PDB: 4LDD) the central VP40 is upside down. In Video 2 the crystal structure of the octameric ring (PDB: 1H2D; Gomis-Ruth et al. 2003 Structure 11:423–33) reveals a 3-nt RNA bound to each N-terminal domain. RNA is illustrated here as the trigger that begins the conformational rearrangement. However it is not yet known what the trigger of this rearrangement is. We thank Dr. Zachary Bornholdt for the use of these models and videos originally published as supplemental figures in Bornholdt et al. 2013 Cell 154:763–74.
More than Meets the Eye: Hidden Structures in the Proteome: Video 2
A video from the 2016 review by Hal Wasserman and Erica Ollmann Saphire "More than Meets the Eye: Hidden Structures in the Proteome" from the Annual Review of Virology.
Shown: Morphs modeling how the VP40 dimer might transition to the matrix-assembling linear hexamer (Video 1) and the RNA-binding octameric ring (this video). In each of these videos N-terminal domains are blue and C-terminal domains are orange. In Video 1 construction of the hexamer form the dimer it is modeled that three VP40 dimers gather at the membrane surface. It is hypothesized that an electrostatic interaction with lipid head groups triggers conformational rearrangement and assembly of the hexamer. Note that in the crystal structure of this hexamer (PDB: 4LDD) the central VP40 is upside down. In this video the crystal structure of the octameric ring (PDB: 1H2D; Gomis-Ruth et al. 2003 Structure 11:423–33) reveals a 3-nt RNA bound to each N-terminal domain. RNA is illustrated here as the trigger that begins the conformational rearrangement. However it is not yet known what the trigger of this rearrangement is. We thank Dr. Zachary Bornholdt for the use of these models and videos originally published as supplemental figures in Bornholdt et al. 2013 Cell 154:763–74.
More than Meets the Eye: Hidden Structures in the Proteome: Video 3
A video from the 2016 review by Hal Wasserman and Erica Ollmann Saphire "More than Meets the Eye: Hidden Structures in the Proteome" from the Annual Review of Virology.
Shown: A modeled morph between the two folds of lymphotactin. Residues 61–70 have been modeled into the final structure to facilitate the final morph and allow the complete α-helix to be included. The beginning structure is the originally disordered Ltn10 monomeric form that functions as a chemokine (PDB: 1J8I). The final structure is one protomer of the biologically active dimer Ltn40 which functions in chemotaxis (PDB: 1J8I).
The Magellanic Stream: Circumnavigating the Galaxy: Figure 4
A video from the 2016 review by Elena D'Onghia and Andrew J. Fox "The Magellanic Stream: Circumnavigating the Galaxy" from the Annual Review of Astronomy and Astrophysics.
Shown: Gas projection in the simulated Magellanic System (red scale). This model reproduces the length of the Magellanic Stream and Leading Arm as well as the Magellanic Bridge connecting the Small and Large Magellanic Clouds (SMC and LMC). In this animation the SMC has completed three passages around the LMC. Adapted from Besla et al. (2012) with permission.
Visual Adaptation: Supplemental Video 1
A supplemental video from the 2015 review by Michael A. Webster "Visual Adaptation" from the Annual Review of Vision Science.
Shown: Demonstrations of adaptation aftereffects described in the review. For each the same image is presented before or after 10 s of adaptation to an adapting image. The aftereffects refer to changes in the appearance of the image following the adaptation. Images illustrating color and blur aftereffects are courtesy of Menka Webster. Images illustrating face aftereffects are from Matsumoto D Ekman P. 1988. Japanese and Caucasian facial expressions of emotion (JACFEE) and neutral faces (JACneuf). Dep. Psychol. San Francisco State Univ.
Livestock's Lure and Liabilities
Herrero et al. "Livestock and the Environment: What Have We Learned in the Past Decade?" Annual Review of Environment and Resources (2015)
Patterns of Gun Violence in the United States
Wintemute. "The Epidemiology of Firearm Violence in the Twenty-First Century United States" Annual Review of Public Health (2015).
Data Visualization and Statistical Graphics in Big Data Analysis: Video 1
A video from the 2016 review by Dianne Cook Eun-Kyung Lee and Mahbubul Majumder "Data Visualization and Statistical Graphics in Big Data Analysis" from the Annual Review of Statistics and Its Application.
Shown: Still image of video showing plane movements across the United States on a normal day of operations January 19 2006. The video includes red-eye planes leaving the West Coast for the East Coast the East Coast waking up and sporadic delayed flights. The code (including links to the data) is available at https://github.com/heike/usflights. An accompanying video at https://vimeo.com/119233996 shows operations during a northeastern snow day March 13 1993. Used with the permission of Heike Hofmann.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 1
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 1 Unwinding of a single molecule of λ DNA by RecBCD.
This video shows unwinding of a single molecule of λ DNA – stained with YOYO-1 attached to a 1-μm polystyrene bead (stained nonspecifically by YOYO-1) and captured by an optical trap by a single RecBCD enzyme at 37°C in the presence of 1 mM ATP; DNA is extend by solution flow from the bottom to the top. This molecule unwound at ∼440 bp/sec and dissociated after ∼26800 bp. Published with permissions from Reference 30.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 2
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 2 Unwinding of a single molecule of DNA by RecBCD.
This video shows translocation of an individual RecBCD molecule along χ-containing λ DNA visualized by virtue of a fluorescent 40-nm particle attached to a biotinylated RecD subunit. Solution flow is left to right. The very bright spot to the left is the 1-μm polystyrene bead to which nanoparticles are bound nonspecifically in the optical trap. Note that the nanoparticle--RecBCD complex can be seen to pause for about 6.6 s and then it continues to translocate but at a much reduced speed (∼145 bp/sec versus ∼1120 bp/sec prior to χ-recognition). Published with permission from Reference 54.
Data Visualization and Statistical Graphics in Big Data Analysis: Video 2
A video from the 2016 review by Dianne Cook Eun-Kyung Lee and Mahbubul Majumder "Data Visualization and Statistical Graphics in Big Data Analysis" from the Annual Review of Statistics and Its Application.
Shown: Use of interactive graphics to explore rankings of statistics departments in the United States. The plots show rating variables as side-by-side dotplots (left) a cluster analysis (center top) and a scatterplot of 5th-percentile rank computed using the S (vertical) and R (horizontal) methods (center bottom) and institution name lookup (right). Selecting an institution highlights (yellow) its values in each of the other plots. Cornell University is highlighted: We can see that its rank by the two methods differs substantially with a good R rank (around 5) but not such a good S rank (around 30). On the ranking criteria the department is around the middle of the pack: It is average in terms of number of publications and citations has few women faculty and students and accepts students with lower GRE scores than most statistics departments.
Data Visualization and Statistical Graphics in Big Data Analysis: Figure 9
A video from the 2016 review by Dianne Cook Eun-Kyung Lee and Mahbubul Majumder "Data Visualization and Statistical Graphics in Big Data Analysis" from the Annual Review of Statistics and Its Application.
Shown: Eulerian parallel coordinate plots (PCPs) of nutritional measurements of chocolates. The Eulerian PCP more strongly indicates a difference between the two types of chocolate milk (orange) and dark (red) and from the scagnostic describing separation displayed by the histogram (blue) we learn that higher values occur when fiber is one of the two variables indicating its importance as a variable. A simple interaction added to this plot using gridSVG highlights the line closest to the mouse cursor so that we can follow it throughout the plot.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 3
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 3 Interrupting and restarting single molecules of RecBCD during DNA unwinding.
This video compares unwinding of three individual molecules of λ DNA by three different single molecules of RecBCD whose initial velocities are comparable. Solution flow is left to right. For each the bright spot to the left is the 1-μm polystyrene bead to which YOYO-1 is bound nonspecifically in the optical trap. Unwinding is transiently paused by moving the molecules into a solution of EDTA (denoted by “Paused” during the video) and then resumed by returning the molecules to a solution of Mg2+:ATP. The change in relative unwinding rate is visually evident. Videos are representative of data collected and reported in Reference 31 although the video itself is previously unpublished.
Ocean Basin Evolution and Global-Scale Plate Reorganization Events Since Pangea Breakup: Supplemental Video 1
A supplemental video from the 2016 review by R. Dietmar Müller Maria Seton Sabin Zahirovic Simon E. Williams Kara J. Matthews Nicky M. Wright Grace E. Shephard Kayla T. Maloney Nicholas Barnett-Moore Maral Hosseinpour Dan J. Bower and John Cannon "Ocean Basin Evolution and Global-Scale Plate Reorganization Events Since Pangea Breakup" from the Annual Review of Earth and Planetary Sciences.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 4
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 4 Unwinding of a single molecule of λ DNA by RecQ detected using fluorescent SSB and imaged using TIRF microscopy.
Initially the dsDNA tethered at each end to the surface of a flow cell is fluorescent due to intercalation of the YO-PRO-1 dye molecules. As a solution containing 200 mM NaCl is introduced into the flow cell the dye dissociates and fluorescence disappears. Subsequently a solution containing 80 nM RecQ and SSBAF488 is introduced into the flow cell to initiate unwinding. The solution fills the channel 24 s into the video. The flow when on goes from left to right in the video. The elapsed time is indicated in hours:minutes:seconds and scale bar is 5 μm. Published with permission from Reference 73.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 5
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 5 Salt-induced intramolecular condensation of SSB-ssDNA imaged using TIRF microscopy.
Video of a single molecule of SSBAF488-coated λ ssDNA tethered at one end and imaged using TIRF microscopy contracting in length upon increasing [NaOAc] from 0 to 100 mM. Solution flow is left to right. The video frames were rendered into a topological intensity map. Time zero corresponds to the time at which the pump was turned on. The dead time of the experiment was approximately 25 s due to the volume in the lines between the syringe valve and the microfluidic chamber. Published with permission from Reference 102.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 6
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 6 Condensation of SSB in the absence of free protein during a transient increase from 0 to 100 mM NaOAc.
Video of a single molecule of SSBAF488-coated λ ssDNA contracting in length as the salt concentration is increased from 0 to 100 mM NaOAc and then subsequently reduced back to zero mM conducted in the absence of free SSBAF488. Solution flow is left to right. The flow cell was extensively washed with buffer to remove free SSB protein before beginning the experiment. Video recording began when the pump was turned on requiring ∼40-50 s for the dead volume to be flushed from the lines to the flow chamber. SSBAF488 was omitted from both of the high-salt washes and from the 0 mM wash. Published with permission from Reference 102.
Mechanics and Single-Molecule Interrogation of DNA Recombination: Supplemental Video 7
A supplemental video from the 2016 review by Jason C. Bell and Stephen C. Kowalczykowski "Mechanics and Single-Molecule Interrogation of DNA Recombination" from the Annual Review of Biochemistry.
Supplemental Video 7 Direct imaging of nucleation and growth of RecA on SSB-coated ssDNA using TIRF microscopy.
This video first shows a flow-extended single molecule of 3′-biotinylated λ ssDNA coated with a fluorescent protein SSBAF488. The molecule was tethered to a streptavidin-coated glass surface within a microfluidic flow cell and visualized using total internal reflection fluorescence microscopy. Solution flow is left to right. SSBAF488 was exchanged with non-fluorescent SSB on the ssDNA in situ and filament assembly was initiated by injecting fluorescein labeled RecA (350 nM) with nucleotide cofactor (ATPγS). Filament assembly proceeded primarily in the absence of flow or laser excitation which were both used only during brief intermittent time-lapsed imaging. Images were processed and rendered into a topographical intensity map for clarity. Published with permission from Reference 110.