Search results for " Ali"
showing 10 items of 2042 documents
CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles
2016
Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for the detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures of modified ribonucleotides relying on both sequence-dependent mismatch patterns and reverse transcription arrests. Common alignment viewers lack specialized functionality, such as filtering, tailored visualization, image export and differential analysis. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modifi…
Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain
2017
We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 11…
Molecular evolution of antioxidant and hypoxia response in long-lived, cancer-resistant blind mole rats: The Nrf2-Keap1 pathway.
2015
The Nrf2-Keap1 pathway is crucial for the cellular antioxidant and hypoxia response in vertebrates. Deciphering its modifications in hypoxia-adapted animals will help understand its functionality under environmental stress and possibly allow for knowledge transfer into biomedical research. The blind mole rat Spalax, a long-lived cancer-resistant rodent, lives in burrows underground and is adapted to severely hypoxic conditions. Here we have conducted a bioinformatical survey of Spalax core genes from the Nrf2-Keap1 pathway on the coding sequence level in comparison to other hypoxia-tolerant and -sensitive rodents. We find strong sequence conservation across all genes, illustrating the pathw…
Performances of Different Metabolic Lactobacillus Groups During the Fermentation of Pizza Doughs Processed from Semolina
2018
The main hypothesis of this work is that facultative and obligate heterofermentative Lactobacillus species can differently impact the final characteristics of pizza. The objective was to evaluate separately the behaviors of the obligate heterofermentative species (OHS), such as Lactobacillus sanfranciscensis, Lactobacillus brevis, and Lactobacillus rossiae, and the facultative heterofermentative species (FHS), including Lactobacillus plantarum, and Lactobacillus curvatus, in the sourdoughs to be used for pizza production. The production of the experimental pizzas was carried out with semolina (Triticum turgidum L. ssp. durum). The acidification process—which was followed by pH, total titrat…
Effect of the inclusion of fresh lemon pulp in the diet of lactating ewes on the properties of milk and cheese
2017
This study investigated the effects of fresh lemon pulp (FLP), as a natural antioxidant in the diet, on the intake of feed and the production of milk and cheese of Valle del Belice lactating ewes during the hot summer in Sicily. A total of 15 second-lambing ewes, kept individually in 3 × 3 m pens, were divided into 3 homogeneous groups fed with 3 diets in a 3 × 3 Latin square design, with 3 experimental phases of 21 days each. The diets were: mixed hay ad libitum plus 600 g/day of concentrate (FLP0); mixed hay ad libitum plus 400 g/day of concentrate and 1 kg/day of FLP (FLP1); and mixed hay ad libitum plus 200 g/day of concentrate and 2 kg/day of FLP (FLP2). Nine experimental Pecorino chee…
Legume grain-based supplements in dairy sheep diet: Effects on milk yield, composition and fatty acid profile
2016
With the aim to find protein sources that are free of genetically modified organisms, the effects of legume grain-based concentrates, used as alternatives of a mixed concentrate feed containing soybean, were evaluated on sheep milk production. Twelve lactating ewes were divided into four groups, fed hay and, according to a 4 × 4 Latin square design, supplied with 800 g/day of a commercial mixed concentrate feed (MCF) containing maize and soybean, or the same amount of isoprotein concentrates consisting of chickpea (CH), faba bean (FB), or pea (PE) mixed with barley. The ewes ingested more of the concentrates with legume grains than the MCF (702, 702, 678 vs 587 g/day DM for CH, FB, PE and M…
Chemical characterization of a variety of cold-pressed gourmet oils available on the Brazilian market
2018
Different specialty extra virgin oils, produced by cold-pressing fruits/nuts (olive, pequi, palm, avocado, coconut, macadamia and Brazil nut) and seeds (grapeseed and canola), and retailed in the Brazilian region of Minas Gerais, were chemically characterized. Specifically, for each type of oil, the fatty acid composition was elucidated by GC-FID, the contents of selected polyphenols and squalene were determined respectively by UHPLC-MS and UHPLC-PDA, whereas minerals were explored by means of ICP-MS. Olive oil was confirmed to have the highest MUFA content due to a valuable level of oleic acid, while oils from grapeseed, Brazil nut and canola were marked by nutritionally important PUFA lev…
Potential Uses of Olive Oil Secoiridoids for the Prevention and Treatment of Cancer: A Narrative Review of Preclinical Studies
2021
The Mediterranean diet (MD) is a combination of foods mainly rich in antioxidants and anti-inflammatory nutrients that have been shown to have many health-enhancing effects. Extra-virgin olive oil (EVOO) is an important component of the MD. The importance of EVOO can be attributed to phenolic compounds, represented by phenolic alcohols, hydroxytyrosol, and tyrosol, and to secoiridoids, which include oleocanthal, oleacein, oleuropein, and ligstroside (along with the aglycone and glycosidic derivatives of the latter two). Each secoiridoid has been studied and characterized, and their effects on human health have been documented by several studies. Secoiridoids have antioxidant, anti-inflammat…
Fast UPLC/PDA determination of squalene in Sicilian P.D.O. pistachio from Bronte: Optimization of oil extraction method and analytical characterizati…
2017
Abstract A fast reversed-phase UPLC method was developed for squalene determination in Sicilian pistachio samples that entry in the European register of the products with P.D.O. In the present study the SPE procedure was optimized for the squalene extraction prior to the UPLC/PDA analysis. The precision of the full analytical procedure was satisfactory and the mean recoveries were 92.8 ± 0.3% and 96.6 ± 0.1% for 25 and 50 mg L−1 level of addition, respectively. Selected chromatographic conditions allowed a very fast squalene determination; in fact it was well separated in ∼0.54 min with good resolution. Squalene was detected in all the pistachio samples analyzed and the levels ranged from 5…
dAPE: a web server to detect homorepeats and follow their evolution.
2016
Abstract Summary Homorepeats are low complexity regions consisting of repetitions of a single amino acid residue. There is no current consensus on the minimum number of residues needed to define a functional homorepeat, nor even if mismatches are allowed. Here we present dAPE, a web server that helps following the evolution of homorepeats based on orthology information, using a sensitive but tunable cutoff to help in the identification of emerging homorepeats. Availability and Implementation dAPE can be accessed from http://cbdm-01.zdv.uni-mainz.de/∼munoz/polyx. Supplementary information Supplementary data are available at Bioinformatics online.