Analysis of qPCR reference genes stability determination methods and a practical approach for efficiency calculation on a turbot (Scphthalmus maximus) gonad dataset

Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray results. Several issues are crucial for a successful qPCR study, particularly the selection of internal reference genes for normalization and efficiency determination. There is no agreement on which method is the best to detect the most stable genes neither on how to perform efficiency determination. In this study we offer a comprehensive evaluation of the characteristics of reference gene selection methods and how to decide which one is more reliable when they show discordant outcomes. Also, we analyze the current efficiency calculation controversy. Our dataset is composed by gonad samples of turbot at different development times reared at different temperatures. Turbot (Scophthalmus maximus) is a relevant marine aquaculture European species with increasing production in the incoming years. Since females largely outgrow males, identification of genes related to sex determination, gonad development and reproductive behavior, and analysis of their expression profiles are of primary importance for turbot industryVersión del edito

Association between cognitive function and supplementation with omega-3 PUFAs and other nutrients in ≥ 75 years old patients: A randomized multicenter study

A few studies have assessed the association between omega-3 polyunsaturated fatty acids (n-3 PUFA) and cognitive impairment (CI) in very old adults. The aim of this study was to evaluate the effect of a multinutrient supplementation rich in n-3 PUFA on the cognitive function in an institutionalized ≥75-year-old population without CI or with mild cognitive impairment (MCI). A multicenter placebo-controlled double-blind randomized trial was conducted between 2012 and 2013. Cognitive function was assessed at baseline and after one year using 4 neuropsychological tests. Nutritional status was assessed using Mini Nutritional Assessment (MNA). Interaction between Mini-Mental State Examination (MMSE) score and nutritional status were analyzed using linear regression models. A total of 99 participants were randomized to receive placebo or pills rich in n-3 PUFA. After 1-year follow-up, both groups decreased their MMSE score (-1.18, SD:0. 53 and -0.82, SD:0. 63, p = 0.67 for the control and the intervention group respectively). The memory subscale of the MMSE showed an improvement (+0.26, SD:0.18) in the intervention group against a worsening in the control group (-0.11, SD: 0.14; p = 0.09 for differences between groups). Patients at intervention group with normal nutritional status (MNA ≥24) showed an improvement in the MMSE (+1.03, p = 0.025 for differences between 1-y and baseline measurements) against a worsening in the group with malnutrition (MNA<24) (-0.4, p = 0.886 for differences between 1-y and baseline; p of interaction p = 0.05). Supplementation with n-3 PUFA did not show an improvement in the global cognitive function in institutionalized elderly people without CI or with MCI. They only suggest an apparent improvement in memory loss if previously they were well nourished

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection are often non-specific, and there is no definitive test for the accurate diagnosis of infection. The 'omics' approaches to identifying biomarkers from the host-response to bacterial infection are promising. In this study, lipidomic analysis was carried out with plasma samples obtained from febrile children with confirmed bacterial infection (n = 20) and confirmed viral infection (n = 20). We show for the first time that bacterial and viral infection produces distinct profile in the host lipidome. Some species of glycerophosphoinositol, sphingomyelin, lysophosphatidylcholine and cholesterol sulfate were higher in the confirmed virus infected group, while some species of fatty acids, glycerophosphocholine, glycerophosphoserine, lactosylceramide and bilirubin were lower in the confirmed virus infected group when compared with confirmed bacterial infected group. A combination of three lipids achieved an area under the receiver operating characteristic (ROC) curve of 0.911 (95% CI 0.81 to 0.98). This pilot study demonstrates the potential of metabolic biomarkers to assist clinicians in distinguishing bacterial from viral infection in febrile children, to facilitate effective clinical management and to the limit inappropriate use of antibiotics

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection ar

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Construction of a bac library from turbot, Scophthalmus maximus, and identification of clones containing candidate sex-determinig genes

The turbot ( Scophthalmus maximus ) is a highly appreciated European aquaculture species. As farming of turbot is growing as an aqua culture enterprise, the identification of genetic regions responsible for economically import ant traits might be importance for future aquaculture of turbot. The sex-determining systems of fish appear to be at a primitive stage of evolution and display an amazing diversity, includi ng male heterogametic, female heterogametic, and temperature dependent systems. F emales of this species reach commercial size 4-6 months before than males, thus the interes t of industry in obtaining all-female populations. Neither mitotic nor meiotic chromosome s have shown sex-associated heteromorphisms in turbot, but the main sex determi ning region of turbot was identified after a detailed QTL and marker association analysis. Her e we describe the construction and characterization of a bacterial artificial chromoso me (BAC) library from turbot and the identification of clones containing genes related t o the sex determining region and to the gonadal differentiation process. The BAC library wa s constructed from the genomic DNA of a highly inbred individual using the vector pIndigo BAC536. The large, high-quality inserts showed a size of at least 100 kb and <5% empty vect ors or non-recombinants were detected. Based on estimated turbot genome size: 800 Mb the l ibrary provides 5x coverage. To our knowledge, this is the first reported Scophthalmus maximus BAC library. The library contains 46.080 clones arrayed in 120 384-well microtiter pl ates. To isolate genes related to sex- determination and differentiation we screened the l ibrary using the 4D-PCR method with slight modifications. Several genes and/or markers associated to the main sex-determining region or related with gonad differentiation were i dentified and are being used for their physical mapping using FISH. Since some of them had been previously mapped, they are being useful to establish the correspondence betwee n the cytogenetic and genetic turbot maps. Using this information the BAC library will be furt her used to analyzed differences in the main sex determining region between males and femal es using positional cloning or chromosome microdissection. This BAC library will b e an essential tool for future projects on genome analysis of productive traits with relevant implications for turbot industry

Laboratory and Astronomical Discovery of Magnesium Dicarbide, MgC2

7 pags., 5 figs., 4 tabs. -- Unified Astronomy Thesaurus concepts: Circumstellar envelopes (237); Metal-containing molecules (2258); Laboratory astrophysics (2004); Carbon stars (199)We report the detection of magnesium dicarbide, MgC2, in the laboratory at centimeter wavelengths and assign 24MgC225MgC2, and 26MgC2 to 14 unidentified lines in the radio spectrum of the circumstellar envelope of the evolved carbon star IRC+10216. The structure of MgC2 is found to be T-shaped with a highly ionic bond between the metal atom and the C2 unit, analogous to other dicarbides containing electropositive elements. A two-temperature excitation model of the MgC2 emission lines observed in IRC+10216 yields a very low rotational temperature of 6 ± 1 K, a kinetic temperature of 22 ± 13 K, and a column density of (1.0 ± 0.3) × 1012 cm−2. The abundance of MgC2 relative to the magnesium-carbon chains MgCCH, MgC4H, and MgC6H is 1:2:22:20 and provides a new constraint on the sequential radiative association-dissociative recombination mechanisms implicated in the production of metal-bearing molecules in circumstellar environments.P.B.C. and M.C.M. are supported by the National Science Foundation (award Nos. AST-1908576 and PHY-2110489). H.G. acknowledges support from the National Science Foundation for participation in this work as part of his independent research and development plan. Any opinions, findings, and conclusions expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. We acknowledge funding support from the Spanish Ministerio de Ciencia e Innovación through grants PID2019-107115GB-C21 and PID2019-106110GB-I00.Peer reviewe

Metabolic balance of microplankton community in the upwelling system of ria de vigo (nw iberian peninsula)

Poster.-- ASLO summer meeting, Santiago de Compostela, 19-24 July 2005N