Biomedical subjects

Yoshinobu Baba

Publications and source records attributed to Yoshinobu Baba.

At least 19 recordsLinked to original sources

PubMed2003

Characterization of electrophoretic behavior of sugar isomers by microchip electrophoresis coupled with videomicroscopy.

The electrophoretic behavior of oligosaccharide isomers was investigated by microchip electrophoresis (micro-CE) coupled with videomicroscopy using maltose, cellobiose, maltriose, and panose as oligosaccharide isomer models. The present study revealed for the first time that the formation of a carbohydrate-phosphate complex is a pH-independent rapid process, whereas the formation of a carbohydrate-borate complex is a highly pH-dependent slow process. As a result, phosphate buffer gave much better separation on oligosaccharide isomers than borate and borate-Tris buffers over a wide pH range in micro-CE. The imaging analysis of the complete process of sample loading and injection with field-amplified stacking (FAS) demonstrated that FAS could be used as an efficient method for manipulating the shape of injected sample plugs, and thus improving the performance of micro-CE in the absence of electroosmotic flow. However, once the ionic strength mismatch between sample and running buffer reached a critical threshold, a further increase in ionic strength mismatch deteriorated the effect of FAS, resulting in a surprising decrease in separation efficiency and peak distortion. Under optimal conditions, high-resolution separation of some oligosaccharide isomers and a complex oligosaccharide mixture released from ribonuclease B was achieved using PMMA microchips with an effective separation channel of 30 mm.

Buffers↗

PubMed2003

Cationic liposome-mediated gene delivery: biophysical study and mechanism of internalization.

To identify factors affecting cationic liposome-mediated gene delivery efficiency, we studied the relationship between the biophysical characteristics of liposome/DNA complexes (lipoplexes) at different (+/-) charge ratios, their structures as monitored by atomic force microscopy (AFM), and their mechanism(s) of internalization into the cells. Significant changes were observed in the particle size and zeta potential of liposomes and their structures assessed by AFM upon addition of DNA, which depended on (+/-) charge ratios. AFM images showed that lipoplexes were formed from extensively fused and apparently homogeneous lipid particles encapsulating DNA. Lipoplexes were found to internalize the cells through the endocytosis pathway. Lipoplex-cell fusion was found to occur mainly at the plasma membrane level; however, this lipoplex-cell membrane fusion was found to be essential for the uptake of the large particles. A new perspective for the internalization of large lipoplex particles into cytoplasm is discussed.

Biophysical Phenomena↗

PubMed2003

Microchip electrophoresis-based separation of DNA.

Miniaturized instruments have developed very quickly in the last decade. This review is focused on the microchip electrophoresis-based separation of DNA. Fundamentals, including the chip format, substrates and fabrication technologies, fluid control, as well as various detection methods, are summarized. Array electrophoresis microchip and the on-chip integration of electrophoresis with other systems are introduced as well. In addition, the application of microchip electrophoresis in DNA sizing, genetic analysis and DNA sequencing are also presented in this paper.

Electrophoresis↗

PubMed2003

Redox potentials of the oriented film of the wild-type, the E194Q-, E204Q- and D96N-mutated bacteriorhodopsins.

The redox potentials of the oriented films of the wild-type, the E194Q-, E204Q- and D96N-mutated bacteriorhodopsins (bR), prepared by adsorbing purple membrane (PM) sheets or its mutant on a Pt electrode, have been examined. The redox potentials (V) of the wild-type bR were -470 mV for the 13-cis configuration of the retinal Shiff base in bR and -757 mV for the all-trans configuration in H(2)O, and -433 mV for the 13-cis configuration and -742 mV for the all-trans configuration in D(2)O. The solvent isotope effect (DeltaV=V(D(2)O)-V(H(2)O)), which shifts the redox potential to a higher value, originates from the cooperative rearrangements of the extensively hydrogen-bonded water molecules around the protonated C=N part in the retinal Schiff base. The redox potential of bR was much higher for the 13-cis configuration than that for the all-trans configuration. The redox potentials for the E194Q mutant in the extracellular region were -507 mV for the 13-cis configuration and -788 mV for the all-trans configuration; and for the E204Q mutant they were -491 mV for the 13-cis configuration and -769 mV for the all-trans configuration. Replacement of the Glu(194) or Glu(204) residues by Gln weakened the electron withdrawing interaction to the protonated C=N bond in the retinal Schiff base. The E204 residue is less linked with the hydrogen-bonded network of the proton release pathway compared with E194. The redox potentials of the D96N mutant in the cytoplasmic region were -471 mV for the 13-cis configuration and -760 mV for the all-trans configuration which were virtually the same as those of the wild-type bR, indicating that the D to N point mutation of the 96 residue had no influence on the interaction between the D96 residue and the C=N part in the Schiff base under the light-adapted condition. The results suggest that the redox potential of bR is closely correlated to the hydrogen-bonded network spanning from the retinal Schiff base to the extracellular surface of bR in the proton transfer pathway.

Bacteriorhodopsins↗

PubMed2003

Anomalously fast migration of triplet-repeat DNA in capillary electrophoresis with linear polymer solution.

We investigated the capillary electrophoretic behavior of single-stranded DNA fragments in methylcellulose solution, and found that triplet-repeat DNA showed anomalously faster mobilities than DNA markers with random sequence. Through the further study on the electrophoretic data, reptation model is proven appropriate to describe the migration of DNA under our experimental conditions. Accordingly, with the equations based on reptation theory, we could obtain the persistence length of DNA fragments and find that these values of triplet-repeat DNAs are larger than that of DNA markers with random sequence, which means the former DNAs are less flexible than the latter ones when they migrate in the electric field. This phenomenon is supposed to result from the characteristic higher-order structure formed by GC base pairs within triplet-repeat DNA, which is further proven by the resumed migration order in accordance with DNA size when the denaturant is added into the sieving matrix.

Base Sequence↗

PubMed2003

Ultrafast analysis of oligosaccharides on microchip with light-emitting diode confocal fluorescence detection.

We have developed a new method for the high-speed separation and high-sensitivity detection of complex oligosaccharides based on microchip electrophoresis (nu-CE) with light-emitting diode (LED) confocal fluorescence detection. Oligosaccharides labeled with 8-aminopyrene-1,3,6-trisulfonate (APTS) were found to strongly adsorb to the surface of polymethylmethacrylate (PMMA) microchips. Accordingly, three classes of major dynamic coating additives were systematically investigated, and cellulose derivatives were found to specifically suppress such adsorption and allow high-performance separation on PMMA chips. Additive concentration, buffer pH and applied field strength were found to be key factors in the high-performance separation& of APTS-labeled oligosaccharides on PMMA chips. Under optimal conditions, 15 oligosaccharides in dextrin hydrolysate can be separated within 45 s with an electrophoretic separation efficiency of over 400 000 theoretical plates per meter. The relative standard deviation (RSD) values of migration times of fourteen oligosaccharides were less than 0.50% between six different channels, and the detection limit for APTS-labeled glucose was about 1.98 x 10(-8) mol/L or 8.61 amol with a signal-to-noise ratio (S/N) of 3. The high speed, high efficiency and high sensitivity of this micro-CE-based method indicate that it can be widely applied to analysis of complex oligosaccharides.

Electrophoresis, Capillary↗

PubMed2003

Reduced viscosity polymer matrices for microchip electrophoresis of double-stranded DNA.

On a polymethylmethacrylate (PMMA) microchip, double-stranded DNA fragments with a wide size range from 50 bp to 20 kbp were separated by two polymer solutions. One was a hydroxypropylmethylcellulose-4000 (HPMC-4000) solution of 1.3% (w/v) to separate fragments below 590 bp, and another was a mixed four molecular weight poly(ethylene oxide) solution at a total concentration of 0.1% to separate fragments above 520 bp. The widths at half height (wh) of the fragments had a good relationship with their migration times (tR) in both polymer solutions. Such a relationship was suitable for obtaining the wh values of unresolved peaks, calculating the resolution of two adjacent fragments, and optimizing microchip separation matrices. Based on the relativity, a low viscosity medium containing 2% HPMC-50 and 8% glucose was optimized for high-performance separation of a phiX174 HaeIII restriction fragment digest.

DNA↗

PubMed2003

Range of separation of potential tool for bioseparation, microchip electrophoresis system, for DNA polymorphisms on the human Y-chromosome.

For the requirement of a high, fast and sufficient technology to suit the needs of 21st century biotechnology, the separation range of a microchip electrophoresis system was studied. Two DNA fragments on the human Y-chromosome, SY594 (82 bp) and 12f2 (88 bp), were successfully separated with a reproducibility of 1.9% and an accuracy of 2.8%. Then, a mixture of 10 DNA markers ranging from 61 bp to 189 bp was successfully separated with high resolution. All of these results demonstrate the superiority of microchip electrophoresis as a tool for 21st century bioseparation.

Chromosomes, Human, Y↗

PubMed2003

Biochemical and microarray analyses of bupivacaine-induced apoptosis.

The mechanism by which apoptosis is induced by local anesthetic bupivacaine, a potent uncoupler of mitochondrial oxidative phosphorylation, was investigated. In promyelocytic leukemia cells HL-60, bupivacaine induced formation of apoptotic bodies and DNA fragmentation in a time- and dose-dependent manner similar to typical apoptosis inducers. Caspase-3, -8 and -9, which play a pivotal role in the initiation and execution of receptor- or mitochondria-mediated apoptosis, were all clearly activated by bupivacaine in good correlation with the degree of DNA fragmentation. However, bupivacaine did not induce either mitochondrial permeability transition (PT) or release of cytochrome c in experiments with isolated mitochondria. These results suggest that an indirect action of bupivacaine on mitochondria occurs and that other mechanisms may be involved in bupivacaine-induced apoptosis. To obtain additional information concerning the mechanism of action involved in bupivacaine-induced apoptosis, a microarray analysis of gene expression in bupivacaine-treated HL-60 cells was carried out. Several apoptosis-related genes were found to be transcriptionally regulated by bupivacaine using a high-density cDNA microarray. The expression levels of heat shock protein 70 (HSP70), c-jun and c-fos genes were remarkably up-regulated and those of c-myc and poly (ADP ribose) polymerase (PARP) were down-regulated in bupivacaine-treated cells. These results are of value in developing a better understanding of the molecular mechanism of bupivacaine-induced apoptosis leading to neuro- or myotoxicity.

Anesthetics, Local↗

PubMed2002

A novel injection method for high-speed proteome analysis by capillary electrophoresis.

We have developed a new sample injection method for capillary electrophoresis (CE) that reduces the required migration time. We demonstrated a pressurization technique that was performed with buffer in the outlet after the electrokinetic sample injection with no buffer in the outlet. To reduce the migration time, the sample injection had to be performed with no buffer in the outlet; water should be pressurized while the buffer is in the outlet. Though the resolution was slightly decreased using this method, the addition of a separation carrier (curdlan) to the run buffer restored the resolution without delaying the migration time. The use of our new sample injection method combined with our high-quality separation carrier will enable us to improve the efficiency of the high-throughput screening (HTS) system for proteome analysis.

Buffers↗

PubMed2002

Analysis of DNA polymorphisms on the human Y-chromosome by microchip electrophoresis.

Validation of microchip electrophoresis in DNA analysis has been carried out using an Agilent 2100 Bioanalyzer. With a DNA 500 Assay Kit, the reproducibility and accuracy of fragment sizing of a 10 bp DNA ladder have been shown to be satisfactory with the relative standard deviation and the relative error mostly below 1.0 and 5.0% (n = 12), respectively. Both intraday and interday validations of fragment sizing and quantitation have also been performed with a 7500 Assay Kit (n = 48). Although the results of quantitation are not as good as that of sizing, due to the manual introduction of samples and markers into the chip wells, they are still sufficient to carry out further analyses of practical samples. Based on such reliable results, fast analysis of DNA polymorphisms on the human Y-chromosome has been realized with microchip electrophoresis. The total analysis times of three genomic polymorphisms on the Y-chromosome, Y Alu polymorphism, 47z/StuI, and 12f2, are all within 100 s, and the relative standard deviation and relative error of fragment sizes are below 3.5 and 3.7%, respectively. In addition, a mixture of nine DNA markers on the human Y-chromosome related to examine the cause of spermatogenic failure have been separated successfully with the smallest fragment size difference of 7 bp. Our results demonstrate the potential of microchip electrophoresis in polymorphism analysis with the advantages of high speed, good reproducibility, high precision, and high resolution.

Chromosomes, Human, Y↗

PubMed2002

Stepwise gradient of linear polymer matrices in microchip electrophoresis for high-resolution separation of DNA.

The stepwise gradient of linear polymer matrices in microchannel electrophoresis is proposed as a means of achieving high-resolution separation of DNA samples containing a wide range of fragment sizes. In this method, multiple discrete steps in terms of polymer type or concentration are created in the microchannel by injecting appropriate solutions in order. The mixing of the various steps is found to be negligible compared to the effective length of separation channel, confirming that a stepwise gradient of matrices is formed. This technique is successfully applied to the analysis of restriction digest fragments and DNA ladders, and is demonstrated to provide higher resolution than the isocratic method, for both small and large fragments simultaneously. Even though the stepwise gradient is created manually, the reproducibility of the migration times of fragments in DNA samples is found to be quite good. Taken the separation of 100 bp DNA ladder in three steps gradient pattern as an example, the relative standard deviations of migration times are respectively less than 0.53% and 3.1% in six consecutive injections in one channel and in different channels. The migration of DNA fragments in gradient mode is shown to be similar to that for the isocratic scheme, allowing the design of each step to be made in reference to existing knowledge. These promising results indicate the great potential of this stepwise gradient method for the analysis of DNA by microchip electrophoresis, offering both high resolution and good reproducibility.

DNA↗

PubMed2002

Investigation of the possibility of geometrical electrophoresis.

We investigate the possibility of geometrical electrophoresis, which is based on nanofabrication techniques. (GEE) utilizes geometrical effects during electrophoresis, which are generated by physical interactions between walls and a macromolecule confined in spaces smaller than the Flory radius. When a polymer is injected into a small space, confinement energy is usually required. However, the confinement energy form depends on the geometry of the space. In the case of electrophoresis, the electric field itself changes depending on the geometry. Using a nanofabricated quartz chip with a curved channel, we investigated electrophoretic behavior of high molecular weight DNA based on the curvature effect.

DNA↗

PubMed2002

DNA separation by microchip electrophoresis using low-viscosity hydroxypropylmethylcellulose-50 solutions enhanced by polyhydroxy compounds.

Low-viscosity polymer solutions have potential for double-stranded (ds) DNA separations in micrototal analysis systems (micro-TAS). In this paper, we report dilute, low-viscosity hydroxypropylmethylcellulose-50 (HPMC-50, 11.5 kDa) solutions containing polyhydroxy additives as separation media. Predominant operational variables, such as applied electric field strength, fluorescent intercalator (YOPro-1) concentration, polymer concentration, and additive concentration, are thoroughly investigated. Fast (within 170 s) and excellent separation of DNA restriction fragments ranging in size from 72 to 1353 base pairs (bp) is achieved in a 30 mm length channel of polymethylmethacrylate (PMMA) microchips at an electric field strength of 300 V/cm, by introducing 8% mannitol, 8% glucose or 10% glycerol additives into a 2% HPMC-50/1 x Tris-borate-EDTA (TBE) solution. The low-viscosity (40 cP) matrix formulation provides both coating of the microchannels and separation of DNA in one step. The performance in the solution surpasses that in highly concentrated HPMC-50 solution. In addition, separation using 1xTris-EDTA buffer in the 2% HPMC-50 matrix containing polyhydroxy additives also exhibits a notably increased performance. This is presumably due to formation of hydrogen-bonding interactions of polyhydroxy additives with HPMC-50 matrix and DNA so as to increase the coupling interactions between matrix and DNA molecules during electrophoresis. The result reflects that boric acid is not a prerequisite in polyhydroxy-enhanced HPMC-50 solution for separation.

Bacteriophage phi X 174↗

PubMed2002

Cell-free protein synthesis on a microchip.

We evaluated the expression of various proteins by using a cell-free protein synthesis system with a rapid translation system, a microtube, and a microchip technique. Protein expression was successfully achieved with a microfabricated reaction chamber on a plastic chip. Proteins were expressed effectively by use of expression vectors for T7 RNA polymerase (pET) instead of a plasmid for in vitro expression vector, which is recommended by the manufacture of the rapid translation system. Expression of the proteins depended on the type of proteins chosen. Two mammalian proteins were synthesized simultaneously with two expression vectors of pET species. Effective application of the cell-free protein synthesis system will enable miniaturization of protein synthesis and mediation between the transcriptome and proteome.

Animals↗

PubMed2002

Requirement of continuous transcription for the synthesis of sufficient amounts of protein by a cell-free rapid translation system.

To understand the key processes of cell-free protein synthesis, the synthesis of adipose-type fatty acid binding protein (A-FABP) by a rapid translation system was examined under various conditions. The synthesis of A-FABP was achieved by using an expression vector of A-FABP containing a T7 promoter. However, synthesis of A-FABP was not observed when an RNA fragment corresponding to the open reading frame of A-FABP was used in the reaction instead of the expression vector. Northern analysis revealed that the RNA that was added to the reaction mixture promptly underwent degradation. On the contrary, when the expression vector of A-FABP was employed, a strong RNA signal was observed over the entire incubation period. Thus, a continuous supply of RNA is needed in order to account for its loss via degradation to achieve the synthesis of reasonable amounts of A-FABP. Furthermore, the effect of continuous exchange of reaction mixture was also evaluated by measurement of the amount of synthesized A-FABP.

Carrier Proteins↗

PubMed2002

Molecular stretching of long DNA in agarose gel using alternating current electric fields.

We demonstrate a novel method for stretching a long DNA molecule in agarose gel with alternating current (AC) electric fields. The molecular motion of a long DNA (T4 DNA; 165.6 kb) in agarose gel was studied using fluorescence microscopy. The effects of a wide range of field frequencies, field strengths, and gel concentrations were investigated. Stretching was only observed in the AC field when a frequency of approximately 10 Hz was used. The maximal length of the stretched DNA had the longest value when a field strength of 200 to 400 V/cm was used. Stretching was not sensitive to a range of agarose gel concentrations from 0.5 to 3%. Together, these experiments indicate that the optimal conditions for stretching long DNA in an AC electric field are a frequency of 10 Hz with a field strength of 200 V/cm and a gel concentration of 1% agarose. Using these conditions, we were able to successfully stretch Saccharomyces cerevisiae chromosomal DNA molecules (225-2,200 kb). These results may aid in the development of a novel method to stretch much longer DNA, such as human chromosomal DNA, and may contribute to the analysis of a single chromosomal DNA from a single cell.

Bacteriophage T4↗

PubMed2002

Effect of cationic liposomes in an in vitro transcription and translation system.

The effects of cationic liposomes complexed with plasmid DNA on the process of transcription was examined using a recently developed rapid cell free translation system. The findings indicate that the liposome itself inhibited the process when the ratio of DNA/liposome typically used in transfection studies was used.

Amino Acid Sequence↗