Harnessing self-assembled peptide nanoparticles in epitope vaccine design

Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.     

Immune plexins and semaphorins: old proteins,new immune functions

Plexins and semaphorins are a large family of proteins that are involved in cell movement and response. The importance of plexins and semaphorins has been emphasized by their discovery in many organ systems including the nervous (Nkyimbeng-Takwi and Chapoval, 2011; McCormick and Leipzig, 2012; Yaron and Sprinzak, 2012), epithelial (Miao et al., 1999; Fujii et al., 2002), and immune systems (Takamatsu and Kumanogoh, 2012) as well as diverse cell processes including angiogenesis (Serini et al., 2009; Sakurai et al., 2012), embryogenesis (Perala et al., 2012), and cancer (Potiron et al., 2009; Micucci et al., 2010). Plexins and semaphorins are transmembrane proteins that share a conserved extracellular semaphorin domain (Hota and Buck, 2012). The plexins and semaphorins are divided into four and eight subfamilies respectively based on their structural homology. Semaphorins are relatively small proteins containing the extracellular semaphorin domain and short intracellular tails. Plexins contain the semaphorin domain and long intracellular tails (Hota and Buck, 2012). The majority of plexin and semaphorin research has focused on the nervous system, particularly the developing nervous system, where these proteins are found to mediate many common neuronal cell processes including cell movement, cytoskeletal rearrangement, and signal transduction (Choi et al., 2008; Takamatsu et al., 2010). Their roles in the immune system are the focus of this review.     

Detection of Tomato Ringspot Nepovirus and a Clostero-like Virus in French Hybrid Vidal 256 Grapevines

Eight- to ten-year old French hybrid Vidal 256 grapevines in southern Maryland produced berries about one-third normal size but did not express any obvious leaf symptoms. Electron microscopy of negatively stained tissue-dip preparations and sectioned material from such vines showed individual and membrane-associated 28 nm spherical virus-like particles and closteroviruslike particles. The spherical particles were characterized as an isolate of tomato ringspot virus (TomRSV-G) that infected a wide range of herbaceous hosts by mechanical inoculation, but did not infect tomato, bean or petunia plants susceptible to the type strain of TomRSV. The closterovirus-like particles did not react, by immunosorbent electron microscopy, with antisera to grapevine virus A (grapevine stem-pitting associated virus of Conti et al. 1980) or the 2200 nm Swiss grapevine leafroll closterovirus (Gugleri et al. 1984).     

Analysis of particle trajectories in aortic artery bifurcations with stenosis

The fluid-particle dynamics in a two-dimensonal symmetric branching channel with local occlusions representing a diseased segment of an aortic artery bifurcation has been analyzed. The validated finite element model simulates the trajectories and landing or impact sites of spherical particles for laminar flow in bifurcation channels with generalized wall conditions. Two hypotheses relating critical wall shear stress levels and plaque formation, previously postulated by Kleinstreuer et al. (1988) and Nazemi et al. (1989), have been confirmed. Low shear stress may contribute to the onset of atherosclerotic lesions and areas of critically low and higher shear stresses are susceptible to accelerated growth of plaque.     

Single-molecule 3D imaging of human plasma intermediate-density lipoproteins reveals a polyhedral structure

Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite pharmacological interest in IDLs, their three-dimensional (3D) structure is still undetermined due to their variation in size, composition, and dynamic structure. To explore the 3D structure of IDLs, we reconstructed 3D density maps from individual IDL particles using cryo-electron microscopy (cryo-EM) and individual-particle electron tomography (IPET, without averaging from different molecules). 3D reconstructions of IDLs revealed an unexpected polyhedral structure that deviates from the generally assumed spherical shape model (Frias et al., 2007; Olson, 1998; Shen et al., 1977). The polyhedral-shaped IDL contains a high-density shell formed by flat surfaces that are similar to those of very-low-density lipoproteins but have sharper dihedral angles between nearby surfaces. These flat surfaces would be less hydrophobic than the curved surface of mature spherical high-density lipoprotein (HDL), leading to a lower binding affinity of IDL to hydrophobic proteins (such as cholesteryl ester transfer protein) than HDL. This is the first visualization of the IDL 3D structure, which could provide fundamental clues for delineating the role of IDL in lipid metabolism and cardiovascular disease.     

Virulence factors in Bacillus thuringiensis: purification and properties of a protein inhibitor of immunity in insects.

We have previously shown that Bacillus thuringiensis subsp. alesti, serotype 3, produces two extracellular inhibitors of the immune system of Saturniid pupae (designated inhibitors A and B; Edlund et al., 1976). Starting from the culture supernatant of a new mutant of B. thuringiensis with a decreased extracellular proteolytic activity, we have now purified immune inhibitor A(InA). The procedure described consists of three steps: ultrafiltration, precipitation with ammonium sulphate and chromatography on hydroxylapatite. Purified InA gave a single band on polyacrylamide gel electrophoresis using either a gel concentration of 7.5% (w/v) and reducing and denaturing conditions or a gradient gel and native conditions. In both cases the apparent molecular weight was 78 000. A certain amount of proteolytic activity was always co-purified with InA but the two activities could be dissociated by heat or EDTA treatment. Antiserum against purified InA gave only one sharp precipitation band on immunodiffusion against InA with or without EDTA. InA inhibited the in vitro killing of Escherichia coli by immune haemolymph but did not affect the killing of Bacillus subtilis. InA was toxic for Drosophila when injected into the abdomen of adult male flies.     

Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis

Heterosis,one of the most important biological phenomena,refers to the phenotypic superiority of a hybrid over its genetically diverse parents with respect to many traits such as biomass,growth rate and yield.Despite its successful application in breeding and agronomic production of many crop and animal varieties,the molecular basis of heterosis remains elusive.The classic genetic explanations for heterosis centered on three hypotheses:dominance (Davenport,1908;Bruce,1910;Keeble and Pellew,1910;Jones,1917),overdominance (East,1908;Shull,1908) and epistasis (Powers,1944;Yu et al.,1997).However,these hypotheses are largely conceptual and not connected to molecular principles,and are therefore insufficient to explain the molecular basis of heterosis (Birchler et al.,2003).Recently,many studies have explored the molecular mechanism of heterosis in plants at a genome-wide level.These studies suggest that global differential gene expression between hybrids and parental lines potentially contributes to heterosis in plants (e.g.,Swanson-Wagner et al.,2006;Zhang et al.,2008;Wei et al.,2009;Song et al.,2010).Research suggests that genetic components,including cis-acting elements and trans-acting factors,are critical regulators of differential gene expression in hybrids (Hochholdinger and Hoecker,2007;Springer and Stupar,2007;Zhang et al.,2008).However,other research indicates that epigenetic components,the regulators of chromatin states and genome activity,also have the potential to impact heterosis (e.g.,Ha et al.,2009;He et al.,2010;Groszmann et al.,2011;Barber et al.,2012;Chodavarapu et al.,2012;Greaves et al.,2012a;Shen et al.,2012).     

Expansion of Polyfunctional HIV-Specific T Cells upon Stimulation with mRNA Electroporated Dendritic Cells in the Presence of Immunomodulatory Drugs

Recently, it has been demonstrated that disease progression during HIV infection is not determined merely by the number of HIV-specific T cells but also by their quality (J. R. Almeida, et al., J. Exp. Med. 204:2473-2485, 2007; C. T. Berger, et al., J. Virol. 85:9334-9345, 2011; M. R. Betts, et al., Blood 107:4781-4789, 2006; V. V. Ganusov, et al., J. Virol. 85:10518-10528, 2011; P. Kiepiela, et al., Nat. Med. 13:46-53, 2007; and F. Pereyra, et al., J. Infect. Dis. 197:563-571, 2008). Therefore, strategies to specifically enhance or induce high-quality, HIV-specific T-cell responses are necessary to develop effective immune therapies. Thalidomide, lenalidomide, and pomalidomide have a strong capacity to boost immune responses and are therefore referred to as immunomodulatory drugs (IMiDs). We evaluated the effects of lenalidomide and pomalidomide on HIV-specific T cells. We found that the presence of IMiDs during in vitro T-cell stimulation with dendritic cells electroporated with Gag- or Nef-encoding mRNA resulted in higher numbers of cytokine-secreting HIV-specific CD8(+) T cells, particularly inducing polyfunctional HIV-specific CD8(+) T cells with an enhanced lytic capacity. Furthermore, CD8(+) T-cell responses were detected upon stimulation with lower antigenic peptide concentrations, and a higher number of Gag epitopes was recognized upon addition of IMiDs. Finally, IMiDs reduced the proliferation of the HIV-specific CD4(+) T cells while increasing the number of polyfunctional CD4(+) T cells. These results provide new information about the effects of IMiDs on antigen-specific T cells and suggest that these drugs increase the efficacy of immune therapies for infectious diseases and cancer.     

177 T-cell vaccine design for Streptococcus pneumoniae: an in silico approach

Streptococcus pneumoniae (pneumococcus) remains an important cause of meningitis, bacteremia, acute otitis media, community acquired pneumonia associated with significant morbidity, and mortality world wide. Conjugated polysaccharide, glycoconjugated, and capsular polysaccharide based vaccines were existent for pneumococcal disease but are still specific and restricted to serotypes of S. pneumoniae. Proteome of eight serotypes of S. pneumoniae was retrieved and identified in common proteins (Munikumar et al., 2012). 18 membrane proteins were distinguished from 1657 common proteins of eight serotypes of S. pneumoniae. Implementing comparative genomic approach and subtractive genomic approach, three membrane proteins were predicted as essential for bacterial survival and non-homologous to human (Munikumar et al., 2012; Umamaheswari et al., 2011). ProPred server was used to propose four promiscuous T-cell epitopes from three membrane proteins and validated through published positive control, SYFPEITHI and immune epitope database (Munikumar et al., in press). The four epitopes docked into peptide binding region of predominant HLA-DRB alleles with good binding affinity in Maestro v9.2. The T-cell epitope 89-VVYLLPILI-97 and HLA-DRB5^?0101 docking complex was with best XPG score (?13.143?kcal/mol). Further, the stability of the complex was checked through molecular dynamics simulations in Desmond v3.3. The simulation results had revealed that the complex was stable throughout 5000?ps (Munikumar et al., in press). Thus, the epitope would be the ideal candidate for T-cell driven subunit vaccine design against selected serotypes of S. pneumoniae.     

Maternal and fetal antibrain antibodies in development and disease

Recent evidence has emerged indicating that the maternal immune response can have a substantial deleterious impact on prenatal development (Croen et al., [2008]: Biol Psychiatry 64:583-588). The maternal immune response is largely sequestered from the fetus. Maternal antibodies, specifically immunoglobulin G (IgG), are passed to the fetus to provide passive immunity throughout much of pregnancy. However, both protective and pathogenic autoantibodies have equal access to the fetus (Goines and Van de Water [2010]: Curr Opin Neurol 23:111-117). If the mother has an underlying autoimmune disease or has reactivity to fetal antigens, autoantibodies produced before or during pregnancy can target tissues in the developing fetus. One such tissue is the fetal brain. The blood brainbarrier (BBB) is developing during the fetal period allowing maternal antibodies to have direct access to the brain during gestation (Diamond et al. [2009]: Nat Rev Immunol; Braunschweig et al. [2011]; Neurotoxicology 29:226-231). It has been proposed that brain injury by circulating brain-specific maternal autoantibodies might underlie multiple congenital, developmental disorders (Lee et al. [2009]: Nat Med 15:91-96). In this review, we will discuss the current state of research in the area of maternal autoantibodies and the development of autism. ? 2012 Wiley Periodicals, Inc. Develop Neurobiol, 2012.     

十种海洋寡毛类纤毛虫:形态学及分类学修订

利用活体观察和蛋白银染色技术对近年来采自青岛、大亚湾、湛江沿岸水体的10个海洋寡毛类纤毛虫种:侧扁急游虫Strombidium apolatum Wilbert & Song,2005、具头急游虫Strombidium capitatum (Leegaard,1995) Kahl,1932、广东急游虫Strombidium guangdongense Liu,et al.,2016、拟卡氏急游虫Strombidiumparacalkinsi (Lei,et al.,1999) Agatha,2004、拟楔尾急游虫Strombidium parastylifer Song,et al.,2009、铃木急游虫Strombidium suzukii Song,et al.,2009、束腰旋游虫Spirostrombidium cinctum (Kahl,1932) Petz,et al.,1995、杨科夫平游虫Parallelostrombidium jankowski (Song,et al.,2009) Song,et al.,2018、卡尔平游虫Parallelostrombidium kahli (Song,et al.,2009) Song,et al.,2018、最小拟盗虫Strombidinopsis minima (Gruber,1884) Song & Bradbury,1998的形态学开展了比较研究,补充和厘定了有关形态特征、纤毛图式以及性状变异等分类学新信息。     

ATP-dependent chromatin remodeling complex SWI/SNF in cardiogenesis and cardiac progenitor cell development

The recent identification of cardiac progenitor cells (CPCs) provides a new paradigm for studying and treating heart disease.To realize the full potential of CPCs for therapeutic purposes,it is essenti...     

"Hydration memory" of lysozyme: a misinterpretation

The effects of sugars and similar additives on the catalytic activity of lysozyme have been attributed (Laretta-Garde et al., Biochim. Biophys. Res. Commun. 155: 816-822 (1988] to a "hydration memory" of the protein for solution conditions to which it was previously exposed. By measuring catalytic activity versus substrate concentration, tryptophan fluorescence and near ultraviolet circular dichroism all in the presence and absence of 50% (w/v) sucrose, we show that the effects can be explained, instead, on the basis of well known properties of proteins.     

Centromere Epigenetics in Plants

The centromere is an essential chromosome site at which the kinetochore forms and loads proteins needed for faithful segregation during the cell cycle and meiosis(Houben et al., 1999;Cleveland et al.,2003;Ma et al.,2007;Birchler and Han,2009).Centromere specific sequences such as tandem repeats or transposable elements evolve quickly both within and between the species but have conserved kinetochore proteins(Henikoff and Furuyama,2010).The universal feature     

Space radiation enhancement linked to geomagnetic disturbances.

Space radiation dosimetry measurements have been made on board the Space Shuttle. A newly developed active detector called "Real-time Radiation Monitoring Device (RRMD)" was used (Doke et al., 1995; Hayashi et al., 1995). The RRMD results indicate that low Linear Energy Transfer (LET) particles steadily penetrate around the South Atlantic Anomaly (SAA) without clear enhancement of dose equivalent and some daily periodic enhancements of dose equivalent due to high LET particles are seen at the lower geomagnetic cutoff regions (Doke et al., 1996). We also have been analyzing the space weather during the experiment, and found that the anomalous high-energy particle enhancement was linked to geomagnetic disturbance due to the high speed solar wind from a coronal hole. Additional analysis and other experiments are necessary for clarification of these phenomena. If a penetration of high-energy particles into the low altitude occurs by common geomagnetic disturbances, the prediction of geomagnetic activity becomes more important in the next Space Station's era.     

Sequence-specific 1H assignment and secondary structure of the bacteriocin AS-48 cyclic peptide

The bacteriocin AS-48 is a cationic peptide (7149 Da) having a broad antimicrobial spectrum, encoded by the 68 kb conjugative plasmid pMB2 from Enterococcus faecalis S-48. It is a unique peptide since it has a cyclic structure, which is achieved by the formation of a tail–head peptide bond after ribosomal synthesis (Gálvez et al., 1989; Martínez-Bueno et al., 1994; Samyn et al., 1994). Preliminary CD and calorimetric studies (data not shown) pointed towards a highly helical and very stable three dimensional structure.All the information gathered until now indicates that the target of AS-48 is the cytoplasmic membrane in which it opens channels or pores, leading to dissipation of the proton motive force and cell death, which in some cases is also followed by bacterial lysis (Gálvez et al., 1991). This peptide is a suitable tool for studying protein–membrane interactions, and it also offers promising perspectives for biotechnological applications.Knowledge of the 3D structure of AS-48 is a first step in the conduct of further structure–function studies. Here we report the complete¹ H NMR assignment of its proton resonances together with the resulting secondary structure pattern as prerequisites for the determination of a high-resolution 3D solution structure.     

NACOB presentation to ASB Young Scientist Award: Postdoctoral. The impact of boundary conditions and mesh size on the accuracy of cancellous bone tissue modulus determination using large-scale finite-element modeling. North American Congress on Biomechanics.

The apparent properties of cancellous bone are determined by a combination of both hard tissue properties and microstructural organization. A method is desired to extract the underlying hard tissue properties from simple mechanical tests, free from the complications of microstructure. It has been suggested that microCT voxel-based large-scale finite element models could be employed to accomplish this goal (van Rietbergen et al., 1995, Journal of Biomechanics, 28, 69-81). This approach has recently been implemented and it is becoming increasingly popular as finite element models increase in size and sophistication (Fyhrie et al., 1997, Proceedings of the 43rd Annual Meeting of the Orthopaedic Research Society, San Francisco, CA, p. 815; van Rietbergen et al., 1997, Proceedings of the 43rd Annual Meeting of the Orthopaedic Research Society, San Francisco, CA, p. 62). However, no direct quantitative measurements of the accuracy of this method applied to porous structures such as cancellous bone have been made. This project demonstrates the feasibility of this approach by quantifying its best-case accuracy in determining the trabecular hard tissue modulus of analogues fabricated of a material with known material properties determined independently by direct testing. In addition we were able to assess the impact of mesh size and boundary conditions on accuracy. We found that the assumption of a frictionless boundary condition in the parallel plate compression loading configuration was a significant source of error that could be overcome with the use of rigid end-caps similar to those used by Keaveny et al. (1997 Journal of Orthopaedic Research, 15(1), 101-110). In conclusion, we found that this approach is an effective method for determining the average trabecular hard tissue properties of human cancellous bone with an expected practical accuracy level better than 5%.     

Role of ICAM-3 in Intercellular Adhesion and Activation of T Lymphocytes

The immune system requires a fine regulation of intercellular communication for its normal function. There are several regulated molecular pathways involved in leukocyte cell interactions (Springer, 1990; Hynes, 1992). Among them, the interaction of the leukocyte integrin LFA-1 (CDlla/CD18) with its ligands provides multiple accessory adhesion signals of capital importance during different functions of the immune response, such as antigen presentation (Harding and Unanue, 1991), T-B lymphocyte interaction (Moy and Brian, 1992), cellular cytotoxicity (Makgoba et al., 1988; Altmann et al., 1989; Davignon et al, 1981; Akella and Hall, 1992), allogenic and autologous mixed lymphocyte reactions (Bagnasco et al., 1990) and recirculation and homing of lymphocytes through tissue endothelium (Hamann et al., 1988; Pals et al, 1988).