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Search Results: 1 - 10 of 1565 matches for " Hiroki Yokota "
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Artificial ants deposit pheromone to search for regulatory DNA elements
Yunlong Liu, Hiroki Yokota
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-221
Abstract: Human chondrogenesis was used as a model system. The results revealed that the ant algorithm was able to identify biologically known binding motifs in chondrogenesis such as AP-1, NFκB, and sox9. Some of the predicted motifs were identical to those previously derived with the genetic algorithm. Unlike the genetic algorithm, however, the ant algorithm was able to evaluate a contribution of individual binding motifs as a spectrum of distributed information and predict core consensus motifs from a wider DNA pool.The ant algorithm offers an efficient, reproducible procedure to predict a role of individual transcription-factor binding motifs using a unique definition of artificial ants.To extract biologically meaningful information from a large amount of gene expression data and genomic information is one of the most challenging tasks in the post Human Genome Project era [1-3]. Since transcriptional processes are regulated combinatorially by multiple regulatory elements, computational modeling is inevitable and an efficient algorithm capable of solving combinatorial optimization problems is desirable [4]. Swarm intelligence is a computational technique that mimics the collective behavior of social insects such as ants and bees [5-7]. Although there is no centralized module that dictates the behavior of individuals, local interactions cause a global optimization pattern to emerge [8-10]. Algorithms based on swarm intelligence have been applied successfully to a large number of hard discrete optimization problems including traveling salesman, quadratic assignment and routing in telecommunications networks [6,8].The ant algorithm is a branch of swarm intelligence techniques inspired by the foraging behavior of ant colonies. Here, the solution in a combinatorial problem is initialized with a population of randomly positioned ants. Each ant represents a particular solution and deposits a varying amount of artificial pheromone based on the fitness of the solution. The concentr
Application of Petri Nets in Bone Remodeling
Lingxi Li and Hiroki Yokota
Gene Regulation and Systems Biology , 2012,
Abstract: Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings.
Application of Petri Nets in Bone Remodeling
Lingxi Li,Hiroki Yokota
Gene Regulation and Systems Biology , 2009,
Abstract: Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings.
Application of Petri Nets in Bone Remodeling
Lingxi Li,Hiroki Yokota
Gene Regulation and Systems Biology , 2009,
Abstract: Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings.
Voltage profile generation for simultaneous multi-protein detection in western blot analysis  [PDF]
Matthew Blair, Mina Wanis, Gaurav Swarnkar, Hiroki Yokota, Stanley Chien
Journal of Biomedical Science and Engineering (JBiSE) , 2012, DOI: 10.4236/jbise.2012.59067
Abstract: Western blotting is a popular technique for examining expression levels of proteins using gel-based electrophoretic fractionation followed by blotting and antibody reactions. Although this is a mature technique, one of the major limitations is the need to prepare an individual electrophoretic gel for each of the protein species to be analyzed. Since most analyses require the detection of multiple protein species, a procedure that allows utilization of a single gel for detecting multiple protein species should significantly save time and resources. In this paper, we developed a novel multiprotein detection device, which enabled simultaneous detection of several proteins species from a single electrophoretic gel. In this device, a protein transfer unit utilized a multi-anode plate that generated a non-uniform voltage profile. This voltage profile enabled uniform transfer regardless of molecular mass of proteins. In vitro experiments using samples, isolated from boneforming osteoblast cells, showed that the expression levels of 5 - 7 different proteins were detectable in the presence and absence of mechanical stimulation that activated genes necessary for bone formation. The result supports the notion that through simultaneous detection of multiple protein species, the described device contributes to reduction in procedural time and sample amounts, as well as a removal of variations among multiple gels.
Development of an Artificial Finger-Like Knee Loading Device to Promote Bone Health  [PDF]
Sandeep Korupolu, Stanley Chien, Hiroki Yokota, Sohel Anwar
Journal of Biomedical Science and Engineering (JBiSE) , 2017, DOI: 10.4236/jbise.2017.1011041
Abstract: This study presents the development of an innovative artificial finger-like device that provides position specific mechanical loads at the end of the long bone and induces mechanotransduction in bone. Bone cells such as osteoblasts are the mechanosensitive cells that regulate bone remodelling. When they receive gentle, periodic mechanical loads, new bone formation is promoted. The proposed device is an under-actuated multi-fingered artificial hand with 4 fingers, each having two phalanges. These fingers are connected by mechanical linkages and operated by a worm gearing mechanism. With the help of 3D printing technology, a prototype device was built mostly using plastic materials. The experimental validation results show that the device is capable of generating necessary forces at the desired frequencies, which are suitable for the stimulation of bone cells and the promotion of bone formation. It is recommended that the device be tested in a clinical study for confirming its safety and efficacy with patients.
Development of a novel protein multi-blotting device  [PDF]
Amin M. Hagyousif, Voon J. Chong, Hiroki Yokota, Stanley Y. P. Chien
Journal of Biomedical Science and Engineering (JBiSE) , 2010, DOI: 10.4236/jbise.2010.312146
Abstract: Blotting is a common technique widely used for molecular analysis in life sciences. The Western blot, in particular, is a process of transferring protein samples from a polyacrylamide gel to a blotting membrane and detecting the levels of specific proteins through reactions with primary and secondary antibodies. The state-of-the-art of Western blotting usually generates one blotting membrane per gel. However, multiple copies of blots are useful in many applications. Two blotting copies from a single protein gel, for instance, can be used for identifying a total amount of proteins of interest as well as its specific subpopulation level such as a phosphorylated isoform. To achieve this multi-blotting operation from a single gel, we modified a blotting procedure and developed a novel blotting device. The device consisted of a multi-anode plate and a microcontroller. It was designed to generate a well-controlled electrophoretic voltage profile, which allowed a quasi-uniform transfer of proteins of any size. The prototype device was built and its operation procedure was described. The experimental results clearly supported the notion that the described device was able to achieve multiple blotting from a single gel and reduce time and cost for protein analysis.
Principal component analysis for predicting transcription-factor binding motifs from array-derived data
Yunlong Liu, Matthew P Vincenti, Hiroki Yokota
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-276
Abstract: The promoter matrix was defined to establish a quantitative relationship between the IL-1-driven mRNA alteration and genomic DNA sequences of the IL-1 responsive genes. The matrix was decomposed with SVD, and the effects of 8 potential TFBMs (5'-CAGGC-3', 5'-CGCCC-3', 5'-CCGCC-3', 5'-ATGGG-3', 5'-GGGAA-3', 5'-CGTCC-3', 5'-AAAGG-3', and 5'-ACCCA-3') were predicted from a pool of 512 random DNA sequences. The prediction included matches to the core binding motifs of biologically known TFBMs such as AP2, SP1, EGR1, KROX, GC-BOX, ABI4, ETF, E2F, SRF, STAT, IK-1, PPARγ, STAF, ROAZ, and NFκB, and their significance was evaluated numerically using Monte Carlo simulation and genetic algorithm.The described SVD-based prediction is an analytical method to provide a set of potential TFBMs involved in transcriptional regulation. The results would be useful to evaluate analytically a contribution of individual DNA sequences.The use of microarrays has led to a significant number of exciting discoveries establishing important links between mRNA expression patterns and cellular states [1,2]. Mathematical and computational models have been developed to understand and characterize the molecular mechanisms underlying expression patterns [3,4]. However, it remains difficult to discover and validate novel transcription-factor binding motifs (TFBMs) in the human genome. The popular approach to identify TFBMs utilizes sequence comparisons among co-expressed genes [5] or across multi-species [6]. Although any consensus motif can be searched among the co-regulated genes in hierarchical clusters [7,8], this approach is not aimed to build a global model with multiple binding motifs. TFBM can be inspected through phylogenetic footprinting [6,9,10], but identifying orthologous genes and their associated regulatory regions are not always possible. Model-based approaches, initially developed using yeast genome [3], encounter difficulty in evaluating the astronomical number of TFBM selections in t
Mechanical Intervention for Maintenance of Cartilage and Bone
Hui B. Sun, Luis Cardoso and Hiroki Yokota
Clinical Medicine Insights: Arthritis and Musculoskeletal Disorders , 2012, DOI: 10.4137/CMAMD.S6982
Abstract: Mechanical loading provides indispensible stimuli for growth and development of the articular cartilage and bone. Interestingly, depending on loading conditions loads applied to the joint can be beneficial as well as harmful to skeletal maintenance and remodeling. Moderate loads to the synovial joint, for instance, suppress the expression levels of matrix metallproteinases (MMPs), while loads above a threshold tend to increase their destructive activities. This report focuses on two recently developed loading modalities from animal studies, joint motion and joint loading. Their unique characteristics and potential usages for maintenance of the articular cartilage and stimulation of bone remodeling are reviewed. Also described are biophysical and molecular mechanisms which likely are responsible for the load-driven maintenance of cartilage and bone, and a possibility of developing load-mediated treatments of osteoporosis and osteoarthritis.
Mechanical Intervention for Maintenance of Cartilage and Bone
Hui B. Sun,Luis Cardoso,Hiroki Yokota
Clinical Medicine Insights: Arthritis and Musculoskeletal Disorders , 2011,
Abstract:
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