2017年6月5日（月）
The 785 nm laser diode is the source
Light coupling setup
The setup (Fig. 4g) consists of a beam deflecting mirror (F), an X/Y stage (G) with a custom-made mount, a fixed-focus collimator (B) screwed into a rotation mount, an iris aperture (C), a 100 mm plano-convex lens (D), a 785 nm PM fibre pigtailed laser diode (A) with a typical output power of 7.5 mW, and a silicon CMOS camera to image the coupling (E).
The 785 nm laser diode is the source of incident light and the fibre is terminated with the fixed-focus collimator in a rotation mount, which is used for selection of s/p polarization. S polarization is chosen in this case. The iris aperture is used to control the beam diameter and, by extension, the range of incident angles introduced by the plano-convex lens used to focus the beam on the surface. A larger beam diameter and angular range broadens the range of in-plane propagation angles for the coupled modes. Finally, the beam is reflected onto the stage-mounted sample by a rotating deflection mirror.
The mirror and X/Y stage allow quick optimization of the input coupling conditions. The silicon CMOS cameras are used to capture the light coupling and splitting.Data published in this paper are available from the University of Southampton repository at Additional Information
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The setup (Fig. 4g) consists of a beam deflecting mirror (F), an X/Y stage (G) with a custom-made mount, a fixed-focus collimator (B) screwed into a rotation mount, an iris aperture (C), a 100 mm plano-convex lens (D), a 785 nm PM fibre pigtailed laser diode (A) with a typical output power of 7.5 mW, and a silicon CMOS camera to image the coupling (E).
The 785 nm laser diode is the source of incident light and the fibre is terminated with the fixed-focus collimator in a rotation mount, which is used for selection of s/p polarization. S polarization is chosen in this case. The iris aperture is used to control the beam diameter and, by extension, the range of incident angles introduced by the plano-convex lens used to focus the beam on the surface. A larger beam diameter and angular range broadens the range of in-plane propagation angles for the coupled modes. Finally, the beam is reflected onto the stage-mounted sample by a rotating deflection mirror.
The mirror and X/Y stage allow quick optimization of the input coupling conditions. The silicon CMOS cameras are used to capture the light coupling and splitting.Data published in this paper are available from the University of Southampton repository at Additional Information
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
2017年6月2日（金）
Examination of the unperturbed 210 ns simulations
Discussion
In the design of optogenetic tools, a fundamental limitation of LOV-based systems is the lack of a digital switch from a non-functional off-state to a highly-function on-state. Rather, optogenetic tools have residual activity in both the Light and Dark states thereby limiting their fidelity. To examine the origins of the lack of a digital LOV-based photoswitch, we wished to computationally examine the allosteric activity of LOV based proteins to extract information relevant to the conformational landscape and configurational entropy of Dark and Light states of VVD. In so doing, we discovered an inherent difference in correlating sampling of conformational space with calculations of configurational entropy. Specifically, where the VVD Dark state samples more conformational space, but the Light state has higher configurational entropy. These analyses shed light on the nature of allostery in LOV based photoswitches.
Examination of the unperturbed 210 ns simulations revealed profound differences between the overall dynamics of VVD Dark and Led SMD Bulbs states. Specifically, the Dark state samples more conformational space during the course of 210 ns simulations than the Light state (Fig. 1B). Further, the Dark state samples conformational space, which lie close to the Light state, thereby likely contributing to residual activity in both states and loss of a digital switch as observed in optogenetic tools. The counterintuitive nature of the conformational sampling of the Dark state, could lie in the need to facilitate a fast switch from the dormant Dark state to active Light state and to reduce barriers in the transition. In such a system, the Dark state samples conformational space poised for activity. Blue-light then populates the Light state that is “locked” into specific conformational space to better serve its signaling function.
In the design of optogenetic tools, a fundamental limitation of LOV-based systems is the lack of a digital switch from a non-functional off-state to a highly-function on-state. Rather, optogenetic tools have residual activity in both the Light and Dark states thereby limiting their fidelity. To examine the origins of the lack of a digital LOV-based photoswitch, we wished to computationally examine the allosteric activity of LOV based proteins to extract information relevant to the conformational landscape and configurational entropy of Dark and Light states of VVD. In so doing, we discovered an inherent difference in correlating sampling of conformational space with calculations of configurational entropy. Specifically, where the VVD Dark state samples more conformational space, but the Light state has higher configurational entropy. These analyses shed light on the nature of allostery in LOV based photoswitches.
Examination of the unperturbed 210 ns simulations revealed profound differences between the overall dynamics of VVD Dark and Led SMD Bulbs states. Specifically, the Dark state samples more conformational space during the course of 210 ns simulations than the Light state (Fig. 1B). Further, the Dark state samples conformational space, which lie close to the Light state, thereby likely contributing to residual activity in both states and loss of a digital switch as observed in optogenetic tools. The counterintuitive nature of the conformational sampling of the Dark state, could lie in the need to facilitate a fast switch from the dormant Dark state to active Light state and to reduce barriers in the transition. In such a system, the Dark state samples conformational space poised for activity. Blue-light then populates the Light state that is “locked” into specific conformational space to better serve its signaling function.
2017年6月2日（金）
In the study presented here
In the study presented here, we applied RRS method on the crystallographic structures of VVD Dark and LED Tube China states to systematically compare the impact of each individual residue on overall protein dynamics, and thoroughly explore potential conformational space that is reachable for VVD protein and could serve as guidance for further mutagenesis studies of this protein.
Results
Root-Mean-Square Deviation (RMSD)
The mass weighted RMSD of all atoms for Dark and Light states of VVD are plotted in Fig. 2A. Initially, the LED Candle Lights state has higher RMSD values than the Dark state agreeing with the expectation that Light state is more flexible than the Dark state. However, the RMSD values of the Dark state exceed the Light state around 120 ns of simulation, suggesting a larger conformational space accessible for the Dark state than the Light state. To illustrate and compare the conformational distributions of both Dark and Light states, we projected two simulations onto a two dimensional(2D) contour plots using RMSD values with reference to the optimized Dark and Light states, respectively (Fig. 2B). The unperturbed Dark and Light state simulations display different distributions on the 2D RMSD plots. For 210 ns of simulations, the Light state displays only one basin of attraction, but the Dark state displays three major basins of attraction, with the far right one adjacent to the LED Candle Lights state on the same plot.
Results
Root-Mean-Square Deviation (RMSD)
The mass weighted RMSD of all atoms for Dark and Light states of VVD are plotted in Fig. 2A. Initially, the LED Candle Lights state has higher RMSD values than the Dark state agreeing with the expectation that Light state is more flexible than the Dark state. However, the RMSD values of the Dark state exceed the Light state around 120 ns of simulation, suggesting a larger conformational space accessible for the Dark state than the Light state. To illustrate and compare the conformational distributions of both Dark and Light states, we projected two simulations onto a two dimensional(2D) contour plots using RMSD values with reference to the optimized Dark and Light states, respectively (Fig. 2B). The unperturbed Dark and Light state simulations display different distributions on the 2D RMSD plots. For 210 ns of simulations, the Light state displays only one basin of attraction, but the Dark state displays three major basins of attraction, with the far right one adjacent to the LED Candle Lights state on the same plot.
2017年6月1日（木）
What might be the function of electrotonic signals
Traveling waves conducted as stereotypical action potentials are energy consuming44. Therefore action potentials dissipate with time and annihilate upon collision4. Electrical solitons dissipate, but because of microstructure and the resultant distribution of charge ‘soakage’, the dissipative energy was shown to be conserved. Furthermore, electrical solitons did not annihilate upon collision because unlike action potentials with the refractory period, the electrotonic signals are maintained by the flux associated with the polarization current flowing through the miscrostructure. Therefore, the model possess attributes like stability and elastic interaction upon head-on collision that differ significantly from stereotypical action potentials attributed to CATV splitter the gating currents through the plasma membrane, including unstable pulses serving as threshold conditions for igniting these stereotypical action potentials45.
What might be the function of electrotonic signals propagating along fine distal branchlets? Electrotonic signals without recovery are suitable in transmitting information through physical interaction of electrical charges held by microstructure and not synaptic inputs46. The stable non-decremented electrotonic signals originating in branchlets could play a functional role in heterosynaptic plasticity. Also electrical solitons conserve energy and so they can decode local information permanently. The stable dynamics of electrotonic signals provide a mechanistic explanation to retrieve long-term memories47. Our view is that backpropagating action potentials48 are unencumbered by solitonic conduction for the reason that they become erratic and CATV splitter unpredictable prone to propagation failures at diameters smaller than 0.5 μm49. Based on the permanence of these electrical solitons, it is unlikely that backpropagating action potentials are involved in higher brain functions such as in conceptual tasks. While for those action potentials that are initiated in thin dendrites (see ref. 50 for a review) we propose two specialized interdependent signals in local information processing: (1) dendritic spikes for encoding/imprinting information and (2) solitons for decoding/retrieval information in distal most dendrites of cortical neurons.
What might be the function of electrotonic signals propagating along fine distal branchlets? Electrotonic signals without recovery are suitable in transmitting information through physical interaction of electrical charges held by microstructure and not synaptic inputs46. The stable non-decremented electrotonic signals originating in branchlets could play a functional role in heterosynaptic plasticity. Also electrical solitons conserve energy and so they can decode local information permanently. The stable dynamics of electrotonic signals provide a mechanistic explanation to retrieve long-term memories47. Our view is that backpropagating action potentials48 are unencumbered by solitonic conduction for the reason that they become erratic and CATV splitter unpredictable prone to propagation failures at diameters smaller than 0.5 μm49. Based on the permanence of these electrical solitons, it is unlikely that backpropagating action potentials are involved in higher brain functions such as in conceptual tasks. While for those action potentials that are initiated in thin dendrites (see ref. 50 for a review) we propose two specialized interdependent signals in local information processing: (1) dendritic spikes for encoding/imprinting information and (2) solitons for decoding/retrieval information in distal most dendrites of cortical neurons.
2017年5月31日（水）
I'm Terry Gross
I'd give a dollar for a dime to play that record one more time. GROSS: What a great song. We've heard a lot of great songs today by Eubie Blake. And it's interesting, you know, right before he died when he became celebrated with the help, Robert Kimball, of the book that you wrote and the shows that you worked on with him, his songs were kind of regaining popularity again. And then in the past few years I feel like he's been forgotten all over again (laughter) so, you know, I'd love to hear more of his songs back in circulation. And I want to thank all of you for helping us bring back some of his songs on the show today. It's really been so pleasurable to hear them performed. Thank you pianist Dick Hyman, singer Vernal Bagneris, theater historian Robert Kimball. Thank you. KIMBALL: Thank you. HYMAN: Thank you, Terry. GROSS: Our tribute to Eubie Blake was originally broadcast in 1998 as part of our series on American popular song. Performances of the new backstage musical "Shuffle Along" continue on Broadway until July 24. The new album "Sissle And Blake Sing Shuffle Along" collecting 1921 one recordings was recently released by Harbinger Records. (SOUNDBITE OF MUSIC) GROSS: Our tribute was conceived, researched and produced with project consultant Margaret Pick of Pacific Vista Productions with assistance from Terry Bronson (ph). It was recorded by engineer Mike DeMark at the studios of WNYC in New York and edited by Tracy Tannenbaum (ph). Ann Marie Baldonado did the rebroadcast editing. FRESH AIR's executive producer is Danny Miller. Tomorrow on FRESH AIR, we talk with Larry Tye about his new biography of Robert F. Kennedy, focusing on his transformation from stalwart anti-communist to liberal icon. I hope you'll join us. I'm Terry Gross.
