The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Nanomedicine delivery: Does protein corona route to the target or off road?

Nanomedicine aims to find novel solutions for urgent biomedical needs. Despite this, one of the most challenging hurdles that nanomedicine faces is to successfully target therapeutic nanoparticles to cells of interest in vivo. As for any biomaterials, once in vivo, nanoparticles can interact with plasma biomolecules, forming new entities for which the name protein coronas (PCs) have been coined. The PC can influence the in vivo biological fate of a nanoparticle. Thus for guaranteeing the desired function of an engineered nanomaterial in vivo, it is crucial to dissect its PC in terms of formation and evolution within the body. In this contribution we will review the 'good' and 'bad' sides of the PC, starting from the scientific aspects to the technological applications

Interaction of nanoparticles with lipid membranes: a multiscale perspective

Freestanding lipid bilayers were challenged with 15 nm Au nanospheres either coated by a citrate layer or passivated by a protein corona. The effect of Au nanospheres on the bilayer morphology, permeability and fluidity presents strong differences or similarities, depending on the observation length scale, from the colloidal to the molecular domains. These findings suggest that the interaction between nanoparticles and lipid membranes should be conveniently treated as a multiscale phenomenon

Surfactant titration of nanoparticle-protein corona

Nanoparticles (NP), when exposed to biological fluids, are coated by specific proteins that form the so-called protein corona. While some adsorbing proteins exchange with the surroundings on a short time scale, described as a "dynamic" corona, others with higher affinity and long-lived interaction with the NP surface form a "hard" corona (HC), which is believed to mediate NP interaction with cellular machineries. In-depth NP protein corona characterization is therefore a necessary step in understanding the relationship between surface layer structure and biological outcomes. In the present work, we evaluate the protein composition and stability over time and we systematically challenge the formed complexes with surfactants. Each challenge is characterized through different physicochemical measurements (dynamic light scattering, ζ-potential, and differential centrifugal sedimentation) alongside proteomic evaluation in titration type experiments (surfactant titration). 100 nm silicon oxide (Si) and 100 nm carboxylated polystyrene (PS-COOH) NPs cloaked by human plasma HC were titrated with 3-[(3-Cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS, zwitterionic), Triton X-100 (nonionic), sodium dodecyl sulfate (SDS, anionic), and dodecyltrimethylammonium bromide (DTAB, cationic) surfactants. Composition and density of HC together with size and ζ-potential of NP-HC complexes were tracked at each step after surfactant titration. Results on Si NP-HC complexes showed that SDS removes most of the HC, while DTAB induces NP agglomeration. Analogous results were obtained for PS NP-HC complexes. Interestingly, CHAPS and Triton X-100, thanks to similar surface binding preferences, enable selective extraction of apolipoprotein AI (ApoAI) from Si NP hard coronas, leaving unaltered the dispersion physicochemical properties. These findings indicate that surfactant titration can enable the study of NP-HC stability through surfactant variation and also selective separation of certain proteins from the HC. This approach thus has an immediate analytical value as well as potential applications in HC engineering

The polyplex, protein corona, cell interplay: Tips and drawbacks

Polyplexes (PX) are soft materials, obtained by blending polycations and nucleic acids, designed for gene delivery applications. While much is known about the transfection properties of PX, their protein corona, the biomolecules interacting with colloids once in a biological environment, represents an underlooked parameter in gene transfection. In this study, linear and branched polyethylenimines (lPEI and bPEI), the golden standard among non-viral vectors, were selected and used throughout the work: their physicochemical properties and protein corona when complexed to DNA were studied and linked to the toxicity and transfection efficiency arisen upon their delivery to cells. Interestingly, lPEIDNA and bPEIDNA complexes were characterized by similar physicochemical features, but different biological behavior. In fact, the biological milieu where cells and PX interact greatly influences their size, stability and transfection abilities. Using PX as a soft material model system, we spotlighted structure-activity relationships and methodologies that can help interpret their biological behavior and guide future studies in the field

The impact of body-weight components on forced spirometry in healthy Italians

Many studies have investigated lung function in relation to age and height among Caucasians, however, most of these studies did not consider the individual components of body weight. The objective of the present study was to study the effect of body weight components [bone-free lean body mass (BF-LBM), bone mineral content (BMC), and fat mass (FM)] measured by dual x-ray absorptiometry (DXA) on the lung-function variables (FVC, FEV1, and PEF) and to derive prediction equations for these variables in healthy adult Italians. Dynamic spirometric tests and body composition analysis by DXA were performed on 58 nonsmoking males, mean age (+/-SE) 26.72 +/- 1.98 years and BMI 25.51 +/- 0.64 kg/m(2), and 60 nonsmoking females matched for age and BMI (29.61 +/- 1.65 years and 26.45 +/- 1.05 kg/m(2), respectively). Bivariate linear regression analysis showed the variables age, height, BF-LBM, BMC, and the interaction term BF-LBM*Height, but not weight and FM, to correlate significantly with lung-function variables for males and for females separately. Multiple linear regression analysis showed that sex, age, height, and BF-LBM*Height were significantly associated with FVC, FEV1, and PEF. The prediction equations developed for FVC, FEV1, and PEF on the basis of the independent variables i.e. sex, age (y), height (m), and BF-LBM*Height (kg . m) had a significantly higher cumulative correlation coefficient and a lower SEE compared with those based on age and height only. The present report suggests that the BF-LBM, expressed independently from height, can be considered for predicting lung-function variables

Colorimetric nanoplasmonic assay to determine purity and titrate extracellular vesicles

Extracellular Vesicles (EVs) - cell secreted vesicles that carry rich molecular information of the parental cell and constitute an important mode of intercellular communication - are becoming a primary topic in translational medicine. EVs (that comprise exosomes and microvesicles/microparticles) have a size ranging from 40 nm to 1 μm and share several physicochemical proprieties, including size, density, surface charge, and light interaction, with other nano-objects present in body fluids, such as single and aggregated proteins. This makes separation, titration, and characterization of EVs challenging and time-consuming. Here we present a cost-effective and fast colorimetric assay for probing by eye protein contaminants and determine the concentration of EV preparations, which exploits the synergy between colloidal gold nanoplasmonics, nanoparticle-protein corona, and nanoparticle-membrane interaction. The assay hits a limit of detection of protein contaminants of 5 ng/μL and has a dynamic range of EV concentration ranging from 35 fM to 35 pM, which matches the typical range of EV concentration in body fluids. This work provides the first example of the exploitation of the nanoparticle-protein corona in analytical chemistry