3,134 publications from this institution
Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.
Abstract Motivation: Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes. Results: We developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process. Availability: ProteinEvolver is written in C, can run in parallel and is freely available from http://code.google.com/p/proteinevolver/. Contact: marenas@cbm.uam.es Supplementary information: Supplementary data are available at Bioinformatics online.
Abstract The populations of Atlantic salmon in the Ulla and Lérez rivers, located in Galicia in northwestern Spain, were close to extinction early in the 1990s. A restoration programme involving supportive breeding has been conducted since 1995, using a mixture of salmon populations from several Galician rivers. The programme utilizes progeny of adults returning to the rivers and wild parr reared in fresh water until maturity. Five microsatellite loci were used to compare genetic variability in the restored populations with that in populations before their collapse in the 1950s. DNA samples were obtained from scale collections (old samples) and from tissue samples of live fish caught in the rivers (modern samples). Average heterozygosities and allelic richness are very similar in modern and old samples. Populations inhabiting the Ulla and Lérez rivers today are more similar than they were in the past, possibly because they originated in the same stock mixture.
Hermida, R. C.1; Calvo, C.2; Ayala, D. E.1; Dominguez, M. J.2; Covelo, M.2; Mojon, A.1; Fernandez, J. R.1; Fontao, M. J.1; Soler, R.1; Lopez, J. E.2 Author Information
Omega-9 fatty acids represent some of the main mono-unsaturated fatty acids (MUFA) found in plant and animal sources.
Food processing sustainability, as well as waste minimization, are key concerns for the modern food industry. A significant amount of waste is generated by the fruit juice industry each year. In addition to the economic losses caused by the removal of these wastes, its impact on the environment is undeniable. Therefore, researchers have focused on recovering the bioactive components from fruit juice processing, in which a great number of phytochemicals still exist in the agro-industrial wastes, to help minimize the waste burden as well as provide new sources of bioactive compounds, which are believed to be protective agents against certain diseases such as cardiovascular diseases, cancer, and diabetes. Although these wastes contain non-negligible amounts of bioactive compounds, information on the utilization of these byproducts in functional ingredient/food production and their impact on the sensory quality of food products is still scarce. In this regard, this review summarizes the most recent literature on bioactive compounds present in the wastes of apple, citrus fruits, berries, stoned fruits, melons, and tropical fruit juices, together with their extraction techniques and valorization approaches. Besides, on the one hand, examples of different current food applications with the use of these wastes are provided. On the other hand, the challenges with respect to economic, sensory, and safety issues are also discussed.
There is a strong association between metabolic syndrome (MS) and increased cardiovascular risk. Moreover, elevated nighttime blood pressure (BP) and non-dipping (subjects with <10% decline in the asleep relative to the awake BP mean) have been also linked to increased cardiovascular morbidity and mortality. We investigated the relation between MS, circadian time of hypertension treatment, and impaired nighttime BP decline in a cross-sectional study on 3352 (1576 men/1776 women) non-diabetic hypertensive subjects, 53.7 ± 13.1 (mean ± SD) yrs of age. Among them, 2056 were ingesting all their prescribed hypertension medication upon awakening, and 1296 were ingesting at least one of their BP medications at bedtime. BP was measured by ambulatory monitoring for 48 consecutive hours to substantiate reproducibility of the dipping pattern. Physical activity was simultaneously monitored every minute by wrist actigraphy to accurately calculate mean BP when awake and asleep for each subject. MS was present in 52.6% of the subjects. The prevalence of an altered non-dipper BP profile was significantly higher among subjects with MS (52.0% vs. 39.5% in subjects without MS, p < .001). Non-dipping was significantly more prevalent among subjects ingesting all BP-lowering medications upon awakening (56.8%) than among those ingesting at least one of their BP medications at bedtime (29.1%; p < .001). Subjects with MS had significantly higher values of uric acid (6.0 vs. 5.3 g/dL, p < .001), plasma fibrinogen (331 vs. 315 mg/dL, p < .001), and erythrocyte sedimentation rate (14.8 vs. 12.4 mm, p < .001). Non-dipping was significantly associated with the presence of MS and treatment upon awakening in a multiple logistic regression model adjusted by significant confounding factors, including age, creatinine, erythrocyte sedimentation rate, and cigarette smoking. This cross-sectional study documents a significant increase of a blunted sleep-time BP decline in treated hypertensive subjects with MS. Even in the presence of MS, treatment at bedtime is significantly associated with lower prevalence of a high-risk non-dipper BP profile.
