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

Deep tissue space-gated microscopy via acousto-optic interaction

© 2020, The Author(s).To extend the imaging depth of high-resolution optical microscopy, various gating operations—confocal, coherence, and polarization gating—have been devised to filter out the multiply scattered wave. However, the imaging depth is still limited by the multiply scattered wave that bypasses the existing gating operations. Here, we present a space gating method, whose mechanism is independent of the existing methods and yet effective enough to complement them. Specifically, we reconstruct an image only using the ballistic wave that is acousto-optically modulated at the object plane. The space gating suppresses the multiply scattered wave by 10–100 times in a highly scattering medium, and thus enables visualization of the skeletal muscle fibers in whole-body zebrafish at 30 days post fertilization. The space gating will be an important addition to optical-resolution microscopy for achieving the ultimate imaging depth set by the detection limit of ballistic wav

The C-terminal region of Bfl-1 sensitizes non-small cell lung cancer to gemcitabine-induced apoptosis by suppressing NF-κB activity and down-regulating Bfl-1

Gemcitabine is used to treat several cancers including lung cancer. However, tumor cells often escape gemcitabine-induced cell death via various mechanisms, which include modulating bcl-2 family members and NF-κB activation. We previously reported that the C-terminal region of Bfl-1 fused with GFP (BC) is sufficient to induce apoptosis in 293T cells. In the present study, we investigated the anti-tumor effect of combined BC gene therapy and gemcitabine chemotherapy in vitro and in vivo using non-small cell lung cancer cell lines and a xenograft model. Cell lines were resistant to low dose gemcitabine (4-40 ng/ml), which induced NF-κB activation and concomitant up-regulation of Bfl-1 (an NF-κB-regulated anti-apoptotic protein). BC induced the apoptosis of A549 and H157 cells with caspase-3 activation. Furthermore, co-treatment with BC and low dose gemcitabine synergistically and efficiently induced mitochondria-mediated apoptosis in these cells. When administered alone or with low dose gemcitabine, BC suppressed NF-κB activity, inhibited the nuclear translocation of p65/relA, and down-regulated Bfl-1 expression. Furthermore, direct suppression of Bfl-1 by RNA interference sensitized cells to gemcitabine-induced cell death, suggesting that Bfl-1 importantly regulates lung cancer cell sensitivity to gemcitabine. BC and gemcitabine co-treatment also showed a strong anti-tumor effect in a nude mouse/A549 xenograft model. These results suggest that lung cancer cells become resistant to gemcitabine via NF-κB activation and the subsequent overexpression of Bfl-1, and that BC, which has both pro-apoptotic and NF-κB inhibitory effects, could be harnessed as a gene therapy to complement gemcitabine chemotherapy in non-small cell lung cancer

Growth of Carbon Nanotubes on Carbon Fiber by Thermal CVD Using Ni Nanoparticles as Catalysts

AbstractNickel nanoparticles and thin film on carbon fiber have been prepared through electroless deposition. Moreover, carbon nanotubes were grown on carbon fiber covered by nickel nanoparticles using thermal chemical vapor deposition. The effects of changes in the thickness of the nickel catalyst layer and the growth temperature of carbon nanotubes were studied systemically, and the results are discussed in the present work

Two novel mutations of Wiskott–Aldrich syndrome: the molecular prediction of interaction between the mutated WASP L101P with WASP-interacting protein by molecular modeling

AbstractWiskott–Aldrich syndrome (WAS) is an X-linked disorder characterized by eczema, thrombocytopenia and increased susceptibility of infections, with mutations of the WAS gene being responsible for WAS and X-linked thrombocytopenia. Herein, two novel mutations of WAS at T336C on exon 3, and at 1326–1329, a G deletion on exon 10, resulting in L101P missense mutation and frameshift mutation 444 stop, respectively, are reported. The affected patients with either mutation showed severe suppression of WAS protein (WASP) levels, T cell proliferation, and CFSE-labeled T cells division. Because WASP L101 have not shown direct nuclear Overhauser effect (NOE) contact with the WASP-interacting protein (WIP) in NMR spectroscopy, molecular modeling was performed to evaluate the molecular effect of WASP P101 to WIP peptide. It is presumed that P101 induced a conformational change in the Q99 residue of WASP and made the side chain of Q99 move away from the WIP peptide, resulting in disruption of the hydrogen bond between Q99 WASP and Y475 WIP. A possible model for the molecular pathogenesis of WAS has been proposed by analyzing the interactions of WASP and WIP using a molecular modeling study

Optical observations of NEA 3200 Phaethon (1983 TB) during the 2017 apparition

The near-Earth asteroid 3200 Phaethon (1983 TB) is an attractive object not only from a scientific viewpoint but also because of JAXA's DESTINY+ target. The rotational lightcurve and spin properties were investigated based on the data obtained in the ground-based observation campaign of Phaethon. We aim to refine the lightcurves and shape model of Phaethon using all available lightcurve datasets obtained via optical observation, as well as our time-series observation data from the 2017 apparition. Using eight 1-2-m telescopes and an optical imager, we acquired the optical lightcurves and derived the spin parameters of Phaethon. We applied the lightcurve inversion method and SAGE algorithm to deduce the convex and non-convex shape model and pole orientations. We analysed the optical lightcurve of Phaethon and derived a synodic and a sidereal rotational period of 3.6039 h, with an axis ratio of a/b = 1.07. The ecliptic longitude (lambda) and latitude (beta) of the pole orientation were determined as (308, -52) and (322, -40) via two independent methods. A non-convex model from the SAGE method, which exhibits a concavity feature, is also presented.Comment: 14 pages, 4 figures, 1 figure in Appendix A. Accepted for publication in Astronomy & Astrophysics (A&A

Multilayer fabrication of unobtrusive poly(dimethylsiloxane) nanobrush for tunable cell adhesion

Precise modulation of polymer brush in its thickness and grafting density can cause unexpected cell behaviors and regulated bioactivities. Herein, a nanoscale poly(dimethylsiloxane) (PDMS) brush was employed to use as a controllable material for cell adhesion. Facile fabrication of ultrathin monolayer PDMS nanobrush on an underlying substrate facilitated regaining cell adhesion through long-range cell attractive forces such as the van der Waals forces. We showed that cell adhesion is diminished by increasing the number of nanobrush layers, causing a gradual decrease of the effectiveness of the long-range force. The result demonstrates that ultrathin PDMS nanobrush can either promote or inhibit cell adhesion, which is required for various biomedical fields such as tissue-engineering, anti-fouling coating, and implantable biomaterials and sensors