Hyunbin Kim

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

BackgroundTransposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.ResultsWe report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.ConclusionsOur study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Optimal Design of Overlapped Ultrasonic Sensor Ring for High Resolution Obstacle Detection

This paper presents the optimal design of an overlapped ultrasonic sensor ring for high resolution obstacle detection of an autonomous mobile robot. It is assumed that a set of low directivity ultrasonic sensors of the same type are arranged along a circle of nonzero radius at a regular spacing with their beams overlapped. First, taking into account the dead angle region, the entire range of obstacle detection is determined with reference to the center of an overlapped ultrasonic sensor ring. Second, the optimal design index of an overlapped ultrasonic sensor ring is defined as the area closeness of three sensing subzones resulting from beam overlap. Third, the lower and upper bounds on the number of ultrasonic sensors are derived, which can guarantee minimal beam overlap and also avoid excessive beam overlap among adjacent ultrasonic sensors. Fourth, employing a commercial low directivity ultrasonic sensor, an optimal design example of an overlapped ultrasonic sensor ring is given along with the ultrasonic sensor ring prototype mounted on top of a mobile robot. Finally, some experimental results using our prototype ultrasonic sensor ring are given to demonstrate the validity and performance of an optimally overlapped ultrasonic sensor ring for high resolution obstacle detection.

Comparative Analysis on Performance Indices of Obstacle Detection for an Overlapped Ultrasonic Sensor Ring

This paper presents a comparative analysis on three different types of performance indices of obstacle detection for an overlapped ultrasonic sensor ring. Due to beam overlap, the entire sensing zone of each ultrasonic sensor can be divided into three smaller sensing subzones, which leads to significant reduction of positional uncertainty in obstacle detection. First, the positional uncertainty in obstacle detection is expressed in terms of the area of a sensing subzone, and type 1 performance index is then defined as the area ratio of side and center sensing subzones. Second, based on the area of a sensing subzone, type 2 performance index is defined taking into account the size of the entire range of obstacle detection as well as the degree of the positional uncertainty in obstacle detection. Third, the positional uncertainty in obstacle detection is now expressed in terms of the length of the uncertainty arc spanning a sensing subzone, and type 3 performance index is then defined as the average value of the uncertainty arc lengths over the entire range of obstacle detection. Fourth, using a commercial low directivity ultrasonic sensor, the changes of three different performance indices depending on the parameter of an overlapped ultrasonic sensor ring are examined and compared.

Pseudorandom Tag Arrangement for Accurate RFID based Mobile Robot Localization

The localization of a mobile robot is one key ingredient for autonomous navigation, along with map building and obstacle detection/ avoidance (Borenstein, J., et al., 1996). Several sensors have long been used for mobile robot localization, but all of them are confronted with their own inherent limitations. Encoder suffers from error accumulation, ultrasonic/ laser sensor demands the line of sight, camera expends complicated processing, and GPS works at low resolution. To cope with these problems of typical sensors, new attempts have been made, which use the RFID system consisting of tags, antenna, and reader for mobile robot localization (Finkenzeller, K., 2000). There have been two different research groups of working on the RFID based mobile robot localization. Both groups assume that a set of tags storing the absolute positional information are deployed throughout a navigation environment. In one group, either active or passive tags are installed along the wall and they are used as beacons or landmarks to guide the navigation of a mobile robot (Kubitz, O., et al., 1997; Kantor, G., et al., 2002; Hahnel, D., et al., 2004; Kulyukin, V., et al., 2004; Penttila, K., et al., 2004; Yamano, K., et al., 2004; Kim, B.K., et al., 2006; Vorst, P., et al., 2008). However, in the other group, passive tags are installed on the floor and they are used to indicate the current position of a mobile robot (Bohn, J., et al., 2004; Choi, J., et al., 2006; Kim, B.K., et al., 2006; Han, S., et al., 2007; Kodaka, K., et al., 2008). This paper belongs to the latter group. When an antenna senses a tag on the floor, there involves the positional uncertainty within the sensing range, which degrades the performance of RFID based mobile robot localization. One simple way of alleviating such a limitation may be to increase the tag distribution density on the floor. If more than one tag is sensed by an antenna at one instant, the current position of a mobile robot can be estimated more accurately by utilizing multiple tag readings (Han, S., et al., 2007; Kodaka, K., et al., 2008). However, the increased tag distribution density may be accompanied by the economical problem of high tag installation cost and the technical problem of incorrect tag readings. For a given tag distribution density, the performance of RFID based mobile robot localization is affected by how a set of tags are arranged over the floor. There have been a variety of tag arrangements considered so far, which can be categorized into three repetitive arrangements, including square, parallelogram, and tilted square. Depending on the

TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

Whole genome annotation errors that omit essential protein-coding genes hinder further research. We developed Target Gene Family Finder (TGFam-Finder), an optimal tool for structural annotation of protein-coding genes containing target domain(s) of interest in eukaryotic genomes. Large-scale re-annotation of 100 publicly available eukaryotic genomes led to the discovery of essential genes that were missed in previous annotations. An average of 117 (346%) and 148 (45%) additional FAR1 and NLR genes were newly identified in 50 plant genomes. Furthermore, 117 (47%) additional C2H2 zinc finger genes were detected in 50 animal genomes including human and mouse. Accuracy of the newly annotated genes was validated by RT-PCR and cDNA sequencing in human, mouse and rice. In the human genome, 26 newly annotated genes were identical with known functional genes. TGFam-Finder along with the new gene models provide an optimized platform for unbiased functional and comparative genomics and comprehensive evolutionary study in eukaryotes.

Development of Traveling Surface Characteristics Extraction Equipment Using Optical Mouse Array

This paper presents the development of the traveling surface characteristics extraction equipment for accurate velocity estimation of a mobile robot using optical mice. In the traveling surface characteristics extraction equipment, a traveling surface sample is rotating relative to stationary optical mice, instead of a mobile robot equipped with optical mice traveling over a floor surface. First, the operational principle of the traveling surface characteristics extraction equipment is explained, Then, the mechanical design & construction, the hardware development, and the software development of the traveling surface characteristics extraction equipment are described in detail.

Optimal Optical Mouse Array for High Performance Mobile Robot Velocity Estimation

This paper presents the optimal array of optical mice for the accurate velocity estimation of a mobile robot. It is assumed that there can be some restriction on the installation of two or more optical mice at the bottom of a mobile robot. First, the velocity kinematics of a mobile robot with an array of optical mice is derived, which maps the velocity of a mobile robot to the velocities of optical mice. Second, taking into account the consistency in physical units, the uncertainty ellipsoid is obtained to represent the error characteristics of the mobile robot velocity estimation owing to noisy optical mouse measurements. Third, a simple but effective performance index is defined as the inverse of the volume of the uncertainty ellipsoid, which can be used for the optimization of the optimal optical mouse placement. Fourth, simulation results for the optimal placement of three optical mice within a given elliptical region are given.