Separation of long DNA chains using non-uniform electric field: a numerical study

We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation demonstrates that the chain captured by an electrode escapes from the binding electric field due to thermal fluctuation. We find that the mobility of chain would depend on the chain length; the mobility sharply increases when the length of a chain exceeds a critical value, which is strongly affected by the amplitude of the applied ac field. Thus we can adjust the length regime, in which this microchannel well separates DNA molecules, without changing the structure of the channel. We also present a theoretical insight into the relation between the critical chain length and the field amplitude.Comment: 12 pages, 9 figure

AJK2011-36009

ABSTRACT We propose a novel cell stimulation device for the analysis of cell responses to chemical stimuli. In order to deliver chemical substances to target single cells, we developed a microfluidic device having microchannels and apertures in the side wall to subject stimuli to laterally trapped cells. The channels were designed to allow simple flow control with single syringe pump. We demonstrated single cell trapping and culturing of pancreatic cell with the device. To test its feasibility in cell stimulation assay, intracellular response of the cell to glucose stimulation was demonstrated

SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level

Compte rendu de « Desrosières, Alain (2014), Prouver et gouverner. Une analyse politique des statistiques publiques »

Prouver et gouverner étudie le rôle des institutions, des conventions et des enjeux normatifs dans la construction d’indicateurs quantitatifs. Desrosières pense qu’on ne peut étudier le développement scientifique des statistiques sans prendre en compte le développement institutionnel – en particulier le rôle de l’État – dans la constitution de cette discipline

Low Cell-Matrix Adhesion Reveals Two Subtypes of Human Pluripotent Stem Cells.

We show that a human pluripotent stem cell (hPSC) population cultured on a low-adhesion substrate developed two hPSC subtypes with different colony morphologies: flat and domed. Notably, the dome-like cells showed higher active proliferation capacity and increased several pluripotent genes' expression compared with the flat monolayer cells. We further demonstrated that cell-matrix adhesion mediates the interaction between cell morphology and expression of KLF4 and KLF5 through a serum response factor (SRF)-based regulatory double loop. Our results provide a mechanistic view on the coupling among adhesion, stem cell morphology, and pluripotency, shedding light on the critical role of cell-matrix adhesion in the induction and maintenance of hPSC

Human Pluripotent Stem Cell-Derived Cardiac Tissue-like Constructs for Repairing the Infarcted Myocardium.

High-purity cardiomyocytes (CMs) derived from human induced pluripotent stem cells (hiPSCs) are promising for drug development and myocardial regeneration. However, most hiPSC-derived CMs morphologically and functionally resemble immature rather than adult CMs, which could hamper their application. Here, we obtained high-quality cardiac tissue-like constructs (CTLCs) by cultivating hiPSC-CMs on low-thickness aligned nanofibers made of biodegradable poly(D,L-lactic-co-glycolic acid) polymer. We show that multilayered and elongated CMs could be organized at high density along aligned nanofibers in a simple one-step seeding process, resulting in upregulated cardiac biomarkers and enhanced cardiac functions. When used for drug assessment, CTLCs were much more robust than the 2D conventional control. We also demonstrated the potential of CTLCs for modeling engraftments in vitro and treating myocardial infarction in vivo. Thus, we established a handy framework for cardiac tissue engineering, which holds high potential for pharmaceutical and clinical applications

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

Simple Fabrication of Metal-Based Piezoelectric MEMS by Direct Deposition of Pb(Zr, Ti)O-3 Thin Films on Titanium Substrates

Piezoelectric Pb(Zr, Ti)O3 (PZT) thin films were directly deposited on cantilever-shaped titanium substrates and evaluated for their piezoelectric properties and actuator performance. Because of the small difference in the thermal expansion coefficient between the PZT and the substrate, and the mitigation of the residual stress, large piezoelectric properties could be obtained for PZT/Ti unimorph actuators. X-ray diffraction measurements clearly revealed that the PZT thin films have a polycrystalline perovskite structure with a random orientation. Observations using a scanning electron microscope (SEM) demonstrated that PZT films, which were 3.8 mum thick, were densely deposited on Pt-coated Ti substrate without pores or cracks. The polarization-electric field (P- E) hysteresis of the PZT film clearly indicates ferroelectricity. The piezoelectric properties of the PZT films were evaluated from the tip displacement of PZT/Ti unimorph cantilevers. Simplified transverse piezoelectric coefficients (e31 * = d31/s11 E, where d31 and s11 E are piezoelectric coefficient and elastic compliance, respectively) were measured, which ranged from -3.6 to 4.3 C/m2 - about three times larger than those of the PZT thin films deposited on stainless-steel substrates. Measurement of resonant frequencies of the cantilevers shows a clear dependence on the cantilever length, which obeys the theoretical equation. This indicates that these cantilevers can be reliably applied as sensors and actuators in a resonance mode

Wide-range frequency selectivity in an acoustic sensor fabricated using a microbeam array with non-uniform thickness

In this study, we have demonstrated the fabrication of a microbeam array (MBA) with various thicknesses and investigated the suitability it for an acoustic sensor with wide-range frequency selectivity. For this, an MBA composed of 64 beams, with thicknesses varying from 2.99–142 µm, was fabricated by using single gray-scale lithography and a thick negative photoresist. The vibration of the beams in air was measured using a laser Doppler vibrometer; the resonant frequencies of the beams were measured to be from 11.5 to 290 kHz. Lastly, the frequency range of the MBA with non-uniform thickness was 10.9 times that of the MBA with uniform thickness