Biotite: new tools for a versatile Python bioinformatics library.

Background: Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. This allows for easy combination of various data analysis, modeling and simulation methods.

Adding hydrogen atoms to molecular models via fragment superimposition.

Background: Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds.

Red and White Wine Lees Show Inhibitory Effects on Liver Carcinogenesis.

Scope: Wine has shown anticarcinogenic benefits in hepatocarcinoma and polyphenols seem to be responsible for these effects. Wine lees are the sediments produced during fermentation and they endow wine with organoleptic and physicochemical properties. However, the anticarcinogenic role of these compounds is still unknown.

Anti/genotoxic, longevity inductive, cytotoxic, and clastogenic-related bioactivities of tomato and lycopene.

The aim of this study was to evaluate some biological activities of tomato as well as lycopene and to consider a new nutraceutic value for this fruit regarding to the protection against genetic damage and as a chemopreventive agent. Genotoxicity, DNA-protection against hydrogen peroxide, and lifespan properties of tomato and lycopene were assessed through wing spot test and longevity assay using the Drosophila in vivo model. Additionally, chemopreventive activity was investigated through cytotoxicity, DNA-fragmentation comet and annexin V FITC/PI assays using HL60 in vitro model.

Association between CFH, CFB, ARMS2, SERPINF1, VEGFR1 and VEGF polymorphisms and anatomical and functional response to ranibizumab treatment in neovascular age-related macular degeneration.

Purpose: We sought to determine if specific genetic single nucleotide polymorphisms (SNPs) influence vascular endothelial growth factor inhibition response to ranibizumab in neovascular age-related macular degeneration (AMD).

Methods: A total of 403 Caucasian patients diagnosed with exudative AMD were included. After a three-injection loading phase, a pro re nata regimen was followed.

Transcriptomic analyses of the anti-adipogenic effects of oleuropein in human mesenchymal stem cells.

Extra virgin olive oil has positive effects on health. Oleuropein is a polyphenolic compound present in olive-tree leaves, fruits (olives) and olive oil. It is responsible for the relevant organoleptic and biological properties of olive oil, including antiadipogenic properties.

Demethylating and anti-hepatocarcinogenic potential of hesperidin, a natural polyphenol of Citrus juices.

Hepatocellular carcinoma (HCC) is a neoplasia representing the fifth most common malignancy worldwide and the third cause of death from cancer. Diets with high content in fruits and vegetables are widely recommended for their health-promoting properties, among them, the protection against diabetes, cancer, and cardiovascular diseases. Hesperidin is the most important phenol in the orange fruit with well-known health benefits.

Extravascular hemolysis and complement consumption in Paroxysmal Nocturnal Hemoglobinuria patients undergoing eculizumab treatment.

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hemolytic anemia characterized by complement-mediated intravascular hemolysis that is effectively treated with eculizumab. However, treatment responses are reported heterogeneous with some patients presenting residual hemolysis and requiring RBC transfusions. Recent reports have shown that both extravascular hemolysis and incomplete C5 blockade can explain these suboptimal hematological responses.

Evaluation of 10 AMD Associated Polymorphisms as a Cause of Choroidal Neovascularization in Highly Myopic Eyes.

Choroidal neovascularization (CNV) commonly occurs in age related macular degeneration and pathological myopia patients. In this study we conducted a case-control prospective study including 431 participants. The aim of this study was to determine the potential association between 10 single nucleotide polymorphisms (SNPs) located in 4 different genetic regions (CFI, COL8A1, LIPC, and APOE), and choroidal neovascularization in age-related macular degeneration and the development of choroidal neovascularization in highly myopic eyes of a Caucasian population.

Effect of Hydroxytyrosol on Human Mesenchymal Stromal/Stem Cell Differentiation into Adipocytes and Osteoblasts.

Background And Aims: Natural phenolic compounds are known for their antioxidant capacity, showing biological activity in numerous physiological processes. Such chemicals have been proposed for prevention or treatment of pathologies like osteoporosis and diabetes. One of these is hydroxytyrosol (HT), which may be involved in the differentiation of human mesenchymal stromal/stem cells (MSCs), which are precursors of osteoblasts and adipocytes.

Transcriptomic Analyses of Adipocyte Differentiation From Human Mesenchymal Stromal-Cells (MSC).

Adipogenesis is a physiological process required for fat-tissue development, mainly involved in regulating the organism energetic-state. Abnormal distribution-changes and dysfunctions in such tissue are associated to different pathologies. Adipocytes are generated from progenitor cells, via a complex differentiating process not yet well understood.

Effects of quercetin, a natural phenolic compound, in the differentiation of human mesenchymal stem cells (MSC) into adipocytes and osteoblasts.

Natural phenols may have beneficial properties against oxidative stress, which is associated with aging and major chronic aging-related diseases, such as loss of bone mineral mass (osteoporosis) and diabetes. The main aim of this study was to analyze the effect of quercetin, a major nutraceutical compound present in the "Mediterranean diet", on mesenchymal stem-cell (MSC) differentiation. Such cells were induced to differentiate into osteoblasts or adipocytes in the presence of two quercetin concentrations (0.

Molecular Basis of Factor H R1210C Association with Ocular and Renal Diseases.

The complement factor H (FH) mutation R1210C, which was described in association with atypical hemolytic uremic syndrome (aHUS), also confers high risk of age-related macular degeneration (AMD) and associates with C3 glomerulopathy (C3G). To reveal the molecular basis of these associations and to provide insight into what determines the disease phenotype in FH-R1210C carriers, we identified FH-R1210C carriers in our aHUS, C3G, and AMD cohorts. Disease status, determined in patients and relatives, revealed an absence of AMD phenotypes in the aHUS cohort and, vice versa, a lack of renal disease in the AMD cohort.

Complement factor H, FHR-3 and FHR-1 variants associate in an extended haplotype conferring increased risk of atypical hemolytic uremic syndrome.

Atypical hemolytic uremic syndrome (aHUS) is a severe thrombotic microangiopathy affecting the renal microvasculature and is associated with complement dysregulation caused by mutations or autoantibodies. Disease penetrance and severity is modulated by inheritance of "risk" polymorphisms in the complement genes MCP, CFH and CFHR1. We describe the prevalence of mutations, the frequency of risk polymorphisms and the occurrence of anti-FH autoantibodies in a Spanish aHUS cohort (n=367).

Evaluation of potential antigenotoxic, cytotoxic and proapoptotic effects of the olive oil by-product "alperujo", hydroxytyrosol, tyrosol and verbascoside.

Olive oil is an integral ingredient of the "Mediterranean diet". The olive oil industry generates large quantities of a by-product called "alperujo" (AL) during the two-phase centrifugation system developed in the early nineties. AL could be a potent exploitable source of natural phenolic antioxidants.

Growth of geographic atrophy on fundus autofluorescence and polymorphisms of CFH, CFB, C3, FHR1-3, and ARMS2 in age-related macular degeneration.

Importance: Identification of the genetic risk factors that contribute to geographic atrophy (GA) could lead to advancements in interventional trials and/or therapeutic approaches for combating vision loss.

Objective: To investigate whether single-nucleotide polymorphisms (SNPs) are associated with the presence and progression of established GA in age-related macular degeneration (AMD).

Design, Setting, And Participants: Prospective, controlled, multicenter study of 154 patients with GA/AMD and 141 age-matched control participants at 8 Spanish hospitals.

Cytotoxic and genotoxic effects of metal(oid)s bioactivated in rocket leaves (Eruca vesicaria subsp. sativa Miller).

Rocket is an important source of essential elements. However, it may also accumulate toxic elements such as metal(oids). The objectives of the present work were (i) to study the uptake of arsenic, lead, cadmium and zinc in rocket grown in contaminated soils, (ii) to establish the genotoxic and cytotoxic activities of this vegetable material, and (iii) to study the modulator role of the glucosinolate and metal contents in the genotoxic/cytotoxic activities.

C3 glomerulopathy-associated CFHR1 mutation alters FHR oligomerization and complement regulation.

C3 glomerulopathies (C3G) are a group of severe renal diseases with distinct patterns of glomerular inflammation and C3 deposition caused by complement dysregulation. Here we report the identification of a familial C3G-associated genomic mutation in the gene complement factor H–related 1 (CFHR1), which encodes FHR1. The mutation resulted in the duplication of the N-terminal short consensus repeats (SCRs) that are conserved in FHR2 and FHR5.

Effects of oocyte quality, incubation time and maturation environment on the number of chromosomal abnormalities in IVF-derived early bovine embryos.

Chromosomal aberrations are one of the major causes of embryo developmental failures in mammals. The occurrence of these types of abnormalities is higher in in vitro-produced (IVP) embryos. The aim of the present study was to investigate the effect of oocyte morphology and maturation conditions on the rate of chromosomal abnormalities in bovine preimplantational embryos.

In vivo biological activity of rocket extracts (Eruca vesicaria subsp. sativa (Miller) Thell) and sulforaphane.

Eruca is thought to be an excellent source of antioxidants like phenolic compounds, carotenoids, glucosinolates and their degradation products, such as isothiocyanates. Sulforaphane is one of the most potent indirect antioxidants of Eruca isolated until the date. In this work we investigate: (i) the safety and DNA protective activity of Eruca extracts and sulforaphane (under and without oxidative stress) in Drosophila melanogaster; and (ii) the influence on D.

Role of citrus juices and distinctive components in the modulation of degenerative processes: genotoxicity, antigenotoxicity, cytotoxicity, and longevity in Drosophila.

It is well established that breakfast beverages contain high quantities of Citrus juices. The purpose of the present study was to assess the nutraceutical value of orange and lemon juices as well as two of their active compounds: hesperidin and limonene. Indicator assays were performed at three levels to evaluate different biological health promoter activities: (i) determination of the safety and DNA-damage protecting ability against free radicals by using the somatic mutation and recombination test (SMART) in Drosophila melanogaster, (ii) study of the modulating role for life span in Drosophila melanogaster, and (iii) measurement of the cytotoxic activity against the human tumor cell line HL60.

A pilot study on the DNA-protective, cytotoxic, and apoptosis-inducing properties of olive-leaf extracts.

Leaves of olive trees are an abundant raw material in the Mediterranean basin. They contain large amounts of potentially useful phytochemicals and could play beneficial roles in health care. In the present study, the principal bioactive phenols in olive-leaf extracts (OLEs) have been identified and quantified, and their genotoxic/antigenotoxic, cytotoxic and apoptotic effects have been assessed.

Targets of red grapes: oxidative damage of DNA and leukaemia cells.

Vitis vinifera is a widespread crop all over the world. The biophenols present in grapes have a remarkable influence on wine quality and also confer potential health-protecting properties to this fruit. The aim of the present work was to assess the beneficial properties of skin, seeds and pulp of red table grapes (RTG) (Vitis vinifera, Palieri Cadiz variety).

Antigenotoxicity, cytotoxicity, and apoptosis induction by apigenin, bisabolol, and protocatechuic acid.

Medicinal plants represent an important resource in new drug research. Antioxidant properties of plants can help to scavenge reactive oxygen species. The objective of this work was to evaluate the genotoxic, antigenotoxic, tumoricidal, and apoptotic effect of some major phenols (apigenin, bisabolol, and protocatechuic acid) from two medicinal plants, Matricaria chamomilla and Uncaria tomentosa.