CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.

BackgroundGenetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species.ResultsHere we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations.ConclusionCSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding

Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea

In August 2016, South Korea experienced a cholera outbreak that caused acute watery diarrhea in three patients. This outbreak was the first time in 15 years that an outbreak was not linked to an overseas source. To identify the cause and to study the epidemiological implications of this outbreak, we sequenced the whole genome of Vibrio cholerae isolates; three from each patient and one from a seawater sample. Herein we present comparative genomic data which reveals that the genome sequences of these four isolates are very similar. Interestingly, these isolates form a monophyletic Glade with V. cholerae strains that caused an outbreak in the Philippines in 2011. The V. cholerae strains responsible for the Korean and Philippines outbreaks have almost identical genomes in which two unique genomic islands are shared, and they both lack SXT elements. Furthermore, we confirm that seawater is the likely source of this outbreak, which suggests the necessity for future routine surveillance of South Korea's seashore.

Polymeric tandem organic light-emitting diodes using a self-organized interfacial layer

The authors have demonstrated efficient polymeric tandem organic light-emitting diodes (OLEDs) with a self-organized interfacial layer, which was formed by differences in chemical surface energy. Hydrophilic poly(styrene sulfonate)-doped poly(3,4-ethylene dioxythiophene) (PEDOT:PSS) was spin coated onto the hydrophobic poly(9,9-dyoctilfluorene) (PFO) surface and a PEDOT:PSS bubble or dome was built as an interfacial layer. The barrier heights of PEDOT:PSS and PFO in the two-unit tandem OLED induced a charge accumulation at the interface in the heterojunction and thereby created exciton recombination at a much higher level than in the one-unit reference. This effect was confirmed in both the hole only and the electron only devices. (c) 2008 American Institute of Physicsopen8

Improved cortical activity and reduced gait asymmetry during poststroke self-paced walking rehabilitation

Background For patients with gait impairment due to neurological disorders, body weight-supported treadmill training (BWSTT) has been widely used for gait rehabilitation. On a conventional (passive) treadmill that runs at a constant speed, however, the level of patient engagement and cortical activity decreased compared with gait training on the ground. To increase the level of cognitive engagement and brain activity during gait rehabilitation, a self-paced (active) treadmill is introduced to allow patients to actively control walking speed, as with overground walking. Methods To validate the effects of self-paced treadmill walking on cortical activities, this paper presents a clinical test with stroke survivors. We hypothesized that cortical activities on the affected side of the brain would also increase during active walking because patients have to match the target walking speed with the affected lower limbs. Thus, asymmetric gait patterns such as limping or hobbling might also decrease during active walking. Results Although the clinical test was conducted in a short period, the patients showed higher cognitive engagement, improved brain activities assessed by electroencephalography (EEG), and decreased gait asymmetry with the self-paced treadmill. As expected, increases in the spectral power of the low γ and β bands in the prefrontal cortex (PFC), premotor cortex (PMC), and supramarginal gyrus (SG) were found, which are possibly related to processing sensory data and planning voluntary movements. In addition, these changes in cortical activities were also found with the affected lower limbs during the swing phase. Since our treadmill controller tracked the swing speed of the leg to control walking speed, such results imply that subjects made substantial effort to control their affected legs in the swing phase to match the target walking speed. Conclusions The patients also showed reduced gait asymmetry patterns. Based on the results, the self-paced gait training system has the potential to train the symmetric gait and to promote the related cortical activities after stroke. Trial registration Not applicableThis work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIT) (No. NRF-2020R1A2C2012641). This study has also been supported by Grant numbers (16-2016-003, 16-2017004) from the SNUBH-KAIST Collaboration Research Fund

Cordycepin induces apoptosis of human ovarian cancer cells by inhibiting CCL5-mediated Akt/NF-κB signaling pathway

The chemokine, CCL5, is a key mediator for the recruitment of immune cells into tumors and tissues. Akt/NF-κB signaling is significantly activated by CCL5. However, the role of NF-κB inactivation in apoptosis induced by negative regulation of CCL5 remains unclear. Here, we analyzed the effect of cordycepin on NF-κB activity in SKOV-3 cells and found that cordycepin-mediated inhibition of NF-κB signaling induced apoptosis in SKOV-3 cells via the serial activation of caspases. In addition, immune-blotting analysis showed that CCL5 is highly expressed in SKOV-3 cells. In addition to activating caspases, we show that, cordycepin prevents TNF-α-induced increase in CCL5, Akt, NF-κB, and c-FLIPL activation and that CCL5 siRNA could inhibit Akt/NF-κB signaling. Moreover, cordycepin negatively regulated the TNF-α-mediated IκB/NF-κB pathway and c-FLIPL activation to promote JNK phosphorylation, resulting in caspase-3 activation and apoptosis. Also, we show that c-FLIPL is rapidly lost in NF-κB activation-deficient. siRNA mediated c-FLIP inhibition increased JNK. SP600125, a selective JNK inhibitor, downregulated p-JNK expression in cordycepin-treated SKOV-3 cells, leading to suppression of cordycepin-induced apoptosis. Thus, these results indicate that cordycepin inhibits CCL5-mediated Akt/NF-κB signaling, which upregulates caspase-3 activation in SKOV-3 cells, supporting the potential of cordycepin as a therapeutic agent for ovarian cancer

Effects of Korean Red Ginseng (Panax ginseng), urushiol (Rhus vernicifera Stokes), and probiotics (Lactobacillus rhamnosus R0011 and Lactobacillus acidophilus R0052) on the gut–liver axis of alcoholic liver disease

AbstractBackgroundRoles of immune reaction and toll-like receptor-4 (TLR-4) have widely been established in the pathogenesis of alcoholic liver disease (ALD).MethodsWe evaluated the biologic efficacy of Korean Red Ginseng (KRG), urushiol, and probiotics (Lactobacillus rhamnosus R0011 and Lactobacillus acidophilus R0052) in mouse models of ALD. Sixty C57BL/6 mice were equally divided into six feeding groups for 10 weeks: normal diet, alcohol, control, alcohol + KRG, alcohol + urushiol, and alcohol + probiotics. Alcohol was administered via a Lieber–DeCarli liquid diet containing 10% alcohol. TLR-4 expression, proinflammatory cytokines, and histology, as well as the results of liver function tests were evaluated and compared.ResultsNo between-group differences were observed with regard to liver function. TLR-4 levels were significantly lower in the KRG, urushiol, and probiotics groups than in the alcohol group (0.37 ± 0.06 ng/mL, 0.39 ± 0.12 ng/mL, and 0.33 ± 0.07 ng/mL, respectively, vs. 0.88 ± 0.31 ng/mL; p < 0.05). Interleukin-1β levels in liver tissues were decreased among the probiotics and KRG groups. The tumor necrosis factor-α level of liver tissue was decreased in the KRG group.ConclusionThe pathological findings showed that alcohol-induced steatosis was significantly reduced by KRG and urushiol. As these agents improve immunologic capacity, they may be considered in potential anti-ALD treatments