Characterization of the transcriptome of fast and slow muscle myotomal fibres in the pacu (Piaractus mesopotamicus)

MDPS and EAM were supported by FAPESP, Proc. n° 12/02489-4 and 2011/09346-1. This work also received funding from CAPES, Proc. n° 2524/12. IAJ and DGDLS were supported by the Marine Alliance for Science and Technology for Scotland pooling initiative and Scottish Funding Council grant number HR09011.Background: The Pacu (Piaractus mesopotamicus) is a member of the Characiform family native to the Prata Basin (South America) and a target for the aquaculture industry. A limitation for the development of a selective breeding program for this species is a lack of available genetic information. The primary objectives of the present study were 1) to increase the genetic resources available for the species, 2) to exploit the anatomical separation of myotomal fibres types to compare the transcriptomes of slow and fast muscle phenotypes and 3) to systematically investigate the expression of Ubiquitin Specific Protease (USP) family members in fast and slow muscle in response to fasting and refeeding. Results: We generated 0.6 Tb of pair-end reads from slow and fast skeletal muscle libraries. Over 665 million reads were assembled into 504,065 contigs with an average length of 1,334 bp and N50=2,772 bp. We successfully annotated nearly 47% of the transcriptome and identified around 15,000 unique genes and over 8000 complete coding sequences. 319 KEGG metabolic pathways were also annotated and 380 putative microsatellites were identified. 956 and 604 genes were differentially expressed between slow and fast skeletal muscle, respectively. 442 paralogues pairs arising from the teleost-specific whole genome duplication were identified, with the majority showing different expression patterns between fibres types (301 in slow and 245 in fast skeletal muscle). 45 members of the USP family were identified in the transcriptome. Transcript levels were quantified by qPCR in a separate fasting and refeeding experiment. USP genes in fast muscle showed a similar transient increase in expression with fasting as the better characterized E3 ubiquitin ligases. Conclusion: We have generated a 53-fold coverage transcriptome for fast and slow myotomal muscle in the pacu (Piaractus mesopotamicus) significantly increasing the genetic resources available for this important aquaculture species. We describe significant differences in gene expression between muscle fibre types for fundamental components of general metabolism, the Pi3k/Akt/mTor network and myogenesis, including detailed analysis of paralogue expression. We also provide a comprehensive description of USP family member expression between muscle fibre types and with changing nutritional status.Publisher PDFPeer reviewe

Investigating the effects of an oral fructose challenge on hepatic ATP reserves in healthy volunteers: a 31P MRS study

Background: Impaired homeostasis of hepatic ATP has been associated with NAFLD. An intravenous fructose infusion has been shown to be an effective challenge to monitor the depletion and subsequent recovery of hepatic ATP reserves using 31P MRS. Aims: The purpose of this study was to evaluate the effects of an oral rather than intravenous fructose challenge on hepatic ATP reserves in healthy subjects. Methods: Self-reported healthy males were recruited. Following an overnight fast, baseline liver glycogen and lipid levels were measured using Magnetic Resonance Spectroscopy (MRS). Immediately after consuming a 500 ml 75 g fructose drink (1275 kJ) subjects were scanned continuously for 90 min to acquire dynamic 31P MRS measurements of liver ATP reserves. Results: A significant effect on ATP reserves was observed across the time course (P < 0.05). Mean ATP levels reached a minimum at 50 min which was markedly lower than baseline (80 ± 17% baseline, P < 0.05). Subsequently, mean values tended to rise but did not reach statistical significance above minimum. The time to minimum ATP levels across subjects was negatively correlated with BMI (R2 ¼ 0.74, P < 0.005). Rates of ATP recovery were not significantly correlated with BMI or liver fat levels, but were negatively correlated with baseline glycogen levels (R2 ¼ 0.7, P < 0.05). Conclusions: Depletion of ATP reserves can be measured non-invasively following an oral fructose challenge using 31P

Orbital state and magnetic properties of LiV_2 O_4

LiV_2 O_4 is one of the most puzzling compounds among transition metal oxides because of its heavy fermion like behavior at low temperatures. In this paper we present results for the orbital state and magnetic properties of LiV_2 O_4 obtained from a combination of density functional theory within the local density approximation and dynamical mean-field theory (DMFT). The DMFT equations are solved by quantum Monte Carlo simulations. The trigonal crystal field splits the V 3d orbitals such that the a_{1g} and e_{g}^{pi} orbitals cross the Fermi level, with the former being slightly lower in energy and narrower in bandwidth. In this situation, the d-d Coulomb interaction leads to an almost localization of one electron per V ion in the a_{1g} orbital, while the e_{g}^{pi} orbitals form relatively broad bands with 1/8 filling. 2The theoretical high-temperature paramagnetic susceptibility chi(T) follows a Curie-Weiss law with an effective paramagnetic moment p_{eff}=1.65 in agreement with the experimental results.Comment: 11 pages, 10 figures, 2 table

On the Application of the Non Linear Sigma Model to Spin Chains and Spin Ladders

We review the non linear sigma model approach (NLSM) to spin chains and spin ladders, presenting new results. The generalization of the Haldane's map to ladders in the Hamiltonian approach, give rise to different values of the $\theta$ parameter depending on the spin S, the number of legs $n_{\ell}$ and the choice of blocks needed to built up the NLSM fields. For rectangular blocks we obtain $\theta = 0$ or $2 \pi S$ depending on wether $n_{\ell}$, is even or odd, while for diagonal blocks we obtain $\theta = 2 \pi S n_{\ell}$. Both results agree modulo $2 \pi$, and yield the same prediction, namely that even ( resp. odd) ladders are gapped (resp. gapless). For even legged ladders we show that the spin gap collapses exponentially with $n_{\ell}$ and we propose a finite size correction to the gap formula recently derived by Chakravarty using the 2+1 NSLM, which gives a good fit of numerical results. We show the existence of a Haldane phase in the two legged ladder using diagonal blocks and finally we consider the phase diagram of dimerized ladders.Comment: 25 pages, Latex, 7 figures in postscript files, Proc. of the 1996 El Escorial Summer School on "Strongly Correlated Magnetic and Superconducting Systems". Some more references are adde

Defining a Minimum Set of Standardized Patient-centered Outcome Measures for Macular Degeneration

Purpose To define a minimum set of outcome measures for tracking, comparing, and improving macular degeneration care. Design Recommendations from a working group of international experts in macular degeneration outcomes registry development and patient advocates, facilitated by the International Consortium for Health Outcomes Measurement (ICHOM). Methods Modified Delphi technique, supported by structured teleconferences, followed by online surveys to drive consensus decisions. Potential outcomes were identified through literature review of outcomes collected in existing registries and reported in major clinical trials. Outcomes were refined by the working group and selected based on impact on patients, relationship to good clinical care, and feasibility of measurement in routine clinical practice. Results Standardized measurement of the following outcomes is recommended: visual functioning and quality of life (distance visual acuity, mobility and independence, emotional well-being, reading and accessing information); number of treatments; complications of treatment; and disease control. Proposed data collection sources include administrative data, clinical data during routine clinical visits, and patient-reported sources annually. Recording the following clinical characteristics is recommended to enable risk adjustment: age; sex; ethnicity; smoking status; baseline visual acuity in both eyes; type of macular degeneration; presence of geographic atrophy, subretinal fibrosis, or pigment epithelial detachment; previous macular degeneration treatment; ocular comorbidities. Conclusions The recommended minimum outcomes and pragmatic reporting standards should enable standardized, meaningful assessments and comparisons of macular degeneration treatment outcomes. Adoption could accelerate global improvements in standardized data gathering and reporting of patient-centered outcomes. This can facilitate informed decisions by patients and health care providers, plus allow long-term monitoring of aggregate data, ultimately improving understanding of disease progression and treatment responses

Muscle fibre size optimisation provides flexibility for energy budgeting in calorie-restricted coho salmon transgenic for growth hormone

The study was supported by the Marine Alliance for Science and Technology for Scotland (Scottish Funding Council grant HR09011) and by the Canadian Biotechnology Strategy (to R.H.D.). Deposited in PMC for immediate releaseCoho salmon (Oncorhynchus kisutch) transgenic for growth hormone (GH) show substantially faster growth than wild-type (WT) fish. We fed GH-transgenic salmon either to satiation (1 year; TF) or the same smaller ration of wild-type fish (2 years; TR), resulting in groups matched for body size to WT salmon. The myotomes of TF and WT fish had the same number and size distribution of muscle fibres, indicating a twofold higher rate of fibre recruitment in the GH transgenics. Unexpectedly, calorie restriction was found to decrease the rate of fibre production in transgenics, resulting in a 20% increase in average fibre size and reduced costs of ionic homeostasis. Genes for myotube formation were downregulated in TR relative to TF and WT fish. We suggest that muscle fibre size optimisation allows the reallocation of energy from maintenance to locomotion, explaining the observation that calorie-restricted transgenics grow at the same rate as WT fish whilst exhibiting markedly higher foraging activity.Publisher PDFPeer reviewe

b-Jet Identification in the D0 Experiment

Algorithms distinguishing jets originating from b quarks from other jet flavors are important tools in the physics program of the D0 experiment at the Fermilab Tevatron p-pbar collider. This article describes the methods that have been used to identify b-quark jets, exploiting in particular the long lifetimes of b-flavored hadrons, and the calibration of the performance of these algorithms based on collider data.Comment: submitted to Nuclear Instruments and Methods in Physics Research

Detector Description and Performance for the First Coincidence Observations between LIGO and GEO

For 17 days in August and September 2002, the LIGO and GEO interferometer gravitational wave detectors were operated in coincidence to produce their first data for scientific analysis. Although the detectors were still far from their design sensitivity levels, the data can be used to place better upper limits on the flux of gravitational waves incident on the earth than previous direct measurements. This paper describes the instruments and the data in some detail, as a companion to analysis papers based on the first data.Comment: 41 pages, 9 figures 17 Sept 03: author list amended, minor editorial change

Search for the standard model Higgs boson in tau final states

We present a search for the standard model Higgs boson using hadronically decaying tau leptons, in 1 inverse femtobarn of data collected with the D0 detector at the Fermilab Tevatron ppbar collider. We select two final states: tau plus missing transverse energy and b jets, and tau+ tau- plus jets. These final states are sensitive to a combination of associated W/Z boson plus Higgs boson, vector boson fusion and gluon-gluon fusion production processes. The observed ratio of the combined limit on the Higgs production cross section at the 95% C.L. to the standard model expectation is 29 for a Higgs boson mass of 115 GeV.Comment: publication versio

Search for pair production of the scalar top quark in the electron-muon final state

We report the result of a search for the pair production of the lightest supersymmetric partner of the top quark ($\tilde{t}_1$) in $p\bar{p}$ collisions at a center-of-mass energy of 1.96 TeV at the Fermilab Tevatron collider corresponding to an integrated luminosity of 5.4 fb$^{-1}$. The scalar top quarks are assumed to decay into a $b$ quark, a charged lepton, and a scalar neutrino ($\tilde{\nu}$), and the search is performed in the electron plus muon final state. No significant excess of events above the standard model prediction is detected, and improved exclusion limits at the 95% C.L. are set in the the ($M_{\tilde{t}_1}$,$M_{\tilde{\nu}}$) mass plane