Jaehyuk Choi

Genome-wide functional analysis of pathogenicity genes in the rice blast fungus.

Rapid translation of genome sequences into meaningful biological information hinges on the integration of multiple experimental and informatics methods into a cohesive platform. Despite the explosion in the number of genome sequences available, such a platform does not exist for filamentous fungi. Here we present the development and application of a functional genomics and informatics platform for a model plant pathogenic fungus, Magnaporthe oryzae. In total, we produced 21,070 mutants through large-scale insertional mutagenesis using Agrobacterium tumefaciens–mediated transformation. We used a high-throughput phenotype screening pipeline to detect disruption of seven phenotypes encompassing the fungal life cycle and identified the mutated gene and the nature of mutation for each mutant. Comparative analysis of phenotypes and genotypes of the mutants uncovered 202 new pathogenicity loci. Our findings demonstrate the effectiveness of our platform and provide new insights on the molecular basis of fungal pathogenesis. Our approach promises comprehensive functional genomics in filamentous fungi and beyond.

EBA: an enhancement of the IEEE 802.11 DCF via distributed reservation

The IEEE 802.11 standard for wireless local area networks (WLANs) employs a medium access control (MAC), called distributed coordination function (DCF), which is based on carrier sense multiple access with collision avoidance (CSMA/CA). The collision avoidance mechanism utilizes the random backoff prior to each frame transmission attempt. The random nature of the backoff reduces the collision probability, but cannot completely eliminate collisions. It is known that the throughput performance of the 802.11 WLAN is significantly compromised as the number of stations increases. In this paper, we propose a novel distributed reservation-based MAC protocol, called early backoff announcement (EBA), which is backward compatible with the legacy DCF. Under EBA, a station announces its future backoff information in terms of the number of backoff slots via the MAC header of its frame being transmitted. All the stations receiving the information avoid collisions by excluding the same backoff duration when selecting their future backoff value. Through extensive simulations, EBA is found to achieve a significant increase in the throughput performance as well as a higher degree of fairness compared to the 802.11 DCF.

Homeobox Transcription Factors Are Required for Conidiation and Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae

The appropriate development of conidia and appressoria is critical in the disease cycle of many fungal pathogens, including Magnaporthe oryzae. A total of eight genes (MoHOX1 to MoHOX8) encoding putative homeobox transcription factors (TFs) were identified from the M. oryzae genome. Knockout mutants for each MoHOX gene were obtained via homology-dependent gene replacement. Two mutants, ΔMohox3 and ΔMohox5, exhibited no difference to wild-type in growth, conidiation, conidium size, conidial germination, appressorium formation, and pathogenicity. However, the ΔMohox1 showed a dramatic reduction in hyphal growth and increase in melanin pigmentation, compared to those in wild-type. ΔMohox4 and ΔMohox6 showed significantly reduced conidium size and hyphal growth, respectively. ΔMohox8 formed normal appressoria, but failed in pathogenicity, probably due to defects in the development of penetration peg and invasive growth. It is most notable that asexual reproduction was completely abolished in ΔMohox2, in which no conidia formed. ΔMohox2 was still pathogenic through hypha-driven appressoria in a manner similar to that of the wild-type. However, ΔMohox7 was unable to form appressoria either on conidial germ tubes, or at hyphal tips, being non-pathogenic. These factors indicate that M. oryzae is able to cause foliar disease via hyphal appressorium-mediated penetration, and MoHOX7 is mutually required to drive appressorium formation from hyphae and germ tubes. Transcriptional analyses suggest that the functioning of M. oryzae homeobox TFs is mediated through the regulation of gene expression and is affected by cAMP and Ca2+ signaling and/or MAPK pathways. The divergent roles of this gene set may help reveal how the genome and regulatory pathways evolved within the rice blast pathogen and close relatives.

A Putative MAP Kinase Kinase Kinase, MCK1, Is Required for Cell Wall Integrity and Pathogenicity of the Rice Blast Fungus, Magnaporthe oryzae

Insertional mutagenesis of Magnaporthe oryzae led to the identification of MCK1, a pathogenicity gene predicted to encode mitogen-activated protein kinase kinase kinase (MAPKKK) homologous to BCK1 in Saccharomyces cerevisiae. Targeted disruption of MCK1 resulted in the fungus undergoing autolysis and showing hypersensitivity to cell-wall-degrading enzyme. The mck1 produced significantly reduced numbers of conidia and developed appressoria in a slightly retarded manner compared with the wild type. Appressorium of the mck1 mutant was unable to penetrate into plant tissues, thereby rendering the mutant nonpathogenic. Cytorrhysis assay and monitoring of lipid mobilization suggested that the appressorial wall was altered, presumably affecting the level of turgor pressure within appressorium. Furthermore, the mck1 mutant failed to grow inside plant tissue. Complementation of the mutated gene restored its ability to cause disease symptoms, demonstrating that MCK1 is required for fungal pathogenicity. Taken together, our results suggest that MCK1 is an MAPKKK involved in maintaining cell wall integrity of M. oryzae, and that remodeling of the cell wall in response to host environments is essential for fungal pathogenesis.

Genome‐wide analysis of T‐DNA integration into the chromosomes of Magnaporthe oryzae

A grobacterium tumefaciens‐ mediated transformation (ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding of T‐DNA integration into the fungal genome remains limited relative to that in plants. Using a model plant‐pathogenic fungus, Magnaporthe oryzae, here we report the most comprehensive analysis of T‐DNA integration events in fungi and the development of an informatics infrastructure, termed a T‐DNA analysis platform (TAP). We identified a total of 1110 T‐DNA‐tagged locations (TTLs) and processed the resulting data via TAP. Analysis of the TTLs showed that T‐DNA integration was biased among chromosomes and preferred the promoter region of genes. In addition, irregular patterns of T‐DNA integration, such as chromosomal rearrangement and readthrough of plasmid vectors, were also observed, showing that T‐DNA integration patterns into the fungal genome are as diverse as those of their plant counterparts. However, overall the observed junction structures between T‐DNA borders and flanking genomic DNA sequences revealed that T‐DNA integration into the fungal genome was more canonical than those observed in plants. Our results support the potential of ATMT as a tool for functional genomics of fungi and show that the TAP is an effective informatics platform for handling data from large‐scale insertional mutagenesis.

A 3.4-

We report a low-power object-adaptive CMOS imager, which suppresses spatial temporal bandwidth. The object-adaptive imager has embedded a feature extraction algorithm for identifying objects of interest. The sensor wakes up triggered by motion sensing and extracts features from the captured image for the detection of object-of-interest (OOI). Full-image capturing operation and image signal transmission are performed only when the interested objects are found, which significantly reduces power consumption at the sensor node. This motion-triggered OOI imaging significantly saves a spatial bandwidth more than 96.5% from the feature output and saves a temporal bandwidth from the motion-triggered wakeup and object adaptive imaging. The sensor consumes low power by employing a reconfigurable differential-pixel architecture with reduced power supply voltage and by implementing the feature extraction algorithm with mixed-signal circuitry in a small area. The chip operates at 0.22 μW/frame in motion-sensing mode and at 3.4 μW/frame for feature extraction, respectively. The object detection from on-chip feature extraction circuits has demonstrated a 94.5% detection rate for human from a set of 200 sample images.

\mu

Wireless Internet access is facilitated by IEEE 802.11 WLANs that, in addition to realizing a specific form of CSMA/CA-distributed coordination function (DCF)- implement a range of performance enhancement features such as multi-rate adaptation that induce cross-layer protocol coupling. Recent works in empirical WLAN performance evaluation have shown that cross-layer interactions can be subtle, sometimes leading to unexpected outcomes. Two such instances are: significant throughput degradation (a bell-shaped throughput curve) resulting from automatic rate fallback (ARF) having difficulty distinguishing collision from channel noise, and scalable TCP performance over DCF that is able to curtail effective multiple access contention in the presence of many contending stations. The latter also mitigates the negative performance effect of ARF. In this paper, we present station-centric Markov chain models of WLAN cross-layer performance aimed at capturing complex interactions between ARF, DCF, and TCP. Our performance analyses may be viewed as multi-protocol extensions of Bianchis IEEE 802.11 model that, despite significantly increased complexity, lead to tractable and accurate performance predictions due to modular coupling. Our results complement empirical and simulation-based findings, demonstrating the versatility and efficacy of station-centric Markov chain analysis for capturing cross-layer WLAN dynamics.

W Object-Adaptive CMOS Image Sensor With Embedded Feature Extraction Algorithm for Motion-Triggered Object-of-Interest Imaging

In this paper, we report a CMOS image sensor for spatial-temporal multiresolution images. This image sensor simultaneously generates two outputs: one for normal images (<30 fps) of stationery background and the other for adaptable frame-rate images (over 960 fps) of moving objects. The moving objects are tracked with a reduced spatial resolution in the region-of-interest (ROI). The entire image is reconstructed from the two images with the details in stationery objects and the suppressed motion blur in moving objects. High frame rate only applies to the ROI; therefore, the proposed scheme can significantly reduce power consumption by adjusting the optimal use of bandwidth. In order to provide real-time decision of ROI, the sensor employs on-chip motion-detection circuits based on the inter-pixel switch operation by storing the previous frame signal in a floating diffusion node. This allows a small pixel implementation without adding any extra in-pixel memory components. A prototype chip has been implemented using a 0.35 mum 1P4M standard CMOS process and multiresolution images have been successfully captured. The fabricated chip operates at 3.3 V and consumes 75 mW in the multiresolution readout of a 256times256 normal image at 30 fps and a 64times64 ROI image at 240 fps.

Cross-Layer Analysis of Rate Adaptation, DCF and TCP in Multi-Rate WLANs

Rate adaptation is one of the basic functionalities in todays 802.11 wireless LANs (WLANs). Although it is primarily designed to cope with the variability of wireless channels and achieve higher system spectral efficiency, its design needs careful consideration of cross-layer dependencies, in particular, link-layer collisions. Most practical rate adaptations focus on the time-varying characteristics of wireless channels, ignoring the impact of link-layer collisions. As a result, they may lose their effectiveness due to unnecessary rate downshift wrongly triggered by the collisions. Some recently proposed rate adaptations use RTS/CTS to suppress the collision effect by differentiating collisions from channel errors. The RTS/CTS handshake, however, incurs significant overhead and is rarely activated in infrastructure WLANs. In this paper, we introduce a new approach for optimizing the operation of rate adaptations by adjusting the rate-increasing and decreasing parameters based on link-layer measurement. To construct the algorithm, we study the impact of rate-increasing and decreasing thresholds on performance and show that dynamic adjustment of thresholds is an effective way to mitigate the collision effect in multi-user environments. Our method does not require additional probing overhead incurred by RTS/CTS exchanges and may be practically deployed without change in firmware. We demonstrate the effectiveness of our solution, comparing with existing approaches through extensive simulations.

A Spatial-Temporal Multiresolution CMOS Image Sensor With Adaptive Frame Rates for Tracking the Moving Objects in Region-of-Interest and Suppressing Motion Blur

This letter presents a novel analytic model that accurately evaluates the performance of a single-hop IEEE 802.11 wireless LAN (WLAN). By using a closed queuing network, we model an IEEE 802.11 WLAN system that consists of a fixed number of stations and derive the saturated throughput of the IEEE 802.11 distributed coordination function (DCF). The ns-2 simulation results show that our new analysis model is very accurate in evaluating the performance of the IEEE 802.11 DCF.