Unique structure (construction and configuration) and evolution of the array of small serum protein genes of Protobothrops flavoviridis snake.

The nucleotide sequence of Protobothrops flavoviridis (Pf) 30534 bp genome segment which contains genes encoding small serum proteins (SSPs) was deciphered. The genome segment contained five SSP genes (PfSSPs), PfSSP-4, PfSSP-5, PfSSP-1, PfSSP-2, and PfSSP-3 in this order and had characteristic configuration and constructions of the particular nucleotide sequences inserted. Comparison between the configurations of the inserted chicken repeat-1 (CR1) fragments of P. flavoviridis and Ophiophagus hannah (Oh) showed that the nucleotide segment encompassing from PfSSP-1 to PfSSP-2 was inverted. The inactive form of PfSSP-1, named PfSSP-1δ(Ψ), found in the intergenic region (I-Reg) between PfSSP-5 and PfSSP-1 had also been destroyed by insertions of the plural long interspersed nuclear elements (LINEs) and DNA transposons. The L2 LINE inserted into the third intron or the particular repetitive sequences inserted into the second intron structurally divided five PfSSPs into two subgroups, the Long SSP subgroup of PfSSP-1, PfSSP-2 and PfSSP-5 or the Short SSP subgroup of PfSSP-3 and PfSSP-4 The mathematical analysis also showed that PfSSPs of the Long SSP subgroup evolved alternately in an accelerated and neutral manner, whereas those of the Short SSP subgroup evolved in an accelerated manner. Moreover, the ortholog analysis of SSPs of various snakes showed that the evolutionary emerging order of SSPs was as follows: SSP-5, SSP-4, SSP-2, SSP-1, and SSP-3 The unique interpretation about accelerated evolution and the novel idea that the transposable elements such as LINEs and DNA transposons are involved in maintaining the host genome besides its own transposition natures were proposed.

Probing Bio-Nano Interactions between Blood Proteins and Monolayer-Stabilized Graphene Sheets.

Meeting proteins is regarded as the starting event for nanostructures to enter biological systems. Understanding their interactions is thus essential for a newly emerging field, nanomedicine. Chemically converted graphene (CCG) is a wonderful two-dimensional (2D) material for nanomedicine, but its stability in biological environments is limited. Systematic probing on the binding of proteins to CCG is currently lacking. Herein, we report a comprehensive study on the interactions between blood proteins and stabilized CCG (sCCG). CCG nanosheets are functionalized by monolayers of perylene leading to significant improvement in their resistance to electrolyte salts and long-term stability, but retain their core structural characteristics. Five types of model human blood proteins including human fibrinogen, γ-globulin, bovine serum albumin (BSA), insulin, and histone are tested. The main driving forces for blood protein binding involve the π-π interacations between the π-plane of sCCG and surface aromatic amonic acid (sAA) residues of proteins. Several key binding parameters including the binding amount, Hill coefficient, and binding constant are determined. Through a detailed analysis of key controlling factors, we conclude that the protein binding to sCCG is determined mainly by the protein size, the number, and the density of the sAA.

Dynamics of statistically confident particle sizes and concentrations in blood plasma obtained by the dynamic light scattering method.

The work is devoted to the study of sizes and concentrations of proteins, and their aggregates in blood plasma samples, using static and dynamic light scattering methods. A new approach is proposed based on multiple repetition of measurements of intensity size distribution and on counting the number of registrations of different sizes, which made it possible to obtain statistically confident particle sizes and concentrations in the blood plasma. It was revealed that statistically confident particle sizes in the blood plasma were stable during 30 h of observations, whereas the concentrations of particles of different sizes varied as a result of redistribution of material between them owing to the protein degradation processes.

Ex situ evaluation of the composition of protein corona of intravenously injected superparamagnetic nanoparticles in rats.

It is now well recognized that the surfaces of nanoparticles (NPs) are coated with biomolecules (e.g., proteins) in a biological medium. Although extensive reports have been published on the protein corona at the surface of NPs in vitro, there are very few on the in vivo protein corona. The main reason for having very poor information regarding the protein corona in vivo is that separation of NPs from the in vivo environment has not been possible by using available techniques. Knowledge of the in vivo protein corona could lead to better understanding and prediction of the fate of NPs in vivo. Here, by using the unique magnetic properties of superparamagnetic iron oxide NPs (SPIONs), NPs were extracted from rat sera after in vivo interaction with the rat's physiological system. More specifically, the in vivo protein coronas of polyvinyl-alcohol-coated SPIONs with various surface charges are defined. The compositions of the corona at the surface of various SPIONs and their effects on the biodistribution of SPIONs were examined and compared with the corona composition of particles incubated for the same time in rat serum.

Atomic force microscopy and analytical ultracentrifugation for probing nanomaterial protein interactions.

Upon contact with the human body, nanomaterials are known to interact with the physiological surroundings, especially with proteins. In this context, we explored analytical methods to provide biologically relevant information, in particular for manufactured nanomaterials as produced by the chemical industry. For this purpose, we selected two batches of SiO(2) nanoparticles as well as four batches of CeO(2) nanoparticles, each of comparably high chemical purity and similar physicochemical properties. Adsorption of serum proteins and bovine serum albumin (BSA) was quantified by SDS-PAGE in combination with densitometry and further investigated by atomic force microscopy (AFM) and analytical ultracentrifugation (AUC). The protein adsorption to SiO(2) nanoparticles was below the limit of detection, regardless of adjusting pH or osmolality to physiological conditions. In contrast, the four CeO(2) nanomaterials could be classified in two groups according to half-maximal protein adsorption. Measuring the work of adhesion and indention by AFM for the BSA-binding CeO(2) nanomaterials revealed the same classification, pointing to alterations in shape of the adsorbed protein. The same trend was also reflected in the agglomeration behavior/dispersibility of the four CeO(2) nanomaterials as revealed by AUC. We conclude that even small differences in physicochemical particle properties may nevertheless lead to differences in protein adsorption, possibly implicating a different disposition and other biological responses in the human body. Advanced analytical methods such as AFM and AUC may provide valuable additional information in this context.

Differential plasma protein binding to metal oxide nanoparticles.

Nanoparticles rapidly interact with the proteins present in biological fluids, such as blood. The proteins that are adsorbed onto the surface potentially dictate the biokinetics of the nanomaterials and their fate in vivo. Using nanoparticles with different sizes and surface characteristics, studies have reported the effects of physicochemical properties on the composition of adsorbed plasma proteins. However, to date, few studies have been conducted focusing on the nanoparticles that are commonly exposed to the general public, such as the metal oxides. Using previously established ultracentrifugation approaches, two-dimensional gel electrophoresis and mass spectrometry, the current study investigated the binding of human plasma proteins to commercially available titanium dioxide, silicon dioxide and zinc oxide nanoparticles. We found that, despite these particles having similar surface charges in buffer, they bound different plasma proteins. For TiO2, the shape of the nanoparticles was also an important determinant of protein binding. Agglomeration in water was observed for all of the nanoparticles and both TiO2 and ZnO further agglomerated in biological media. This led to an increase in the amount and number of different proteins bound to these nanoparticles. Proteins with important biological functions were identified, including immunoglobulins, lipoproteins, acute-phase proteins and proteins involved in complement pathways and coagulation. These results provide important insights into which human plasma proteins bind to particular metal oxide nanoparticles. Because protein absorption to nanoparticles may determine their interaction with cells and tissues in vivo, understanding how and why plasma proteins are adsorbed to these particles may be important for understanding their biological responses.

Characterization of granulations of calcium and apatite in serum as pleomorphic mineralo-protein complexes and as precursors of putative nanobacteria.

Calcium and apatite granulations are demonstrated here to form in both human and fetal bovine serum in response to the simple addition of either calcium or phosphate, or a combination of both. These granulations are shown to represent precipitating complexes of protein and hydroxyapatite (HAP) that display marked pleomorphism, appearing as round, laminated particles, spindles, and films. These same complexes can be found in normal untreated serum, albeit at much lower amounts, and appear to result from the progressive binding of serum proteins with apatite until reaching saturation, upon which the mineralo-protein complexes precipitate. Chemically and morphologically, these complexes are virtually identical to the so-called nanobacteria (NB) implicated in numerous diseases and considered unusual for their small size, pleomorphism, and the presence of HAP. Like NB, serum granulations can seed particles upon transfer to serum-free medium, and their main protein constituents include albumin, complement components 3 and 4A, fetuin-A, and apolipoproteins A1 and B100, as well as other calcium and apatite binding proteins found in the serum. However, these serum mineralo-protein complexes are formed from the direct chemical binding of inorganic and organic phases, bypassing the need for any biological processes, including the long cultivation in cell culture conditions deemed necessary for the demonstration of NB. Thus, these serum granulations may result from physiologically inherent processes that become amplified with calcium phosphate loading or when subjected to culturing in medium. They may be viewed as simple mineralo-protein complexes formed from the deployment of calcification-inhibitory pathways used by the body to cope with excess calcium phosphate so as to prevent unwarranted calcification. Rather than representing novel pathophysiological mechanisms or exotic lifeforms, these results indicate that the entities described earlier as NB most likely originate from calcium and apatite binding factors in the serum, presumably calcification inhibitors, that upon saturation, form seeds for HAP deposition and growth. These calcium granulations are similar to those found in organisms throughout nature and may represent the products of more general calcium regulation pathways involved in the control of calcium storage, retrieval, tissue deposition, and disposal.

Effect of blood and mucus on tympanostomy tube biofilm formation.

OBJECTIVES/HYPOTHESIS: Tympanostomy tube (TT) biofilm formation may lead to refractory otorrhea and occlusion. The aim of this study was to determine whether TT biofilm formation may be promoted by mucus or blood exposure. STUDY DESIGN: In vitro, controlled. METHODS: Fluoroplastic TTs were exposed to blood, mucoid effusion, or saline. Half were allowed to dry. TTs were cultured with Pseudomonas aeruginosa. After 4 days, gentamicin was added to kill planktonic bacteria. Biofilm formation was assessed by quantitative bacterial counts and scanning electron microscopy. RESULTS: Mucus pretreatment (dry and wet) did not increase biofilm formation. Both dry and wet blood exposure increased biofilm formation by bacterial counts (P < .0001). Biofilm formation was demonstrated by electron microscopy in all groups. CONCLUSIONS: P. aeruginosa biofilm formation on fluoroplastic TTs is enhanced by blood exposure. Care should be taken to minimize bleeding with TT placement to reduce the risk of biofilm formation.

An investigation of vibration-induced protein desorption mechanism using a micromachined membrane and PZT plate.

A micromachined vibrating membrane is used to remove adsorbed proteins on a surface. A lead zirconate titanate (PZT) composite (3 x 1 x 0.5 mm) is attached to a silicon membrane (2,000 x 500 x 3 microm) and vibrates in a flexural plate wave (FPW) mode with wavelength of 4,000/3 microm at a resonant frequency of 308 kHz. The surface charge on the membrane and fluid shear stress contribute in minimizing the protein adsorption on the SiO(2) surface. In vitro characterization shows that 57 +/- 10% of the adsorbed bovine serum albumin (BSA), 47 +/- 13% of the immunoglobulin G (IgG), and 55.3~59.2 +/- 8% of the proteins from blood plasma are effectively removed from the vibrating surface. A simulation study of the vibration-frequency spectrum and vibrating amplitude distribution matches well with the experimental data. Potentially, a microelectromechanical system (MEMS)-based vibrating membrane could be the tool to minimize biofouling of in vivo MEMS devices.

PVA-DNA cryogel membranes: characterization, swelling, and transport studies.

Double-stranded (ds) DNA from salmon testes has been incorporated into PVA hydrogels obtained by a technique of repeated freezing and thawing. The cryogels obtained are free of potential toxic species like chemical cross-linkers, and consequently, they can be used in pharmaceutical or medical applications. These cryogels show a good mechanical resistance and a white and opaque appearance caused by a heterogeneous porous structure. Encapsulated DNA molecules can be in a compacted or an extended conformation in the PVA matrix and can be controlled by tailoring the degree of crystallinity of the PVA network; this is supported by fluorescence microscopy and UV and FTIR spectroscopic studies. The two forms of encapsulated DNA were observed for different types of matrixes: an extended one in a more crystalline network and a globular one in a more amorphous one. Different associations of base pairs have also been observed. PVA cryogel crystallinity could be tailored by the cryogel contact with different salt solutions. Cryogel surface (scanning electron microscopy) and bulk morphology (porosimetry), swelling, DNA retention, and delivery kinetics have also been studied. All these investigations clearly show strong interactions between PVA and DNA.

Early stages of human plasma proteins adsorption probed by Atomic Force Microscope.

Atomic Force Microscope (AFM) as a surface characterization technique has offered a great impulse in the advance of biocompatible materials. In this study AFM was implemented for the investigation of the early stages of adsorption of two human plasma proteins on titanium and hydrogenated carbon biocompatible thin films. The plasma proteins that were used were Human Serum Albumin and Fibrinogen, two of the most important proteins in human plasma. The concentration of the protein solutions was the same as that in human plasma. As the examined samples were soft, non-contact AFM mode was used to avoid their destruction. In order for the early stages of protein adsorption to be assessed, small incubation times were applied. AFM measurements in liquid buffer were also carried out, allowing the observation of the protein behaviour in an environment much closer to their native one. In addition, there was an assessment of the adsorption mechanism of the proteins on the above-mentioned biomaterials.

Rhizopus oryzae fungus cells producing L(+)-lactic acid: kinetic and metabolic parameters of free and PVA-cryogel-entrapped mycelium.

Spores of the filamentous fungus Rhizopus oryzae were entrapped in macroporous poly(vinyl alcohol) cryogel (PVA-cryogel). To prepare immobilised biocatalyst capable of producing L(+)-lactic acid (LA), the fungus cells were cultivated inside the carrier beads. The growth parameters and metabolic activity of the suspended (free) and immobilised cells producing LA in a batch process were comparatively investigated. The immobilised cells possessed increased resistance to high concentrations of accumulated product and gave much higher yields of LA in the iterative working cycle than the free cells did. Detailed kinetic analysis of the changes in the intracellular adenosine triphosphate concentration, specific rate of growth, substrate consumption and LA production showed that the fungus cells entrapped in PVA-cryogel are more attractive for biotechnological applications compared to the free cells.

Preparation and characterization of novel biocompatible cryogels of poly (vinyl alcohol) and egg-albumin and their water sorption study.

Polyvinyl alcohol (PVA) and egg albumin are water-soluble, biocompatible and biodegradable polymers and have been widely employed in biomedical fields. In this paper, novel physically cross-linked hydrogels composed of poly (vinyl alcohol) and egg albumin were prepared by cyclic freezing/thawing processes of aqueous solutions containing PVA and egg albumin. The FTIR analysis of prepared cryogels indicated that egg albumin was successfully introduced into the formed hydrogel possibly via hydrogen bonds among hydroxyl groups, amide groups and amino groups present in PVA and egg albumin. The gels were also characterized thermally and morphologically by DSC and SEM-techniques, respectively. The prepared so called 'cryogels' were evaluated for their water uptake potential and influence of various factors such as chemical architecture of the spongy hydrogels, pH and temperature of the swelling bath were investigated on the degree of water sorption by the cryogels. The effect of salt solution and various simulated biological fluids on the swelling of cryogel was also studied. The in vitro biocompatibility of the prepared cryogel was also judged by methods such as protein (BSA) adsorption, blood clot formation and percentage hemolysis measurements.

Binding mitochondria to cryogel monoliths allows detection of proteins specifically released following permeability transition.

Following proapoptotic signals such as calcium-induced mitochondrial permeability transition or translocation of proapoptotic proteins, mitochondria induce cell death through release of apoptogenic proteins. The mechanism of release and the identity of the released proteins are currently debated. Earlier attempts at identification of the apoptogenic proteins have been hampered by a high nonspecific background. Our aim was to develop a novel method where background release was eliminated, allowing proteins specifically released from mitochondria following proapoptotic stimulation to be identified. Liver mitochondria were immobilized and washed on cryogel monoliths prior to induction of protein release (calcium or Bid/Bax). Immobilized mitochondria exhibited normal morphology and swelling response and retained respiratory activity. The released proteins were collected, concentrated, separated on polyacrylamide gels which were cut into pieces, trypsin-digested, and analyzed using liquid chromatography-tandem mass spectrometry. Control samples contained no protein, and stimulation with calcium and Bid/Bax resulted in identification of 68 and 82 proteins, respectively. We conclude that, in combination with the robust proteomic approach, immobilization on cryogel monoliths is a fruitful approach for studying specific protein release from isolated mitochondria. We propose that this method is a powerful tool to further characterize the role of mitochondria in cell death induction.

The 17A structure of the 420 kDa lobster clottable protein by single particle reconstruction from cryoelectron micrographs.

Crustaceans form clots by the rapid crosslinking of a hemolymph clottable protein (CP) to form long, branched polymers. Clotting limits hemolymph loss from wounds as well as playing a part in the innate immune response. CP is a 420 kDa homodimer with a large quantity of associated lipid, primarily the carotenoid pigment astaxanthin. The three-dimensional structure of CP from the lobster Panulirus interruptus has been determined to 17 A resolution by single particle reconstruction from electron micrographs of the protein embedded in vitreous ice. The most prominent feature of this structure is a large cavity spanning the length of the molecule, which is the likely lipid binding pocket. The EM structure has been used in a low resolution molecular replacement search with data from orthorhombic CP crystals, and a solution is presented which describes the crystal packing.

Biostability and biocompatibility of a surface-grafted phospholipid monolayer on a solid substrate.

We have previously demonstrated phosphorylcholine monolayer chemically grafted onto a methacryloyl-terminated solid substrate by in situ polymerization. The in situ polymerization was carried out at the interface between a pre-assembled acrylated phospholipid monolayer produced by vesicle fusion and a methacryloyl-terminated substrate using a water-soluble initiator, 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPD). Herein, we examined the biostability and biocompatibility of a surface-grafted phospholipid monolayer (poly-PC) on a methacryloyl-terminated substrate using a "wash off' test, in vitro protein adsorption and in vivo cage implantation for time intervals of 4, 7, 14 and 21 days, respectively. In order to compare the biostability and biocompatibility of phospholipid surfaces on solid substrates, we used two types of phospholipid surfaces: a physically adsorbed phospholipid monolayer (PC) and a poly-PC. Atomic force microscopy and water contact angle measurements indicated that the poly-PC surface was more stable in PBS, Triton X-100 and to EO gas sterilization than the PC surface. The adsorption of proteins such as albumin, fibrinogen, IgG and human plasma proteins on the poly-PC surfaces were significantly reduced, in vitro. Moreover, the poly-PC surface greatly reduced macrophage adhesion and the formation of foreign body giant cells, in vivo.

Competitive plasma protein adsorption onto fluorinated polyimide surfaces.

A series of fluorinated polyimides cured at different temperatures was prepared, and plasma protein adsorption and platelet adhesion onto the polyimide films were evaluated in vitro using scanning electron microscopy, a micro-bicinchoninic acid protein assay, and a gold-colloid-labeled immunoassay. In particular, we focused on competitive plasma protein adsorption onto polyimide film because elucidation of the competitive adsorption mechanism is needed for a good understanding of in vivo biocompatibility of polyimide. Interestingly, the trend of IgG adsorption onto the polyimide surface measured in human plasma was completely contrary to that observed with IgG dissolved in PBS, and the adsorption increased with an increase in the curing temperature. We propose that the human plasma F(c) region in IgG might selectively adsorb onto polyimide film cured at high temperatures because of competitive plasma protein adsorption to the surface.

Isolation and characterization of haemoporin, an abundant haemolymph protein from Aplysia californica.

In the present study, we show the isolation and characterization of the protein haemoporin, which constitutes the second most abundant protein fraction in the haemolymph of the marine gastropod Aplysia californica. Although Aplysia is commonly used to investigate the molecular basis of learning, not much is known about the proteins in its haemolymph, which is in contact with the neurons owing to the open circulatory system of molluscs. In the native state, haemoporin is a macromolecular complex forming a cylinder with a central solvent-filled pore. The native complex most probably is a homopentamer made up from 70 kDa subunits with a molecular mass of 360 kDa and a sedimentation coefficient of 11.7 S. Prediction of the secondary structure by CD spectroscopy revealed that haemoporin contains 36% alpha-helices and 19% beta-strands. An absorption band in the 300-400 nm region indicates that haemoporin probably contains a bound substance. Haemoporin also contains a below average amount of tryptophan as evident from absorption and fluorescence spectra. The specific absorption coefficient at 280 nm (a (280 nm, 1 mg/ml)) varies between 0.42 and 0.59 l x g(-1) x cm(-1) depending on the method. The function of the protein is not yet known, but there are structural parallels between haemoporin and a pore protein reported previously in the haemolymph of another marine gastropod Megathura crenulata. The alanine-rich N-terminal sequence (AAVPEAAAEATAEAAPVSEF) is unique among protein sequences and indicates an alpha-helical structure. Whereas one side of the helix is hydrophobic and faces the interior of the protein, the other side contains a glutamic cluster, which may form the channel of the pore in the quaternary structure. Thus both proteins might belong to a new class of haemolymph proteins present in the haemolymph of marine gastropods.

Molecular basis of non-self recognition by the horseshoe crab tachylectins.

The self/non-self discrimination by innate immunity through simple ligands universally expressed both on pathogens and hosts, such as monosaccharides and acetyl group, depends on the density or clustering patterns of the ligands. The specific recognition by the horseshoe crab tachylectins with a propeller-like fold or a propeller-like oligomeric arrangement is reinforced by the short distance between the individual binding sites that interact with pathogen-associated molecular patterns (PAMPs). There is virtually no conformational change in the main or side chains of tachylectins upon binding with the ligands. This low structural flexibility of the propeller structures must be very important for specific interaction with PAMPs. Mammalian lectins, such as mannose-binding lectin and ficolins, trigger complement activation through the lectin pathway in the form of opsonins. However, tachylectins have no effector collagenous domains and no lectin-associated serine proteases found in the mammalian lectins. Furthermore, no complement-like proteins have been found in horseshoe crabs, except for alpha(2)-macroglobulin. The mystery of the molecular mechanism of the scavenging pathway of pathogens in horseshoe crabs remains to be solved.

Structural conversion between open and closed forms of radixin: low-angle shadowing electron microscopy.

The function of ERM (ezrin/radixin/moesin) proteins as general cross-linkers between actin filaments and plasma membranes is regulated downstream of Rho, through the transition between active and inactive forms. To directly examine the conformational change between the active and inactive forms of ERM proteins, we applied low-angle rotary-shadowing electron microscopy to the radixin molecules, wild-type, T564A-non-phosphorylated-type, and T564E-phosphorylated-type, since most of the active forms are reportedly stabilized in cells by the C-terminal threonine phosphorylation. As a result, the T564A- and wild-type radixin molecules yielded the globular closed forms, approximately 8-14 nm in diameter, with some striations on their surfaces. In contrast, the T564E-radixin molecules tended to take elongated open forms, in which two globular structures measuring approximately 8 nm and approximately 5 nm in diameter were associated with both ends of the filamentous structures. The filamentous structure took either a approximately 20-25 nm-long straight course or a folded course. Taken together with the biochemical and the crystal structural results obtained to date, the closed and open forms represent the inactive and active forms of radixin as cross-linkers between actin filaments and plasma membranes.