Works Published in 2006
Displaying works 21 - 40 of 73 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2006 journal article
Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers
Biochemical and Biophysical Research Communications, 348(1), 245–252.
Contributors: W. Yoshida *, K. Sode* & K. Ikebukuro *
author keywords: homogeneous DNA sensing; enzyme-inhibiting DNA aptamers; aptameric enzyme subunit; SARS detection; thrombin-inhibiting aptamer
MeSH headings : Aptamers, Peptide; Base Sequence; Biosensing Techniques; DNA / analysis; DNA / genetics; Humans; Molecular Sequence Data; Nucleic Acid Conformation; Protein Subunits / analysis; Sequence Analysis, DNA / methods; Thrombin / analysis; Thrombin / antagonists & inhibitors; Thrombin / genetics
TL;DR:
A novel aptameric enzyme subunit (AES) which can detect target DNAs has been developed and was able to detect targetDNAs by measuring the thrombin activity in a homogeneous solution without bound/free separation, and the lower detection limit was 20nM.
(via Semantic Scholar)
europepmc.org (repository)
Source: ORCID
Added: October 9, 2020
2006 journal article
Development of a compact high-density microbial hydrogen reactor for portable bio-fuel cell system
International Journal of Hydrogen Energy, 31(11), 1484–1489.
Contributors: M. Ishikawa*, S. Yamamura *, Y. Takamura *, K. Sode* , E. Tamiya * & M. Tomiyama*
author keywords: biohydrogen; bioreactor; cell immobilization; bio-fuel cell
TL;DR:
The encapsulation of hydrogen producing bacterium, Escherichia coli strain MC13-4, in alginate gel beads provided approximately three-fold increase in hydrogen production in comparison with the free cell suspension.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: October 9, 2020
2006 journal article
Cloning and functional expression of glucose dehydrogenase complex of Burkholderia cepacia in Escherichia coli
Journal of Biotechnology, 123(2), 127–136.
Contributors: T. Tsuya*, S. Ferri*, M. Fujikawa*, H. Yamaoka* & K. Sode*
author keywords: electron transfer subunit; gene cluster; glucose dehydrogenase; respiration
MeSH headings : Amino Acid Sequence; Burkholderia cepacia / enzymology; Burkholderia cepacia / genetics; Cell Respiration / physiology; Cloning, Molecular / methods; Enzyme Activation; Escherichia coli / physiology; Glucose / metabolism; Glucose 1-Dehydrogenase / analysis; Glucose 1-Dehydrogenase / chemistry; Glucose 1-Dehydrogenase / genetics; Glucose 1-Dehydrogenase / metabolism; Molecular Sequence Data; Protein Engineering / methods; Recombinant Proteins / chemistry; Recombinant Proteins / metabolism
TL;DR:
The deduced beta subunit amino acid sequence contains three typical heme-binding motifs and was 44-49% identical to the cytochrome c subunits of other FAD-dependent dehydrogenase complexes.
(via Semantic Scholar)
Source: ORCID
Added: October 9, 2020
2006 journal article
Characterization and application of aptamers for Taq DNA polymerase selected using an evolution-mimicking algorithm
Biotechnology Letters, 28(23), 1939–1944.
Contributors: T. Noma *, K. Sode* & K. Ikebukuro *
author keywords: aptamer; evolution-mimicking algorithm; hot-start PCR
MeSH headings : Algorithms; Aptamers, Nucleotide; Base Sequence; Biotechnology / methods; DNA, Viral / genetics; Evolution, Molecular; HIV-1 / genetics; Ligands; Models, Genetic; Molecular Sequence Data; Mutation; Oligonucleotides / chemistry; Polymerase Chain Reaction; Taq Polymerase / chemistry; Taq Polymerase / genetics
TL;DR:
This study characterized the most potent aptamer and demonstrated its applicability and improved the specificity of detection of a low-copy-number target gene in PCR using these DNA polymerases.
(via Semantic Scholar)
Source: ORCID
Added: October 9, 2020
2006 journal article
Aptameric enzyme subunit for biosensing based on enzymatic activity measurement
Analytical Chemistry, 78(10), 3296–3303.
Contributors: W. Yoshida *, K. Sode* & K. Ikebukuro *
MeSH headings : Adenosine / chemistry; Aptamers, Nucleotide / chemistry; Aptamers, Nucleotide / metabolism; Base Sequence; Biosensing Techniques / methods; Calibration; Circular Dichroism; Nucleic Acid Conformation; Protease Inhibitors / chemistry; Protease Inhibitors / metabolism; Protein Subunits / antagonists & inhibitors; Protein Subunits / chemistry; Protein Subunits / metabolism; Thrombin / antagonists & inhibitors; Thrombin / metabolism
TL;DR:
The aptameric enzyme subunit (AES), which is a DNA aptamer composed of an enzyme-inhibiting aptamer and a target molecule-binding aptamer, has been developed for the biosensing of target molecules and adenosine was successfully detected by measuring the thrombin activity in a homogeneous solution without bound/free separation.
(via Semantic Scholar)
Source: ORCID
Added: October 9, 2020
2006 journal article
Analysis of the evolution of the thrombin-inhibiting DNA aptamers using a genetic algorithm
Biotechnology Letters, 28(23), 1933–1937.
Contributors: K. Ikebukuro *, W. Yoshida *, T. Noma * & K. Sode*
author keywords: aptamer; genetic algorithm; G-quartet structure; inhibitor; systematic; evolution of ligands by exponential enrichment
MeSH headings : Algorithms; Aptamers, Nucleotide; Biotechnology / methods; Chemistry, Physical / methods; DNA / chemistry; Fibrinogen / chemistry; Humans; Ligands; Models, Genetic; Molecular Conformation; Mutation; Nucleic Acid Conformation; RNA / chemistry; Thrombin / antagonists & inhibitors; Thrombin / chemistry
TL;DR:
This method randomized the sequences of the duplex region of this thrombin-inhibiting DNA aptamer and carried out selection based on inhibitory activity using a genetic algorithm, and obtained ligands with greater inhibitory activities than that of the original aptamer.
(via Semantic Scholar)
Source: ORCID
Added: October 9, 2020
2006 journal article
Active site analysis of fructosyl amine oxidase using homology modeling and site-directed mutagenesis
Biotechnology Letters, 28(23), 1895–1900.
Contributors: S. Miura*, S. Ferri*, W. Tsugawa *, S. Kiin & K. Sode*
author keywords: biosensor; diabetes; fructosyl amine oxidase; HbA1c; substrate specificity
MeSH headings : Amino Acid Oxidoreductases / chemistry; Amino Acid Sequence; Bacillus / enzymology; Binding Sites; Biotechnology / methods; Diabetes Mellitus / metabolism; Glycated Hemoglobin / chemistry; Kinetics; Molecular Sequence Data; Mutagenesis, Site-Directed; Pichia / enzymology; Protein Conformation; Sarcosine Oxidase / chemistry; Sequence Homology, Amino Acid; Substrate Specificity
TL;DR:
A three-dimensional structural model of fructosyl amine oxidase from the marine yeast Pichia N1-1 was generated using the crystal structure of monomeric sarcosine oxidation from Bacillus sp.
(via Semantic Scholar)
Source: ORCID
Added: October 9, 2020
2006 journal article
A screening method for DNA aptamers that bind to specific, unidentified protein in tissue samples
Biotechnology Letters, 28(17), 1377–1381.
Contributors: T. Noma *, K. Ikebukuro *, K. Sode* , T. Ohkubo*, Y. Sakasegawa*, N. Hachiya *, K. Kaneko*
author keywords: aptamer; electrophoresis blotting; multiple target proteins; systematic evolution of ligands by exponential enrichment
MeSH headings : Animals; Aptamers, Nucleotide / metabolism; Chickens; Gene Library; Muscle, Skeletal / metabolism; Oligonucleotides / metabolism; Protein Binding; Proteomics / methods
TL;DR:
To select aptamers that bind to a specific unidentified protein in tissues for protein analysis, a screening method was developed using chicken skeletal muscle as a model, suggesting this screening method might be useful for selecting aptamer for proteome analysis.
(via Semantic Scholar)
Source: ORCID
Added: October 9, 2020
2006 journal article
Impact of finger posture on mapping from muscle activation to joint torque
Clinical Biomechanics, 21(4), 361–369.
author keywords: index finger; moment arm; joints
MeSH headings : Adult; Computer Simulation; Electric Stimulation; Fingers / anatomy & histology; Fingers / physiology; Humans; Isometric Contraction / physiology; Models, Biological; Muscle, Skeletal / anatomy & histology; Muscle, Skeletal / innervation; Muscle, Skeletal / physiology; Posture / physiology; Torque
TL;DR:
The data suggest that substantial changes in muscle moment arms occur with posture, and this postural dependence should be considered when constructing biomechanical models of the hand or planning tendon transfers for the fingers.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Weakness Is the Primary Contributor to Finger Impairment in Chronic Stroke
Archives of Physical Medicine and Rehabilitation, 87(9), 1262–1269.
author keywords: hand; human; muscle spasticity; muscle weakness; rehabilitation; stroke
MeSH headings : Biomechanical Phenomena; Chronic Disease; Electromyography; Fingers; Hand Strength; Humans; Middle Aged; Muscle Weakness / classification; Muscle Weakness / etiology; Severity of Illness Index; Stroke / classification; Stroke / physiopathology
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2006 journal article
Kinematics of point-to-point finger movements
Experimental Brain Research, 174(1), 29–34.
author keywords: trajectories; fingertip; motor planning
MeSH headings : Adult; Aged; Biomechanical Phenomena; Cues; Data Interpretation, Statistical; Female; Fingers / physiology; Hand / anatomy & histology; Hand / physiology; Humans; Male; Middle Aged; Movement / physiology
TL;DR:
Directional dependence of the curvature of the chosen finger-only trajectory observed in the initial protocol is incompatible with motor planning based solely on kinematic constraints, instead mechanical properties of the finger are likely incorporated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2006 journal article
Effects of changing wrist positions on finger flexor hypertonia in stroke survivors
Muscle & Nerve, 33(2), 183–190.
author keywords: length dependence; muscle spindle; spasticity; stretch reflex; stroke; velocity dependence
MeSH headings : Adult; Aged; Electromyography; Female; Fingers / anatomy & histology; Fingers / physiology; Humans; Male; Metacarpophalangeal Joint / physiology; Metacarpophalangeal Joint / physiopathology; Middle Aged; Movement / physiology; Muscle Hypertonia / physiopathology; Muscle Spasticity / physiopathology; Muscle Spindles / physiology; Muscle, Skeletal / anatomy & histology; Muscle, Skeletal / physiology; Muscle, Skeletal / physiopathology; Reflex, Stretch / physiology; Stroke / physiopathology; Wrist / physiology
TL;DR:
The results support the hypothesis that finger flexor hypertonia is primarily of neural origin, and that it accurately reflects spindle receptor firing properties, and there were significant interactions between velocity and length.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Electric field-mediated enhancement of in vivo transport of plasmid DNA in tumor interstitium
Journal of Biomechanics, 39, S377.
Source: Crossref
Added: August 28, 2020
2006 journal article
A single molecule detection method for understanding mechanisms of electric field-mediated interstitial transport of genes
Bioelectrochemistry, 69(2), 248–253.
author keywords: single molecule detection; DNA electromobility; interstitial transport; electric field-mediated gene delivery; non-viral gene delivery
MeSH headings : DNA / chemistry; DNA / radiation effects; Dose-Response Relationship, Radiation; Electromagnetic Fields; Electroporation / methods; Molecular Probe Techniques; Motion; Radiation Dosage; Stress, Mechanical; Transfection / methods
TL;DR:
A reproducible single molecule detection method is developed to observe the electromobility of DNA in a range of pulsed, high field strength electric fields typically used during electric field-mediated gene delivery and suggests the existence of a minimum pulse amplitude required to initiate electrophoretic transport.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Electric Fields in Tumors Exposed to External Voltage Sources: Implication for Electric Field-Mediated Drug and Gene Delivery
Annals of Biomedical Engineering, 34(10), 1564–1572.
author keywords: drug and gene delivery; electroporation; electrogenetherapy; electrochemotherapy
MeSH headings : Animals; Biomedical Engineering; Cell Line, Tumor; Drug Delivery Systems; Electric Impedance; Electric Stimulation; Electrochemotherapy; Electroporation; Female; Genetic Therapy; In Vitro Techniques; Mammary Neoplasms, Experimental / physiopathology; Mammary Neoplasms, Experimental / therapy; Melanoma, Experimental / physiopathology; Melanoma, Experimental / therapy; Mice; Mice, Inbred BALB C; Mice, Inbred C57BL; Phantoms, Imaging
TL;DR:
The distribution of the electric field in mouse tumors and tissue phantoms exposed to a large range of electric stimuli, and the resistances of tumor, skin, and electrode-tissue interface are investigated to help improve electric field-mediated drug and gene delivery in solid tumors.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2006 journal article
Nonlinear Dependence of Hydraulic Conductivity on Tissue Deformation During Intratumoral Infusion
Annals of Biomedical Engineering, 34(7), 1173–1181.
author keywords: collagen concentration; hydraulic conductivity; intratumoral infusion; drug and gene delivery
MeSH headings : Animals; Antineoplastic Agents / administration & dosage; Biological Transport; Cell Line, Tumor; Collagen / metabolism; Elasticity; Gene Transfer Techniques; Genetic Therapy; Humans; Infusions, Parenteral / methods; Mice; Models, Biological; Neoplasm Transplantation; Neoplasms, Experimental / metabolism; Neoplasms, Experimental / therapy
TL;DR:
Results from numerical simulations based on the poroelastic model suggest that both the existence of Pt and the nonlinear relationships between Q and Pinf could be explained by infusion-induced tissue deformation that anisotropically affected the hydraulic conductivity of tissues.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Fiber architecture and biaxial mechanical behavior of porcine urinary bladder extracellular matrix
Journal of Biomechanics, 39, S391.
Source: Crossref
Added: August 28, 2020
2006 journal article
Effect of storage upon material properties of lyophilized porcine extracellular matrix derived from the urinary bladder
Journal of Biomedical Materials Research Part B: Applied Biomaterials, 78B(2), 327–333.
author keywords: stability; suture; scaffold; permeability; mechanical properties; urinary bladder; extracellular matrix
MeSH headings : Animals; Bioprosthesis; Extracellular Matrix; Freeze Drying; Materials Testing; Swine; Time Factors; Urinary Bladder
TL;DR:
Examination of material properties for lyophilized forms of an ECM scaffold derived from the porcine urinary bladder shows that structural changes in the UBM device may slowly occur as a function of prolonged storage and storage temperature.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Toolbox for the design of optimized microfluidic components
Lab on a Chip, 6(4), 540.
MeSH headings : Microfluidic Analytical Techniques / instrumentation; Microfluidic Analytical Techniques / methods; Microfluidics; Models, Theoretical; Viscosity
TL;DR:
A computational "toolbox" for the a priori design of optimized microfluidic components consisting of a microchannel under low-Reynolds number, pressure-driven flow, with an arrangement of grooves cut into the top and bottom to generate a tailored cross-channel flow is presented.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Diagnosis on disc
Nature, 440(7081), 159–160.
MeSH headings : Immunoassay / economics; Immunoassay / instrumentation; Immunoassay / methods; Miniaturization / instrumentation; Miniaturization / methods; Sensitivity and Specificity
TL;DR:
A simple, low-cost technique that can identify and quantify many different antigens simultaneously need high-resolution imaging capability and could be music to the authors' ears.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
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