A 3-dimensional model building by homology of the HFE protein: molecular consequences and application to antibody development

Genetic hemochromatosis (GH) is a common inherited disease of iron metabolism affecting 2-5 in 1000 individuals of European origin. A candidate gene for GH, namely HFE has been recently characterized. Structural studies of the protein product of the HFE gene are of major interest for a better understanding of the molecular physiopathology in iron overload. We have built a 3-dimensional model of the HFE protein based on congruent with40% homology of sequence identity with HLA-Aw68, another MHC class I molecule. This work presents the first 3-dimensional structure of HFE available in the public domain (http://swift.embl-heidelberg.de/service/francois). The 3-dimensional characteristics of the protein complexed with the beta2-microglobulin are presented. The model has been used to predict immunogenic loops and to develop an antibody able to recognize a protein exhibiting the same molecular weight as HFE. Structural consequences of two common mutations are debated and evolutionary hypotheses are considered in the discussion of the particular biological activity of HFE. This study shows that a strategy based on homology modeling is sufficient to undertake biological investigations.     

The effect of functionalization of mesoporous silica nanoparticles on the interaction and stability of confined enzyme

Immobilization of enzymes into the mesoporous nanomaterials results in formation of more stable and even more active versions of biocatalysts. The effect of surface functionalization of mesoporous silica nanoparticles (MSNs) on its adsorption characteristics and stability of superoxide dismutase (SOD) was investigated. For this purpose, non-functionalized (KIT-6) and aminopropyl-functionalized cubic Ia3d mesoporous silica ([n-PrNH(2)-KIT-6]) nanoparticles with 3-dimensional pores were used as supports. It was observed that the amount of enzyme adsorbed on/within MSNs is dependent on the initial enzyme concentration for both KIT-6 and [n-PrNH(2)-KIT-6] mesoporous silicas. However a stronger interaction between SOD and [n-PrNH(2)-KIT-6] was observed relative to KIT-6. Increasing temperature favors a larger amount of SOD immobilization into KIT-6, while it was negligible for [n-PrNH(2)-KIT-6]. Immobilized SOD was more stable against urea and thermal denaturation relative to free enzyme and this improvement of stability was more pronounced for SOD into the [n-PrNH(2)-KIT-6] than KIT-6. These results may be useful in determining the mechanism(s) of protein immobilization and stabilization into the solid supports.     

DFA7, a New Method to Distinguish between Intron-Containing and Intronless Genes

Intron-containing and intronless genes have different biological properties and statistical characteristics. Here we propose a new computational method to distinguish between intron-containing and intronless gene sequences. Seven feature parameters , , , , , , and based on detrended fluctuation analysis (DFA) are fully used, and thus we can compute a 7-dimensional feature vector for any given gene sequence to be discriminated. Furthermore, support vector machine (SVM) classifier with Gaussian radial basis kernel function is performed on this feature space to classify the genes into intron-containing and intronless. We investigate the performance of the proposed method in comparison with other state-of-the-art algorithms on biological datasets. The experimental results show that our new method significantly improves the accuracy over those existing techniques.     

细胞膜仿生修饰纳米粒肿瘤治疗的研究进展

大量研究证明,细胞膜仿生修饰通过将不同细胞膜包被于纳米粒表面,赋予纳米粒新的生物学功能.纳米粒被细胞膜仿生修饰后,获得了细胞膜表面丰富的蛋白质并保留了纳米粒的高载药能力,延长体内循环时间,使纳米粒具有逃避免疫系统,跨越各种生理屏障的能力.本文总结了近年来细胞膜仿生修饰纳米粒用于肿瘤治疗的最新进展,讨论了细胞膜仿生修饰纳...     

Studies on quantum dots synthesized in aqueous solution for biological labeling via electrostatic interaction

3-Mercaptopropyl acid-stabilized CdTe nanoparticles synthesized in aqueous solution are effectively bound to a biomacromolecule, papain, via electrostatic interaction. The conjugation between the nanoparticles and the papain is demonstrated by UV-Vis absorption, photoluminescence spectroscopy, transmission electron microscopy, and fluorescence micrographs. The biological activity of papain is maintained after the conjugation. The effects of the quantity of papain and the size of nanoparticles on the fluorescence characteristics of the CdTe-papain bioconjugates were studied.     

Fabrication of curcumin-loaded zein nanoparticles stabilized by sodium caseinate/sodium alginate: Curcumin solubility,thermal properties,rheology, and stability

Curcumin is a polyphenol with multiple biological activities, but its extremely poor water solubility severely limits its application in the food industry. The purposes of this work were to study the effect of nano-encapsulation on the water solubility of curcumin (C), the interaction of curcumin with zein (Z), the thermal properties, rheological properties, and the stability under different environmental pressures of the nanoparticles. The results of particle size, zeta potential, and surface hydrophobicity (H₀) indicated that the combination of coating materials including sodium caseinate (SC) and sodium alginate (SA) with zein nanoparticles by electrostatic interaction led to a gradual increase in the particle size of composite nanoparticles and a decrease in surface hydrophobicity. The nano-encapsulation significantly improved the water solubility of curcumin and causing its crystal structure to change to an amorphous state. Fourier transform infrared spectroscopy confirmed that curcumin bound to zein through hydrogen bonding. Rheological test results showed that the coating materials combined with zein led to an increase in the apparent viscosity of the nanoparticles. The stability analysis results indicated that the composite nanoparticles with a sodium alginate coating have excellent stability of pH, salt solution and storage, and excellent anti-gastrointestinal fluids digestion characteristics when compared to pure protein nanoparticles.     

Chemotactic assay for biological effects of silver nanoparticles

A method is proposed for assessing the biocidal efficacy of water-dispersed nanoparticles of silver. It is based on negative chemotaxis of the plasmodia of the slime mold Physarum polycephalum. Biocidal and repellent effects were compared for silver nanoparticles, Ag⁺ ions, and AOT in solution and in the agar gel. In such characteristics as increasing the period of auto-oscillations of contractile activity, decreasing the area of spreading on substrate, and substrate preference in spatial tests, silver nanoparticles proved to be substantially more effective than Ag⁺ and AOT. The lethal concentrations of the nanoparticles were close to those found earlier for bacteria and viruses. The chemotactic tests allow quantitative assessment of the biological reaction and monitoring its dynamics; in resolution, they are superior to the tests based on the lethal action of biocidal agents.     

Recent developments in colorimetric immunoassays using nanozymes and plasmonic nanoparticles

Enzyme-linked immunosorbent assay (ELISA) is a popular detection technique for the screening and diagnosis of diseases. The sensitivity of ELISA can be increased by the incorporation of nanoparticles. Through this article, we discuss the utilization of nanoparticles in ELISA. Nanoparticles possess an intrinsic biological peroxidase-like activity which allows it to act as an enzyme mimic for the development of an improved analysis method. Different nanoparticles (gold nanoparticles, silver nanoparticles, etc.) carry different peroxidase-mimic characteristics. Besides this, nanoparticles can also perform as a colorimetric substrate in ELISA where it gives a more prominent color change compared to the commonly used colorimetric substrate TMB. This article also focuses on the mechanisms behind this color change including aggregation, in situ nanoparticle growth, seeding, and etching.     

Gold Nanoparticle Uptake by Tumour Cells of B16 Mouse Melanoma

Because of their photo-optical distinctiveness and biocompatibility, gold nanoparticles have proven to be powerful tools in various nanomedical applications. In this article, we discuss the advantage of gold nanoparticles in image diagnostic application of melanoma. It has demonstrated the potential role of gold nanoparticles in the study of tumour tissue architecture and the utility of gold nanoparticles in the hystopathological exam of B16 melanoma with the benefit of fluorescence emission of gold nanoparticles in UV spectrum. The optical properties of colloidal gold nanoparticles allow spectroscopic detection and identification of melanoma cells. The method proposed is easy, inexpensive and reliable for hystopathological analysis of melanoma. The fluorescence images in the cryosections of tissues depicted a strong luminescence property of gold nanoparticles uptaken in melanoma, results that confirm the role of the gold nanoparticles in biological labelling and imaging applications. To emphasize the AuNPs influence over the biological tissues, a study of the chemical bonds configuration was performed using Raman spectrometry.     

Formation of silver nanoparticles in water samples from Antarctic Lake Untersee

Comparative integral assessment of the biological characteristics of the water samples of ice-covered Antarctic Lake Untersee was carried out using a new nanobiotechnological approach based on registration of biogenic nanoparticles of reduced silver Ag⁰. Formation of reduced silver nanoparticles occurred in all samples containing aboriginal microorganisms, while nanoparticles were not formed in the samples from which bacterial cells were removed. Size distribution of biogenic silver nanoparticles varied in the samples from five water horizons. The method proposed provides for rapid detection of live microbiological objects in the samples by detection of formation of biogenic nanoparticles of reduced silver. The method was termed OBNG (Observation of Biogenic Nanoparticles Growth).     

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty

This model-based design of experiments (MBDOE) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study. The ideal global solution for this experiment design problem is generally computationally intractable because of parametric uncertainties in the mathematical model of the biological system. Others have addressed this issue by limiting the solution to a local estimate of the model parameters. Here we present an approach that is independent of the local parameter constraint. This approach is made computationally efficient and tractable by the use of: (1) sparse grid interpolation that approximates the biological system dynamics, (2) representative parameters that uniformly represent the data-consistent dynamical space, and (3) probability weights of the represented experimentally distinguishable dynamics. Our approach identifies data-consistent representative parameters using sparse grid interpolants, constructs the optimal input sequence from a greedy search, and defines the associated optimal measurements using a scenario tree. We explore the optimality of this MBDOE algorithm using a 3-dimensional Hes1 model and a 19-dimensional T-cell receptor model. The 19-dimensional T-cell model also demonstrates the MBDOE algorithm’s scalability to higher dimensions. In both cases, the dynamical uncertainty region that bounds the trajectories of the target system states were reduced by as much as 86% and 99% respectively after completing the designed experiments in silico. Our results suggest that for resolving dynamical uncertainty, the ability to design an input sequence paired with its associated measurements is particularly important when limited by the number of measurements.     

A new generation of polymer nanoparticles for drug delivery.

One of the main interests of using polymer nanoparticles as drug carrier systems is to control the delivery of the drugs including their biodistribution. During the last decade, it was clearly demonstrated that surface properties of nanoparticles were the key factor which determined the in vivo fate of such a carrier. Thus, the purpose of this work was to develop a new method which allows the easy fabrication of nanoparticles with versatile surface properties using polysaccharides. This preparation was based on the use of a redox radical polymerization reaction applied for the first time to the emulsion polymerization of alkylcyanoacrylates in aqueous continuous media. The dispersion of nanoparticles was very stable. The nanoparticle surfaces were coated with polysaccharides and their characteristics can be modulated by the type and the molecular weight of the polysaccharides used during the synthesis. Interestingly the biological properties of the polysaccharide immobilized on the nanoparticle surface can be preserved opening very interesting perspectives for such nanoparticles. This method also offers a new strategy for the design of modular biomimetic nanoparticles as drug carrier systems with multiple functions. One of the applications considered in this work was to use these nanoparticles coupled with haemoglobin as an oxygen carrier.     

生物脱氮中工程纳米颗粒的毒害作用及减毒措施的研究进展

氮化合物在生命代谢过程中扮演着重要的角色,但过多的无机氮会导致水体恶化进而影响人类健康,生物脱氮技术可高效去除环境中的无机氮且不引起二次污染.随着工程纳米颗粒在生活中的广泛应用,导致其大量释放到土壤及水体中,极大地阻碍了废水处理中的生物脱氮过程,因此,微生物脱氮过程中工程纳米颗粒的毒害作用及减毒措施成了近年来的研究热点...     

Bioluminescent assay for toxicological assessment of nanomaterials

A new method for assessing biotoxicity of nanomaterials, based on the use of soluble bioluminescent coupled enzyme system NAD(P)?H:FMN oxidoreductase and luciferase, is proposed. The results of this study indicate a significant adverse biological effect exerted by nanoparticles at the molecular level. It was found that the most toxic nanoparticles the nanoparticles are based on copper and copper oxide, as well as single-walled carbon nanotubes and multi-walled carbon nanofibers, which are referred to hazard class II.     

Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing.

Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer a global approach to the study of the cell. Using the integrated approach offered by 2-dimensional gel protein databases it is now possible to reveal phenotype specific protein (or proteins), to microsequence them, to search for homology with previously identified proteins, to clone the cDNAs, to assign partial protein sequence to genes for which the full DNA sequence and the chromosome location is known, and to study the regulatory properties and function of groups of proteins that are coordinately expressed in a given biological process. Human 2-dimensional gel protein databases are becoming increasingly important in view of the concerted effort to map and sequence the entire genome.     

Gold Nanoparticles Attenuates Antimycin A-Induced Mitochondrial Dysfunction in MC3T3-E1 Osteoblastic Cells

Gold nanoparticles have shown promising biological applications due to their unique properties. Understanding the interaction mechanisms between nanomaterials and biological cells is important for the control and manipulation of these interactions for biomedical applications. In the present study, we investigated the effects of gold nanoparticles on the differentiation of osteoblastic MC3T3-E1 cells and antimycin A-induced mitochondrial dysfunction. The results showed that gold nanoparticles (5, 10, and 20 nm) caused a significant elevation of cell growth, alkaline phosphatase activity, collagen synthesis, and osteocalcin content in the cells (P?<?0.05). Moreover, pretreatment with gold nanoparticles prior to antimycin A exposure significantly reduced antimycin A-induced cell damage by preventing mitochondrial membrane potential dissipation, complex IV inactivation, ATP loss, cytochrome c release, cardiolipin peroxidation, and reactive oxygen species generation. Taken together, our study indicated that gold nanoparticles may improve the differentiation and have protective effects on mitochondrial dysfunction of osteoblastic cells.     

Inactivation of S. epidermidis, B. subtilis, and E. coli bacteria bioaerosols deposited on a filter utilizing airborne silver nanoparticles

In the present study, a control methodology utilizing airborne silver nanoparticles is suggested and tested with respect to its potential to control Gram-positive Staphylococcus epidermidis and Bacillus subtilis, and Gram-negative Escherichia coli bacteria bioaerosols deposited on filters. As it is known that the Gram-negative bacteria are sensitive to airflow exposure, the main focus of this study for testing the airborne silver nanoparticles effect was the Gram-positive Staphylococcus epidermidis and Bacillus subtilis bacteria bioaerosols whereas Escherichia coli bioaerosols were utilized for comparison. Airborne bacteria and airborne silver nanoparticles were quantitatively generated in an experimental system. Bioaerosols deposited on the filter were exposed to airborne silver nanoparticles. The physical and biological properties of the airborne bacteria and airborne silver nanoparticles were measured via aerosol measurement devices. From the experimental results, it was demonstrated that this method utilizing airborne silver nanoparticles offers potential as a bioaerosol control methodology.     

Concanavalin A‐immobilized magnetic nanoparticles for selective enrichment of glycoproteins and application to glycoproteomics in hepatocelluar carcinoma cell line

Protein glycosylation is one of the most important PTMs in biological organism. Lectins such as concanavalin A (Con A) have been widely applied to N‐glycosylated protein investigation. In this study, we developed Con A‐immobilized magnetic nanoparticles for selective separation of glycoproteins. At first, a facile immobilization of Con A on aminophenylboronic acid‐functionalized magnetic nanoparticles was performed by forming boronic acid‐sugar‐Con A bond in sandwich structure using methyl α‐D ‐mannopyranoside as an intermedium. The selective capture ability of Con A‐modified magnetic nanoparticles for glycoproteins was tested using standard glycoproteins and cell lysate of human hepatocelluar carcinoma cell line 7703. In total 184 glycosylated sites were detected within 172 different glycopeptides corresponding to 101 glycoproteins. Also, the regeneration of the protein‐immobilized nanoparticles can easily be performed taking advantage of the reversible binding mechanism between boronic acid and sugar chain. The experiment results demonstrated that Con A‐modified magnetic nanoparticles by the facile and low‐cost synthesis provided a convenient and efficient enrichment approach for glycoproteins, and are promising candidates for large‐scale glycoproteomic research in complicated biological samples.     

A 2-dimensional geometry for biological time

This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the usual (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The “visual” representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3-dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for “representation time”, with a cognitive significance.     

Toxicology of engineered nanomaterials: Focus on biocompatibility,biodistribution and biodegradation

Background

It is widely believed that engineered nanomaterials will be increasingly used in biomedical applications. However, before these novel materials can be safely applied in a clinical setting, their biocompatibility, biodistribution and biodegradation needs to be carefully assessed.

Scope of Review

There are a number of different classes of nanoparticles that hold promise for biomedical purposes. Here, we will focus on some of the most commonly studied nanomaterials: iron oxide nanoparticles, dendrimers, mesoporous silica particles, gold nanoparticles, and carbon nanotubes.

Major Conclusions

The mechanism of cellular uptake of nanoparticles and the biodistribution depend on the physico-chemical properties of the particles and in particular on their surface characteristics. Moreover, as particles are mainly recognized and engulfed by immune cells special attention should be paid to nano–immuno interactions. It is also important to use primary cells for testing of the biocompatibility of nanoparticles, as they are closer to the in vivo situation when compared to transformed cell lines.

General Significance

Understanding the unique characteristics of engineered nanomaterials and their interactions with biological systems is key to the safe implementation of these materials in novel biomedical diagnostics and therapeutics. This article is part of a Special Issue entitled Nanotechnologies - Emerging Applications in Biomedicine.