Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice.

The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.

Safety and Efficacy of Aspiration Thrombectomy or Pharmacomechanical Thrombectomy after Catheter-Directed Thrombolysis for the Treatment of Acute Iliofemoral Deep Vein Thrombosis.

PURPOSE: To evaluate the safety and efficacy of additional aspiration thrombectomy (AT) or pharmacomechanical thrombectomy (PMT) after catheter-directed thrombolysis (CDT) for the treatment of acute iliofemoral deep vein thrombosis (AIFDVT). MATERIALS AND METHODS: Between May 2017 and December 2018, 40 patients with AIFDVT were enrolled. Twenty underwent AT after CDT (CDTAT), while the remaining 20 underwent PMT using an AngioJetTM device after CDT (CDTPMT). Thrombus clearance was assessed using computed tomography venography at 1 week after the procedure, as follows: grade I, ≤50%; grade II, 51% to 75%; grade III, >75%. Grade III was considered a successful outcome. Treatment outcomes (thrombus clearance, thrombolytic therapy duration, urokinase dose, major complications, residual filter thrombosis, and Villalta score) were compared between the groups. RESULTS: Successful thrombus clearance was achieved in 95% of the patients in both groups. Significant decreases in the thrombolytic therapy duration (P=0.018) and urokinase dose (P=0.014) were noted in the CDTPMT group. Major complications were not noted in both groups. Residual filter thrombi >10 mm were found in 6 filters in the CDTAT group and in 1 filter in the CDTPMT group (P=0.038). The Villalta scores at 6 months were 1.47±1.24 and 1.12±0.92 in the CDTAT and CDTPMT groups, respectively (P=0.372). CONCLUSION: Both methods may be safe and effective management options for patients with AIFDVT. CDTPMT can reduce urokinase dosage, time and remained filter thrombus compared to CDTAT. Studies conducted in the future should compare the effects of overnight CDT followed by PMT with those of single-session PMT on patients with AIFDVT.

Surgical Removal of the Inferior Vena Cava Filter Using Minimal Cavotomy: A Case Report.

The use of retrievable inferior vena cava (IVC) filters has markedly increased in the recent years. However, the failure rate for the retrieval of the IVC filters using the endovascular method is reported to be up to 19%. Open surgical removal of the IVC filters is technically challenging and may require longitudinal cavotomy, clamping, and repair of the IVC. Here, we present a case of successful open surgical removal of the IVC filter using minimal cavotomy. This technique is an effective method after a failed endovascular removal attempt.

The Advantage of Common Femoral Endarterectomy Alone or Combined with Endovascular Treatment.

PURPOSE: Although common femoral artery endarterectomy (CFAE) is regarded as the standard treatment modality for common femoral artery (CFA) disease, availability of advanced endovascular techniques has resulted in an increased number of CFA disease being treated. We evaluated clinical outcomes in a contemporary series of patients who were treated for CFA disease using endarterectomy alone or combined with endovascular treatment. MATERIALS AND METHODS: We retrospectively reviewed 46 patients from November 2001 through December 2007. The treated lesions were divided into 4 groups based on operative procedure: group I (n=11), CFAE alone; group II (n=15), CFAE and iliac artery (IA) endovascular treatment; group III (n=6), CFAE and superficial femoral artery (SFA) endovascular treatment; group IV (n=14), CFAE and IA and SFA endovascular treatment or bypass surgery. RESULTS: The degree of CFA steno-occlusion was not different among the groups. The 3-year primary patency rates of each group were 88.9±10.5%, 60.0±14.5%, 62.5±21.3%, and 83.9±10.4%, respectively. The 3-year primary assisted patency rates were 100%, 70.0±13.0%, 62.5±21.3%, and 89.3±10.4%, while 3-year secondary patency rates were 100%, 80.0±13.0%, 62.5±21.3%, and 92.3±7.4%, respectively. There was no procedure-related mortality. Significant improvement of ankle-brachial index was achieved in all groups. CONCLUSION: CFAE alone is the treatment of choice for excellent patency and clinical improvement in steno-occlusive lesions confined to the CFA. In multiple steno-occlusive diseases, this procedure could be combined with endovascular procedures to reduce the operative risk in conditions with high morbidity.

Simultaneous Hybrid Operation Common Femoral Endarterectomy and Endovascular Treatment in Multilevel Peripheral Arterial Disease with Critical Limb Ischemia.

The purpose of revascularization in lower extremity arterial occlusive disease is to prevent amputation and improve walking ability. Many surgical techniques for peripheral vascular disease (PAD) have been reported. The hybrid operation composed of open surgery and endovascular procedure has been increasingly used for multilevel revascularization. The goal of this study is to evaluate feasibility of simultaneous hybrid femoral endarterectomy and endovascular treatment in patients who need multilevel revascularization with critical limb ischemia. Between March 2011 and July 2014, 38 consecutive patients (43 limbs) with multilevel peripheral arterial disease in critical limb ischemia were treated by simultaneous hybrid operation by single surgeon. The hybrid operation which combines common femoral artery endarterectomy and additive interventional procedure was simultaneously performed for multilevel revascularization. The measurements of primary outcome were primary patency rates, secondary patency rates, and limb salvage rates. Patients who underwent single procedure of surgery or intervention were excluded. The mean age was 72.48 years old and 92.1% were male. The primary and secondary patency rates at 24 months were 67.3 and 72.1%, respectively. The preoperative mean ABI of 0.51 ± 0.27 increased to postoperative mean ABI of 0.88 ± 0.35. The limb salvage rate was 95.3%. Major amputation was performed in 2 out of 43 limbs. There was no early postoperative mortality. The simultaneous hybrid operation for multilevel revascularization may be feasible to treat in multilevel PAD with high technical success and limb salvage rates, thus providing an attractive alternative to larger open surgery or endovascular procedures.

Management of inferior vena cava thrombosis after blunt liver injury.

Inferior vena cava (IVC) thrombosis after traumatic liver injury is an extremely rare condition, and only 12 cases have been reported in the English literature since 1911. We report a case of a 26-year-old man who presented with IVC thrombosis after blunt liver injury. IVC thrombosis was incidentally detected by computed tomography 15 days after conservative management of blunt liver injury. The patient denied any symptoms of thrombophlebitis and did not have any evidence of hypercoagulable state. We placed an IVC filter via the right jugular vein and started the anticoagulation treatment. The patient recovered successfully without operative treatment and IVC thrombosis disappeared completely two months later. We suggest that that the possibility of IVC thrombosis should be considered in patients with a large hematoma of the liver, which may cause compression of the IVC.

Comparison of functional gene annotation of Toxascaris leonina and Toxocara canis using CLC genomics workbench.

The ascarids, Toxocara canis and Toxascaris leonina, are probably the most common gastrointestinal helminths encountered in dogs. In order to understand biological differences of 2 ascarids, we analyzed gene expression profiles of female adults of T. canis and T. leonina using CLC Genomics Workbench, and the results were compared with those of free-living nematode Caenorhabditis elegans. A total of 2,880 and 7,949 ESTs were collected from T. leonina and T. canis, respectively. The length of ESTs ranged from 106 to 4,637 bp with an average insert size of 820 bp. Overall, our results showed that most functional gene annotations of 2 ascarids were quite similar to each other in 3 major categories, i.e., cellular component, biological process, and molecular function. Although some different transcript expression categories were found, the distance was short and it was not enough to explain their different lifestyles. However, we found distinguished transcript differences between ascarid parasites and free-living nematodes. Understanding evolutionary genetic changes might be helpful for studies of the lifestyle and evolution of parasites.

Early experience of thoracic endovascular aortic repair: a local single hospital experience.

PURPOSE: The purpose of this retrospective study was to evaluate the short- to mid-term results of thoracic endovascular aortic repair (TEVAR) in Wonkwang University School of Medicine & Hospital. METHODS: Between February 2009 and May 2011, 8 consecutive patients had undergone endovascular stent-grafting for thoracic aortic diseases. Five patients were treated for traumatic thoracic aortic injuries, two patients were treated for thoracic aneurysms and one patient was treated for a pseudoaneurysm due to penetrating aortic ulcers. Attempted stent-graft deployment was performed electively in 6 patients and emergently in 2. Follow-up was performed at 1-month, 6-month, 1-year, and annually thereafter. RESULTS: Technical success rates were achieved in 87.5% and the 30-day mortality rate was 0%. Mean hospital length of stay after TEVAR was 30 days in traumatic thoracic aortic injuries and 10 days in thoracic aneurismal diseases. Intra-operative Type I endoleak due to migration at deflation was visualized in 1 patient, which was treated by insertion of another stent-graft. During follow-up, a major complication was encountered in one patient who received carotid-subclavian bypass to relieve left arm ischemia. After 5 months he was treated with arch replacement for aortic arch aneurysm with type I endoleak at proximal site after endovascular treatment. The 30-day mortality rate was 0%. However, 1 case of mortality (12.5%) was observed during the follow-up period. CONCLUSION: The short and mid-term results of endovascular repair of thoracic aortic diseases are promising. TEVAR is an effective procedure in the management of thoracic aortic diseases.

Comparative analysis of expressed sequence tags from Flammulina velutipes at different developmental stages.

Flammulina velutipes is a popular edible basidiomycete mushroom found in East Asia and is commonly known as winter mushroom. Mushroom development showing dramatic morphological changes by different environmental factors is scientifically and commercially interesting. To create a genetic database and isolate genes regulated during mushroom development, cDNA libraries were constructed from three developmental stages of mycelium, primordium, and fruit body in F. velutipes. We generated a total of 5,431 expressed sequence tags (ESTs) from randomly selected clones from the three cDNA libraries. Of these, 3,332 different unique genes (unigenes) were consistent with 2,442 (73%) singlets and 890 (27%) contigs. This corresponds to a redundancy of 39%. Using a homology search in the gene ontology database, the EST unigenes were classified into the three categories of molecular function (28%), biological process (29%), and cellular component (6%). Comparative analysis found great variations in the unigene expression pattern among the three different unigene sets generated from the cDNA libraries of mycelium, primordium, and fruit body. The 19-34% of total unigenes were unique to each unigene set and only 3% were shared among all three unigene sets. The unique and common representation in F. velutipes unigenes from the three different cDNA libraries suggests great differential gene expression profiles during the different developmental stages of F. velutipes mushroom.

Proteome analysis of the m. longissimus dorsi between fattening stages in Hanwoo steer.

The objective of this study was to identify proteins in the m. longissimus dorsi between early (12 months of age) and late (27 months of age) fattening stages of Hanwoo (Korean cattle) steers. Using two-dimensional electrophoresis and mass spectrometry, 8 proteins of 11 differentially expressed spots between the 12 and 27 month age groups were identified in the loin muscle. Among those that were differentially expressed, zinc finger 323 and myosin light chain were highly expressed in late-fattening stage, and two catabolic enzymes, triosephosphate isomerase (TPI) and succinate dehydrogenase (SDH) were expressed more in the early versus the late-fattening stage. In particular, the quantification of TPI and SDH by immunoblotting correlated well with fat content. Our data suggested that TPI and SDH are potential candidates as markers and their identification provides new insight into the molecular mechanisms and pathways associated with intramuscular fat contents of bovine skeletal muscle.

Isolation of Genes Specifically Expressed in Different Developmental Stages of Pleurotus ostreatus Using Macroarray Analysis.

The oyster mushroom (Pleurotus ostreatus) is one of the most important edible mushrooms worldwide. The mechanism of P. ostreatus fruiting body development has been of interest both for the basic understanding of the phenotypic change of the mycelium-fruiting body and to improve breeding of the mushrooms. Based on our previous publication of P. ostreatus expressed sequence tag database, 1,528 unigene clones were used in macroarray analysis of mycelium, fruiting body and basidiospore developmental stages of P. ostreatus. Gene expression profile databases generated by evaluating expression levels showed that 33, 10, and 94 genes were abundantly expressed in mycelium, fruiting body and basidiospore developmental stages, respectively. Among them, the genes specifically expressed in the fruiting body stage were further analyzed by reverse transcription-polymerase chain reaction and Northern blot to investigate temporal and spatial expression patterns. These results provide useful information for future studies of edible mushroom development.

Effect of Casing Layer on Growth Promotion of the Edible Mushroom Pleurotus ostreatus.

Various bacteria were isolated from the casing layer soil of the culture bed of P. ostreatus and their role in fruiting body induction of the edible mushroom, P. ostreatus, was investigated. Analysis of the bacterial community isolated from the casing layer soil revealed that the composition of genera and number of cultivable bacteria were different for each sterilizing treatment. Bordetella was predominant in the bulk soil whereas Flavobacterium was predominant after sterilization of the casing layer soil. Fluorescent Pseudomonas was predominant in the non-sterilized casing layer soil. Total number of the bacterial genera in the casing layer soil was higher than that in the bulk soil. In particular, an increase in the fluorescent Pseudomonas population was observed in the non-sterilized casing layer accompanied by induction of fruiting body and enhanced mushroom production yield. The results suggested that specific bacterial populations in the casing layer play an important role in the formation of primodia and the development of basidiome in P. ostreatus.