First Report of Powdery Mildew Caused by Golovinomyces sonchicola on Ixeris chinensis in Korea

Ixeris chinensis (Thunb.) Nakai, known as Chinese ixeris, is distributed from Siberia to Japan, including Korea, Taiwan, and China. The whole plant has been used in folk medicine in Asia (4). In Korea, the plants of Chinese ixeris have been gathered and used as a wild root vegetable. During summer to autumn of 2011, Chinese ixeris leaves were found to be heavily infected with a powdery mildew in several locations of Korea. Symptoms first appeared as thin white colonies, which subsequently developed into abundant hyphal growth on both sides of the leaves, leading to drying of the leaves. The same symptoms on Chinese ixeris leaves were continuously observed in 2012 and 2013. Voucher specimens (n = 10) were deposited at Korea University Herbarium (KUS). Hyphal appressoria were moderately lobed or nipple-shaped. Conidiophores arose from the lateral part of the hyphae, measured 100 to 270 × 10 to 12.5 μm, and produced 2 to 6 immature conidia in chains with a sinuate outline. Basal parts of foot-cells in conidiophores were curved. Conidia were barrel-shaped to ellipsoid, measured 26 to 36 × 13 to 19 μm (length/width ratio = 1.7 to 2.4), lacked fibrosin bodies, and showed reticulate wrinkling of the outer walls. Primary conidia were ovate with conical-obtuse apex and subtruncate base. Germ tubes were produced on the perihilar position of conidia. Chasmothecia were not observed. The morphological characteristics were typical of the Euoidium type anamorph of the genus Golovinomyces, and the fungus measurements and structures were consistent with those of G. sonchicola U. Braun & R.T.A. Cook (1). To confirm the identification, internal transcribed spacer (ITS) region of rDNA sequences from a representative material (KUS-F26212) was amplified using primers ITS5/P3 and sequenced (3). The resulting 416-bp sequence was deposited in GenBank (Accession No. KF819857). A GenBank BLAST search revealed that the isolate showed >99% sequence similarity with those of G. cichoracearum from Sonchus spp. (e.g., AB453762, AF011296, JQ010848, etc.). G. sonchicola is currently confined to G. cichoracearum s. lat. on Sonchus spp., based on molecular sequence analyses (1). Pathogenicity was confirmed through inoculation by gently pressing a diseased leaf onto leaves of five healthy potted Chinese ixeris. Five non-inoculated plants served as controls. Inoculated plants developed symptoms after 6 days, whereas the controls remained symptomless. The fungus present on the inoculated plants was identical morphologically to that originally observed on diseased plants. Powdery mildew infections of I. chinensis associated with Golovinomyces have been known in China (2). To our knowledge, this is the first report of powdery mildew disease caused by G. sonchicola on I. chinensis in Korea. Farming of Chinese ixeris has recently started on a commercial scale in Korea. Though no statistical data are available, we postulate the cultivation area in Korea to be approximately 200 ha, mostly growing without chemical controls. Occurrence of powdery mildews poses a potential threat to safe production of this vegetable, especially in organic farming. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No.11. CBS, Utrecht, 2012. (2) F. L. Tai. Bull. Chinese Bot. Sci. 2:16, 1936. (3) S. Takamatsu et al. Mycol. Res. 113:117, 2009. (4) S. J. Zhang et al. J. Nat. Prod. 69:1425, 2006.

Association Analysis of TEC Polymorphisms with Aspirin-Exacerbated Respiratory Disease in a Korean Population

The tyrosine-protein kinase Tec (TEC) is a member of non-receptor tyrosine kinases and has critical roles in cell signaling transmission, calcium mobilization, gene expression, and transformation. TEC is also involved in various immune responses, such as mast cell activation. Therefore, we hypothesized that TEC polymorphisms might be involved in aspirin-exacerbated respiratory disease (AERD) pathogenesis. We genotyped 38 TEC single nucleotide polymorphisms in a total of 592 subjects, which comprised 163 AERD cases and 429 aspirin-tolerant asthma controls. Logistic regression analysis was performed to examine the associations between TEC polymorphisms and the risk of AERD in a Korean population. The results revealed that TEC polymorphisms and major haplotypes were not associated with the risk of AERD. In another regression analysis for the fall rate of forced expiratory volume in 1 second (FEV₁) by aspirin provocation, two variations (rs7664091 and rs12500534) and one haplotype (TEC_BL2_ht4) showed nominal associations with FEV₁ decline (p = 0.03-0.04). However, the association signals were not retained after performing corrections for multiple testing. Despite TEC playing an important role in immune responses, the results from the present study suggest that TEC polymorphisms do not affect AERD susceptibility. Findings from the present study might contribute to the genetic etiology of AERD pathogenesis.

Screening for 392 polymorphisms in 141 pharmacogenes

Pharmacogenomics is the study of the association between inter-individual genetic differences and drug responses. Researches in pharmacogenomics have been performed in compliance with the use of several genotyping technologies. In this study, a total of 392 single-nucleotide polymorphisms (SNPs) located in 141 pharmacogenes, including 21 phase I, 13 phase II, 18 transporter and 5 modifier genes, were selected and genotyped in 150 subjects using the GoldenGate assay or the SNaPshot technique. These variants were in Hardy-Weinberg equilibrium (HWE) (P>0.05), except for 22 SNPs. Genotyping of the 392 SNPs revealed that the minor allele frequencies of 47 SNPs were <0.05, 105 SNPs were monomorphic and 22 variants were not in HWE. Also, based on previous studies, we predicted the association between the polymorphisms of certain pharmacogenes, such as cytochrome P450 2D6, cytochrome P450 2C9, vitamin K epoxide reductase complex, subunit 1, cytochrome P450 2C19, human leukocyte antigen, class I, B and thiopurine S-methyltransferase, and drug efficacy. In conclusion, our study demonstrated the allele distribution of SNPs in 141 pharmacogenes as determined by high-throughput screening. Our results may be helpful in developing personalized medicines by using pharmacogene polymorphisms.

Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors

BACKGROUND

The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS) for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs), which are abundant in solid tumors, can be utilized for identification of rearranged ends.

METHOD

As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB) in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP) microarray method entailing CNB-region refinement by competitor DNA.

RESULT

Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9%) were identified, and two polymerase chain reaction (PCR)-amplifiable rearrangements were obtained in six cases (66.7%). And significantly, TNGS-CNB, with its high positive identification rate (82.6%) of PCR-amplifiable rearrangements at candidate sites (19/23), just from filtering of aligned sequences, requires little effort for validation.

CONCLUSION

Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.

First Report of Powdery Mildew Caused by Erysiphe heraclei on Parsley in Korea

Parsley, Petroselinum crispum (Mill.) Nyman, is a minor but important leaf crop in Korea. In June 2010, parsley plants (cv. Paramount) showing typical symptoms of powdery mildew were found with approximately 90% incidence (percentage of plants showing symptoms) in polyethylene-film-covered greenhouses in an organic farm in Icheon County of Korea. Symptoms first appeared as thin white colonies, which subsequently showed abundant growth on the leaves with chlorosis and crinkling. Most diseased plantings were unmarketable and shriveled without being harvested. The damage due to powdery mildew infections on parsley has reappeared in Icheon County and Gangneung City with confirmation of the causal agent made again in 2011 and 2012. Voucher specimens were deposited in the Korea University Herbarium (KUS). Appressoria on the mycelium were multilobed or moderately lobed. Conidiophores were cylindrical, 75 to 125 × 8 to 10 μm, straight in foot-cells, and produced conidia singly, followed by 2 to 3 cells. Conidia were oblong-elliptical to oblong, 32 to 55 × 14 to 20 μm with a length/width ratio of 1.7 to 2.9, lacked fibrosin bodies, and produced germ tubes on the perihilar position, with angular/rectangular wrinkling of the outer walls. First-formed conidia were apically conical, basally subtruncate to rounded, and generally smaller than the secondary conidia. Chasmothecia were not found. These structures are typical of the powdery mildew Pseudoidium anamorph of the genus Erysiphe. The specific measurements and morphological characteristics were consistent with those of E. heraclei DC. (1). To confirm the identity of the causal fungus, the complete ITS region of rDNA from isolate KUS-F25037 was amplified with primers ITS5 and P3 (3) and sequenced directly. The resulting 606-bp sequence was deposited in GenBank (Accession No. KF680162). A GenBank BLAST search of this sequence revealed 100% identity with that of E. heraclei on Anethum graveolens from Korea (JN603995) and >99% similarity with those of E. heraclei on Daucus carota from Mexico (GU252368), Pimpinella affinis from Iran (AB104513), Anthriscus cerefolium from Korea (KF111807), and many other parsley family (Apiaceae) plants. Pathogenicity was verified through inoculation by gently pressing diseased leaves onto leaves of five healthy potted parsley plants. Five non-inoculated plants served as negative controls. Inoculated plants developed symptoms after 7 days, whereas the control plants remained symptomless. The fungus present on the inoculated plants was morphologically identical to that originally observed on diseased plants. Parsley powdery mildew caused by E. heraclei has been known in Europe, North America, Brazil, and Japan (2,4). To our knowledge, this is the first report of powdery mildew infections by E. heraclei on parsley in Korea. Since cultivation of parsley was only recently started on a commercial scale in Korea, powdery mildew infections pose a serious threat to safe production of this herb, especially those grown in organic farming where chemical options are limited. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11. CBS, Utrecht, 2012. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab., Online publication, ARS, USDA, retrieved September 17, 2013. (3) S. Takamatsu et al. Mycol. Res. 113:117, 2009. (4) Y. Tsuzaki and K. Sogou. Proc. Assoc. Plant Prot. Shikoku 24:47, 1989.

First Report of Powdery Mildew Caused by Erysiphe elevata on Catalpa bignonioides in Korea

Catalpa bignonioides Walter, known as southern catalpa or Indian bean tree, is native to the southeastern United States and are planted as shade trees throughout the world. In August 2009, typical powdery mildew symptoms on several leaves of the plants below 5% disease incidence were observed in a public garden of Hongcheon County of Korea. In 2011 to 2013, hundreds of southern catalpa trees were found heavily damaged by a powdery mildew with 90 to 100% disease incidence in a park of Incheon City of Korea, about 140 km apart from Hongcheon County. Symptoms appeared as circular to irregular white patches, which subsequently showed abundant mycelial growth on both sides of leaves and herbaceous stems. Severe infections caused poor growth and premature loss of leaves, resulting in reduced aesthetic value. Voucher specimens (n = 6) were deposited in the Korea University Herbarium (KUS). Appressoria on the mycelium were well-developed, lobed, and solitary or in opposite pairs. Conidiophores composed of 3 to 4 cells were 70 to 100 × 7.5 to 10 μm, and produced conidia singly. Foot-cells of conidiophores were flexuous or nearly straight, and 20 to 40 μm long. Conidia were oblong to oblong-elliptical, measured 30 to 42 × 13 to 20 μm (n = 30) with a length/width ratio of 1.6 to 2.5, devoid of distinct fibrosin bodies, and showed angular/rectangular wrinkling of outer walls. Primary conidia were apically rounded, basally subtruncate, and generally smaller than the secondary conidia. Germ tubes were produced on the end of conidia. Chasmothecia were not observed. These structures are typical of the Pseudoidium anamorph of the genus Erysiphe. The specific measurements and characteristics were compatible with those of E. elevata (Burrill) U. Braun & S. Takam. (1,2). To confirm the identification, the complete internal transcribed spacer (ITS) region of rDNA from KUS-F27676 was amplified with primers ITS5 and P3 (4) and sequenced directly. The resulting 675-bp sequence was deposited in GenBank (Accession No. KF840721). A GenBank BLAST search of the ITS sequence showed >99% similarity with isolates of E. elevata on C. bignonioides (Accession Nos. AY587012 to AY587014). Pathogenicity was confirmed through inoculation by gently dusting conidia onto leaves of five healthy southern catalpa seedlings. Five non-inoculated plants served as controls. Inoculated and non-inoculated plants were maintained in a greenhouse at 24 to 28°C in isolation. Inoculated plants developed symptoms after 6 days, whereas the control plants remained symptomless. The fungus present on the inoculated plants was identical morphologically to that originally observed on diseased plants. E.elevata is a North American powdery mildew on Catalpa species which was recently introduced into Europe (1,2,3). To our knowledge, this is the first report of powdery mildew caused by E. elevata on C. bignonioides in Asia as well as in Korea. The disease would be a serious threat to the widespread ornamental plantings of C. bignonioides in Korea. References: (1) N. Ale-Agha et al. Mycol. Prog. 3:291, 2004. (2) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No.11. CBS, Utrecht, 2012. (3) D. F. Farr and A. Y. Rossman. Fungal Databases, Syst. Mycol. Microbiol. Lab., Online publication. ARS, USDA. Retrieved November 4, 2013. (4) S. Takamatsu et al. Mycol. Res. 113:117, 2009.

First Report of Powdery Mildew Caused by Cystotheca wrightii on Quercus glauca in Korea

Quercus glauca Thunb. (syn. Cyclobalanopsis glauca (Thunb.) Oerst.), known as ring-cupped oak or Japanese blue oak, is a dominant tree species commonly found in evergreen forests in East Asia (2). In May 2012, hundreds of Q. glauca were found heavily affected by a powdery mildew in several locations of Jeju Islands, Korea. Symptoms on overwintered leaves appeared as circular to irregular blackish violet to dark brown felt-like growths with numerous chasmothecia on abaxial leaf surfaces. New infections on current-year leaves started in early summer and were characterized by typical white patches with abundant sporulation on abaxial leaf surfaces. In early autumn, with formation of special aerial hyphae and without further sporulation, the patches turned light brown to brown. Formation of chasmothecia was noticed from late autumn. The adaxial leaf surface was free of powdery mildew growths and exhibited yellowing and discoloration. Voucher specimens were deposited in the Korea University Herbarium (KUS). Special aerial hyphae were falcate to curved, aseptate, at first hyaline, later deep brown to purplish brown, thick-walled, and 80 to 140 × 6 to 15 μm. Conidiophores were 175 to 245 × 10 to 12 μm, and produced 2 to 4 immature conidia in chains with a sinuate outline. Foot-cells of conidiophores were cylindrical and 80 to 120 μm long. Conidia were lemon- to barrel-shaped, 26 to 35 × 17 to 24 μm with a length/width ratio of 1.2 to 1.6, and devoid of fibrosin bodies. Primary conidia were apically conical and basally subtruncate. Germ tubes produced in the lateral to perihilar position of conidia were long and slender (3 μm wide). Chasmothecia were scattered or gregarious, partly embedded with special aerial hyphae, dark brown, spherical, 55 to 70 μm in diameter, and contained a single ascus. Chasmothecial peridia consisted of two layers. Exoperidia (outer layer) were composed of dark brown, polygonal cells 10 to 20 μm wide. Endoperidia (inner layer) consisted of hyaline, polygonal cells 10 to 15 μm wide. Appendages were basally attached, mycelioid, rare or few, and pale brown to rusty brown. Asci were short stalked, 55 to 72 × 35 to 46 μm, had a terminal oculus 10 to 20 μm wide, and contained 8 ascospores. Ascospores were oblong-elliptical, 22 to 27 × 10 to 12.5 μm, subhyaline, and contained 1 or 2 oil drops. The specific measurements and characteristics (especially falcate aerial hyphae) were consistent with those of Cystotheca wrightii Berk. & M.A. Curtis (1). Fungal DNA was extracted by the Chelex method. The internal transcribed spacer (ITS) region of rDNA of KUS-F27309 was amplified with primers ITS5/P3 and sequenced directly (4). The resulting 589-bp sequence was deposited in GenBank (Accession No. KF735066). A BLAST search in GenBank showed that the Korean isolate had 100% homology with C. wrightii on Q. glauca from Japan (AB000932). Powdery mildews of Q. glauca associated with C. wrightii have been known in Japan, Taiwan, and China (1,3), but not in Korea. Finding of C. wrightii on Q. glauca could pose a potential threat to other evergreen oak species in southern part of Korea. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11, CBS, Utrecht, Netherlands, 2012. (2) X. Y. Chen et al. Acta Bot. Sin. 39:149, 1997. (3) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab., Online publication, ARS, USDA, retrieved 21 October, 2013. (4) S. Takamatsu et al. Mycol. Res. 113:117, 2009.

Genome-wide association study identifies ALLC polymorphisms correlated with FEV₁ change by corticosteroid

OBJECTIVES

Asthma can be suppressed by inhaled corticosteroids (ICS). However, response to ICS shows marked inter-individual variability. This study is aimed to identify the genetic variants associated with the change in the percentage of forced expiratory volume in 1second (%ΔFEV1) following ICS treatment.

METHODS

A genome-wide association study was performed in a Korean asthmatic cohort. To further investigate these genetic associations, 11 additional single-nucleotide polymorphisms (SNPs) on the allantoicase (ALLC) gene were selected from the HapMap database and genotyped in the same asthmatic patients in the follow-up study.

RESULTS

In a genome-wide study, we identified the lowest P-value in ALLC, but none of the SNPs met the genome-wide association criteria (P<1.0×10(-8)). However, among 25 SNPs on ALLC in the follow-up study, 6 variants showed significant associations with the mean %ΔFEV1 in the study subjects (P<3.73×10(-6)).

CONCLUSIONS

Although the associated signals could not overcome the genome-wide multiple correction due to small sample size (n=189), our results suggest that associated SNPs of ALLC might be genetic predictors of response to ICS, at least with respect to ΔFEV1 in Korean asthmatics.

First Report of Leaf Spot Caused by Pseudocercospora pruni-persicicola on Sweet Cherry in Korea

Sweet cherry, Prunus avium (L.) L., is not much cultivated in Korea, with only 150 ha planted for domestic consumption. In September 2012, a previously unknown leaf spot was observed with nearly 100% incidence on trees (cv. Seneca) planted in a plastic greenhouse in Iksan City of Korea. Interestingly, the same cultivar as well as other cultivars planted outdoors did not show these symptoms. Leaf spots were irregular to subcircular, dark brown with or without a yellow halo, and becoming coalesced to cause leaf blight and premature defoliation. A cercosporoid fungus was consistently associated with disease symptoms. Fungal structures within the lesion developed on both leaf sides but mostly on the upper side. Stromata were well-developed, globular, dark brown, composed of textura angularis-globosa, and 30 to 80 μm in diameter. Conidiophores were densely fasciculate, pale olivaceous to pale brown, subcylindrical, geniculate-sinuous, 8 to 24 × 3 to 4 μm, and aseptate to 2-septate. Conidiogenous loci were inconspicuous, neither thickened nor darkened. Conidia were olivaceous, generally darker than conidiophores, cylindrical to obclavate, almost straight to mildly curved, short obconically truncate at the base, obtuse at the apex, 1- to 10-septate, constricted at the septa, 12 to 86 × 3.5 to 5 μm, guttulate, and had unthickened, not darkened hila. Morphological characteristics of the fungus were consistent with previous descriptions of Pseudocercospora pruni-persicicola (J.M. Yen) J.M. Yen (1,3). A voucher specimen was deposited in the Korea University herbarium (Accession No. KUS-F27264) and a monoconidial isolate was deposited in the Korean Agricultural Culture Collection (Accession No. KACC47019). The complete internal transcribed spacer (ITS) region of rDNA was amplified with the primers ITS1/ITS4 (4) and sequenced. The resulting 505-bp sequence was deposited in GenBank (Accession No. KF670713). A BLAST search in GenBank revealed that the sequence showed >99% similarity with sequences of many Pseudocercospora species, indicating the close phylogenetic relationship of species in this genus. To conduct a pathogenicity test, a conidial suspension (~1 × 10⁴ conidia/ml) was prepared in sterile water by harvesting conidia from 2-week-old cultures on V8 juice agar, and the suspension was sprayed until runoff onto the leaves of five healthy seedlings. Control plants were sprayed with sterile water. The plants were covered with plastic bags to maintain a relative humidity of 100% for 48 h and then transferred to a greenhouse. Necrotic spots appeared on the inoculated leaves 20 days after inoculation, and were identical to the ones observed in the field. P. pruni-persicicola was re-isolated from symptomatic leaf tissues, fulfilling Koch's postulates. Control plants remained symptomless. The fungus has previously been recorded on Prunus persica (L.) Stokes in Taiwan (2,3). To our knowledge, this is the first report of this fungus on P. avium globally as well as in Korea. The disease poses a new threat to the sweet cherry industry in Korea. References: (1) U. Braun and V. A. Melnik. Cercosporoid Fungi from Russia and Adjacent Countries. Rus. Acad. Sci., St.-Petersburg, 1997. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab., Online publication, ARS, USDA, Retrieved August 24, 2013. (3) J. M. Yen. Rev. Mycol. 42:57, 1978. (4) T. J. White et al. PCR Protocols. Academic Press, San Diego, CA, 1990.

Functional polymorphism in aldehyde dehydrogenase-2 gene associated with risk of tuberculosis

Background

The well-known genetic polymorphisms in ADH1B(His47Arg) and ALDH2(Glu487Lys) have dramatic effects on the rate of metabolizing alcohol and acetaldehyde. We investigated possible involvement of these functional polymorphisms in other common complex-trait diseases.

Methods

The genetic effects of these two polymorphisms on hepatitis, asthma, type-2 diabetes mellitus (T2DM), and tuberculosis (TB) were examined in a Korean population.

Results

We demonstrated that the well-known functional polymorphism of a primary alcohol-metabolizing enzyme (ALDH2 Glu487Lys) has a strong genetic association with the risk of TB. The frequency of the minor allele (ALDH2*487Lys) was found to be much lower in TB patients (freq. = 0.099/n = 477) than among controls (freq. = 0.162/n = 796) (P = 0.00001, OR (95% confidential interval) = 0.57 (0.45-0.74)). Our data may indicate that TB was once an endemic disease, which exerted selection pressure for higher frequencies of ALDH2*487Lys in Asian populations. In addition, the calculated attributable fraction (AF) indicates that 39.5% of TB patients can attribute their disease to the detrimental effects of ALDH2Glu487Glu.

Conclusion

Our results suggest that this polymorphism is one of the genetic components of TB, at least in the Korean population.

First Report of Powdery Mildew Caused by Podosphaera spiraeae on Japanese Spiraea in China

Japanese spiraea (Spiraea japonica L.f.), belonging to Rosaceae, is widely planted for its ornamental value in China. Since July 2011, powdery mildew infections on leaves and stems of Japanese spiraea have been noticed in some parks and gardens of Chengyang District in Qingdao City, China (GPS coordinates 36°31'04.22″ N, 120°39'41.92″ E). Symptoms first appeared as white spots covered with mycelium on both side of the leaves and young stems. As the disease progressed, abundant mycelial growth covered the whole shoots and caused growth reduction and leaf distortion with or without reddening. A voucher specimen was deposited in the herbarium of Qingdao Agricultural University (Accession No. HMQAU13013). Hyphae were flexuous to straight, branched, septate, 5 to 7 μm wide, and had nipple-shaped appressoria. Conidiophores arising from the upper surface of hyphal cells produced 2 to 5 immature conidia in chains with a crenate outline. Foot-cells of conidiophores were straight, 60 to 125 × 7 to 9 μm, and followed by 1 to 2 shorter cells. Conidia were ellipsoid-ovoid to doliiform, measured 25 to 32 × 12 to 15 μm with a length/width ratio of 1.8 to 2.6, and had distinct fibrosin bodies. Chasmothecia were not found. The structures and measurements were compatible with the anamorphic state of Podosphaera spiraeae (Sawada) U. Braun & S. Takam. as described before (1). The identity of HMQAU13013 was further confirmed by analysis of nucleotide sequences of the internal transcribed spacer (ITS) regions amplified using the primers ITS1/ITS4 (4). The resulting 564-bp sequence was deposited in GenBank (Accession No. KF500426). A GenBank BLAST search of complete ITS sequence showed 100% identity with that of P. spiraeae on S. cantoniensis (AB525940). A pathogenicity test was conducted through inoculation by gently pressing a diseased leaf onto five healthy leaves of a potted Japanese spiraea. Five non-inoculated leaves served as controls. The plants were maintained in a greenhouse at 22°C. Inoculated leaves developed typical symptoms of powdery mildew after 5 days, but the non-inoculated leaves remained symptomless. The fungus presented on the inoculated plant was morphologically identical to that originally observed on diseased plants, fulfilling Koch's postulates. Powdery mildew of S. japonica caused by P. spiraeae has been recorded in Japan, Poland, and Switzerland (2,3). To our knowledge, this is the first report of powdery mildew caused by P. spiraeae on Japanese spiraea in China. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No.11. CBS, Utrecht, 2012. (2) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ September 10, 2013. (3) T. Kobayashi. Index of Fungi Inhabiting Woody Plants in Japan. Host, Distribution and Literature. Zenkoku-Noson-Kyoiku Kyokai Publishing Co. Ltd., Tokyo, 2007. (4) S. Matsuda and S. Takamatsu. Mol. Phylogenet. Evol. 27:314, 2003.

CD58 polymorphisms associated with the risk of neuromyelitis optica in a Korean population

BACKGROUND

Neuromyelitis optica (NMO) is a serious inflammatory demyelinating disease (IDD), characterized by the inflammation and demyelination of optic nerves and spinal cords, which subsequently leads to the loss of function. In a previous genome-wide association study, cluster of differentiation 58 (CD58) region was found to be susceptible for the risk of multiple sclerosis (MS) in Caucasian, and the association between CD58 variants and MS was replicated in Americans. However, no study has been conducted to explore the possible association between CD58 and NMO yet. Thus, this study aimed to investigate the association of CD58 polymorphisms with the risk of NMO in a Korean population.

METHODS

Using TaqMan assay, 6 single nucleotide polymorphisms (SNPs) were genotyped in 98 NMO patients and 237 normal controls (N = 336). Logistic regression analysis was conducted to find a possible association between CD58 polymorphisms and NMO.

RESULTS

The analysis results showed that 6 variations (rs2300747, rs1335532, rs12044852, rs1016140, CD58_ht1, and CD58_ht3) showed significant associations (P = 0.002 ~ 0.008, P(corr) = 0.01 ~ 0.04).

CONCLUSION

The genetic variations in CD58 may be associated with the susceptibility of NMO in a Korean population. Based on previous studies, we suspect that the A allele of rs2300747 may decrease CD58 RNA expression, thus increasing NMO risk. Also, we deduced that the G allele of rs1016140 caused an increase of T cell activity, which in turn eased the access of AQP4 antibody into central nervous system (CNS) and ultimately leading to NMO development.

First Report of Powdery Mildew Caused by Erysiphe cruciferarum on Chinese Cabbage in China

Chinese cabbage, Brassica rapa ssp. pekinensis (syn. Brassica pekinensis (Lour.) Rupr.), in the Brassicaceae, is an important vegetable grown on about 3 million ha in China. Since 2012, a powdery mildew has been found infecting Chinese cabbage plants (cv. Qingyanchunbai No. 1) after bolting for seed production from autumn through spring 2013 in a greenhouse in Qingdao, China. Symptoms first appeared as circular to irregular white patches on both sides of the leaves, and on stems and pods, often thinly covering the whole surface. A voucher specimen was deposited in the herbarium of Qingdao Agricultural University (Accession No. HMQAU12216). Hyphae were thin-walled, smooth, hyaline, and 4 to 6 μm wide. Appressoria on the mycelia were well developed, lobed, solitary, or in pairs. Conidiophores were erect, cylindrical, 45 to 110 μm long, and comprised 3 to 4 cells. Foot-cells of conidiophores were straight, cylindrical, 16 to 28 μm long, and 7.6 to 10 μm wide. Singly-produced conidia were oblong to cylindrical or somewhat ellipsoid-doliiform, 32 to 56 × 12 to 18 μm, with a length/width ratio of 1.8 to 3.8, with angular/rectangular wrinkling of the outer wall surface, and lacked distinct fibrosin bodies. Germ tubes were produced in the perihilar position of conidia. No chasmothecia were found. These structures are typical of the powdery mildew Pseudoidium anamorph of Erysiphe (2). The specific measurements and characteristics (especially short foot-cells of conidiophores) were consistent with previous records of Erysiphe cruciferarum Opiz ex L. Junell (2,3). To confirm the identification, the complete internal transcribed spacer (ITS) region of rDNA of isolate HMQAU12216 was amplified (4) and sequenced directly. The resulting 649-bp sequence was deposited in GenBank (Accession No. KC878683). A GenBank BLAST search of ITS sequences showed an exact match with those of E. cruciferarum on B. oleracea var. acephala (GU721075) and Oidium sp. on B. pekinensis (AB522714). A pathogenicity test was conducted by gently pressing a symptomatic leaf loaded with conidia onto a leaf of each five, healthy, potted, 40-day-old plants (cv. Qingyanchunbai No. 1). Five non-inoculated plants served as a control treatment. Inoculated plants were isolated from non-inoculated plants in separate rooms in a greenhouse at 20 ± 2°C. Inoculated plants developed signs and symptoms after 10 days, whereas the control plants remained symptomless. The fungus present on the inoculated plants was identical morphologically to that originally observed on diseased plants, thus fulfilling Koch's postulates. Though many Brassica spp. have been known to be infected with E. cruciferarum throughout the world, powdery mildew of Chinese cabbage caused by E. cruciferarum has been reported only in Finland, Germany, and Korea (1,3). To our knowledge, this is the first report of powdery mildew caused by E. cruciferarum on Chinese cabbage in China. Though occurrence of the powdery mildew on Chinese cabbage was noticed in an experimental breeding plot, this finding poses a potential threat to production of this vegetable in China. References: (1) U. Braun. The Powdery Mildews (Erysiphales) of Europe. Gustav Fischer Verlag, Jena, Germany, 1995. (2) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11. CBS, Utrecht, 2012. (3) H. J. Jee et al. Plant Pathol. 57:777, 2008. (4) S. Matsuda and S. Takamatsu. Mol. Phylogen. Evol. 27:314, 2003.

First Report of Powdery Mildew Caused by Erysiphe heraclei on Chervil in Korea

Chervil (Anthriscus cerefolium (L.) Hoffm.), belonging to the family Apiaceae, is an aromatic annual herb that is native to the Caucasus. It is widely used as a flavoring agent for culinary purposes. This herb was recently introduced in Korea. In April 2013, plants showing typical symptoms of powdery mildew disease were observed in a polyethylene film-covered greenhouse in Seoul, Korea. White mycelium bearing conidia formed irregular patches on leaves and stems. Mycelial growth was amphigenous. Severe infections caused leaf withering and premature senescence. Voucher specimens were deposited in the Korea University Herbarium (KUS). Hyphae were septate, branched, with moderately lobed appressoria. Conidiophores presented 3 to 4 cells and measured 85 to 148 × 7 to 9 μm. Foot-cells of conidiophores were 37 to 50 μm long. Conidia were produced singly, oblong-elliptical to oblong, measured 30 to 50 × 13 to 18 μm with a length/width ratio of 2.0 to 3.3, lacked conspicuous fibrosin bodies, and with angular/rectangular wrinkling of the outer walls. Germ tubes were produced in the subterminal position of conidia. Chasmothecia were not found. These structures are typical of the powdery mildew Pseudoidium anamorph of the genus Erysiphe. The specific measurements and morphological characteristics were consistent with those of E. heraclei DC. (1). To confirm identity of the causal fungus, the complete internal transcribed spacer (ITS) region of rDNA of KUS-F27279 was amplified with primers ITS5 and P3 (4) and sequenced directly. The resulting 561-bp sequence was deposited in GenBank (Accession No. KF111807). A GenBank BLAST search of this sequence showed >99% similarity with those of many E. heraclei isolates, e.g., Pimpinella affinis (AB104513), Anethum graveolens (JN603995), and Daucus carota (EU371725). Pathogenicity was confirmed through inoculation by gently pressing a diseased leaf onto leaves of five healthy potted chervil plants. Five non-inoculated plants served as a control treatment. Plants were maintained in a greenhouse at 22 ± 2°C. Inoculated plants developed signs and symptoms after 6 days, whereas the control plants remained healthy. The fungus present on the inoculated plants was identical morphologically to that originally observed on diseased plants. Chervil powdery mildews caused by E. heraclei have been reported in Europe (Bulgaria, France, Germany, Hungary, Italy, Romania, Switzerland, and the former Soviet Union) and the United States (2,3). To our knowledge, this is the first report of powdery mildew caused by E. heraclei on chervil in Asia as well as in Korea. The plant is cultivated in commercial farms for its edible leaves in Korea. Occurrence of powdery mildew is a threat to quality and marketability of this herb, especially those grown in organic farming where chemical control options are limited. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series No. 11, CBS, Utrecht, 2012. (2) D. F. Farr and A. Y. Rossman. Fungal Databases, Syst. Mycol. Microbiol. Lab., Online publication. ARS, USDA. Retrieved July 29, 2013. (3) S. T. Koike and G. S. Saenz. Plant Dis. 88:1163, 2004. (4) S. Takamatsu et al. Mycol. Res. 113:117, 2009.

Association analysis of member RAS oncogene family gene polymorphisms with aspirin intolerance in asthmatic patients

Member RAS oncogene family (RAB1A), a member of the RAS oncogene family, cycles between inactive GDP-bound and active GTP-bound forms regulating vesicle transport in exocytosis. Thus, functional alterations of the RAB1A gene may contribute to aspirin intolerance in asthmatic sufferers. To investigate the relationship between single-nucleotide polymorphisms (SNPs) in the RAB1A gene and aspirin-exacerbated respiratory disease (AERD), asthmatics (n=1197) were categorized into AERD and aspirin-tolerant asthma (ATA). All subjects were diagnosed as asthma on the basis of the Global Initiative for Asthma (GINA) guidelines. AERD was defined as asthmatics showing 15% or greater decreases in forced expiratory volume in one second (FEV(1)) or naso-ocular reactions by the oral acetyl salicylic acid (ASA) challenge (OAC) test. In total, eight SNPs were genotyped. Logistic regression analysis identified that the minor allele frequency of +14444 T>G and +41170 C>G was significantly higher in the AERD group (n=181) than in the ATA group (n=1016) (p=0.0003-0.03). Linear regression analysis revealed a strong association between the SNPs and the aspirin-induced decrease in FEV(1) (p=0.0004-0.004). The RAB1A gene may play a role in the development of AERD in asthmatics and the genetic polymorphisms of the gene have the potential to be used as an indicator of this disease.

Associations of CD6, TNFRSF1A and IRF8 polymorphisms with risk of inflammatory demyelinating diseases

AIMS

Multiple sclerosis (MS) and neuromyelitis optica (NMO) are inflammatory autoimmune diseases that affect the central nervous system. Several genome-wide and candidate gene studies have identified genetic polymorphisms associated with the risk of MS or NMO. In particular, two recently published studies of meta-analysis in European-origin populations have suggested associations of single-nucleotide polymorphisms (SNPs) in CD6, TNFRSF1A and IRF8 with MS. The aim of our study was to assess the associations between SNPs in these three genes and the risk of inflammatory demyelinating disease (IDD) including MS and NMO. To the best of our knowledge, this is the first time such a study has been performed in an Asian population.

METHODS

A total of 21 SNPs of CD6, TNFRSF1A and IRF8 were genotyped in 178 IDD cases (79 MS and 99 NMO patients) and 237 normal controls in a Korean population.

RESULTS

Logistic analyses revealed that one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577 and rs1800693, P = 0.01-0.03) were associated with NMO. However, there was no association of IRF8 polymorphisms with IDD, including MS and NMO. Using further information from the SNP Function Prediction website, two exonic splicing enhancers (ESEs), including the polymorphic site of rs767455, were predicted to be binding sites for splicing factors (SRp55, SF2/ASF2 and SF2/ASF1).

CONCLUSION

Although additional studies are needed, our findings could provide information regarding the genetic aetiology of IDD in the Korean population.

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci

OBJECTIVE

A highly polygenic aetiology and high degree of allele-sharing between ancestries have been well elucidated in genetic studies of rheumatoid arthritis. Recently, the high-density genotyping array Immunochip for immune disease loci identified 14 new rheumatoid arthritis risk loci among individuals of European ancestry. Here, we aimed to identify new rheumatoid arthritis risk loci using Korean-specific Immunochip data.

METHODS

We analysed Korean rheumatoid arthritis case-control samples using the Immunochip and genome-wide association studies (GWAS) array to search for new risk alleles of rheumatoid arthritis with anticitrullinated peptide antibodies. To increase power, we performed a meta-analysis of Korean data with previously published European Immunochip and GWAS data for a total sample size of 9299 Korean and 45,790 European case-control samples.

RESULTS

We identified eight new rheumatoid arthritis susceptibility loci (TNFSF4, LBH, EOMES, ETS1-FLI1, COG6, RAD51B, UBASH3A and SYNGR1) that passed a genome-wide significance threshold (p<5×10(-8)), with evidence for three independent risk alleles at 1q25/TNFSF4. The risk alleles from the seven new loci except for the TNFSF4 locus (monomorphic in Koreans), together with risk alleles from previously established RA risk loci, exhibited a high correlation of effect sizes between ancestries. Further, we refined the number of single nucleotide polymorphisms (SNPs) that represent potentially causal variants through a trans-ethnic comparison of densely genotyped SNPs.

CONCLUSIONS

This study demonstrates the advantage of dense-mapping and trans-ancestral analysis for identification of potentially causal SNPs. In addition, our findings support the importance of T cells in the pathogenesis and the fact of frequent overlap of risk loci among diverse autoimmune diseases.

Comprehensive variant screening of the UGT gene family

PURPOSE

UGT1A1, UGT2B7, and UGT2B15 are well-known pharmacogenes that belong to the uridine diphosphate glucuronyltransferase gene family. For personalized drug treatment, it is important to study differences in the frequency of core markers across various ethnic groups. Accordingly, we screened single nucleotide polymorphisms (SNPs) of these three genes and analyzed differences in their frequency among five ethnic groups, as well as attempted to predict the function of novel SNPs.

MATERIALS AND METHODS

We directly sequenced 288 subjects consisting of 96 Korean, 48 Japanese, 48 Han Chinese, 48 African American, and 48 European American subjects. Subsequently, we analyzed genetic variability, linkage disequilibrium (LD) structures and ethnic differences for each gene. We also conducted in silico analysis to predict the function of novel SNPs.

RESULTS

A total of 87 SNPs were detected, with seven pharmacogenetic core SNPs and 31 novel SNPs. We observed that the frequencies of UGT1A1 *6 (rs4148323), UGT1A1 *60 (rs4124874), UGT1A1 *93 (rs10929302), UGT2B7 *2 (rs7439366), a part of UGT2B7 *3 (rs12233719), and UGT2B15 *2 (rs1902023) were different between Asian and other ethnic groups. Additional in silico analysis results showed that two novel promoter SNPs of UGT1A1 -690G>A and -689A>C were found to potentially change transcription factor binding sites. Moreover, 673G>A (UGT2B7), 2552T>C, and 23269C>T (both SNPs from UGT2B15) changed amino acid properties, which could cause structural deformation.

CONCLUSION

Findings from the present study would be valuable for further studies on pharmacogenetic studies of personalized medicine and drug response.

Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations

OBJECTIVE

Crohn's disease (CD) is an intractable inflammatory bowel disease (IBD) of unknown cause. Recent meta-analysis of the genome-wide association studies (GWAS) and Immunochip data identified 163 susceptibility loci to IBD in Caucasians, however there are limited studies in other populations.

METHODS

We performed a GWAS and two validation studies in the Korean population comprising a total of 2311 patients with CD and 2442 controls.

RESULTS

We confirmed four previously reported loci: TNFSF15, IL23R, the major histocompatibility complex region, and the RNASET2-FGFR1OP-CCR6 region. We identified three new susceptibility loci at genome-wide significance: rs6856616 at 4p14 (OR=1.43, combined p=3.60×10(-14)), rs11195128 at 10q25 (OR=1.42, combined p=1.55×10(-10)) and rs11235667 at 11q13 (OR=1.46, combined p=7.15×10(-9)), implicating ATG16L2 and/or FCHSD2 as novel susceptibility genes for CD. Further analysis of the 11q13 locus revealed a non-synonymous single nucleotide polymorphism (SNP) (R220W/rs11235604) in the evolutionarily conserved region of ATG16L2 with stronger association (OR=1.61, combined p=2.44×10(-12)) than rs11235667, suggesting ATG16L2 as a novel susceptibility gene for CD and rs11235604 to be a potential causal variant of the association. Two of the three SNPs (rs6856616 (p=0.00024) and rs11195128 (p=5.32×10(-5))) showed consistent patterns of association in the International IBD Genetics Consortium dataset. Together, the novel and replicated loci accounted for 5.31% of the total genetic variance for CD risk in Koreans.

CONCLUSIONS

Our study provides new biological insight to CD and supports the complementary value of genetic studies in different populations.

First Report of Leaf Spot Caused by a Phoma sp. on Schisandra chinensis in Korea

Schisandra chinensis (Turcz.) Baill. is a deciduous woody vine native to northern China and the Russian Far East. Its berries have long been used in traditional Asian medicine. In Korea, S. chinensis is one of 10 major medicinal crops and, as of 2011, the production is 6,892 metric tons from 1,749 ha of cultivation area (1). During summer to autumn of 2011 and 2012, leaf spots were observed on S. chinensis (cv. Cheongsun) with disease incidence of 100% in many locations of Jangsu County, Korea. Early symptoms appeared as small, circular, and pale brown spots. Each spot increased in size, became grayish brown and necrotic, and finally developed concentric rings with a definite margin. Some spots coalesced to cover nearly half of the leaves, often becoming torn and giving a shot hole effect. The infected leaf tissue contained blackish pycnidia from which masses of conidia were released in a humid environment. The pycnidia were brown, globose to pyriform, ostiolate, and 45 to 160 μm in diameter. Conidia were hyaline, smooth, oval to ellipsoidal, aseptate or medianly 1-septate, very occasionally 2-septate, slightly constricted at the septa, 4 to 11 × 2.5 to 5 μm, and contained small oil drops. These morphological characteristics were consistent with the generic concept of Phoma (2). Three monoconidial isolates were successfully cultured by diluting conidia mass in sterile water and streaking conidia suspension on potato dextrose agar (PDA). A representative isolate was deposited in the Korean Agricultural Culture Collection (Accession No. KACC47113) and used for pathogenicity test and molecular analysis. Inoculum for a pathogenicity test was prepared by harvesting conidia from 30-day-old cultures (12-h diurnal cycle, 25°C) and a conidial suspension in water (1.1 × 10⁷ conidia/ml) was sprayed onto leaves of three healthy seedlings (cv. Cheongsun). Three seedlings serving as controls were sprayed until runoff with sterile distilled water. The plants were separately covered with plastic bags for 48 h in a glasshouse. After 10 days, typical leaf spot symptoms developed on the leaves inoculated with the fungus. Phoma sp. was re-isolated from those lesions, confirming Koch's postulates. No symptoms were observed on controls. The pathogenicity test was conducted twice. Fungal DNA was extracted, and the complete internal transcribed spacer (ITS) region of rDNA was amplified with the primers ITS1/ITS4 and sequenced directly. The resulting 520-bp sequence was deposited in GenBank (Accession No. KC928322). The sequence showed over 99% similarity with many Phoma species from various substrates, but no exact matches. Phoma leaf spot of S. chinensis was once recorded in Korea without pathogenicity test and culture deposition (3). Phoma glomerata was recorded as a causal fungus of leaf spot disease on S. chinensis in China (4). The Korean isolates differ from P. glomerata in having larger conidia and are separated from it in ITS sequence data. Therefore, we tentatively place the Korean isolates as unidentified Phoma sp. To our knowledge, this is the first confirmed report of leaf spot disease caused by a Phoma sp. in Korea. References: (1) Anonymous. Statistics of Cultivation and Production of Industrial Crops in 2011. Korean Ministry for Food, Agriculture, Forestry and Fisheries. 2012. (2) M. M. Aveskamp et al. Mycologia 101:363, 2009. (3) E. J. Lee et al. Compendium of Medicinal Plant Diseases with Color Plates. Nat. Inst. Agric. Sci., Suwon, Korea. 1991. (4) X. Wang et al. Plant Dis. 96:289, 2012.

Screening of Genetic Polymorphisms of CYP3A4 and CYP3A5 Genes

Given the CYP3A4 and CYP3A5's impact on the efficacy of drugs, the genetic backgrounds of individuals and populations are regarded as an important factor to be considered in the prescription of personalized medicine. However, genetic studies with Korean population are relatively scarce compared to those with other populations. In this study, we aimed to identify CYP3A4/5 polymorphisms and compare the genotype distributions among five ethnicities. To identify CYP3A4/5 SNPs, we first performed direct sequencing with 288 DNA samples which consisted of 96 Koreans, 48 European-Americans, 48 African-Americans, 48 Han Chinese, and 48 Japanese. The direct sequencing identified 15 novel SNPs, as well as 42 known polymorphisms. We defined the genotype distributions, and compared the allele frequencies among five ethnicities. The results showed that minor allele frequencies of Korean population were similar with those of the Japanese and Han Chinese populations, whereas there were distinct differences from European-Americans or African-Americans. Among the pharmacogenetic markers, frequencies of CYP3A4*1B (rs2740574) and CYP3A5*3C (rs776742) in Asian groups were different from those in other populations. In addition, minor allele frequency of CYP3A4*18 (rs28371759) was the highest in Korean population. Additional in silico analysis predicted that two novel non-synonymous SNPs in CYP3A5 (+27256C>T, P389S and +31546T>G, I488S) could alter protein structure. The frequency distributions of the identified polymorphisms in the present study may contribute to the expansion of pharmacogenetic knowledge.

Polymorphisms of ATF6B Are Potentially Associated With FEV1 Decline by Aspirin Provocation in Asthmatics

Purpose

Endoplasmic reticulum (ER) stress has recently been observed to activate NF-kappaB and induce inflammatory responses such as asthma. Activating transcription factor 6β (ATF6B) is known to regulate ATFα-mediated ER stress response. The aim of this study is to investigate the associations of ATF6B genetic variants with aspirin-exacerbated respiratory disease (AERD) and its major phenotype, % decline of FEV1 by aspirin provocation.

Methods

Four common single nucleotide polymorphisms (SNPs) of ATF6B were genotyped and statistically analyzed in 93 AERD patients and 96 aspirin-tolerant asthma (ATA) as controls.

Results

Logistic analysis revealed that 2 SNPs (rs2228628 and rs8111, P=0.008; corrected P=0.03) and 1 haplotype (ATF6B-ht4, P=0.005; corrected P=0.02) were significantly associated with % decline of FEV1 by aspirin provocation, whereas ATF6B polymorphisms and haplotypes were not associated with the risk of AERD.

Conclusions

Although further functional and replication studies are needed, our preliminary findings suggest that ATF6B may be related to obstructive phenotypes in response to aspirin exposure in adult asthmatics.