High-throughput avian molecular sexing by SYBR green-based real-time PCR combined with melting curve analysis

<p>Abstract</p> <p>Background</p> <p>Combination of <it>CHD </it>(chromo-helicase-DNA binding protein)-specific polymerase chain reaction (PCR) with electrophoresis (PCR/electrophoresis) is the most common avian molecular sexing technique but it is lab-intensive and gel-required. Gender determination often fails when the difference in length between the PCR products of <it>CHD-Z </it>and <it>CHD-W </it>genes is too short to be resolved.</p> <p>Results</p> <p>Here, we are the first to introduce a PCR-melting curve analysis (PCR/MCA) to identify the gender of birds by genomic DNA, which is gel-free, quick, and inexpensive. <it>Spilornis cheela hoya </it>(<it>S. c. hoya</it>) and <it>Pycnonotus sinensis </it>(<it>P. sinensis</it>) were used to illustrate this novel molecular sexing technique. The difference in the length of <it>CHD </it>genes in <it>S. c. hoya </it>and <it>P. sinensis </it>is 13-, and 52-bp, respectively. Using Griffiths' P2/P8 primers, molecular sexing failed both in PCR/electrophoresis of <it>S. c. hoya </it>and in PCR/MCA of <it>S. c. hoya </it>and <it>P. sinensis</it>. In contrast, we redesigned sex-specific primers to yield 185- and 112-bp PCR products for the <it>CHD-Z </it>and <it>CHD-W </it>genes of <it>S. c. hoya</it>, respectively, using PCR/MCA. Using this specific primer set, at least 13 samples of <it>S. c. hoya </it>were examined simultaneously and the Tm peaks of <it>CHD-Z </it>and <it>CHD-W </it>PCR products were distinguished.</p> <p>Conclusion</p> <p>In this study, we introduced a high-throughput avian molecular sexing technique and successfully applied it to two species. This new method holds a great potential for use in high throughput sexing of other avian species, as well.</p

Water vapor deposition from the inner gas coma onto the nucleus of Comet 67P/Churyumov-Gerasimenko

Rosetta has detected water ice existing on the surface of Comet 67P/Churyumov-Gerasimenko in various types of features. One of particular interest is the frost-like layer observed at the edge of receding shadows during the whole mission, interpreted as the recondensation of a thin layer of water ice. Two possible mechanisms, (1) subsurface ice sublimation and (2) gas coma deposition, have been proposed for producing this recondensation process and diurnal cycles of water ice. Previous studies have demonstrated both mechanisms based on simplified models. More precise and modern models are yet insufficient when addressing the gas-coma-deposition mechanism. We aim to study the recondensation from the inner water gas coma of the 67P/Churyumov-Gerasimenko with more physical constraints including the OSIRIS images, nucleus shape model, and insolation conditions. We compute, for the first time, the backflux distributions from the coma with various boundary conditions. Numerical simulations of this gas-coma-deposition process show that the equivalent water ice deposition can be up to several microns in an hour of accumulation time close to the perihelion passage, which is comparable with the simulation results of the other subsurface-ice sublimation mechanism

Control of lethal browning of tissue culture plantlets of Cavendish banana cv. Formosana with ascorbic acid

Cavendish banana cv. Formosana is a high yielding commercial cultivar resistant to race 4 of Fusarium oxysporum f. sp. cubense. Mass micropropagation of this cultivar has a serious problem of high mortality due to lethal browning of plantlets. The mineral contents in leaves and corms of diseased and healthy plantlets were similar. Amendment of culture medium with anion exchange resins, cation exchange resins, polyvinylpyrrolidone or activated charcoal did not reduce the disease incidence. However, addition of ascorbic acid to the surface of culture medium not only prevented the development of lethal browning but also greatly increased the number of plantlets produced. Even at 0.005% ascorbic acid was able to reduce the disease incidence by more than 60% and caused over 8-fold increase in number of plantlets produced. When cultures raised from 12 different Formosana corms were tested, ascorbic acid was able to reduce disease incidence by an average of 83%, and increase the number of plantlets in each test. When diseased plantlets were transferred to culture medium with ascorbic acid, all of them recovered, and resumed normal growth and multiplication, while all control plantlets on culture medium without ascorbic acid died after one month

Modeling water waves beyond perturbations

In this chapter, we illustrate the advantage of variational principles for modeling water waves from an elementary practical viewpoint. The method is based on a `relaxed' variational principle, i.e., on a Lagrangian involving as many variables as possible, and imposing some suitable subordinate constraints. This approach allows the construction of approximations without necessarily relying on a small parameter. This is illustrated via simple examples, namely the Serre equations in shallow water, a generalization of the Klein-Gordon equation in deep water and how to unify these equations in arbitrary depth. The chapter ends with a discussion and caution on how this approach should be used in practice.Comment: 15 pages, 1 figure, 39 references. This document is a contributed chapter to an upcoming volume to be published by Springer in Lecture Notes in Physics Series. Other author's papers can be downloaded at http://www.denys-dutykh.com

Magnetism in the dilute Kondo lattice model

The one dimensional dilute Kondo lattice model is investigated by means of bosonization for different dilution patterns of the array of impurity spins. The physical picture is very different if a commensurate or incommensurate doping of the impurity spins is considered. For the commensurate case, the obtained phase diagram is verified using a non-Abelian density-matrix renormalization-group algorithm. The paramagnetic phase widens at the expense of the ferromagnetic phase as the $f$-spins are diluted. For the incommensurate case, antiferromagnetism is found at low doping, which distinguishes the dilute Kondo lattice model from the standard Kondo lattice model.Comment: 11 pages, 2 figure

Specific characters of 16S rRNA gene and 16S-23S rRNA internal transcribed spacer sequences of Xylella fastidiosa pear leaf scorch strains

Pear leaf scorch, the only Xylella fastidiosa-induced disease reported from Taiwan, was found in area where the variety Hengshan (Pyrus pyrifolia) was grown. Strains of pear leaf scorch Xyl. fastidiosa (XF-PLS) shared similarities to strains of other host origins in the requirement of complex medium and the exhibition of rippled cell walls, however, recent serological and molecular biology studies showed difference among them. Five strains of XF-PLS were compared with 20 other strains originally isolated from almond, oleander, pecan, plum, peach, mulberry, grapes, citrus, coffee, and sycamore by sequence analyses of the 16S rRNA gene and 16S-23S rRNA internal transcribed spacer region (ITS). When sequences of 16S rRNA gene based on fragment size of 1,537-1,540 bp were compared, the similarity index among 5 XF-PLS strains was 99.3-99.8%, whereas it was 97.8-98.6% between XF-PLS strains and strains from other hosts. When sequences of 16S-23S rRNA ITS based on fragment size of 510-540 bp were compared, the similarity index among 5 XF-PLS strains was 99.0-100%, whereas it was 80.7-82% between XF-PLS strains and strains from other hosts. Multiple sequence alignments led to the identification of 5 polymorphic nucleotides in the 16S rRNA gene among the 25 Xyl. fastidiosa strains, and there were considerable variations in the nucleotide sequences of 16S-23S rRNA ITS between XF-PLS and the other 20 Xyl. fastidiosa strains. The phylogenetic trees revealed that XF-PLS strains were separated from strains of other hosts. Strains of other hosts were divided into four subgroups: strains from (1) oleander, (2) grape, almond M23 and mulberry, (3) citrus and coffee, and (4) pecan, peach, plum, sycamore and almond M12. Results indicate that XF-PLS strains were not closely related to the above-mentioned strains from other hosts and could possibly belong to a new subspecies of Xyl. fastidiosa

Cavitation of Electrons Bubbles in Liquid Helium Below saturation Pressure

We have used a Hartree-type electron-helium potential together with a density functional description of liquid $^4$He and $^3$He to study the explosion of electron bubbles submitted to a negative pressure. The critical pressure at which bubbles explode has been determined as a function of temperature. It has been found that this critical pressure is very close to the pressure at which liquid helium becomes globally unstable in the presence of electrons. It is shown that at high temperatures the capillary model overestimates the critical pressures. We have checked that a commonly used and rather simple electron-helium interaction yields results very similar to those obtained using the more accurate Hartree-type interaction. We have estimated that the crossover temperature for thermal to quantum nucleation of electron bubbles is very low, of the order of 6 mK for $^4$He.Comment: 22 pages, 9 figure

Translational development of an ADAMTS-5 antibody for osteoarthritis disease modification

SummaryObjective/MethodAggrecanase activity, most notably ADAMTS-5, is implicated in pathogenic cartilage degradation. Selective monoclonal antibodies (mAbs) to both ADAMTS-5 and ADAMTS-4 were generated and in vitro, ex vivo and in vivo systems were utilized to assess target engagement, aggrecanase inhibition and modulation of disease-related endpoints with the intent of selecting a candidate for clinical development in osteoarthritis (OA).ResultsStructural mapping predicts the most potent mAbs employ a unique mode of inhibition by cross-linking the catalytic and disintegrin domains. In a surgical mouse model of OA, both ADAMTS-5 and ADAMTS-4-specific mAbs penetrate cartilage following systemic administration, demonstrating access to the anticipated site of action. Structural disease modification and associated alleviation of pain-related behavior were observed with ADAMTS-5 mAb treatment. Treatment of human OA cartilage demonstrated a preferential role for ADAMTS-5 inhibition over ADAMTS-4, as measured by ARGS neoepitope release in explant cultures. ADAMTS-5 mAb activity was most evident in a subset of patient-derived tissues and suppression of ARGS neoepitope release was sustained for weeks after a single treatment in human explants and in cynomolgus monkeys, consistent with high affinity target engagement and slow ADAMTS-5 turnover.ConclusionThis data supports a hypothesis set forth from knockout mouse studies that ADAMTS-5 is the major aggrecanase involved in cartilage degradation and provides a link between a biological pathway and pharmacology which translates to human tissues, non-human primate models and points to a target OA patient population. Therefore, a humanized ADAMTS-5-selective monoclonal antibody (GSK2394002) was progressed as a potential OA disease modifying therapeutic

A CsI(Tl) Scintillating Crystal Detector for the Studies of Low Energy Neutrino Interactions

Scintillating crystal detector may offer some potential advantages in the low-energy, low-background experiments. A 500 kg CsI(Tl) detector to be placed near the core of Nuclear Power Station II in Taiwan is being constructed for the studies of electron-neutrino scatterings and other keV-MeV range neutrino interactions. The motivations of this detector approach, the physics to be addressed, the basic experimental design, and the characteristic performance of prototype modules are described. The expected background channels and their experimental handles are discussed.Comment: 34 pages, 11 figures, submitted to Nucl. Instrum. Method