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

A quantitative real time PCR method to analyze T cell receptor Vβ subgroup expansion by staphylococcal superantigens

<p>Abstract</p> <p>Background</p> <p>Staphylococcal enterotoxins (SEs), SE-like (SEl) toxins, and toxic shock syndrome toxin-1 (TSST-1), produced by <it>Staphylococcus aureus</it>, belong to the subgroup of microbial superantigens (SAgs). SAgs induce clonal proliferation of T cells bearing specific variable regions of the T cell receptor β chain (Vβ). Quantitative real time PCR (qRT-PCR) has become widely accepted for rapid and reproducible mRNA quantification. Although the quantification of Vβ subgroups using qRT-PCR has been reported, qRT-PCR using both primers annealing to selected Vβ nucleotide sequences and SYBR Green I reporter has not been applied to assess Vβ-dependent expansion of T cells by SAgs.</p> <p>Methods</p> <p>Human peripheral blood mononuclear cells were stimulated with various SAgs or a monoclonal antibody specific to human CD3. Highly specific expansion of Vβ subgroups was assessed by qRT-PCR using SYBR Green I reporter and primers corresponding to selected Vβ nucleotide sequences.</p> <p>Results</p> <p>qRT-PCR specificities were confirmed by sequencing amplified PCR products and melting curve analysis. To assess qRT-PCR efficiencies, standard curves were generated for each primer set. The average slope and R²of standard curves were -3.3764 ± 0.0245 and 0.99856 ± 0.000478, respectively, demonstrating that the qRT-PCR established in this study is highly efficient. With some exceptions, SAg Vβ specificities observed in this study were similar to those reported in previous studies.</p> <p>Conclusions</p> <p>The qRT-PCR method established in this study produced an accurate and reproducible assessment of Vβ-dependent expansion of human T cells by staphylococcal SAgs. This method could be a useful tool in the characterization T cell proliferation by newly discovered SAg and in the investigation of biological effects of SAgs linked to pathogenesis.</p

Multi-Color Luminescence Transition of Upconversion Nanocrystals via Crystal Phase Control with SiO2 for High Temperature Thermal Labels

Upconversion nanocrystals (UCNs)-embedded microarchitectures with luminescence color transition capability and enhanced luminescence intensity under extreme conditions are suitable for developing a robust labeling system in a high-temperature thermal industrial process. However, most UCNs based labeling systems are limited by the loss of luminescence owing to the destruction of the crystalline phase or by a predetermined luminescence color without color transition capability. Herein, an unusual crystal phase transition of UCNs to a hexagonal apatite phase in the presence of SiO2 nanoparticles is reported with the enhancements of 130-fold green luminescence and 52-fold luminance as compared to that of the SiO2-free counterpart. By rationally combining this strategy with an additive color mixing method using a mask-less flow lithography technique, single to multiple luminescence color transition, scalable labeling systems with hidden letters-, and multi-luminescence colored microparticles are demonstrated for a UCNs luminescence color change-based high temperature labeling system

Thermal Effects of Microwave Reduced-Graphene-Oxide Coated Polyester Fabric on a Simulated Human Skin in Cool and Neutral Air Temperatures

Batteryless wearable technology has wide applications. In particular, human body surface temperature controlling fabrics can help regulate skin temperature in heat or cold. This study investigated surface temperature distribution of the fabrics coated with reduced graphene oxide (rGO) on simulated human body skin conditions at 18 degrees C (cool) and 27 degrees C (neutral) ambient air temperatures. Polyester fabrics were spin-coated with a graphene-oxide (GO) solution of 0.2 wt%. Preparation of rGO was processed by using a microwave oven (MW-rGO). Non-treated fabric (CON) was compared to GO and MW-rGO. The surface temperature of a hot plate was maintained at 35 degrees C or 40 degrees C. The test fabrics were put on the heated hot plate or non-heated-outer portions of the hot plate. Surface temperatures of MW-rGO on the heated hot plate at an air temperature of 18 degrees C (cool) were higher than those of non-treated fabric (CON) under the same conditions (p < 0.01). No effects from the graphene treatment were found on non-heated portions of the graphene oxide fabric (GO) or the reduced graphene oxide fabric (MW-rGO). On the non-heated portions, surface temperatures were higher at the location closer to the hot plate compared to the location farther from the hot plate (p < 0.05). These results partially represent thermal effects of MW-rGO under a specific environment and heat source. Our findings enable an application of reduced graphene oxide to body temperature regulating clothing.

Pattern of distant recurrence according to the molecular subtypes in Korean women with breast cancer

<p>Abstract</p> <p>Background</p> <p>Distant recurrence is one of the most important risk factors in overall survival, and distant recurrence is related to a complex biologic interaction of seed and soil factors. The aim of the study was to investigate the association between the molecular subtypes and patterns of distant recurrence in patients with breast cancer.</p> <p>Methods</p> <p>In an investigation of 313 women with breast cancer who underwent surgery from 1994 and 2000, the expressions of estrogen and progestrone receptor (ER/PR), and human epithelial receptor-2 (HER2) were evaluated. The subtypes were defined as luminal-A, luminal-HER2, HER2-enriched, and triple negative breast cancer (TNBC) according to ER, PR, and HER2 status.</p> <p>Results</p> <p>Bone was the most common site of distant recurrence. The incidence of first distant recurrence site was significantly different among the subtypes. Brain metastasis was more frequent in the luminal-HER2 and TNBC subtypes. In subgroup analysis, overall survival in patients with distant recurrence after 24 months after surgery was significantly different among the subtypes.</p> <p>Conclusions</p> <p>Organ-specific metastasis may depend on the molecular subtype of breast cancer. Tailored strategies against distant metastasis concerning the molecular subtypes in breast cancer may be considered.</p

Total Gastrectomy in Gastric Conduit Cancer

We report a very rare case of surgery on gastric conduit cancer. A 67-year-old male patient underwent esophagectomy and intrathoracic esophagogastrostomy for squamous cell carcinoma of the lower thoracic esophagus 27 months ago. Upon follow-up, a gastric carcinoma at the intra-abdominal part of the gastric conduit was found on an esophagogastroduodenoscopy. We performed total gastrectomy and esophagocolonojejunostomy in the manner of Roux-en-Y anastomosis. The postoperative course was not eventful and an esophagogram on the 10th postoperative day showed no leakage or stenosis of the passage. The patient was discharged on the 17th day with no complications