Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

This is the final version of the article. Available from Nature Publishing Group via the DOI in this record.Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the overall accuracies of an input read dataset, alignment and SNP-calling method providing an isolate in that dataset has a corresponding, or closely related reference sequence available. In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate. We benchmark this method against other SNP callers using our FDR method with three fungal genomes, finding that it was able achieve a high level of accuracy. These tools are available at http://cfdr.sourceforge.net/.R.A.F. was funded by the Natural Environment Research Council (NERC). D.A.H. and M.C.F. were supported by the Wellcome Trust. No additional external funding received for this study

Lipid-Based Antimicrobial Delivery-Systems for the Treatment of Bacterial Infections

Many nanotechnology-based antimicrobials and antimicrobial-delivery-systems have been developed over the past decades with the aim to provide alternatives to antibiotic treatment of infectious-biofilms across the human body. Antimicrobials can be loaded into nanocarriers to protect them against de-activation, and to reduce their toxicity and potential, harmful side-effects. Moreover, antimicrobial nanocarriers such as micelles, can be equipped with stealth and pH-responsive features that allow self-targeting and accumulation in infectious-biofilms at high concentrations. Micellar and liposomal nanocarriers differ in hydrophilicity of their outer-surface and inner-core. Micelles are self-assembled, spherical core-shell structures composed of single layers of surfactants, with hydrophilic head-groups and hydrophobic tail-groups pointing to the micellar core. Liposomes are composed of lipids, self-assembled into bilayers. The hydrophilic head of the lipids determines the surface properties of liposomes, while the hydrophobic tail, internal to the bilayer, determines the fluidity of liposomal-membranes. Therefore, whereas micelles can only be loaded with hydrophobic antimicrobials, hydrophilic antimicrobials can be encapsulated in the hydrophilic, aqueous core of liposomes and hydrophobic or amphiphilic antimicrobials can be inserted in the phospholipid bilayer. Nanotechnology-derived liposomes can be prepared with diameter

Phagocytosis of Bacteria Adhering to a Biomaterial Surface in a Surface Thermodynamic Perspective

Bacterial biofilms can increase the pathogenicity of infection and constitute a major problem in modern health-care, especially on biomaterial implants and devices. Biofilms are difficult to eradicate by the host immune system, even with antibiotics, and have been the number one cause of biomaterial implant and device failure for decades. Therefore, it is important to understand how immune cells interact with adhering pathogens. This study firstly aims to develop a simple method to quantify phagocytosis of six different strains of staphylococci adhering on a surface with phase-contrast-microscopy. Phagocytosis of adhering staphylococci to a glass surface by phagocytes was quantified in a parallel plate flow chamber, and expressed as a phagocytosis rate, accounting for the number of adhering staphylococci initially present and for the duration of phagocytosis. Murine macrophages were more effective in clearing staphylococci from a surface than human phagocytes, which require differentiation from their monocyte or promyelocytic state during an experiment. Direct visualization of internalization of a GFP-modified S. aureus strain inside phagocytes confirmed the validity of the method proposed. As a second aim, the differences in phagocytosis rates observed were investigated on a surface thermodynamic basis using measured contact angles of liquids on macroscopic lawns of staphylococci and phagocytes, confirming that phagocytosis of adhering pathogens can be regarded as a surface phenomenon. In addition, surface thermodynamics revealed that phagocytosis of adhering pathogens is determined by an interplay of physical attraction between pathogens and phagocytes and the influence of chemo-attractants. For future studies, these results will help to place in vitro experiments and murine infection models in better perspective with respect to human ones

Liposomes with Water as a pH-Responsive Functionality for Targeting of Acidic Tumor and Infection Sites

A lipid named DCPA was synthesized under microwave-assisted heating. DCPA possesses a pyridine betaine, hydrophilic group that can be complexed with water through hydrogen bonding (DCPA-H2O). DCPA-H2O liposomes became protonated relatively fast already at p

Proton-mediated burst of dual-drug loaded liposomes for biofilm dispersal and bacterial killing

Exposure of infectious biofilms to dispersants induces high bacterial concentrations in blood that may cause sepsis. Preventing sepsis requires simultaneous biofilm dispersal and bacterial killing. Here, self-targeting DCPA(2-(4-((1,5-bis(octadecenoyl)1,5-dioxopentan-2-yl)carbamoyl)pyridin-1-ium-1-yl)acetate) liposomes with complexed water were self-assembled with ciprofloxacin loaded in-membrane and PEGylated as a lipid-membrane component, together with bromelain loaded in-core. Inside biofilms, DCPA-H2O and PEGylated ciprofloxacin became protonated, disturbing the balance in the lipid-membrane to cause liposome-burst and simultaneous release of bromelain and ciprofloxacin. Simultaneous release of bromelain and ciprofloxacin enhanced bacterial killing in Staphylococcus aureus biofilms as compared with free bromelain and/or ciprofloxacin. After tail-vein injection in mice, liposomes accumulated inside intra-abdominal staphylococcal biofilms. Subsequent liposome-burst and simultaneous release of bromelain and ciprofloxacin yielded degradation of the biofilm matrix by bromelain and higher bacterial killing without inducing septic symptoms as obtained by injection of free bromelain and ciprofloxacin. This shows the advantage of simultaneous release from liposomes of bromelain and ciprofloxacin inside a biofilm

Prevalence of antibodies to Leishmania infantum and Toxoplasma gondii in horses from the north of Portugal

Leishmania infantum and Toxoplasma gondii are protozoa with zoonotic and economic importance. Prevalences of antibodies to these agents were assessed in 173 horses from the north of Portugal. Antibodies to L. infantum were detected by the direct agglutination test (DAT); seven (4.0%) horses were seropositive with DAT titres of 200 (n = 5), 800 (n = 1) and ≥ 1600 (n = 1). Antibodies to T. gondii were assayed by the modified agglutination test (MAT); 23 (13.3%) horses were seropositive with MAT titres of 20 (n = 13), 40 (n = 5), 80 (n = 3) and ≥ 160 (n = 2). No statistical differences were found among equine categories of gender (female, male and gelding), age (1.5-6, 7-12 and 13-30 years), type of housing (indoors and mixed/outdoors), ability (recreation, farming and sports) and clinical status (apparently healthy and sick) for both agents. Horses are exposed to and may be infected with L. infantum and T. gondii in the north of Portuga

FROM PIGMENTS TO PAINTS: STUDYING ORIGINAL MATERIALS FROM THE ATELIER OF THE ARTIST MARIANO FORTUNY Y MADRAZO

We present the first study related to the painting materials used by Mariano Fortuny y Madrazo (Granada 1871 - Venice 1949). This eclectic artist, whose activities ranged from photography to painting, produced his own tempera colours Tempere Fortuny. His atelier in Palazzo Pesaro degli Orfei in Venice still conserves several kinds of painting materials employed in different stages of paint manufacture: from raw colourant materials (e.g. pigments and dyes) to a ready-to-use paint tube containing a complex mixture of pigment, binder ad additives. Micro samples collected from 29 “raw” materials and 2 handcrafted coloured paint mixtures were characterised by XRF, FT-IR and PyGCMS analysis. Through this multi-analytical approach, both inorganic and organic fractions were detected. According to the obtained results, Mariano Fortuny used both traditional and innovative materials- commercial products which were available at his time and sold for artistic practice and paint manufacture. This study allowed to understand the procedures followed by Fortuny in the production of his own colours, in particular highlighting the technical expedients the artist used in binding medium processing. These pieces of information prove Fortuny’s deep proficiency in paint manufacture and explain why his own Tempere were appreciated by his contemporaries.We present the first study related to the painting materials used by Mariano Fortuny y Madrazo (Granada 1871 - Venice 1949). This eclectic artist, whose activities ranged from photography to painting, produced his own tempera colours Tempere Fortuny. His atelier in Palazzo Pesaro degli Orfei in Venice still conserves several kinds of painting materials employed in different stages of paint manufacture: from raw colourant materials (e.g. pigments and dyes) to a ready-to-use paint tube containing a complex mixture of pigment, binder ad additives. Micro samples collected from 29 “raw” materials and 2 handcrafted coloured paint mixtures were characterised by XRF, FT-IR and PyGCMS analysis. Through this multi-analytical approach, both inorganic and organic fractions were detected. According to the obtained results, Mariano Fortuny used both traditional and innovative materials- commercial products which were available at his time and sold for artistic practice and paint manufacture. This study allowed to understand the procedures followed by Fortuny in the production of his own colours, in particular highlighting the technical expedients the artist used in binding medium processing. These pieces of information prove Fortuny’s deep proficiency in paint manufacture and explain why his own Tempere were appreciated by his contemporaries