DTranNER: biomedical named entity recognition with deep learning-based label-label transition model.

BACKGROUND: Biomedical named-entity recognition (BioNER) is widely modeled with conditional random fields (CRF) by regarding it as a sequence labeling problem. The CRF-based methods yield structured outputs of labels by imposing connectivity between the labels. Recent studies for BioNER have reported state-of-the-art performance by combining deep learning-based models (e.g., bidirectional Long Short-Term Memory) and CRF. The deep learning-based models in the CRF-based methods are dedicated to estimating individual labels, whereas the relationships between connected labels are described as static numbers; thereby, it is not allowed to timely reflect the context in generating the most plausible label-label transitions for a given input sentence. Regardless, correctly segmenting entity mentions in biomedical texts is challenging because the biomedical terms are often descriptive and long compared with general terms. Therefore, limiting the label-label transitions as static numbers is a bottleneck in the performance improvement of BioNER. RESULTS: We introduce DTranNER, a novel CRF-based framework incorporating a deep learning-based label-label transition model into BioNER. DTranNER uses two separate deep learning-based networks: Unary-Network and Pairwise-Network. The former is to model the input for determining individual labels, and the latter is to explore the context of the input for describing the label-label transitions. We performed experiments on five benchmark BioNER corpora. Compared with current state-of-the-art methods, DTranNER achieves the best F1-score of 84.56% beyond 84.40% on the BioCreative II gene mention (BC2GM) corpus, the best F1-score of 91.99% beyond 91.41% on the BioCreative IV chemical and drug (BC4CHEMD) corpus, the best F1-score of 94.16% beyond 93.44% on the chemical NER, the best F1-score of 87.22% beyond 86.56% on the disease NER of the BioCreative V chemical disease relation (BC5CDR) corpus, and a near-best F1-score of 88.62% on the NCBI-Disease corpus. CONCLUSIONS: Our results indicate that the incorporation of the deep learning-based label-label transition model provides distinctive contextual clues to enhance BioNER over the static transition model. We demonstrate that the proposed framework enables the dynamic transition model to adaptively explore the contextual relations between adjacent labels in a fine-grained way. We expect that our study can be a stepping stone for further prosperity of biomedical literature mining.

Urinary Neutrophil Gelatinase-Associated Lipocalin as a Biomarker for Renal Injury in Liver Transplant Recipients Using Calcineurin Inhibitors.

BACKGROUND: Urinary neutrophil gelatinase-associated lipocalin (uNGAL) is an early biomarker of renal injury. We examined the feasibility of using uNGAL as an early predictor of renal impairment in patients under calcineurin inhibitors in liver transplant recipients. METHODS: From urine samples obtained from liver transplant recipients, the glomerular filtration rate (GFR) at the time of urine sampling was compared with that at 5 to 7 months later. Patients were divided into 3 groups according to initial GFR and then divided into 2 groups according to the uNGAL level of 25 ng/mL. Progression of renal injury (PRI) was defined as a decrease in the GFR of more than 5 mL/min/1.73 m2 in the mild or moderate groups, or if a normal group patient shifted to the mild or moderate group. RESULTS: Fifty-one patients were enrolled. The mean uNGAL level was higher in the moderate group than in the normal and mild groups (18.38 ± 14.31 vs 7.74 ± 8.13; P < .01). A proportion of uNGAL-high was also higher in the moderate group than in the mild group (40% vs 5%; P = .03). uNGAL-high was a risk factor for 6-month PRI (odds ratio, 60.375; 95% confidence interval, 1.283-4088.25; P = .037) and 1-year PRI (odds ratio, 21.311; % confidence interval, 0.947-479.578; P = .054). CONCLUSIONS: A uNGAL of >25 ng/mg can be a marker for moderate renal impairment (GFR of 30-59 mL/min/1.73 m2) and a predictor of PRI at 6 months in patients using calcineurin inhibitors. Renal protection strategies should be considered in liver transplant recipients with a uNGAL of >25 ng/mg in spot urine sampling.

Initial experience with purely laparoscopic living-donor right hepatectomy.

BACKGROUND: There may be concerns about purely laparoscopic donor right hepatectomy (PLDRH) compared with open donor right hepatectomy, especially when performed by surgeons accustomed to open surgery. This study aimed to describe technical tips and pitfalls in PLDRH. METHODS: Data from donors who underwent PLDRH at Seoul National University Hospital between December 2015 and July 2017 were analysed retrospectively. Endpoints analysed included intraoperative events and postoperative complications. All operations were performed by a single surgeon with considerable experience in open living donor hepatectomy. RESULTS: A total of 26 donors underwent purely laparoscopic right hepatectomy in the study interval. No donor required transfusion during surgery, whereas two underwent reoperation. In two donors, the dissection plane at the right upper deep portion of the midplane was not correct. One donor experienced portal vein injury during caudate lobe transection, and one developed remnant left hepatic duct stenosis. One donor experienced remnant portal vein angulation owing to a different approach angle, and one experienced arterial damage associated with the use of a laparoscopic energy device. One donor had postoperative bleeding due to masking of potential bleeding foci owing to intra-abdominal pressure during laparoscopy. Two donors experienced right liver surface damage caused by a xiphoid trocar. CONCLUSION: Purely laparoscopic donor hepatectomy differs from open donor hepatectomy in terms of angle and caudal view. Therefore, surgeons experienced in open donor hepatectomy must gain adequate experience in laparoscopic liver surgery and make adjustments when performing PLDRH.

Pure laparoscopic living donor hepatectomy: Focus on 55 donors undergoing right hepatectomy.

Although laparoscopic donor hepatectomy is increasingly common, few centers with substantial experience have reported the results of pure laparoscopic donor right hepatectomy (PLDRH). Here, we report the experiences of 60 consecutive liver donors undergoing pure laparoscopic donor hepatectomy (PLDH), with most undergoing right hepatectomy. None of the 60 donors who underwent PLDH had intraoperative complications and none required transfusions, reoperation, or conversion to open hepatectomy. Forty-five donors who underwent PLDRH between November 2015 and December 2016 were compared with 42 who underwent conventional donor right hepatectomy (CDRH) between May 2013 and February 2014. The total operation time was longer (330.7 vs 280.0 minutes; P < .001) and the percentage with multiple bile duct openings was higher (53.3% vs 26.2%; P = .010) in the PLDRH group. However, the length of postoperative hospital stay (8.4 vs 8.2 days; P = .495) and rate of complications (11.9% vs 8.9%; P = .733) and re-hospitalizations (4.8% vs 4.4%; P = 1.000) were similar in both groups. PLDH, including PLDRH, is feasible when performed by a highly experienced surgeon and transplant team. Further evaluation, including long-term results, may support these preliminary findings of comparative outcomes for donors undergoing PLDRH and CDRH.

Efficacy and Safety of Generic Mycophenolate Mofetil (My-rept) 500-Milligram Tablets in Primary Liver Transplant Recipients.

BACKGROUND: Generic immunosuppressants may be cost-effective if clinical outcomes are equivalent to the brand-name medications. Mycophenolate mofetil in the form of My-rept may be cost-effective being a generic immunosuppressant, which is available as a 500-mg tablet as well as a 250-mg capsule (Chong Kun Dang Pharmaceutical Corporation, Seoul, Korea). OBJECTIVE: This study aimed to evaluate the efficacy, safety, cost-effectiveness, and convenience of My-rept 500-mg tablets in liver transplant recipients. SETTING: The setting was an outpatient liver transplantation clinic of a tertiary hospital in Korea. METHOD: A phase 4, single-center, open-label, noncomparative study was undertaken. A total of 50 patients were recruited. Acute transplant rejection, changes in blood chemistry, white blood cell count, assessments of renal function, occurrence of adverse drug reactions, and other characteristics of the patients were recorded for 24 weeks. After study termination, a satisfaction survey was conducted. RESULTS: All enrolled patients and their liver grafts had survived for 24 weeks post-transplantation. No episodes of acute rejection were reported. Nine patients (18.8%) presented with adverse drug reactions that had been commonly reported with the use of other mycophenolate mofetil products, and no serious adverse drug reactions were reported. CONCLUSION: In conclusion, the My-rept 500-mg tablet appears to be feasible and convenient for administration to recipients of a liver transplant.

Surgical Techniques of Allogeneic Liver Transplantation in a Nonhuman Primate Model.

Herein, we report our experience of performing allogeneic orthotopic liver transplantation (LT) in nonhuman primates. We designed an allogeneic ABO-compatible orthotopic LT model in monkeys in a manner similar to that used in humans. We applied almost the same surgical procedures used for human conventional deceased donor LT. A total of 6 monkeys underwent allogeneic LT. One cynomolgus monkey aged 45 months (3.4 kg) and 5 rhesus macaque monkeys aged 50.2 ± 14.8 months (5.40 ± 0.33 kg) were used as recipients. In the donor surgery, the liver was perfused in situ through the aorta using cold histidine-tryptophan-ketoglutarate solution. The portal vein (diameter, 5-10 mm), supra- and infra-hepatic inferior vena cava (IVC) (diameter, 12-15 mm), and common bile duct (diameter, 1.5-3.0 mm) were dissected out. The hepatic artery was kept in continuity with the celiac trunk and abdominal aorta up to the iliac bifurcation (diameter, 5-6 mm). The mean graft weight was 102.0 g (94.8-111.0 g). Recipient surgery was conducted in parallel. After recipient hepatectomy, the graft was implanted. The suprahepatic IVC and portal vein were anastomosed to those of the graft. After reperfusion, the infrahepatic IVC was anastomosed. The aorta conduit of the graft was anastomosed to the infrarenal aorta of the recipient in a retrocolic end-to-side manner. Biliary reconstruction was performed in a duct-to-duct anastomosis with cholecystectomy. Mean operative time was 107.0 minutes for donor and 198.2 minutes for recipient. There was one operative death due to unknown cause. In conclusion, for allogeneic orthotopic LT in nonhuman primate model, we can apply almost the same procedure used for human conventional deceased donor LT in a similar manner.

Survival benefit of liver resection for Barcelona Clinic Liver Cancer stage B hepatocellular carcinoma.

BACKGROUND: Although transarterial chemoembolization is recommended as the standard treatment for Barcelona Clinic Liver Cancer stage B hepatocellular carcinoma (BCLC-B HCC), other treatments including liver resection have been used. This study aimed to determine the survival benefit of treatment strategies including resection for BCLC-B HCC compared with non-surgical treatments. METHODS: The nationwide multicentre database of the Korean Liver Cancer Association was reviewed. Patients with BCLC-B HCC who underwent liver resection as a first or second treatment within 2 years of diagnosis and patients who received non-surgical treatment were selected randomly. Survival outcomes of propensity score-matched groups were compared. RESULTS: Among 887 randomly selected patients with BCLC-B HCC, 83 underwent liver resection as first or second treatment and 597 had non-surgical treatment. After propensity score matching, the two groups were well balanced (80 patients in each group). Overall median survival in the resection group was better than that for patients receiving non-surgical treatment (50·9 versus 22·1 months respectively; P < 0·001). The 1-, 2-, 3- and 5-year overall survival rates in the resection group were 90, 88, 75 and 63 per cent, compared with 79, 48, 35 and 22 per cent in the no-surgery group (P < 0·001). In multivariable analysis, non-surgical treatment only (hazard ratio (HR) 3·35, 95 per cent c.i. 2·16 to 5·19; P < 0·001), albumin level below 3·5 g/dl (HR 1·96, 1·22 to 3·15; P = 0·005) and largest tumour size greater than 5·0 cm (HR 1·81, 1·20 to 2·75; P = 0·005) were independent predictors of worse overall survival. CONCLUSION: Treatment strategies that include liver resection offer a survival benefit compared with non-surgical treatments for potentially resectable BCLC-B HCC.

Four-Year Experience With Extracorporeal Membrane Oxygenation for Kidney Transplant Patients With Severe Refractory Cardiopulmonary Insufficiency.

BACKGROUND: Kidney transplant (KT) recipients are vulnerable to infections because of their immunosuppressive treatments, and they occasionally exhibit serious acute cardiopulmonary dysfunction. The purpose of this study was to report the clinical outcomes of using extracorporeal membrane oxygenation (ECMO) in KT recipients and to identify risk factors for ECMO weaning failure. METHODS: We retrospectively reviewed the electronic medical records of KT patients who experienced severe cardiopulmonary dysfunction refractory to conventional therapy and received ECMO at the Asan Medical Center Surgical Intensive Care Unit between December 2010 and December 2014. RESULTS: During the 4-year study period, 12 KT patients required ECMO management. Six of these patients were successfully weaned from ECMO; the mean duration of ECMO support was 9.1 days (range, 3.5-15.1 days). Indications for ECMO included pneumonia (8 cases required venovenous ECMO and 1 case required venoarterial [VA] ECMO), stress-induced cardiomyopathy due to fungemia (1 case required VA ECMO), and septic shock due to either urinary tract infection or unknown origin (2 cases required VA ECMO). In assessing risk factors leading to a failure of ECMO weaning, the pH on arterial blood gas analysis performed just before the beginning of this intervention was significantly lower in the nonsurvivors than in the survivors (P = .046). CONCLUSIONS: ECMO can be a beneficial rescue therapy in immunosuppressed patients with cardiopulmonary dysfunction refractory to treatment. Severe acidosis before the administration of EMCO is a major determinant of ECMO weaning failure.

Tranexamic acid and blood loss during and after cesarean section: a meta-analysis.

OBJECTIVE: A meta-analysis of randomized controlled trials (RCTs) was conducted to evaluate whether tranexamic acid (TXA) could significantly reduce blood loss during and after cesarean section (CS) when compared with no TXA. STUDY DESIGN: MEDLINE (PubMed), EMBASE, Cochrane Central Register of Controlled Trials and Web of Science were searched to identify RCTs that compared intravenous TXA with no TXA before CS for blood loss. The related data were extracted by two independent authors. The fixed or random-effect methods were used to combine data. RESULT: Eleven RCTs were included in this analysis with a total of 1276 women in TXA group and 1255 in no TXA (control) group. Total blood loss during and after CS was significantly less in TXA group than in control group (mean difference (MD) -141.61 ml, 95% confidence interval (CI) -207.09 to -76.14, P<0.01). There was a significant reduction in intraoperative and postpartum blood loss in TXA group as compared with control group (MD -143.36 ml, 95% CI -220.38 to -66.35, P<0.01; and MD -38.20 ml, 95% CI -59.27 to -17.12, P<0.01, respectively). Declines in hemoglobin and hematocrit values after CS were both significantly less in TXA group than in control group. The difference of postpartum hemorrhage rate was statistically significant between groups (risk ratio (RR) 0.57, 95% CI 0.37 to 0.89, P=0.01). The need for blood transfusion was significantly less in TXA group than control group (RR 0.23, 95% CI 0.10 to 0.57, P<0.01). CONCLUSION: Our results demonstrate that TXA offers an advantage over no TXA in reducing blood loss during and after CS.

Pretransplant serum levels of C-reactive protein predict prognoses in patients undergoing liver transplantation for hepatocellular carcinoma.

BACKGROUND: Preoperative absolute C-reactive protein (CRP) has been shown to correlate with prognoses in various malignancies, including hepatocellular carcinoma (HCC). METHODS: The aim of this study was to investigate whether pretransplant CRP levels predict prognoses in patients undergoing liver transplantation (LT) for HCC. We retrospectively analyzed clinicopathological factors in 211 patients with available pretransplant serum CRP levels who underwent LT for HCC between January 2005 and April 2012. RESULTS: By means of receiver operating characteristic curve analysis, a CRP level of >0.3 mg/dL was considered to be elevated. By multivariate analysis, the high CRP level, the maximal tumor size >5 cm, the presence of intrahepatic metastasis, and positive findings in pretransplant (18)fluoro-2-deoxy-D-glucose positron emission tomography/computed tomography ((18)F-FDG PET/CT) were related to tumor recurrence, whereas the high CRP level, the presence of intrahepatic metastasis, and positive findings in pretransplant (18)F-FDG PET/CT were related to poor overall survival. When subgroup analysis was conducted according to the Milan criteria, the high CRP level was an independent factor for predicting poor outcomes in patients with HCC beyond the Milan criteria (P = .001 for recurrence-free survival and P = .010 for overall survival), and not for patients within the criteria. CONCLUSIONS: Pretransplant serum CRP levels can predict prognoses in patients undergoing LT for HCC, especially in patients with HCC exceeding the Milan criteria.

Surgical treatment of central venous catheter related septic deep venous thrombosis.

OBJECTIVE/BACKGROUND: The aim of this study was to evaluate the clinical features and outcomes of catheter related central venous thrombosis and whether a surgical approach can be an effective treatment modality in selected cases that are refractory to conservative management. METHODS: This was a retrospective review of the 46 consecutive patients who were suspected of having central venous catheter related infected deep venous thrombosis and who met the eligibility criteria. RESULTS: Conservative management achieved clinical improvement in 26 (56.5%) patients and failed in 20 (43.5%), of whom surgical thrombectomy was performed in 13. The remaining seven patients died before surgery could be performed or their clinical condition was too poor. Apart from one case of wound hematoma (7.7%), post-operative complications that related to the surgical procedure were not observed. Patency of the involved vein was re-established in 12 of the 13 (92.3%) surgically treated patients, and clinical improvement was achieved in 11 (84.6%). In particular, the five patients whose blood cultures revealed Candida species exhibited prompt defervescence after surgical thrombectomy. CONCLUSION: Although conservative management is the first therapy of choice in patients with central venous catheter related infected thrombosis, surgical treatment that removes the septic material can be regarded as a last resort in critically ill patients with septic thrombophlebitis that is refractory to conservative management.

Mortalin (GRP75/HSPA9) upregulation promotes survival and proliferation of medullary thyroid carcinoma cells.

Medullary thyroid carcinoma (MTC) is a neuroendocrine tumor mainly caused by mutations in the rearranged during transfection (RET) proto-oncogene. For therapy of advanced MTC, the Food and Drug Administration recently approved vandetanib and cabozantinib, the tyrosine kinase inhibitors targeting RET, vascular endothelial growth factor receptor, epidermal growth factor receptor and/or c-MET. Nevertheless, not all patients respond to these drugs, demanding additional therapeutic strategies. We found that mortalin (HSPA9/GRP75), a member of HSP70 family, is upregulated in human MTC tissues and that its depletion robustly induces cell death and growth arrest in MTC cell lines in culture and in mouse xenografts. These effects were accompanied by substantial downregulation of RET, induction of the tumor-suppressor TP53 and altered expression of cell cycle regulatory machinery and apoptosis markers, including E2F-1, p21(CIP1), p27(KIP1) and Bcl-2 family proteins. Our investigation of the molecular mechanisms underlying these effects revealed that mortalin depletion induces transient MEK/ERK (extracellular signal-regulated kinase) activation and altered mitochondrial bioenergetics in MTC cells, as indicated by depolarized mitochondrial membrane, decreased oxygen consumption and extracellular acidification and increased oxidative stress. Intriguingly, mortalin depletion induced growth arrest partly via the MEK/ERK pathway, whereas it induced cell death by causing mitochondrial dysfunction in a Bcl-2-dependent manner. However, TP53 was not necessary for these effects except for p21(CIP1) induction. Moreover, mortalin depletion downregulated RET expression independently of MEK/ERK and TP53. These data demonstrate that mortalin is a key regulator of multiple signaling and metabolic pathways pivotal to MTC cell survival and proliferation, proposing mortalin as a novel therapeutic target for MTC.

Genome-wide Association Study for Warner-Bratzler Shear Force and Sensory Traits in Hanwoo (Korean Cattle).

Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p<1.3×10(-6)) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.

Genetic variants in the CYP24A1 gene are associated with prostate cancer risk and aggressiveness in a Korean study population.

BACKGROUND: Vitamin D-deactivating enzyme CYP24A1 had controversial effects on prostate cancer risk; the genetic study also showed the controversial results. Therefore, we identified the relationships between polymorphisms in CYP24A1 and prostate cancer in a Korean cohort. METHODS: We evaluated the association between 21 single-nucleotide polymorphisms (SNPs) in the CYP24A1 and prostate cancer in Korean men (272 prostate cancers and 173 controls). BPH patients with high PSA or abnormal digital rectal examination who underwent negative prostate biopsy were enrolled in the control group. Twenty-one SNPs in the CYP24A1 were selected from the International HapMap database and the NCBI database with calculation of minor allele frequency and linkage disequilibrium, preferably including the SNPs that were nonsynonymous and located within exons. We also investigated the association between 21 SNPs in the CYP24A1 gene and known clinical characteristics, such as the PSA level, clinical stage, pathological stage and Gleason score. RESULTS: The statistical analysis suggested that five CYP24A1 sequence variants (rs2248461-odds ratio (OR): 0.63, rs2248359-OR: 0.65, rs6022999-OR: 0.65, rs2585428-OR: 0.46, rs4809959-OR: 0.52) had a significant association with prostate cancer risk after multiple comparisons by a method of false discovery rate. Logistic analyses of the CYP24A1 polymorphisms with several prostate cancer-related factors showed that several SNPs were significant: four SNPs to PSA level, three to clinical stage, two to pathological stage and two SNPs to the Gleason score. CONCLUSIONS: The results of this study suggest that some CYP24A1 gene polymorphisms might be associated with the risk of prostate cancer in Korean men. Five CYP24A1 sequence variants showed the significance to predict prostate cancer, and several SNPs of CYP24A1 gene had an important finding to predict prostate cancer-related factors. However, these results should be validated in future large-scale studies.

First Report of Fusarium succisae Causing Flower Rot on Thread-leaf Coreopsis.

In July 2010, flower rot of thread-leaf coreopsis (Coreopsis verticillata) was found in a garden in the Icheon City, Korea. The disease affected about 20 to 50% of a 100 m2 area. The disease was characterized by the appearance of pinkish mycelia on the stigmata and inflorescences of flowers. In some cases, flowers failed to bloom or turned brown before opening fully. Fragments (each 5 × 5 mm) of the symptomatic tissue were surface-sterilized with 1% NaOCl for 1 min, and then rinsed twice in sterilized distilled water. The tissue pieces were placed on water agar (WA) and incubated at 25°C for 4 to 6 days. Twenty-two isolates of Fusarium species were obtained from the diseased flowers. All isolates were identified as Fusarium succisae based on their morphological characteristics on carnation leaf agar (CLA) medium and DNA sequences of the translation elongation factor 1-alpha gene (1). Macroconidia and sporodochia were sparsely produced on CLA medium. Microconidia were abundant, borne in false heads, oval or allantoid and sometimes pyriform, and measured 4.2 to 13 × 2.2 to 5.4 µm. Chlamydospores were absent. The EF-1α gene was amplified from three isolates by PCR assay and the amplification products were sequenced (2). The nucleotide sequences obtained were deposited in GenBank with accession numbers KF514658, KF514659, and KF514660. BLASTn analysis showed 99% homology with the EF-1α sequence of F. succisae NRRL13613 (GenBank Accession No. AF160291). Pathogenicity tests were conducted with inoculation of flowers on Coreopsis verticillata. Spore suspension was prepared by flooding 7-day-old cultures on potato dextrose agar with sterilized 2% (w/v) sugar solution. When the plants started to have buds, the isolates were inoculated by placing one drop (20 µl) of spore suspension (1 × 106 spores ml-1) into the buds. Fifteen buds of the plants were arranged into three replications. The control was treated with sterilized 2% sugar solution. Inoculated plants were kept in a greenhouse at 25/20°C (12 h/12 h). Three weeks after inoculation, the symptoms were observed on buds with mycelial production. Control plants had no mycelia on buds. F. succisae was re-isolated from the inoculated flowers. To our knowledge, this is the first report of flower rot of thread-leaf coreopsis caused by F. succisae. References: (1) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Publishing, Ames, IA, 2006. (2) K. O'Donnell et al. Proc. Nat. Acad. Sci. 95:2044, 1998.

Exome Sequencing and High-Density Microarray Testing in Monozygotic Twin Pairs Discordant for Features of VACTERL Association.

Exome sequencing offers an efficient and affordable method to interrogate genetic factors involved in human disease. Performing exome sequencing of monozygotic twins discordant for VACTERL (Vertebral anomalies, Anal atresia, Cardiac malformations, Tracheo-Esophageal fistula, Renal anomalies, and Limb abnormalities) association-type congenital malformations was hypothesized to potentially reveal discordant variants that could demonstrate disease cause(s). After demonstrating monozygosity, we applied high-density microarrays and exome sequencing to 2 twin pairs in which 1 twin had features of VACTERL association while the other was phenotypically normal (demonstrated through comprehensive clinical and radiological evaluation). No obvious discordant genotypic results were found that would explain phenotypic discordance. We conclude that VACTERL association is a complex disease, and while performing microarray analysis and exome sequencing on phenotypically discordant monozygotic twins may hypothetically reveal genetic causes of disorders, challenges remain in applying these methods in this circumstance.

First Report of Fusarium oxysporum f. sp. lycopersici Race 3 Causing Fusarium Wilt on Tomato in Korea.

In July 2010, fusarium wilt symptoms of tomato (Lycopersicon esculentum Mill.) plants were found in two commercial greenhouses in the Damyang area of Korea. Approximately 1% of 7,000 to 8,000 tomato plants were wilted and chlorotic in each greenhouse. The vascular tissue was usually dark brown and the discoloration extended to the apex. Fragments (each 5 × 5 mm) of the symptomatic tissue were surface-sterilized with 1% NaOCl for 1 min, then rinsed twice in sterilized distilled water (SDW). The tissue pieces were placed on water agar and incubated at 25°C for 4 to 6 days. Nine Fusarium isolates were obtained from four diseased plants, of which three isolates were identified as F. oxysporum based on morphological characteristics on carnation leaf agar medium and DNA sequences of the translation elongation factor 1-alpha (EF-1α) gene (2). Macroconidia were mostly 3- to 5-septate, slightly curved, and 28 to 53 × 2.8 to 5.2 µm. Microconidia were abundant, borne in false heads or short monophialides, generally single-celled, oval to kidney shaped, and 5 to 23 × 3 to 5 µm. Chlamydospores were single or in short chains. The EF-1α gene was amplified from three isolates by PCR assay using ef1 and ef2 primers (3), and the amplification products were sequenced. The nucleotide sequences obtained were deposited in GenBank (Accession Nos. KC491844, KC491845, and KC491846). BLASTn analysis showed 99% homology with the EF-1α sequence of F. oxysporum f. sp. lycopersici MN-24 (HM057331). Pathogenicity tests and race determination were conducted using root-dip inoculation (4) on seedlings of tomato differential cultivars: Ponderosa (susceptible to all races), Momotaro (resistant to race 1), Walter (resistant to races 1 and 2), and I3R-1 (resistant to all races). A spore suspension was prepared by flooding 5-day-old cultures on potato dextrose agar with SDW. Plants at the first true-leaf stage were inoculated by dipping the roots in the spore suspension (1 × 106 conidia/ml) for 10 min. Inoculated plants were transplanted into pots containing sterilized soil, and maintained in the greenhouse at 25/20°C (12/12 h). Twenty-four seedlings of each cultivar were arranged into three replications. An equal number of plants of each cultivar dipped in water were used as control treatments. Disease reaction was evaluated 3 weeks after inoculation, using a disease index on a scale of 0 to 4 (0 = no symptoms, 1 = slightly swollen and/or bent hypocotyl, 2 = one or two brown vascular bundles in the hypocotyl, 3 = at least two brown vascular bundles and growth distortion, 4 = all vascular bundles brown and the plant either dead or very small and wilted). All isolates caused symptoms of fusarium wilt on all cultivars except I3R-1, indicating that the isolates were race 3. The pathogen was reisolated from the discolored vascular tissue of symptomatic plants. Control plants remained asymptomatic, and the pathogen was not reisolated from the vascular tissue. Fusarium wilt of tomato caused by isolates of F. oxysporum f. sp. lycopersici races 1 and 2 has been reported previously; however, race 3 has not been reported in Korea (1). To our knowledge, this is the first report of isolates of F. oxysporum f. sp. lycopersici race 3 on tomato in Korea. References: (1) O. S. Hur et al. Res. Plant Dis. 18:304, 2012 (in Korean). (2) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Publishing, Ames, IA, 2006. (3) K. O'Donnell et al. Proc. Nat. Acad. Sci. 95:2044, 1998. (4) M. Rep et al. Mol. Microbiol. 53:1373, 2004.

Phylogenetic Analysis of a Privately-owned Korean Native Chicken Population Using mtDNA D-loop Variations.

The use of Korean native chicken is increasing, and the discovery of new genetic resources is very important from both economic and genetic conservation points of view. In this study, mtDNA D-loop sequences from 272 privately-owned Korean native chickens from a Hyunin farm were investigated. Seventeen nucleotide substitutions were identified from the sequence analysis and they were classified as 6 haplotypes. Previously investigated haplotypes in five Korean native chicken populations have been compared with the Hyunin chicken population. The results indicated that two haplotypes, H10 and H15, in the Hyunin chicken population were not previously identified in other Korean native chicken populations, representing 33.09% (90/272) and 1.1% (3/272) of the Hyunin population, respectively. On the other hand, four other haplotypes were identical to those of a previous study of Korean native chicken populations. This result is indicative of conservation strategies of Hyunin chicken populations for expanding the genetic diversity in the Korean native chicken population.