Bart E. Vos, Luka C. Liebrand, Mahsa Vahabi, Andreas Biebricher, Gijs J. L. Wuite, Erwin J. G. Peterman, Nicholas A. Kurniawan, Fred C. MacKintosh and Gijsje H. Koenderink
Fibrous networks are ideal functional materials since they provide mechanical rigidity at low weight. Here, we demonstrate that fibrous networks of the blood clotting protein fibrin undergo a strong and irreversible increase in their mechanical rigidity in response to uniaxial compression. This rigidification can be precisely controlled by the level of applied compressive strain, providing a means to program the network rigidity without having to change its composition. To identify the underlying mechanism we measure single fiber–fiber interactions using optical tweezers. We further develop a minimal computational model of cohesive fiber networks that shows that stiffening arises due to the formation of new bonds in the compressed state, which develop tensile stress when the network is re-expanded. The model predicts that the network stiffness after a compression cycle obeys a power-law dependence on tensile stress, which we confirm experimentally. This finding provides new insights into how biological tissues can adapt themselves independently of any cellular processes, offering new perspectives to inspire the design of reprogrammable materials.
DOI
Monday, November 20, 2017
Optical trapping of nanoparticles with tunable inter-distance using a multimode slot cavity
Lin Wang, Yongyin Cao, Tongtong Zhu, Rei Feng, Fangkui Sun, and Weiqiang Ding
Optical trapping of nano-objects (i.e., the nano-tweezers) has been investigated intensively. Most of those nano-tweezers, however, were focused on the trapping of a single nanoparticle, while the interactions between them were seldom considered. In this work, we propose a nano-tweezers in a slot photonic crystal cavity supporting multiple modes, where the relative positions of two trapped nanoparticles can be tuned by selective excitation of different resonant mode. Results show that both the nanoparticles are trapped at the center of the cavity when the first order mode is excited. When the incident source is tuned to the second order mode, however, these two nanoparticles push each other and are trapped stably at two separated positions. Also, the inter-distance between them can be tuned precisely by changing the relative power of the two modes. This provides a potential method to control the interactions between two nano-objects via optically tuning the separation between them, and may have applications in various related disciplinary.
DOI
Optical trapping of nano-objects (i.e., the nano-tweezers) has been investigated intensively. Most of those nano-tweezers, however, were focused on the trapping of a single nanoparticle, while the interactions between them were seldom considered. In this work, we propose a nano-tweezers in a slot photonic crystal cavity supporting multiple modes, where the relative positions of two trapped nanoparticles can be tuned by selective excitation of different resonant mode. Results show that both the nanoparticles are trapped at the center of the cavity when the first order mode is excited. When the incident source is tuned to the second order mode, however, these two nanoparticles push each other and are trapped stably at two separated positions. Also, the inter-distance between them can be tuned precisely by changing the relative power of the two modes. This provides a potential method to control the interactions between two nano-objects via optically tuning the separation between them, and may have applications in various related disciplinary.
DOI
The temporal evolution process from fluorescence bleaching to clean Raman spectra of single solid particles optically trapped in air
Zhiyong Gong, Yong-Le Pan, Gorden Videen, Chuji Wang
We observe the entire temporal evolution process of fluorescence and Raman spectra of single solid particles optically trapped in air. The spectra initially contain strong fluorescence with weak Raman peaks, then the fluorescence was bleached within seconds, and finally only the clean Raman peaks remain. We construct an optical trap using two counter-propagating hollow beams, which is able to stably trap both absorbing and non-absorbing particles in air, for observing such temporal processes. This technique offers a new method to study dynamic changes in the fluorescence and Raman spectra from a single optically trapped particle in air.
DOI
DOI
Engineering Cell Surface Function with DNA Origami
Ehsan Akbari, Molly Y. Mollica, Christopher R. Lucas, Sarah M. Bushman, Randy A. Patton, Melika Shahhosseini, Jonathan W. Song, Carlos E. Castro
A specific and reversible method is reported to engineer cell-membrane function by embedding DNA-origami nanodevices onto the cell surface. Robust membrane functionalization across epithelial, mesenchymal, and nonadherent immune cells is achieved with DNA nanoplatforms that enable functions including the construction of higher-order DNA assemblies at the cell surface and programed cell–cell adhesion between homotypic and heterotypic cells via sequence-specific DNA hybridization. It is anticipated that integration of DNA-origami nanodevices can transform the cell membrane into an engineered material that can mimic, manipulate, and measure biophysical and biochemical function within the plasma membrane of living cells.
DOI
A specific and reversible method is reported to engineer cell-membrane function by embedding DNA-origami nanodevices onto the cell surface. Robust membrane functionalization across epithelial, mesenchymal, and nonadherent immune cells is achieved with DNA nanoplatforms that enable functions including the construction of higher-order DNA assemblies at the cell surface and programed cell–cell adhesion between homotypic and heterotypic cells via sequence-specific DNA hybridization. It is anticipated that integration of DNA-origami nanodevices can transform the cell membrane into an engineered material that can mimic, manipulate, and measure biophysical and biochemical function within the plasma membrane of living cells.
DOI
Wednesday, November 15, 2017
Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution
Hailey L. Gahlon, Louis J. Romano, and David Rueda
Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.
DOI
Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.
DOI
A review on optical actuators for microfluidic systems
Tie Yang, Yue Chen and Paolo Minzioni
During the last few decades microfluidic systems have become more and more popular and their relevance in different fields is continually growing. In fact, the use of microchannels allows a significant reduction of the required sample-volume and opens the way to a completely new set of possible investigations, including the study of the properties of cells, the development of new cells' separation techniques and the analysis of single-cell proteins. One of the main differences between microscopic and macroscopic systems is obviously dictated by the need for suitable actuation mechanisms, which should allow precise control of microscopic fluid volumes and of micro-samples inside the fluid. Even if both syringe-pump and pneumatic-pump technologies significantly evolved and they currently enable sub-μL samples control, completely new approaches were recently developed for the manipulation of samples inside the microchannel. This review is dedicated to describing different kinds of optical actuators that can be applied in microfluidic systems for sample manipulation as well as for pumping. The basic principles underlying the optical actuation mechanisms will be described first, and then several experimental demonstrations will be reviewed and compared.
DOI
During the last few decades microfluidic systems have become more and more popular and their relevance in different fields is continually growing. In fact, the use of microchannels allows a significant reduction of the required sample-volume and opens the way to a completely new set of possible investigations, including the study of the properties of cells, the development of new cells' separation techniques and the analysis of single-cell proteins. One of the main differences between microscopic and macroscopic systems is obviously dictated by the need for suitable actuation mechanisms, which should allow precise control of microscopic fluid volumes and of micro-samples inside the fluid. Even if both syringe-pump and pneumatic-pump technologies significantly evolved and they currently enable sub-μL samples control, completely new approaches were recently developed for the manipulation of samples inside the microchannel. This review is dedicated to describing different kinds of optical actuators that can be applied in microfluidic systems for sample manipulation as well as for pumping. The basic principles underlying the optical actuation mechanisms will be described first, and then several experimental demonstrations will be reviewed and compared.
DOI
Stochastic Optical Trapping and Manipulation of Micro Object with Neural-Network Adaptation
Xiang Li ; Chien Chern Cheah
Optical tweezers are capable of manipulating micro/nano objects without any physical contact, and therefore widely used in biomedical engineering and biological science. While much progress has been achieved in automated optical manipulation of micro objects, Brownian motion is commonly ignored in the stability analysis in order to simplify the control problem. However, random Brownian perturbations exist in micromanipulation problem and therefore may result in failure of optical trapping due to the escape of micro object from the trap. In addition, it is usually assumed in the development of controller that the model of trapping stiffness is known, but the model is difficult to obtain because of its spatially varying feature around the centre of laser beam and variations with laser power and dimensions of objects. In this paper, a neural-network control method is proposed for optical trapping and manipulation of micro object, in the presence of stochastic perturbations and unknown trapping stiffness. The unknown trapping stiffness and dynamic parameters of micro objects, which vary with different laser power settings and sizes of the objects, are approximated by using adaptive neural networks. The stability analysis is carried out from stochastic perspectives, by considering the effect of Brownian motion in the dynamic model. Both experimental results and simulation results are presented.
DOI
Optical tweezers are capable of manipulating micro/nano objects without any physical contact, and therefore widely used in biomedical engineering and biological science. While much progress has been achieved in automated optical manipulation of micro objects, Brownian motion is commonly ignored in the stability analysis in order to simplify the control problem. However, random Brownian perturbations exist in micromanipulation problem and therefore may result in failure of optical trapping due to the escape of micro object from the trap. In addition, it is usually assumed in the development of controller that the model of trapping stiffness is known, but the model is difficult to obtain because of its spatially varying feature around the centre of laser beam and variations with laser power and dimensions of objects. In this paper, a neural-network control method is proposed for optical trapping and manipulation of micro object, in the presence of stochastic perturbations and unknown trapping stiffness. The unknown trapping stiffness and dynamic parameters of micro objects, which vary with different laser power settings and sizes of the objects, are approximated by using adaptive neural networks. The stability analysis is carried out from stochastic perspectives, by considering the effect of Brownian motion in the dynamic model. Both experimental results and simulation results are presented.
DOI
Radiation forces of beams generated by Gaussian mirror resonator on a Rayleigh dielectric sphere
Bin Tang, Kai Chen, Lirong Bian, Xin Zhou, Li Huang & Yi Jin
Optical trapping and manipulating of micron-sized particles have attracted enormous interests due to the potential applications in biotechnology and nanoscience. In this work, we investigate numerically and theoretically the radiation forces acting on a Rayleigh dielectric particle produced by beams generated by Gaussian mirror resonator (GMR) in the Rayleigh scattering regime. The results show that the focused beams generated by GMR can be used to trap and manipulate the particles with both high and low index of refractive near the focus point. The influences of optical parameters of the beams generated by GMR on the radiation forces are analyzed in detail. Furthermore, the conditions for trapping stability are also discussed in this paper.
DOI
Optical trapping and manipulating of micron-sized particles have attracted enormous interests due to the potential applications in biotechnology and nanoscience. In this work, we investigate numerically and theoretically the radiation forces acting on a Rayleigh dielectric particle produced by beams generated by Gaussian mirror resonator (GMR) in the Rayleigh scattering regime. The results show that the focused beams generated by GMR can be used to trap and manipulate the particles with both high and low index of refractive near the focus point. The influences of optical parameters of the beams generated by GMR on the radiation forces are analyzed in detail. Furthermore, the conditions for trapping stability are also discussed in this paper.
DOI
Ferdinando Borghese (26 May 1940–19 January 2017)
M.A. Iatì, R. Saija, O.M. Maragò, P. Denti
Here we summarize the life and scientific legacy of Ferdinando Borghese (1940–2017). He has been a pioneer in the theory and modeling of light scattering by nonspherical particles and clusters in the framework of the transition matrix approach. His work has found applications in many research fields ranging from interstellar dust to aerosol science, plasmonics, and optical trapping.
DOI
Here we summarize the life and scientific legacy of Ferdinando Borghese (1940–2017). He has been a pioneer in the theory and modeling of light scattering by nonspherical particles and clusters in the framework of the transition matrix approach. His work has found applications in many research fields ranging from interstellar dust to aerosol science, plasmonics, and optical trapping.
DOI
Dimerization regulates both deaminase-dependent and deaminase-independent HIV-1 restriction by APOBEC3G
Michael Morse, Ran Huo, Yuqing Feng, Ioulia Rouzina, Linda Chelico & Mark C. Williams
APOBEC3G (A3G) is a human enzyme that inhibits human immunodeficiency virus type 1 (HIV-1) infectivity, in the absence of the viral infectivity factor Vif, through deoxycytidine deamination and a deamination-independent mechanism. A3G converts from a fast to a slow binding state through oligomerization, which suggests that large A3G oligomers could block HIV-1 reverse transcriptase-mediated DNA synthesis, thereby inhibiting HIV-1 replication. However, it is unclear how the small number of A3G molecules found in the virus could form large oligomers. Here we measure the single-stranded DNA binding and oligomerization kinetics of wild-type and oligomerization-deficient A3G, and find that A3G first transiently binds DNA as a monomer. Subsequently, A3G forms N-terminal domain-mediated dimers, whose dissociation from DNA is reduced and their deaminase activity inhibited. Overall, our results suggest that the A3G molecules packaged in the virion first deaminate viral DNA as monomers before dimerizing to form multiple enzymatically deficient roadblocks that may inhibit reverse transcription.
APOBEC3G (A3G) is a human enzyme that inhibits human immunodeficiency virus type 1 (HIV-1) infectivity, in the absence of the viral infectivity factor Vif, through deoxycytidine deamination and a deamination-independent mechanism. A3G converts from a fast to a slow binding state through oligomerization, which suggests that large A3G oligomers could block HIV-1 reverse transcriptase-mediated DNA synthesis, thereby inhibiting HIV-1 replication. However, it is unclear how the small number of A3G molecules found in the virus could form large oligomers. Here we measure the single-stranded DNA binding and oligomerization kinetics of wild-type and oligomerization-deficient A3G, and find that A3G first transiently binds DNA as a monomer. Subsequently, A3G forms N-terminal domain-mediated dimers, whose dissociation from DNA is reduced and their deaminase activity inhibited. Overall, our results suggest that the A3G molecules packaged in the virion first deaminate viral DNA as monomers before dimerizing to form multiple enzymatically deficient roadblocks that may inhibit reverse transcription.
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