Direct Integration of Micromachined Pipettes in a Flow Channel for Single DNA Molecule Study by Optical Tweezers

We have developed a micromachined flow cell consisting of a flow channel integrated with micropipettes. The flow cell is used in combination with an optical trap setup (optical tweezers) to study mechanical and structural properties of λ-DNA molecules. The flow cell was realized using silicon micromachining including the so-called buried channel technology to fabricate the micropipettes, the wet etching of glass to create the flow channel,\ud and the powder blasting of glass to make the fluid connections. The volume of the flow cell is 2 µl. The pipettes have a length of 130 m, a width of 5–10 µm, a round opening of 1 um and can be processed with different shapes. Using this flow cell we stretched single molecules (λ-DNA) showing typical force-extension curves also found with conventional techniques. These pipettes can be\ud also used for drug delivery, for injection of small gas bubbles into a liquid flow to monitor the streamlines, and for the mixing of liquids to study diffusion effects. The paper describes the design, the fabrication and testing of the flow cell

Integrated microfluidic biosensing platform for simultaneous confocal microscopy and electrophysiological measurements on bilayer lipid membranes and ion channels

Combining high-resolution imaging and electrophysiological recordings is key for various types of experimentation on lipid bilayers and ion channels. Here, we propose an integrated biosensing platform consisting of a microfluidic cartridge and a dedicated chip-holder to conduct such dual measurements on suspended lipid bilayers, in a user-friendly manner. To illustrate the potential of the integrated platform, we characterize lipid bilayers in terms of thickness and fluidity while simultaneously monitoring single ion channel currents. For that purpose, POPC lipid bilayers are supplemented with a fluorescently-tagged phospholipid (NBD-PE, 1% mol) for Fluorescence Recovery After Photobleaching (FRAP) measurements and a model ion channel (gramicidin, 1 nM). These combined measurements reveal that NBD-PE has no effect on the lipid bilayer thickness while gramicidin induces thinning of the membrane. Furthermore, the presence of gramicidin does not alter the lipid bilayer fluidity. Surprisingly, in lipid bilayers supplemented with both probes, a reduction in gramicidin open probability and lifetime is observed compared to lipid bilayers with gramicidin only, suggesting an influence of NBD-PE on the gramicidin ion function. Altogether, our proposed microfluidic biosensing platform in combination with the herein presented multi-parametric measurement scheme paves the way to explore the interdependent relationship between lipid bilayer properties and ion channel function

Modular ATR FT-IR microreactor chip for optimizing reaction conditions

A silicon chip for attenuated total reflection (ATR) Fourier transform infrared (FT-IR) spectroscopy in combination with a modular PDMS herringbone mixer and a microreactor has been successfully fabricated and tested. The modular design allows the chip to be used for a variety of reactions. A model synthesis of 1-butyl-2,5-dimethyl-1H-pyrrole from hexane-2,5-dione with 1-butylamine has been performed on chip. When plotting the natural logarithm of the peak area corresponding to the ketone stretch vibration at 1710cm-1, against the residence time, a linear curve can be fitted, suggesting this step to be a first order reaction

Modular ATR FT-IR microreactor chip for optimizing reaction conditions

A silicon chip for attenuated total reflection (ATR) Fourier transform infrared (FT-IR) spectroscopy in combination with a modular PDMS herringbone mixer and a microreactor has been successfully fabricated and tested. The modular design allows the chip to be used for a variety of reactions. A model synthesis of 1-butyl-2,5-dimethyl-1H-pyrrole from hexane-2,5-dione with 1-butylamine has been performed on chip. When plotting the natural logarithm of the peak area corresponding to the ketone stretch vibration at 1710cm-1, against the residence time, a linear curve can be fitted, suggesting this step to be a first order reaction

Self-organized network evolution coupled to extremal dynamics

The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the dynamics of the Bak-Sneppen evolution model with the rules of the so-called fitness network model for establishing the topology of a network; each vertex is assigned a fitness, and the vertex with minimum fitness and its neighbours are updated in each iteration. At the same time, the links between the updated vertices and all other vertices are drawn anew with a fitness-dependent connection probability. We show analytically and numerically that the system self-organizes to a non-trivial state that differs from what is obtained when the two processes are decoupled. A power-law decay of dynamical and topological quantities above a threshold emerges spontaneously, as well as a feedback between different dynamical regimes and the underlying correlation and percolation properties of the network.Comment: Accepted version. Supplementary information at http://www.nature.com/nphys/journal/v3/n11/suppinfo/nphys729_S1.htm

SDN-Actors:Modeling and Verification of SDN Programs

Software-Defined Networking (SDN) is a recent networking paradigm that has become increasingly popular in the last decade. It gives unprecedented control over the global behavior of the network and provides a new opportunity for formal methods. Much work has appeared in the last few years on providing bridges between SDN and verification. This paper advances this research line and provides a link between SDN and traditional work on formal methods for verification of distributed software—actor-based modelling. We show how SDN programs can be seamlessly modelled using actors, and thus existing advanced model checking techniques developed for actors can be directly applied to verify a range of properties of SDN networks, including consistency of flow tables, violation of safety policies, and forwarding loops.Depto. de Sistemas Informáticos y ComputaciónFac. de InformáticaTRUEpu

A tomato xylem sap protein represents a new family of small cysteine-rich proteins with structural similarity to lipid transfer proteins

AbstractThe coding sequence of a major xylem sap protein of tomato was identified with the aid of mass spectrometry. The protein, XSP10, represents a novel family of extracellular plant proteins with structural similarity to plant lipid transfer proteins. The XSP10 gene is constitutively expressed in roots and lower stems. The decline of XSP10 protein levels in tomato infected with a fungal vascular pathogen may reflect breakdown or modification by the pathogen

The medicinal treatment of COVID-19:a brief update

Much has changed in the medical treatment of COVID-19 after the first patient with an infection with SARS-CoV-2 in the Netherlands was diagnosed in February 2020. On the basis of limited data, at first only off-label use of (hydroxy)chloroquine seemed to be a treatment option. However, now based on the findings of several randomized studies, other medicines have been included in the Dutch guidelines about the treatment of COVID-19. In this article, we will briefly discuss the current state of affairs with regard to the drugs (hydroxy) chloroquine, remdesivir and corticosteroids. Again, it appears that only well-executed randomized clinical trials can determine the status of various supposedly effective drugs.</p

Calculation of The Band Gap Energy and Study of Cross Luminescence in Alkaline-Earth Dihalide Crystals

The band gap energy as well as the possibility of cross luminescence processes in alkaline-earth dihalide crystals have been calculated using the ab initio Perturbed-Ion (PI) model. The gap is calculated in several ways: as a difference between one-electron energy eigenvalues and as a difference between total energies of appropriate electronic states of the crystal, both at the HF level and with inclusion of Coulomb correlation effects. In order to study the possibility of ocurrence of cross luminescence in these materials, the energy difference between the valence band and the upmost core band for some representative crystals has been calculated. Both calculated band gap energies and cross luminescence predictions compare very well with the available experimental results.Comment: LaTeX file containing 8 pages plus 1 postscript figure. Final version accepted for publication in The Journal of the Physical Society of Japan. It contains a more complete list of references, as well as a more detailed comparison with previous theoretical investigations on the subjec

Supersonic water masers in 30 Doradus

We report on extremely high velocity molecular gas, up to -80 km/s relative to the ambient medium, in the giant star-formation complex 30 Doradus in the Large Magellanic Cloud (LMC), as observed in new 22 GHz H2O maser emission spectra obtained with the Mopra radio telescope. The masers may trace the velocities of protostars, and the observed morphology and kinematics indicate that current star formation occurs near the interfaces of colliding stellar-wind blown bubbles. The large space velocities of the protostars and associated gas could result in efficient mixing of the LMC. A similar mechanism in the Milky Way could seed the galactic halo with relatively young stars and gas.Comment: 11 pages plus 1 PS and 1 EPS figure, uses AASTeX preprint style; accepted for publication in Astrophysical Journal Letter