Visualization and Differential Analysis of Protein Expression Data Using R.

Data analysis is essential to derive meaningful conclusions from proteomic data. This chapter describes ways of performing common data visualization and differential analysis tasks on gel-based proteomic datasets using a freely available statistical software package (R). A workflow followed is illustrated using a synthetic dataset as example

Supplementing taurine to plant-based diets improves lipid digestive capacity and amino acid retention of Senegalese sole (Solea senegalensis) juveniles

Recent studies reported positive effects of taurine supplementation to plant protein-based diets on fish growth performance and feed conversion ratio but the mechanisms involved remain unclear. The objective of this work was to provide a first insight on the importance of taurine on dietary protein and lipid absorption and utilisation, in Senegalese sole (Solea senegalensis) juveniles fed plant-based diets. Seven practical diets were tested: a fishmeal-based diet (FM) and a plant protein-based formula (PP85) to which taurine was added in graded levels: 0.2% (TAU1), 0.3% (TAU2), 0.4% (TAUS), 0.7% (TAU4) and 1.5% (TAU5). Short-term metabolic trials were performed by tube-feeding the different experimental diets labelled with different tracers: C-14-taurine, C-14-triolein (as tracer of dietary triacylglycerol) and a mixture of C-14-amino acids. Feeding sole juveniles with the PP85 diet affected taurine metabolism, since a higher proportion of dietary taurine was directed to gallbladder and probably used for bile salt synthesis. Consistent with this, fish receiving the plant-based low taurine-content diets (PP85 and TAU1) displayed a poor triacyglycerol digestion capacity. A higher proportion of C-14-amino acids was retained in fish muscle when fed the TAU5 compared to the PP85 diet. These short-term trials suggested that taurine supplementation to a plant-based diet might be beneficial to sole performance by enhancing bile salt synthesis and triacylglycerol digestion as well as muscle amino acid retention. However, this dietary supplementation should be tested in long-term trials to verify the effect on fish growth and to assess the beneficial effects on protein and lipid metabolism suggested here. Statement of relevance in the general field of aquaculture (limited to 60 characters): Adding taurine to a plant-based diet is beneficial for sole (C) 2016 Elsevier B.V. All rights reserved.National Funds through Fundacao para a Ciencia e Tecnologia [PTDC/MAR/117047/2010]Fundacao para a Ciencia e Tecnologia, Portugal [SFRH/BDP/65578/2009]info:eu-repo/semantics/acceptedVersio

Proteomics as a tool to develop molecular indicators of nutritional condition in farmed gilthead seabream

Gilthead seabream is the main aquaculture species produced in Portugal, as well as in the Mediterranean. However, the winter disease syndrome, a series of metabolic and immune system disorders caused by low temperatures, affects seabream culture, leading to important industrial losses, either as mortalities or growth decreases during spring. These effects can be minimized through dietary optimisation, either improving diets for the end of summer season, or feeding seabream with a fortified diet during autumn/winter. However, the development of a fortified diet for autumn/winter is hindered by the lack of tools to evaluate fish metabolic and physiological condition. Nevertheless, the recent development of new generation molecular tools provides good perspectives to supply molecular indicators of condition that would support this task

Interannual memory effects for spring NDVI in semi-arid South Africa

Almost 20 years of Normalized Difference Vegetative Index (NDVI) and precipitation (PPT) data are analysed to better understand the interannual memory effects on vegetation dynamics observed at regional scales in Southern Africa (SA). The study focuses on a semi-arid region (25°S–31°S; 21°E–26°E) during the austral early summer (September–December). The memory effects are examined using simple statistical approaches (linear correlations and regressions) which require the definition of an early summer vegetation predictand (December NDVI minus September NDVI) and a consistent set of potential predictors (rainfall amount, number of rainy days, rainfall intensity, NDVI and Rain-Use-Efficiency) considered with 4 to 15-month time-lag. An analysis over six SA sub-regions, corresponding to the six major land-cover types of the area reveals two distinct memory effects. A “negative” memory effect (with both rainfall and vegetation) is detected at 7 to 10-month time-lag while a “positive” memory effect (with vegetation only) is observed at 12 to 14-month time-lag. These results suggest that interannual memory effects in early summer vegetation dynamics of semi-arid South Africa may preferably be driven by biological rather than hydrological mechanisms

Enhanced dietary formulation to mitigate winter thermal stress in gilthead sea bream (Sparus aurata): a 2D-DIGE plasma proteome study

Low water temperatures during winter are common in farming of gilthead sea bream in the Mediterranean. This causes metabolic disorders that in extreme cases can lead to a syndrome called "winter disease." An improved immunostimulatory nutritional status might mitigate the effects of this thermal metabolic stress. A trial was set up to assess the effects of two different diets on gilthead sea bream physiology and nutritional state through plasma proteome and metabolites. Four groups of 25 adult gilthead sea bream were reared during winter months, being fed either with a control diet (CTRL) or with a diet called "winter feed" (WF). Proteome results show a slightly higher number of proteins upregulated in plasma of fish fed the WF. These proteins are mostly involved in the immune system and cell protection mechanisms. Lipid metabolism was also affected, as shown both by plasma proteome and by the cholesterol plasma levels. Overall, the winter feed diet tested seems to have positive effects in terms of fish condition and nutritional status, reducing the metabolic effects of thermal stress

Nutrition, quality and performance in marine fish larvae

O cultivo de larvas de peixes marinhos é caracterizado por altas mortalidades e por problemas de qualidade, nomeadamente malformações esqueléticas. A solução de parte destes problemas passa por uma melhor compreensão dos requisitos nutricionais. Este trabalho pretende fazer uma revisão de trabalhos recentes que demonstram como os aminoácidos, os ácidos gordos e a vitamina K, mas também o regime alimentar, podem influenciar a qualidade e a performance das larvas de peixes marinhos

A Role of the Fast ATP-gated P2X1 Cation Channel in Thrombosis of Small Arteries In Vivo

The P2X1 receptor is a fast ATP-gated cation channel expressed in blood platelets, where its role has been difficult to assess due to its rapid desensitization and the lack of pharmacological tools. In this paper, we have used P2X1−/− and wild-type mouse platelets, treated with apyrase to prevent desensitization, to demonstrate the function of P2X1 in the response to thrombogenic stimuli. In vitro, the collagen-induced aggregation and secretion of P2X1-deficient platelets was decreased, as was adhesion and thrombus growth on a collagen-coated surface, particularly when the wall shear rate was elevated. In vivo, the functional role of P2X1 could be demonstrated using two models of platelet-dependent thrombotic occlusion of small arteries, in which blood flow is characterized by a high shear rate. The mortality of P2X1−/− mice in a model of systemic thromboembolism was reduced and the size of mural thrombi formed after a laser-induced vessel wall injury was decreased as compared with normal mice, whereas the time for complete thrombus removal was shortened. Overall, the P2X1 receptor appears to contribute to the formation of platelet thrombi, particularly in arteries in which shear forces are high

Mild dyslipidemia accelerates tumorigenesis through expansion of Ly6Chi monocytes and differentiation to pro-angiogenic myeloid cells

Cancer and cardiovascular disease (CVD) share common risk factors such as dyslipidemia, obesity and inflammation. However, the role of pro-atherogenic environment and its associated low-grade inflammation in tumor progression remains underexplored. Here we show that feeding C57BL/6J mice with a non-obesogenic high fat high cholesterol diet (HFHCD) for two weeks to induce mild dyslipidemia, increases the pool of circulating Ly6Chi monocytes available for initial melanoma development, in an IL-1β-dependent manner. Descendants of circulating myeloid cells, which accumulate in the tumor microenvironment of mice under HFHCD, heighten pro-angiogenic and immunosuppressive activities locally. Limiting myeloid cell accumulation or targeting VEGF-A production by myeloid cells decrease HFHCD-induced tumor growth acceleration. Reverting the HFHCD to a chow diet at the time of tumor implantation protects against tumor growth. Together, these data shed light on cross-disease communication between cardiovascular pathologies and cancer

Fibrin monomers evaluation during hospitalization for COVID-19 is a predictive marker of in-hospital mortality

BackgroundCoagulopathy is one of the main triggers of severity and worsening of Coronavirus disease 2019 (COVID-19) particularly in critically ill patients. D-dimer has been widely used to detect COVID-19 coagulation disorders and has been correlated with outcomes such as disease severity and in-hospital mortality. Involvement of other fibrin degradation products, particularly fibrin monomers (FM), remains an ongoing question.MethodsWe performed a monocentric study of adult patients with COVID-19, who were admitted either in the medical ward (MW) or in the intensive care unit (ICU) and who had FM measurements performed on them during the first wave of COVID-19 outbreak. We analyzed the positivity of FM levels (FM > 7 µg/mL) to assess the ability of FM monitoring during the first days of hospitalization to predict COVID-19 outcomes.ResultsIn our cohort, 935 FM measurements were performed in 246 patients during their first 9 days of hospitalization. During patient follow-up, the FM levels were higher in patients admitted directly to the ICU than in those admitted to the MW. Moreover, we observed significantly increased levels of FM in patients when the data were stratified for in-hospital mortality. At hospital admission, only 27 (11%) patients displayed a positive value for FM; this subgroup did not differ from other patients in terms of severity (indicated by ICU referral at admission) or in-hospital mortality. When analyzing FM positivity in the first 9 days of hospitalization, we found that 37% of patients had positive FM at least once during hospitalization and these patients had increased in-hospital mortality (p = 0.001). Thus, we used non-adjusted Kaplan–Meier curves for in-hospital mortality according to FM positivity during hospitalization and we observed a statistically significant difference for in-hospital mortality (hazard ratio = 1.48, 95% CI: 1.25–1.76, p < 0.001). However, we compared the AUC of FM positivity associated with a ratio of D-dimer >70% and found that this combined receiver operating characteristic (ROC) curve was superior to the FM positivity ROC curve alone.ConclusionMonitoring of FM positivity in hospitalized patients with COVID-19 could be a reliable and helpful tool to predict the worsening condition and mortality of COVID-19

Cytomegalovirus distribution and evolution in hominines

Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.Peer Reviewe