RNA-seq analysis of single bovine blastocysts

Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results: We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions: This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.EEA BalcarceFil: Chitwood, James L. University of California Davis. Department of Animal Science; Estados UnidosFil: Rincon, Gonzalo. University of California Davis. Department of Animal Science; Estados UnidosFil: Kaiser, German Gustavo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Medrano, Juan F. University of California Davis. Department of Animal Science; Estados UnidosFil: Ross, Pablo J. University of California Davis. Department of Animal Science; Estados Unido

Measurement of the Rate of Muon Capture in Hydrogen Gas and Determination of the Proton's Pseudoscalar Coupling gPg_P

The rate of nuclear muon capture by the proton has been measured using a new experimental technique based on a time projection chamber operating in ultra-clean, deuterium-depleted hydrogen gas at 1 MPa pressure. The capture rate was obtained from the difference between the measured $\mu^-$ disappearance rate in hydrogen and the world average for the $\mu^+$ decay rate. The target's low gas density of 1% compared to liquid hydrogen is key to avoiding uncertainties that arise from the formation of muonic molecules. The capture rate from the hyperfine singlet ground state of the $\mu p$ atom is measured to be $\Lambda_S=725.0 \pm 17.4 s^{-1}$, from which the induced pseudoscalar coupling of the nucleon, $g_P(q^2=-0.88 m_\mu^2)=7.3 \pm 1.1$, is extracted. This result is consistent with theoretical predictions for $g_P$ that are based on the approximate chiral symmetry of QCD.Comment: submitted to Phys.Rev.Let

Increases in Vein Length Compensate for Leaf Area Lost to Lobing in Grapevine

Premise:Leaf lobing and leaf size vary considerably across and within species,including among grapevines (Vitisspp.), some of the best‐studied leaves. Weexamined the relationship between leaf lobing and leaf area across grapevinepopulations that varied in extent of leaf lobing.Methods:We used homologous landmarking techniques to measure 2632 leavesacross 2 years in 476 unique, genetically distinct grapevines fromfive biparentalcrosses that vary primarily in the extent of lobing. We determined to what extent leafarea explained variation in lobing, vein length, and vein to blade ratio.Results:Although lobing was the primary source of variation in shape across theleaves we measured, leaf area varied only slightly as a function of lobing. Rather, leafarea increases as a function of total major vein length, total branching vein length, andvein to blade ratio. These relationships are stronger for more highly lobed leaves, withthe residuals for each model differing as a function of distal lobing.Conclusions:For leaves with different extents of lobing but the same area, the morehighly lobed leaves have longer veins and higher vein to blade ratios, allowing themto maintain similar leaf areas despite increased lobing. Thesefindings show howmore highly lobed leaves may compensate for what would otherwise result in areduced leaf area, allowing for increasedphotosynthetic capacity through similarleaf siz

Measurement of the Positive Muon Lifetime and Determination of the Fermi Constant to Part-per-Million Precision

We report a measurement of the positive muon lifetime to a precision of 1.0 parts per million (ppm); it is the most precise particle lifetime ever measured. The experiment used a time-structured, low-energy muon beam and a segmented plastic scintillator array to record more than 2 x 10^{12} decays. Two different stopping target configurations were employed in independent data-taking periods. The combined results give tau_{mu^+}(MuLan) = 2196980.3(2.2) ps, more than 15 times as precise as any previous experiment. The muon lifetime gives the most precise value for the Fermi constant: G_F(MuLan) = 1.1663788 (7) x 10^-5 GeV^-2 (0.6 ppm). It is also used to extract the mu^-p singlet capture rate, which determines the proton's weak induced pseudoscalar coupling g_P.Comment: Accepted for publication in Phys. Rev. Let

Improved Measurement of the Positive Muon Lifetime and Determination of the Fermi Constant

The mean life of the positive muon has been measured to a precision of 11 ppm using a low-energy, pulsed muon beam stopped in a ferromagnetic target, which was surrounded by a scintillator detector array. The result, tau_mu = 2.197013(24) us, is in excellent agreement with the previous world average. The new world average tau_mu = 2.197019(21) us determines the Fermi constant G_F = 1.166371(6) x 10^-5 GeV^-2 (5 ppm). Additionally, the precision measurement of the positive muon lifetime is needed to determine the nucleon pseudoscalar coupling g_P.Comment: As published version (PRL, July 2007

Muon Physics: A Pillar of the Standard Model

Since its discovery in the 1930s, the muon has played an important role in our quest to understand the sub-atomic theory of matter. The muon was the first second-generation standard-model particle to be discovered, and its decay has provided information on the (Vector -Axial Vector) structure of the weak interaction, the strength of the weak interaction, G_F, and the conservation of lepton number (flavor) in muon decay. The muon's anomalous magnetic moment has played an important role in restricting theories of physics beyond the standard standard model, where at present there is a 3.4 standard-deviation difference between the experiment and standard-model theory. Its capture on the atomic nucleus has provided valuable information on the modification of the weak current by the strong interaction which is complementary to that obtained from nuclear beta decay.Comment: 8 pages, 9 figures. Invited paper for the Journal of Physical Society in Japan (JPSJ), Special Topics Issue "Frontiers of Elementary Particle Physics, The Standard Model and beyond

Characterisation of a Desmosterol Reductase Involved in Phytosterol Dealkylation in the Silkworm, Bombyx mori

Most species of invertebrate animals cannot synthesise sterols de novo and many that feed on plants dealkylate phytosterols (mostly C29 and C28) yielding cholesterol (C27). The final step of this dealkylation pathway involves desmosterol reductase (DHCR24)-catalysed reduction of desmosterol to cholesterol. We now report the molecular characterisation in the silkworm, Bombyx mori, of such a desmosterol reductase involved in production of cholesterol from phytosterol, rather than in de novo synthesis of cholesterol. Phylogenomic analysis of putative desmosterol reductases revealed the occurrence of various clades that allowed for the identification of a strong reductase candidate gene in Bombyx mori (BGIBMGA 005735). Following PCR-based cloning of the cDNA (1.6 kb) and its heterologous expression in Saccharomyces cerevisae, the recombinant protein catalysed reduction of desmosterol to cholesterol in an NADH- and FAD- dependent reaction

Multi-dimensional Leaf Phenotypes Reflect Root System Genotype in Grafted Grapevine Over the Growing Season

Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock\u27s influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown