Massive parallel sequencing of short tandem repeats in the Korean population.

STR analysis using capillary electrophoresis has been the most widely used method for forensic DNA typing. Recently, massive parallel sequencing (MPS) technique has been emerging as an innovative tool to supplement or replace the conventional CE process. In this study, we evaluated the application of commercial MiSeqFGx™ forensic signature kit (Illumina Inc., San Diego, CA, USA) in the Korean population, including performance comparison with CE-based STR profiling kits. The genotyping results of 209 unrelated random Korean individuals were summarized according to the International Society for Forensic Genetics guideline. The study revealed that 26 novel sequence variations in autosomal STR were newly found that had not been previously reported in other forensic literature. This indicates that MPS may be an effective supplementary tool for forensic DNA typing and the database to increase the discriminatory power of individual identification.

Differential pre-amplification of STR loci for fragmented forensic DNA profiling.

DNA profiling of short tandem repeats (STR) has been successfully used for the identification of individuals in forensic samples, accidents and natural disasters. However, STR profiling of DNA isolated from old crime scenes and damaged biological samples is difficult due to DNA degradation and fragmentation. Here, we show that pre-amplification of STR loci using biotinylated primers for the STR loci is an efficient strategy to obtain STR profiling results from fragmented forensic samples. Analysis of STR loci with longer amplicon sizes is generally hampered, since these relatively long loci are vulnerable to DNA fragmentation. This problem was overcome by using reduced or increased primer concentrations for loci with shorter or longer amplicon sizes, respectively, in our pre-amplification strategy. In addition, pre-amplification of STR loci into two groups of short or long amplicon size increases the efficiency of STR profiling from highly fragmented forensic DNA samples. Therefore, differential pre-amplification of STR loci is an effective way to obtain DNA profiling results from fragmented forensic samples.

SH3RF2 functions as an oncogene by mediating PAK4 protein stability.

SH3RF (SH3-domain-containing RING finger protein) family members, SH3RF1-3, are multidomain scaffold proteins involved in promoting cell survival and apoptosis. In this report, we show that SH3RF2 is an oncogene product that is overexpressed in human cancers and regulates p21-activated kinase 4 (PAK4) protein stability. Immunohistochemical analysis of 159 colon cancer tissues showed that SH3RF2 expression levels are frequently elevated in cancer tissues and significantly correlate with poor prognostic indicators, including increased invasion, early recurrence and poor survival rates. We also demonstrated that PAK4 protein is degraded by the ubiquitin-proteasome system and that SH3RF2 inhibits PAK4 ubiquitination via physical interaction-mediated steric hindrance, which results in the upregulation of PAK4 protein. Moreover, ablation of SH3RF2 expression attenuates TRADD (TNFR-associated death domain) recruitment to tumor necrosis factor-α (TNF-α) receptor 1 and hinders downstream signals, thereby inhibiting NF-κB (nuclear factor-kappaB) activity and enhancing caspase-8 activity, in the context of TNF-α treatment. Notably, ectopic expression of SH3RF2 effectively prevents apoptosis in cancer cells and enhances cell migration, colony formation and tumor growth in vivo. Taken together, our results suggest that SH3RF2 is an oncogene that may be a definitive regulator of PAK4. Therefore, SH3RF2 may represent an effective therapeutic target for cancer treatment.

Optimization of STR locus enrichment for STR profiling of fragmented DNA.

DNA degradation is a major obstacle in gaining an accurate profile with standard DNA typing technology. Although alternative genotyping strategies such as mini-STRs and SNPs have proven to be more successful in profiling degraded DNA, these approaches also have limitations. Here, we show that locus enrichment by hybridization of degraded genomic DNA with an STR locus-specific biotinylated oligonucleotide is a powerful approach to overcome problems in STR typing of highly degraded DNA. An experimental investigation of factors affecting the efficiency of this method indicates that the choice of primer and molar ratio of primers to genomic DNA are critical factors in improving enrichment of the STR locus before genotyping with multiplex kits. In addition, we find that indirect capture rather than direct capture with magnetic beads yields better enrichment efficiency for STR locus enrichments. Using these strategies, we demonstrate an improvement in STR typing of DNA from cultured cells damaged by exposure to sunlight or UV. We suggest that this approach could be applied to highly degraded forensic samples alone or in combination with mini-STRs.

Parsonage-Turner Syndrome Following Typhoid Vaccination.

Parsonage-Turner syndrome is a rare neurological disease of varying etiology characterized by severe shoulder pain, muscle weakness, and atrophy. Mechanisms are unclear, but are thought to be genetic and immune-mediated reactions. Rarely, Parsonage-Turner syndrome occurs as a side effect of vaccination. A 20-year-old male who worked as a soldier visited the military hospital because of shoulder pain after vaccination against typhoid and was diagnosed with Parsonage-Turner syndrome based on electromyography and joint magnetic resonance imaging. Pain was controlled with a nerve block. Intravenous immunoglobulin was administered for improvement of neurologic symptoms. This case suggests that Parsonage-Turner syndrome should be considered as a side effect of vaccination. To the best of our knowledge, this is the first report of Parsonage-Turner syndrome following vaccination in Korea.

Particulate Matter Exposure During Oocyte Maturation: Cell Cycle Arrest, ROS Generation, and Early Apoptosis in Mice.

Particulate matter (PM) is a general atmospheric pollutant released into the air by an anthropogenic and naturally derived mixture of substances. Current studies indicate that fine dust can result in different health defects, including endothelial dysfunction, asthma, lung cancer, cardiovascular diseases, uterine leiomyoma, deterioration in sperm quality, and overall birth impairment. However, the most prominent effects of PM10 (diameter < 10 µM) exposure on the female reproductive system, especially with respect to oocyte maturation, remain unclear. In the present study, maturing mouse oocytes were treated with PM10 and the phenotypes of the resulting toxic effects were investigated. Exposure to PM10 led to impairment of maturation capacity by inducing cell cycle arrest and blocking normal polar body extrusion during in vitro maturation and activation of fertilization of mouse oocytes. Additionally, defects in tubulin formation and DNA alignment were observed in PM10-treated oocytes during metaphase I to anaphase/telophase I transition. Moreover, PM10 induced reactive oxygen species generation, mitochondrial dysfunction, DNA damage, and early apoptosis. Taken together, these results indicate that PM10 exposure leads to a decline in oocyte quality and affects the subsequent embryonic development potential of mammalian oocytes.

Potential Applications of Non-thermal Plasma in Animal Husbandry to Improve Infrastructure.

Infrastructure in animal husbandry refers to fundamental facilities and services necessary for better living conditions of animals and its economy to function through better productivity. Mainly, infrastructure can be divided into two categories: hard infrastructure and soft infrastructure. Physical infrastructure, such as buildings, roads, and water supplying systems, belongs to hard infrastructure. Soft infrastructure includes services which are required to maintain economic, health, cultural and social standards of animal husbandry. Therefore, the proper management of infrastructure in animal husbandry is necessary for animal welfare and its economy. Among various technologies to improve the quality of infrastructure, non-thermal plasma (NTP) technology is an effectively applicable technology in different stages of animal husbandry. NTP is mainly helpful in maintaining better health conditions of animals in several ways via decontamination from microorganisms present in air, water, food, instruments and surfaces of animal farming systems. Furthermore, NTP is used in the treatment of waste water, vaccine production, wound healing in animals, odor-free ventilation, and packaging of animal food or animal products. This review summarizes the recent studies of NTP which can be related to the infrastructure in animal husbandry.

Maximization of dextransucrase activity expressed in E. coli by mutation and its functional characterization.

A novel dextransucrase gene, DSRN, was obtained by ultrasoft X-ray treatment of the DSRB742 gene. The DSRN gene was further mutated via site-directed mutagenesis producing four mutants: DSRN1 (F196S), DSRN2 (Y346N), DSRN3 (K395T) and DSRN4 (P980T). Dextransucrases derived from DSRB742 and its mutants were expressed in E. coli and affinity-purified using dextran to give 80% purity. They had specific activities of 0.6-17 U/mg with Km values of 18-88 mM. DSRB742 had the lowest (0.02 s(-1) x mM(-1)) and DSRN1 had the highest (0.13 s(-1) x mM(-1)) Kcat/Km values. DSRN3 had the highest enzymatic transglycosylation efficiency with maltose (63% of theoretical), gentiobiose (39%), or salicine (40%).

Comparison of clinical efficacy between ultra-LABAs and ultra-LAMAs in COPD: a systemic review with meta-analysis of randomized controlled trials.

BACKGROUND: A single long-acting bronchodilator, ultra-long acting muscarinic antagonist (ultra-LAMA) or ultra-long acting ß2-agonist (ultra-LABA) is preferred for the initial treatment of patients with chronic obstructive pulmonary disease (COPD); however, there are few head-to-head comparative studies between the two. Here, a meta-analysis of randomized controlled trials was performed to compare the clinical efficacy between ultra-LABA and ultra-LAMA in patients with moderate-to-severe COPD. METHODS: MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials were searched (to March 1, 2017) to identify all published randomized controlled trials. RESULTS: Of the 12,906 articles found by searching the databases, we obtained data from 10,591 patients with COPD (LABA, n=5,058; LAMA, n=5,533) in seven published studies. Our results showed that COPD exacerbation were significantly lower in patients taking ultra-LAMA than those taking ultra-LABA (odds ratio =0.857, P=0.0008). However, no significant differences were observed between ultra-LAMA and ultra-LABA patients regarding improvement in trough forced expiratory volume in 1 s, the transitional dyspnea index, or St. George's Respiratory Questionnaire score. CONCLUSIONS: This study suggests that COPD exacerbation occurred less often in patients taking an ultra-LAMA than in those taking an ultra-LABA with similar efficacy of lung function and quality of life.

Enhanced anti-oxidative effect of fermented Korean mistletoe is originated from an increase in the contents of caffeic acid and lyoniresinol.

Viscum album var. coloratum (Korean mistletoe; KM) is an herbal medicine that is used worldwide for the treatment of various immunological disorders and cancers. KM extract showed enhanced anti-oxidative effects in 2,2-diphenyl-1-picrylhydrazyl, Trolox equivalent antioxidant capacity, and 5-(and-6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate acetyl ester assays after being fermented with a crude enzyme extract from a soybean paste fungus, Aspergillus kawachii. High-performance liquid chromatography analysis showed four increased peaks in enzyme treated KM. The increased peaks were isolated and identified as caffeic acid (1), hesperetin (2), syringaldehyde (3), and lyoniresinol (4). Among the four compounds, only 1 and 4 showed strong anti-oxidative activity. Therefore, the fermentation increased the contents of 1 and 4, which consequently increased the anti-oxidative activity of KM.

A Case of Statin-Induced Interstitial Pneumonitis due to Rosuvastatin.

Statins lower the hyperlipidemia and reduce the incidence of cardiovascular events and related mortality. A 60-year-old man who was diagnosed with a transient ischemic attack was started on acetyl-L-carnitine, cilostazol, and rosuvastatin. After rosuvastatin treatment for 4 weeks, the patient presented with sudden onset fever, cough, and dyspnea. His symptoms were aggravated despite empirical antibiotic treatment. All infectious pathogens were excluded based on results of culture and polymerase chain reaction of the bronchoscopic wash specimens. Chest radiography showed diffuse ground-glass opacities in both lungs, along with several subpleural ground-glass opacity nodules; and a foamy alveolar macrophage appearance was confirmed on bronchoalveolar lavage. We suspected rosuvastatin-induced lung injury, discontinued rosuvastatin and initiated prednisolone 1 mg/kg tapered over 2weeks. After initiating steroid therapy, his symptoms and radiologic findings significantly improved. We suggest that clinicians should be aware of the potential for rosuvastatin-induced lung injury.

Infected Aortic Aneurysm caused by Mycobacterium bovis after Intravesical Bacillus Calmette-Guérin Treatment for Bladder Cancer.

A 70-year-old man presented with lower back pain and cyanotic changes in his left lower extremity. He was diagnosed with infected aortic aneurysm and infectious spondylitis. He had received intravesical Bacillus Calmette-Guérin (BCG) therapy up to 1 month before the onset of symptoms. The aneurysm was excised and an aorto-biiliac interposition graft was performed. Mycobacterium tuberculosis complex was cultured in the surgical specimens. Real-time polymerase chain reaction (PCR) targeting the senX3-regX3 region, and multiplex PCR using dual-priming oligonucleotide primers targeting the RD1 gene, revealed that the organism isolated was Mycobacterium bovis BCG. The patient took anti-tuberculosis medication for 1 year, and there was no evidence of recurrence at 18 months follow-up.

High-throughput STR analysis for DNA database using direct PCR.

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner.

Stabilization of HIPK2 by escape from proteasomal degradation mediated by the E3 ubiquitin ligase Siah1.

Homeodomain-interacting protein kinase 2 (HIPK2) induces apoptosis and, thus, is maintained at a low level via ubiquitin-mediated proteolysis. In a yeast two-hybrid screen, we identified Siah1, a RING finger E3 ubiquitin ligase, as an interacting protein of HIPK2. Siah1 targeted HIPK2 for poly-ubiquitination-mediated proteasomal degradation. Degradation of HIPK2 by Siah1 was blocked by forced expression of either Mixed Lineage Kinase-3 or Epstein-Barr viral protein LMP-1, as well as by DNA damaging stimuli. These findings effectively illustrate the regulatory mechanisms underlying HIPK2 stabilization by escape from Siah1-mediated degradation, and that Siah1 is an integration target for several internal or external stimuli for HIPK2 stabilization.

Synthesis of gelatin-containing PHBV nanofiber mats for biomedical application.

Electrospinning is one of the fabrication method to form ultra-fine fiber in a nano-scale made of synthetic and natural extracellular matrix components for tissue-engineering applications. In this study, a nanofibrous scaffold was obtained by co-electrospinning poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and gelatin in 2,2,2-trifluoroethanol (TFE) at a ratio of 50/50. The resulting fiber diameters were in the range of 400-1,000 nm without any beads. The nanofiber surfaces were characterized by attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), electron spectroscopy for chemical analysis (ESCA), and atomic force microscopy. It was found, from cell culture experiments, that NIH 3T3 cells on the PHBV/gelatin nanofibrous scaffold more proliferated than on the PHBV nanofibrous scaffold.

Electrospun PHBV/collagen composite nanofibrous scaffolds for tissue engineering.

Electrospinning has recently emerged as a leading technique for the formation of nanofibrous structures made of synthetic and natural extracellular matrix components. In this study, nanofibrous scaffolds were obtained by electrospinning a combination of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and type-I collagen in 1,1,1,3,3,3-hexafluoro-2-isopropanol (HIFP). The resulting fibers ranged from 300 to 600 nm in diameter. Their surfaces were characterized by attenuated total reflection Fourier transform infrared spectroscopy, electron spectroscopy for chemical analysis and atomic force microscopy. The PHBV and collagen components of the PHBV/collagen nanofibrous scaffold were biodegraded by PHB depolymerase and a type-I collagenase aqueous solution, respectively. The cell culture experiments indicated that the PHBV/collagen nanofibrous scaffold accelerated the adhesion and growth of NIH3T3 cells more effectively than the PHBV nanofibrous scaffold, thus making the former a good scaffold for tissue engineering.