manipulating-living-cells-to-construct-stable-3d-cellular-assembly

Manipulating Living Cells to Construct Stable 3D Cellular Assembly Without Artificial Scaffold

Regenerative medicine and tissue engineering offer several advantages for the treatment of intractable diseases, and several studies have demonstrated the ...

Doshisha University

The erosion rates of extraction electrodes of ion sources due to ion beam irradiation are largely affected by amount of projectiles retained in the electrodes. A Monte Carlo simulation code ACAT has been used to calculate sputtering yields and reflection coefficients by simulating the accumulation effect of projectiles in a target material. The results for Xe projectiles-C target combination have indicated that both sputtering yields and reflection coefficients are largely enhanced by Xe retention, particularly at larger incident angle for the surface normal with low incident energy.

Erosion of accel grids of ion engine due to sputtering.

Atomic collision processes associated with surface production of negative hydrogen ions (H(-)) by particle reflection at molybdenum surface immersed in hydrogen plasma have been investigated. To calculate sputtering yields of Cs, as well as energy spectra and angular distributions of reflected hydrogen atoms from molybdenum surface by H(+) ion and Cs(+) ion bombardments, a Monte Carlo simulation code ACAT (Atomic Collision in Amorphous Target) was run with the corresponding surface conditions. A fractal surface model has been developed and adopted to ACAT for evaluating the effect due to roughness of target material. The results obtained with ACAT have indicated that the retention of hydrogen atoms leads to the reduction in sputtering yields of Cs, and the surface roughness does largely affect the sputtering yields of Cs.

Effects of adsorption and roughness upon the collision processes at the convertor surface of a plasma sputter negative ion source.

The effects of nucleoid proteins Fis and Dps of Escherichia coli on the higher order structure of a giant DNA were studied, in which Fis and Dps are known to be expressed mainly in the exponential growth phase and stationary phase, respectively. Fis causes loose shrinking of the higher order structure of a genome-sized DNA, T4 DNA (166 kbp), in a cooperative manner, that is, the DNA conformational transition proceeds through the appearance of a bimodal size distribution or the coexistence of elongated coil and shrunken globular states. The effective volume of the loosely shrunken state induced by Fis is 30-60 times larger than that of the compact state induced by spermidine, suggesting that cellular enzymes can access for DNA with the shrunken state but cannot for the compact state. Interestingly, Dps tends to inhibit the Fis-induced shrinkage of DNA, but promotes DNA compaction in the presence of spermidine. These characteristic effects of nucleotide proteins on a giant DNA are discussed by adopting a simple theoretical model with a mean-field approximation. 

Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps.

We observed single DNA molecules at different ethanol concentrations by using fluorescence microscopy. Large single DNA molecules undergo reentrant conformational transitions from elongated coil into folded globule and then into elongated coil state, accompanied by the increase of the concentration of ethanol in a low-salt aqueous environment. The second transition from globule into the coil state occurs at around 70 % (v/v) ethanol. From circular dichroism (CD) measurements, it is confirmed that the reentrant transition of the higher order structure proceeds together with the transitions of the secondary structure from B to C and, then, from C to A in a cooperative manner. The determined mechanism of the reentrant transition is discussed in relation to the unique characteristics of solutions with higher ethanol content, for which clathrate-like nanostructures of alcohol molecules are generated in the surrounding water. 

Highly Concentrated Ethanol Solutions: Good Solvents for DNA as Revealed by Single-Molecule Observation.

Our observation reveals the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA 166 kbp) by fluorescence microscopy. It was found that divalent cations, Mg(2+) and Ca(2+), inhibit DNA compaction induced by a trivalent cation, spermidine (SPD(3+)). On the other hand, in the absence of SPD(3+), divalent cations cause the shrinkage of DNA. As the control experiment, we have confirmed the minimum effect of monovalent cation, Na(+) on the DNA higher-order structure. We interpret the competition between 2+ and 3+ cations in terms of the change in the translational entropy of the counterions. For the compaction with SPD(3+), we consider the increase in translational entropy due to the ion-exchange of the intrinsic monovalent cations condensing on a highly charged polyelectrolyte, double-stranded DNA, by the 3+ cations. In contrast, the presence of 2+ cation decreases the gain of entropy contribution by the ion-exchange between monovalent and 3+ ions. 

Divalent cation shrinks DNA but inhibits its compaction with trivalent cation.

DNA double-strand breaks (DSBs) caused by ultrasound were evaluated in a quantitative manner by single-molecule fluorescence microscopy. We compared the effect of time-interval (or pulse) sonication to that of continuous wave (CW) sonication at a fixed frequency of 30 kHz. Pulses caused fewer DSBs than CW sonication under the same total input ultrasound energy when the pulse repetition period was above the order of a second. In contrast, pulses caused more DSBs than CW sonication for pulse widths shorter than a second. These effect of ultrasound on DNA were interpreted in terms of the time-dependent decay in the probability of breakage during the duration of a pulse. We propose a simple phenomenological model by considering a characteristic decay in the probability of DSBs during single-pulse sonication, which reproduces the essence of the experimental trend. In addition, a data analysis revealed a characteristic scaling behavior between the number of pulses and the number of DSBs.

Double-Strand Breaks in Genome-Sized DNA Caused by Ultrasound.

Polyamines have various biological functions including marked effects on the structure and function of genomic DNA molecules. Changes in the higher-order structure of DNA caused by polyamines are expected to be closely related to genetic activity. To clarify this issue, we examined the relationship between gene expression and the higher-order structure of DNA under different polyamine concentrations.

Opposite effect of polyamines on In vitro gene expression: Enhancement at low concentrations but inhibition at high concentrations.

Although biopsy is one of the most important methods for diagnosis in diseases, there is ambiguity based on the information obtained from the visual inspection of tissue slices. Here, we studied the effect of external extension on tissue slices from mouse liver with different stages of disease: Healthy normal state, Simple steatosis, Non-alcoholic steatohepatitis and Hepatocellular carcinoma. We found that the cracking pattern of a tissue slice caused by extension can provide useful information for distinguishing among the disease states. Interestingly, slices with Hepatocellular carcinoma showed a fine roughening on the cracking pattern with a characteristic length of the size of cells, which is much different than the cracking pattern for slices with non-cancerous steatosis, for which the cracks were relatively straight. The significant difference in the cracking pattern depending on the disease state is attributable to a difference in the strength of cell-cell adhesion, which would be very weak under carcinosis. As it is well known that the manner of cell-cell adhesion neatly concerns with the symptoms in many diseases, it may be promising to apply the proposed methodology to the diagnosis of other diseases.

Cracking pattern of tissue slices induced by external extension provides useful diagnostic information.

We report the successful generation of directional liquid-flow under stationary laser irradiation at a fixed position in a chamber. We adopt a homogeneous solution consisting of a mixture of water and triethylamine (TEA), with a composition near the critical point for phase segregation. When geometrical asymmetry is introduced around the laser focus in the chamber, continuous directional flow is generated, accompanied by the emergence of water-rich microdroplets at the laser focus. The emerging microdroplets tend to escape toward the surrounding bulk solution and then merge/annihilate into the homogeneous solution. The essential features of the directional flow are reproduced through a simple numerical simulation using fluid dynamic equations.

Article	Year
Erosion of accel grids of ion engine due to sputtering. The Review of scientific instruments\| PubMed ID: 20192416	2010
Effects of adsorption and roughness upon the collision processes at the convertor surface of a plasma sputter negative ion source. The Review of scientific instruments\| PubMed ID: 22380231	2012
Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps. Biophysical journal\| PubMed ID: 23972855	2013
Highly Concentrated Ethanol Solutions: Good Solvents for DNA as Revealed by Single-Molecule Observation. Chemphyschem : a European journal of chemical physics and physical chemistry\| PubMed ID: 26891092	2016
Divalent cation shrinks DNA but inhibits its compaction with trivalent cation. The Journal of chemical physics\| PubMed ID: 27250329	2016
Double-Strand Breaks in Genome-Sized DNA Caused by Ultrasound. Chemphyschem : a European journal of chemical physics and physical chemistry\| PubMed ID: 28170150	2017
Opposite effect of polyamines on In vitro gene expression: Enhancement at low concentrations but inhibition at high concentrations. PloS one\| PubMed ID: 29494707	2018
Cracking pattern of tissue slices induced by external extension provides useful diagnostic information. Scientific reports\| PubMed ID: 30111854	2018
Optical Fluid Pump: Generation of Directional Flow via Microphase Segregation/Homogenization. The journal of physical chemistry letters\| PubMed ID: 30222363	2018

Takahiro Kenmotsu

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