Your article is protected by copyright and all rights are held exclusively by Springer-Verlag. Th... more Your article is protected by copyright and all rights are held exclusively by Springer-Verlag. This e-offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your work, please use the accepted author's version for posting to your own website or your institution's repository. You may further deposit the accepted author's version on a funder's repository at a funder's request, provided it is not made publicly available until 12 months after publication.
The accuracy of the Content should not be relied upon and should be independently verified with p... more The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden.
Fungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a p... more Fungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a part of host innate immunity. Recent studies proposed peroxidases as components of antioxidant defense system. However, the role of fungal peroxidases during interaction with host plants has not been explored at the genomic level. Here, we systematically identified peroxidase genes and analyzed their impact on fungal pathogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. Phylogeny reconstruction placed 27 putative peroxidase genes into 15 clades. Expression profiles showed that majority of them are responsive to in planta condition and in vitro H2O2. Our analysis of individual deletion mutants for seven selected genes including MoPRX1 revealed that these genes contribute to fungal development and/or pathogenesis. We identified significant and positive correlations among sensitivity to H2O2, peroxidase activity and fungal pathogenicity. In-depth analysis of MoPRX1 demonstrate...
Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. H... more Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mbp, and contains 14268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. C. rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the inc...
Database : the journal of biological databases and curation, 2015
Over the past two decades, epigenetics has evolved into a key concept for understanding regulatio... more Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11 576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenet...
ABSTRACT Over the last decade or so, face recognition has become a popular area of research in co... more ABSTRACT Over the last decade or so, face recognition has become a popular area of research in computer vision and one of the most successful applications of image analysis and understanding. In addition, recognition of faces under varied poses has been a challenging area of research due to the complexity of pose dispersion in feature space. This paper presents a novel and robust pose-invariant face recognition method. In this approach, first, the facial region is detected using the TSL color model. The direction of face or pose is estimated using facial features and the estimated pose vector is decomposed into X-Y-Z axes. Second, the input face is mapped by a deformable template using these vectors and the 3D CANDIDE face model. Finally, the mapped face is transformed to the frontal face which appropriates for face recognition by the estimated pose vector. Through the experiments, we come to validate the application of face detection model and the method for estimating facial poses. Moreover, the tests show that recognition rate is greatly boosted through the normalization of the poses.
Recognition of faces under varied poses has been a challenging area of research due to the comple... more Recognition of faces under varied poses has been a challenging area of research due to the complex dispersion of poses in feature space when compared to that of frontal faces. This paper presents a novel and robust pose-invariant face recognition method in order to improvise over existing face recognition techniques. First, we apply the TSL color model for detecting facial
Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall bi... more Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basi...
In wireless sensor networks (WSNs), reducing energy consumption of resource constrained sensor no... more In wireless sensor networks (WSNs), reducing energy consumption of resource constrained sensor nodes is one of the most important issues. In this paper, we propose a task aware (TA) MAC protocol, which improves energy efficiency and throughput by introducing a channel access scheme depending on traffic load in WSNs. The amount of traffic load of a sensor node can be estimated by its task activity, where a task is an operation that the sensor node performs based on the schedule set by data dissemination procedures in advance. In addition, the sensor node collects neighbor nodes' task activities and determines its channel access probability using the collected information. Consequently, the sensor node can choose a more suitable channel access probability which is adaptive to its traffic load as well as neighbor's traffic load. We carry out performance analysis using a p-persistent MAC protocol. The results reveal that the TA-MAC protocol exhibits less collisions than the normal p-persistent MAC protocol and thus it achieves energy efficient operations. Also, it can been seen that the TA-MAC protocol improves system throughput compared with other protocols.
We sought to determine whether electrical stimulation (ES) with subthreshold, continuous, low-fre... more We sought to determine whether electrical stimulation (ES) with subthreshold, continuous, low-frequency impulses is a viable clinical method for improving functional recovery after facial nerve crush injury. In 10 rabbits, bilateral crush injuries were made on the facial nerve by compression for 30 s with mosquito forceps, causing complete facial paralysis. Subthreshold continuous direct current ES with 20-Hz square-wave pulses was applied to the proximal stump on one side for 4 weeks. Vibrissae movement returned significantly earlier on the ES side, with a less variable recovery time. Electrophysiologically, the stimulated side had a significantly shorter latency, longer duration, and faster conduction velocity. Light and transmission electron microscopy revealed that the electrical stimulation also markedly decreased Wallerian degeneration. The average numbers of fluorescent, double-labeled nerve cells were significantly different between the ES and non-ES sides. This study shows ...
Electrokinetic remediation (also known as electrokinetics) is a promising technology for removing... more Electrokinetic remediation (also known as electrokinetics) is a promising technology for removing metals from fine-grained soils. However, few studies have been conducted regarding the transport behavior of multi-metals during electrokinetics. We investigated the transport of As, Cu, Pb, and Zn from soils during electrokinetics, the metal fractionation before and after electrokinetics, the relationships between metal transport and fractionation, and the effects of electrolyte conditioning. The main transport mechanisms of the metals were electroosmosis and electromigration during the first two weeks and electromigration during the following weeks. The direction of electroosmotic flow was from the anode to the cathode, and the metals in the dissolved and reducible-oxides fractions were transported to the anode or cathode by electromigration according to the chemical speciation of the metal ions in the pore water. Moreover, a portion of the metals that were initially in the residual f...
Purpose: Mitochondrial disease (MD) and Duchenne muscular dystrophy (DMD) are often associated wi... more Purpose: Mitochondrial disease (MD) and Duchenne muscular dystrophy (DMD) are often associated with cardiomyopathy, but the myocardial variability has not been isolated to a specific characteristic. We evaluated the left ventricular (LV) mass by echocardiography to identify the general distribution and functional changes of the myocardium in patients with MD or DMD. Methods: We retrospectively evaluated the echocardiographic data of 90 children with MD and 42 with DMD. Using two-dimensional echocardiography, including time-motion (M) mode and Doppler measurements, we estimated the LV mass, ratio of early to late mitral filling velocities (E/A), ratio of early mitral filling velocity to early diastolic mitral annular velocity (E/Ea), stroke volume, and cardiac output. A "z score" was generated using the lambda-mu-sigma method to standardize the LV mass with respect to body size. Results: The LV mass-for-height z scores were significantly below normal in children with MD (-1.02±1.52, P<0.001) or DMD (-0.82±1.61, P=0.002), as were the LV mass-for-lean body-mass z scores. The body mass index (BMI)-for-age z scores were far below normal and were directly proportional to the LV mass-for-height z scores in both patients with MD (R=0.377, P<0.001) and those with DMD (R =0.330, P=0.033). The LV mass-for-height z score correlated positively with the stroke volume index (R =0.462, P<0.001) and cardiac index (R =0.358, P<0.001). Conclusion: LV myocardial atrophy is present in patients with MD and those with DMD and may be closely associated with low BMI. The insufficient LV mass for body size might indicate deterioration of systolic function in these patients.
2011 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS), 2011
The Internet topological connectivity becomes denser over time. However the de facto routing prot... more The Internet topological connectivity becomes denser over time. However the de facto routing protocol of the global Internet, BGP, lets each BGP router select and propagate only a single best path to each destination network. This leads to a common concern that the rich connectivity is not fully utilized and the lack of alternative paths can reduce a network's robustness to failures as well as flexibility in traffic engineering, and can lead to slow adaptation to topological changes. Yet there have been few quantitative measurement studies on path diversity in today's operational Internet. In this paper we use iBGP routing data collected from a Tier1 ISP, ISPA, over a 2-year time period to quantify BGP next-hop diversity for all destinations. Our results show that ISPA reaches the majority of prefixes through multiple next-hop routers. We use several case studies of prefixes with different diversity degrees to identify two major factors that impact the number of observed next-hops: the ISP's path preference and the number of peering routers between large ISPs. This observation provides operational input to the current efforts on augmenting BGP to increase path diversity.
The lichen-forming fungus Cladonia macilenta strain KoLRI003786 is capable of producing an acetyl... more The lichen-forming fungus Cladonia macilenta strain KoLRI003786 is capable of producing an acetylcholinesterase inhibitor, biruloquinone, which effectively prevents neurodegeneration in Alzheimer's disease. Laying the foundation to unravel the biruloquinone biosynthetic pathway, we present the 37.11-Mb draft genome sequence of strain KoLRI003786.
Genomes contain a large number of unique genes which have not been found in other species. Althou... more Genomes contain a large number of unique genes which have not been found in other species. Although the origen of such "orphan" genes remains unclear, they are thought to be involved in species-specific adaptive processes. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7) prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7) during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. ...
Laccases, multi-copper-containing proteins, can catalyze the oxidation of phenolic substrates and... more Laccases, multi-copper-containing proteins, can catalyze the oxidation of phenolic substrates and have diverse functions such as a virulence factor in fungi. However, limited information can be found on the role of laccases in the interaction of Heterobasidion annosum s.s. to its host plant. Due to genome availability of the close-related species Heterobasidion irregulare, which contains 18 predicted laccase-encoding genes, phylogenetic analysis and gene expression profiling were performed. Eighteen laccase genes could be classified into 4 groups based on protein domains and phylogenetic analysis. However, there is no clear indication between phylogeny and domain compositions in laccases, and lifestyles of fungal species. The results of qRT-PCR showed that the expression of 8 laccase genes was highly up-regulated in Scots pine seedlings at 1 wpi. These data suggested that they might be involved in early stage of host infection. In addition, up-regulation of gene expression under glu...
Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated ... more Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated transformation (ATMT), making it the only known genetically tractable lichen-forming fungus to date. We report another advancement in lichen genetics, a draft genome assembly for U. muehlenbergii with a size of 34,812,353 bp and a GC content of 47.12%, consisting of seven scaffolds.
DNA methylation is an important epigenetic modification that regulates development of plants and ... more DNA methylation is an important epigenetic modification that regulates development of plants and mammals. To investigate the roles of DNA methylation in fungal development, we profiled genome-wide methylation patterns at single-nucleotide resolution during vegetative growth, asexual reproduction, and infection-related morphogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. We found that DNA methylation occurs in and around genes as well as transposable elements and undergoes global reprogramming during fungal development. Such reprogramming of DNA methylation suggests that it may have acquired new roles other than controlling the proliferation of TEs. Genetic analysis of DNA methyltransferase deletion mutants also indicated that proper reprogramming in methylomes is required for asexual reproduction in the fungus. Furthermore, RNA-seq analysis showed that DNA methylation is associated with transcriptional silencing of transposable elements and transcript abundance of g...
Your article is protected by copyright and all rights are held exclusively by Springer-Verlag. Th... more Your article is protected by copyright and all rights are held exclusively by Springer-Verlag. This e-offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your work, please use the accepted author's version for posting to your own website or your institution's repository. You may further deposit the accepted author's version on a funder's repository at a funder's request, provided it is not made publicly available until 12 months after publication.
The accuracy of the Content should not be relied upon and should be independently verified with p... more The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden.
Fungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a p... more Fungal pathogens have evolved antioxidant defense against reactive oxygen species produced as a part of host innate immunity. Recent studies proposed peroxidases as components of antioxidant defense system. However, the role of fungal peroxidases during interaction with host plants has not been explored at the genomic level. Here, we systematically identified peroxidase genes and analyzed their impact on fungal pathogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. Phylogeny reconstruction placed 27 putative peroxidase genes into 15 clades. Expression profiles showed that majority of them are responsive to in planta condition and in vitro H2O2. Our analysis of individual deletion mutants for seven selected genes including MoPRX1 revealed that these genes contribute to fungal development and/or pathogenesis. We identified significant and positive correlations among sensitivity to H2O2, peroxidase activity and fungal pathogenicity. In-depth analysis of MoPRX1 demonstrate...
Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. H... more Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mbp, and contains 14268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. C. rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the inc...
Database : the journal of biological databases and curation, 2015
Over the past two decades, epigenetics has evolved into a key concept for understanding regulatio... more Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11 576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenet...
ABSTRACT Over the last decade or so, face recognition has become a popular area of research in co... more ABSTRACT Over the last decade or so, face recognition has become a popular area of research in computer vision and one of the most successful applications of image analysis and understanding. In addition, recognition of faces under varied poses has been a challenging area of research due to the complexity of pose dispersion in feature space. This paper presents a novel and robust pose-invariant face recognition method. In this approach, first, the facial region is detected using the TSL color model. The direction of face or pose is estimated using facial features and the estimated pose vector is decomposed into X-Y-Z axes. Second, the input face is mapped by a deformable template using these vectors and the 3D CANDIDE face model. Finally, the mapped face is transformed to the frontal face which appropriates for face recognition by the estimated pose vector. Through the experiments, we come to validate the application of face detection model and the method for estimating facial poses. Moreover, the tests show that recognition rate is greatly boosted through the normalization of the poses.
Recognition of faces under varied poses has been a challenging area of research due to the comple... more Recognition of faces under varied poses has been a challenging area of research due to the complex dispersion of poses in feature space when compared to that of frontal faces. This paper presents a novel and robust pose-invariant face recognition method in order to improvise over existing face recognition techniques. First, we apply the TSL color model for detecting facial
Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall bi... more Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basi...
In wireless sensor networks (WSNs), reducing energy consumption of resource constrained sensor no... more In wireless sensor networks (WSNs), reducing energy consumption of resource constrained sensor nodes is one of the most important issues. In this paper, we propose a task aware (TA) MAC protocol, which improves energy efficiency and throughput by introducing a channel access scheme depending on traffic load in WSNs. The amount of traffic load of a sensor node can be estimated by its task activity, where a task is an operation that the sensor node performs based on the schedule set by data dissemination procedures in advance. In addition, the sensor node collects neighbor nodes' task activities and determines its channel access probability using the collected information. Consequently, the sensor node can choose a more suitable channel access probability which is adaptive to its traffic load as well as neighbor's traffic load. We carry out performance analysis using a p-persistent MAC protocol. The results reveal that the TA-MAC protocol exhibits less collisions than the normal p-persistent MAC protocol and thus it achieves energy efficient operations. Also, it can been seen that the TA-MAC protocol improves system throughput compared with other protocols.
We sought to determine whether electrical stimulation (ES) with subthreshold, continuous, low-fre... more We sought to determine whether electrical stimulation (ES) with subthreshold, continuous, low-frequency impulses is a viable clinical method for improving functional recovery after facial nerve crush injury. In 10 rabbits, bilateral crush injuries were made on the facial nerve by compression for 30 s with mosquito forceps, causing complete facial paralysis. Subthreshold continuous direct current ES with 20-Hz square-wave pulses was applied to the proximal stump on one side for 4 weeks. Vibrissae movement returned significantly earlier on the ES side, with a less variable recovery time. Electrophysiologically, the stimulated side had a significantly shorter latency, longer duration, and faster conduction velocity. Light and transmission electron microscopy revealed that the electrical stimulation also markedly decreased Wallerian degeneration. The average numbers of fluorescent, double-labeled nerve cells were significantly different between the ES and non-ES sides. This study shows ...
Electrokinetic remediation (also known as electrokinetics) is a promising technology for removing... more Electrokinetic remediation (also known as electrokinetics) is a promising technology for removing metals from fine-grained soils. However, few studies have been conducted regarding the transport behavior of multi-metals during electrokinetics. We investigated the transport of As, Cu, Pb, and Zn from soils during electrokinetics, the metal fractionation before and after electrokinetics, the relationships between metal transport and fractionation, and the effects of electrolyte conditioning. The main transport mechanisms of the metals were electroosmosis and electromigration during the first two weeks and electromigration during the following weeks. The direction of electroosmotic flow was from the anode to the cathode, and the metals in the dissolved and reducible-oxides fractions were transported to the anode or cathode by electromigration according to the chemical speciation of the metal ions in the pore water. Moreover, a portion of the metals that were initially in the residual f...
Purpose: Mitochondrial disease (MD) and Duchenne muscular dystrophy (DMD) are often associated wi... more Purpose: Mitochondrial disease (MD) and Duchenne muscular dystrophy (DMD) are often associated with cardiomyopathy, but the myocardial variability has not been isolated to a specific characteristic. We evaluated the left ventricular (LV) mass by echocardiography to identify the general distribution and functional changes of the myocardium in patients with MD or DMD. Methods: We retrospectively evaluated the echocardiographic data of 90 children with MD and 42 with DMD. Using two-dimensional echocardiography, including time-motion (M) mode and Doppler measurements, we estimated the LV mass, ratio of early to late mitral filling velocities (E/A), ratio of early mitral filling velocity to early diastolic mitral annular velocity (E/Ea), stroke volume, and cardiac output. A "z score" was generated using the lambda-mu-sigma method to standardize the LV mass with respect to body size. Results: The LV mass-for-height z scores were significantly below normal in children with MD (-1.02±1.52, P<0.001) or DMD (-0.82±1.61, P=0.002), as were the LV mass-for-lean body-mass z scores. The body mass index (BMI)-for-age z scores were far below normal and were directly proportional to the LV mass-for-height z scores in both patients with MD (R=0.377, P<0.001) and those with DMD (R =0.330, P=0.033). The LV mass-for-height z score correlated positively with the stroke volume index (R =0.462, P<0.001) and cardiac index (R =0.358, P<0.001). Conclusion: LV myocardial atrophy is present in patients with MD and those with DMD and may be closely associated with low BMI. The insufficient LV mass for body size might indicate deterioration of systolic function in these patients.
2011 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS), 2011
The Internet topological connectivity becomes denser over time. However the de facto routing prot... more The Internet topological connectivity becomes denser over time. However the de facto routing protocol of the global Internet, BGP, lets each BGP router select and propagate only a single best path to each destination network. This leads to a common concern that the rich connectivity is not fully utilized and the lack of alternative paths can reduce a network's robustness to failures as well as flexibility in traffic engineering, and can lead to slow adaptation to topological changes. Yet there have been few quantitative measurement studies on path diversity in today's operational Internet. In this paper we use iBGP routing data collected from a Tier1 ISP, ISPA, over a 2-year time period to quantify BGP next-hop diversity for all destinations. Our results show that ISPA reaches the majority of prefixes through multiple next-hop routers. We use several case studies of prefixes with different diversity degrees to identify two major factors that impact the number of observed next-hops: the ISP's path preference and the number of peering routers between large ISPs. This observation provides operational input to the current efforts on augmenting BGP to increase path diversity.
The lichen-forming fungus Cladonia macilenta strain KoLRI003786 is capable of producing an acetyl... more The lichen-forming fungus Cladonia macilenta strain KoLRI003786 is capable of producing an acetylcholinesterase inhibitor, biruloquinone, which effectively prevents neurodegeneration in Alzheimer's disease. Laying the foundation to unravel the biruloquinone biosynthetic pathway, we present the 37.11-Mb draft genome sequence of strain KoLRI003786.
Genomes contain a large number of unique genes which have not been found in other species. Althou... more Genomes contain a large number of unique genes which have not been found in other species. Although the origen of such "orphan" genes remains unclear, they are thought to be involved in species-specific adaptive processes. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7) prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7) during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. ...
Laccases, multi-copper-containing proteins, can catalyze the oxidation of phenolic substrates and... more Laccases, multi-copper-containing proteins, can catalyze the oxidation of phenolic substrates and have diverse functions such as a virulence factor in fungi. However, limited information can be found on the role of laccases in the interaction of Heterobasidion annosum s.s. to its host plant. Due to genome availability of the close-related species Heterobasidion irregulare, which contains 18 predicted laccase-encoding genes, phylogenetic analysis and gene expression profiling were performed. Eighteen laccase genes could be classified into 4 groups based on protein domains and phylogenetic analysis. However, there is no clear indication between phylogeny and domain compositions in laccases, and lifestyles of fungal species. The results of qRT-PCR showed that the expression of 8 laccase genes was highly up-regulated in Scots pine seedlings at 1 wpi. These data suggested that they might be involved in early stage of host infection. In addition, up-regulation of gene expression under glu...
Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated ... more Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated transformation (ATMT), making it the only known genetically tractable lichen-forming fungus to date. We report another advancement in lichen genetics, a draft genome assembly for U. muehlenbergii with a size of 34,812,353 bp and a GC content of 47.12%, consisting of seven scaffolds.
DNA methylation is an important epigenetic modification that regulates development of plants and ... more DNA methylation is an important epigenetic modification that regulates development of plants and mammals. To investigate the roles of DNA methylation in fungal development, we profiled genome-wide methylation patterns at single-nucleotide resolution during vegetative growth, asexual reproduction, and infection-related morphogenesis in a model plant pathogenic fungus, Magnaporthe oryzae. We found that DNA methylation occurs in and around genes as well as transposable elements and undergoes global reprogramming during fungal development. Such reprogramming of DNA methylation suggests that it may have acquired new roles other than controlling the proliferation of TEs. Genetic analysis of DNA methyltransferase deletion mutants also indicated that proper reprogramming in methylomes is required for asexual reproduction in the fungus. Furthermore, RNA-seq analysis showed that DNA methylation is associated with transcriptional silencing of transposable elements and transcript abundance of g...
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