Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes

The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.

Relation of Uric Acid to Serum Levels of High-Sensitivity C-Reactive Protein, Triglycerides, and High-Density Lipoprotein Cholesterol and to Hepatic Steatosis

Increased uric acid (UA) is strongly linked to cardiovascular disease. However, the independent role of UA is still debated because it is associated with several cardiovascular risk factors including obesity and metabolic syndrome. This study assessed the association of UA with increased high-sensitivity C-reactive protein (hs-CRP), increased ratio of triglyceride to high-density lipoprotein cholesterol (TG/HDL), sonographically detected hepatic steatosis, and their clustering in the presence and absence of obesity and metabolic syndrome. We evaluated 3,518 employed subjects without clinical cardiovascular disease from November 2008 through July 2010. Prevalence of tis-CRP >= 3 mg/L was 19%, that of TG/HDL >= 3 was 44%, and that of hepatic steatosis was 43%. In multivariable logistic regression after adjusting for traditional cardiovascular risk factors and confounders, highest versus lowest UA quartile was associated with hs-CRP >= 3 mg/L (odds ratio [OR] 1.52, 95% confidence interval [CI] 1.01 to 2.28, p = 0.04), TG/HDL >= 3 (OR 3.29, 95% CI 2.36 to 4.60, p <0.001), and hepatic steatosis (OR 3.10, 95% CI 2.22 to 4.32, p <0.001) independently of obesity and metabolic syndrome. Association of UA with hs-CRP >= 3 mg/L became nonsignificant in analyses stratified by obesity. Ascending UA quartiles compared to the lowest UA quartile demonstrated a graded increase in the odds of having 2 or 3 of these risk conditions and a successive decrease in the odds of having none. In conclusion, high UA levels were associated with increased TG/HDL and hepatic steatosis independently of metabolic syndrome and obesity and with increased hs-CRP independently of metabolic syndrome. (C) 2012 Elsevier Inc. All rights reserved. (Am J Cardiol 2012;110:1787-1792)

Effect of pulse repetition rate and number of pulses in the analysis of polypropylene and high density polyethylene by nanosecond infrared laser induced breakdown spectroscopy

Pulse repetition rates and the number of laser pulses are among the most important parameters that do affect the analysis of solid materials by laser induced breakdown spectroscopy, and the knowledge of their effects is of fundamental importance for suggesting analytical strategies when dealing with laser ablation processes of polymers. In this contribution, the influence of these parameters in the ablated mass and in the features of craters was evaluated in polypropylene and high density polyethylene plates containing pigment-based PbCrO4. Surface characterization and craters profile were carried out by perfilometry and scanning electron microscopy. Area, volume and profile of craters were obtained using Taylor Map software. A laser induced breakdown spectroscopy system consisted of a Q-Switched Nd:YAG laser (1064 nm, 5 ns) and an Echelle spectrometer equipped with ICCD detector were used. The evaluated operating conditions consisted of 10, 25 and 50 laser pulses at 1, 5 and 10 Hz, 250 mJ/pulse (85 J cm(-2)), 2 mu s delay time and 6 mu s integration time gate. Differences in the topographical features among craters of both polymers were observed. The decrease in the repetition rate resulted in irregular craters and formation of edges, especially in polypropylene sample. The differences in the topographical features and ablated masses were attributed to the influence of the degree of crystallinity, crystalline melting temperature and glass transition temperature in the ablation process of the high density polyethylene and polypropylene. It was also observed that the intensities of chromium and lead emission signals obtained at 10 Hz were two times higher than at 5 Hz by keeping the number of laser pulses constant. (C) 2011 Elsevier B. V. All rights reserved.

Transiting exoplanets from the CoRoT space mission XX. CoRoT-20b: A very high density, high eccentricity transiting giant planet

We report the discovery by the CoRoT space mission of a new giant planet, CoRoT-20b. The planet has a mass of 4.24 +/- 0.23 M-Jup and a radius of 0.84 +/- 0.04 R-Jup. With a mean density of 8.87 +/- 1.10 g cm(-3), it is among the most compact planets known so far. Evolutionary models for the planet suggest a mass of heavy elements of the order of 800 M-circle plus if embedded in a central core, requiring a revision either of the planet formation models or both planet evolution and structure models. We note however that smaller amounts of heavy elements are expected by more realistic models in which they are mixed throughout the envelope. The planet orbits a G-type star with an orbital period of 9.24 days and an eccentricity of 0.56. The star's projected rotational velocity is v sin i = 4.5 +/- 1.0 km s(-1), corresponding to a spin period of 11.5 +/- 3.1 days if its axis of rotation is perpendicular to the orbital plane. In the framework of Darwinian theories and neglecting stellar magnetic breaking, we calculate the tidal evolution of the system and show that CoRoT-20b is presently one of the very few Darwin-stable planets that is evolving toward a triple synchronous state with equality of the orbital, planetary and stellar spin periods.

Plasma lipases and lipid transfer proteins increase phospholipid but not free cholesterol transfer from lipid emulsion to high density lipoproteins.

Abstract Background Plasma lipases and lipid transfer proteins are involved in the generation and speciation of high density lipoproteins. In this study we have examined the influence of plasma lipases and lipid transfer protein activities on the transfer of free cholesterol (FC) and phospholipids (PL) from lipid emulsion to human, rat and mouse lipoproteins. The effect of the lipases was verified by incubation of labeled (3H-FC,14C-PL) triglyceride rich emulsion with human plasma (control, post-heparin and post-heparin plus lipase inhibitor), rat plasma (control and post-heparin) and by the injection of the labeled lipid emulsion into control and heparinized functionally hepatectomized rats. Results In vitro, the lipase enriched plasma stimulated significantly the transfer of 14C-PL from emulsion to high density lipoprotein (p<0.001) but did not modify the transfer of 3H-FC. In hepatectomized rats, heparin stimulation of intravascular lipolysis increased the plasma removal of 14C-PL and the amount of 14C-PL found in the low density lipoprotein density fraction but not in the high density lipoprotein density fraction. The in vitro and in vivo experiments showed that free cholesterol and phospholipids were transferred from lipid emulsion to plasma lipoproteins independently from each other. The incubation of human plasma, control and control plus monoclonal antibody anti-cholesteryl ester transfer protein (CETP), with 14C-PL emulsion showed that CETP increases 14C-PL transfer to human HDL, since its partial inhibition by the anti-CETP antibody reduced significantly the 14C-PL transfer (p<0.05). However, comparing the nontransgenic (no CETP activity) with the CETP transgenic mouse plasma, no effect of CETP on the 14C-PL distribution in mice lipoproteins was observed. Conclusions It is concluded that: 1-intravascular lipases stimulate phospholipid transfer protein mediated phospholipid transfer, but not free cholesterol, from triglyceride rich particles to human high density lipoproteins and rat low density lipoproteins and high density lipoproteins; 2-free cholesterol and phospholipids are transferred from triglyceride rich particles to plasma lipoproteins by distinct mechanisms, and 3 - CETP also contributes to phospholipid transfer activity in human plasma but not in transgenic mice plasma, a species which has high levels of the specific phospholipid transfer protein activity.

Observability of high density tracing molecular lines in lensed galaxies with the Atacama large millimeter array

Lo scopo di questo lavoro di tesi è indagare le capacità di ALMA di osservare il continuo e le righe molecolari di emissione di HCN, HCO+ e HNC, in galassie lensate ad alto z, nelle prime fasi della loro formazione. Per farlo vengono utilizzate osservazioni ALMA di righe di emissione molecolare, relative a dati pubblici di Ciclo 0. Queste osservazioni vengono utilizzate per simulare in modo realistico l’emissione da parte di galassie ad alto z e la risposta osservativa del telescopio, assumendo diverse possibili geometrie di lensing. Inoltre le recenti osservazioni ALMA sono state utilizzate per aggiornare le relazioni già esistenti tra la luminosità FIR e la luminosità delle righe molecolari. Queste recenti osservazioni con maggiore sensibilità e risoluzione angolare, sembrano essere in buon accordo con le precedenti osservazioni. Per realizzare questo progetto di tesi, sono stati scaricati dall’archivio ALMA i dati non calibrati relativi a due sorgenti ben studiate: NGC1614, rappresentativa delle galassie di tipo starburst ed IRAS 20551-4250, un AGN oscurato. Il processo di calibrazione è stato ripetuto per esaminare le proprietà dei cubi di dati utilizzando il pacchetto Common Astronomy Software Applications (CASA). Le righe spettrali osservate e l’emissione del continuo sono state successivamente estrapolate ad alto z riscalando adeguatamente le distanze, le dimensioni delle sorgenti e le frequenze di emissione. In seguito è stato applicato un modello di lensing gravitazionale basato su quello di Lapi et al. (2012). Sono state considerate diverse configurazioni tra lente e sorgente per ottenere diverse geometrie delle immagini e diversi fattori di amplificazione. Infine stato utilizzato il software CASA per simulare le osservazioni ALMA in modo da verificare le capacità osservative del telescopio al variare della geometria del sistema. Per ogni riga molecolare e per l’emissione del continuo sono state determinate la sensibilit e la risoluzione che possono essere raggiunte con le osservazioni ALMA e sono state analizzate alcune strategie osservative per effettuare survey di righe spettrali in oggetti lensati. Inoltre stata analizzata la possibilit di caratterizzare oggetti starburst ed AGN dai rapporti tra le righe di emissione delle molecole traccianti di alta densit. Le prestazioni di ALMA consentiranno di distinguere e stimare i contributi relativi di SB ed AGN in galassie lensate a z > 2.5, quindi vicine alla loro presunta epoca di formazione (Lapi et al. 2010), in meno di 5 minuti di osservazione per qualsiasi fattore di magnificazione. Nel presente lavoro sono state inoltre discusse alcune strategie osservative per condurre survey o followup per osservare le righe di HCN(4-3), HCO+(4-3) e HNC(4-3) in galassie lensate a redshift 2.5 < z < 3, dimostrando che sono possibili per campioni statisticamente significativi in tempi relativamente brevi.

EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA

In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data manipulations, referred to as preprocessing, can influence the quality of the ultimate measurements. In the last few years, the high-throughput measurement of gene expression is the most popular application of microarray technology. For this application, various groups have demonstrated that the use of modern statistical methodology can substantially improve accuracy and precision of gene expression measurements, relative to ad-hoc procedures introduced by designers and manufacturers of the technology. Currently, other applications of microarrays are becoming more and more popular. In this paper we describe a preprocessing methodology for a technology designed for the identification of DNA sequence variants in specific genes or regions of the human genome that are associated with phenotypes of interest such as disease. In particular we describe methodology useful for preprocessing Affymetrix SNP chips and obtaining genotype calls with the preprocessed data. We demonstrate how our procedure improves existing approaches using data from three relatively large studies including one in which large number independent calls are available. Software implementing these ideas are avialble from the Bioconductor oligo package.

Compositional protein analysis of high density lipoproteins in hypercholesterolemia by shotgun LC-MS/MS and probabilistic peptide scoring

A protein of a biological sample is usually quantified by immunological techniques based on antibodies. Mass spectrometry offers alternative approaches that are not dependent on antibody affinity and avidity, protein isoforms, quaternary structures, or steric hindrance of antibody-antigen recognition in case of multiprotein complexes. One approach is the use of stable isotope-labeled internal standards; another is the direct exploitation of mass spectrometric signals recorded by LC-MS/MS analysis of protein digests. Here we assessed the peptide match score summation index based on probabilistic peptide scores calculated by the PHENYX protein identification engine for absolute protein quantification in accordance with the protein abundance index as proposed by Mann and co-workers (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome Res. 12, 1231-1245). Using synthetic protein mixtures, we demonstrated that this approach works well, although proteins can have different response factors. Applied to high density lipoproteins (HDLs), this new approach compared favorably to alternative protein quantitation methods like UV detection of protein peaks separated by capillary electrophoresis or quantitation of protein spots on SDS-PAGE. We compared the protein composition of a well defined HDL density class isolated from plasma of seven hypercholesterolemia subjects having low or high HDL cholesterol with HDL from nine normolipidemia subjects. The quantitative protein patterns distinguished individuals according to the corresponding concentration and distribution of cholesterol from serum lipid measurements of the same samples and revealed that hypercholesterolemia in unrelated individuals is the result of different deficiencies. The presented approach is complementary to HDL lipid analysis; does not rely on complicated sample treatment, e.g. chemical reactions, or antibodies; and can be used for projective clinical studies of larger patient groups.

Links between body mass index, total body fat, cholesterol, high-density lipoprotein, and insulin sensitivity in patients with obesity related to depression, anger, and anxiety

OBJECTIVE: Define links between psychosocial parameters and metabolic variables in obese females before and after a low-calorie diet. METHOD: Nine female obese patients (age 36.1 +/- 7.1 years, body mass index [BMI] > 30 kg/m2) were investigated before and after a 6-week low-calorie diet accompanied by behavior therapy. Blood lipids, insulin sensitivity (Bergman protocol), fat distribution (by dual-energy X-ray absorptiometry [DEXA]), as well as psychological parameters such as depression, anger, anxiety, symptom load, and well-being, were assessed before and after the dieting period. RESULTS: The females lost 9.6 +/- 2.8 kg (p < .0001) of body weight, their BMI was reduced by 3.5 +/- 0.3 kg/m2 (p < .0001), and insulin sensitivity increased from 3.0 +/- 1.8 to 4.3 +/- 1.5 mg/kg (p = .05). Their abdominal fat content decreased from 22.3 +/- 5.5 to 18.9 +/- 4.5 kg (p < .0001). In parallel, psychological parameters such as irritability (p < .05) and cognitive control (p < .0001) increased, whereas feelings of hunger (p < .05), externality (p < .05), interpersonal sensitivity (p < .01), paranoid ideation (p < .05), psychoticism (p < .01), and global severity index (p < .01) decreased. Prospectively, differences in body fat (percent) were correlated to nervousness (p < .05). Waist-to-hip ratio (WHR) differences were significantly correlated to sociability (p < .05) and inversely to emotional instability (p < .05), whereas emotional instability was inversely correlated to differences in insulin sensitivity (p < .01). DISCUSSION: Weight reduction may lead to better somatic risk factor control. Women with more nervousness and better sociability at the beginning of a diet period may lose more weight than others.

High-density electrode array for imaging in vitro electrophysiological activity

The development of a high-density active microelectrode array for in vitro electrophysiology is reported. Based on the Active Pixel Sensor (APS) concept, the array integrates 4096 gold microelectrodes (electrode separation 20 microm) on a surface of 2.5 mmx2.5 mm as well as a high-speed random addressing logic allowing the sequential selection of the measuring pixels. Following the electrical characterization in a phosphate solution, the functional evaluation has been carried out by recording the spontaneous electrical activity of neonatal rat cardiomyocytes. Signals with amplitudes from 130 microVp-p to 300 microVp-p could be recorded from different pixels. The results demonstrate the suitability of the APS concept for developing a new generation of high-resolution extracellular recording devices for in vitro electrophysiology.

Inverse relationship between fractionated electrograms and atrial fibrosis in persistent atrial fibrillation: combined magnetic resonance imaging and high-density mapping

OBJECTIVES This study sought to evaluate the relationship between fibrosis imaged by delayed-enhancement (DE) magnetic resonance imaging (MRI) and atrial electrograms (Egms) in persistent atrial fibrillation (AF). BACKGROUND Atrial fractionated Egms are strongly related to slow anisotropic conduction. Their relationship to atrial fibrosis has not yet been investigated. METHODS Atrial high-resolution MRI of 18 patients with persistent AF (11 long-lasting persistent AF) was registered with mapping geometry (NavX electro-anatomical system (version 8.0, St. Jude Medical, St. Paul, Minnesota)). DE areas were categorized as dense or patchy, depending on their DE content. Left atrial Egms during AF were acquired using a high-density, 20-pole catheter (514 ± 77 sites/map). Fractionation, organization/regularity, local mean cycle length (CL), and voltage were analyzed with regard to DE. RESULTS Patients with long-lasting persistent versus persistent AF had larger left atrial (LA) surface area (134 ± 38 cm(2) vs. 98 ± 9 cm(2), p = 0.02), a higher amount of atrial DE (70 ± 16 cm(2) vs. 49 ± 10 cm(2), p = 0.01), more complex fractionated atrial Egm (CFAE) extent (54 ± 16 cm(2) vs. 28 ± 15 cm(2), p = 0.02), and a shorter baseline AF CL (147 ± 10 ms vs. 182 ± 14 ms, p = 0.01). Continuous CFAE (CFEmean [NavX algorithm that quantifies Egm fractionation] <80 ms) occupied 38 ± 19% of total LA surface area. Dense DE was detected at the left posterior left atrium. In contrast, the right posterior left atrium contained predominantly patchy DE. Most CFAE (48 ± 14%) occurred at non-DE LA sites, followed by 41 ± 12% CFAE at patchy DE and 11 ± 6% at dense DE regions (p = 0.005 and p = 0.008, respectively); 19 ± 6% CFAE sites occurred at border zones of dense DE. Egms were less fractionated, with longer CL and lower voltage at dense DE versus non-DE regions: CFEmean: 97 ms versus 76 ms, p < 0.0001; local CL: 153 ms versus 143 ms, p < 0.0001; mean voltage: 0.63 mV versus 0.86 mV, p < 0.0001. CONCLUSIONS Atrial fibrosis as defined by DE MRI is associated with slower and more organized electrical activity but with lower voltage than healthy atrial areas. Ninety percent of continuous CFAE sites occur at non-DE and patchy DE LA sites. These findings are important when choosing the ablation strategy in persistent AF.