Identification of myosin heavy chain isoforms in porcine longissimus dorsi muscle by electrophoresis and mass spectrometry

Myosin heavy chain (MHC) isoforms have been considered as makers for muscle fiber types in relation to meat quality, whereas MHC isoforms in porcine skeletal muscle have not been fully identified. The improved technique of SDS‐PAGE and 2DE were used to separate porcine MHC isoforms. Western blotting with monoclonal antibodies including BA‐F8 (anti‐MHC slow/I), SC‐71 (anti‐MHC 2a and 2x), 10F5 (anti‐MHC 2b), and BF‐35 (anti‐MHC slow/I and 2a) and MS were used to confirm MHC migration rate and identify MHC isoforms from separated bands and spots. Up to 45% w/v of glycerol, 8% w/v of acrylamide content, and 25 h of electrophoretic time at 70 V allowed a clear separation of MHC isoforms. Major MHC isoforms such as slow, 2a, 2x, and 2b were clearly separated by SDS‐PAGE. A total of 23 MHC spots were separated and identified by 2DE and MS. Therefore, four MHC isoforms such as slow/I, 2a, 2x, and 2b could be identified by the improved SDS‐PAGEtechnique, 2DE and MS. Therefore, these techniques allow more accurate and accessible analysis in muscle fiber typing and in relationship between MHC isoforms, muscle fiber characteristics, and pork quality.     

Complex Formation between the Lumenal Domain of Adenovirus E3–19k Protein and the Extracellular Domain of Class I MHC Molecule In Vitro

The Ad2 E3–19k protein inhibits the transport of newly synthesized class I MHC molecules to the cell surface, thereby interfering with antigen presentation. The details of the interaction between E3–19k protein and class I MHC molecules have not been well‐defined. In this present study, we describe the use of gel filtration HPLC for confirming the binding interaction of two domain proteins, E3–19k and MHC class I antigen, and subsequently the characterization of protein complex by SDS‐PAGE. Our results demonstrate the complex formation between Ad2 lumenal E3–19k (108 amino acids, wt 108) and HLA‐A*0201 molecule in vitro. Titration experiments will be employed in the future to determine stoichiometry and verify the specific interactions.     

Microfluidic biofunctionalisation protocols to form multi‐valent interactions for cell rolling and phenotype modification investigations

In this study, we propose a fast, simple method to biofunctionalise microfluidic systems for cellomic investigations based on micro‐fluidic protocols. Many available processes either require expensive and time‐consuming protocols or are incompatible with the fabrication of microfluidic systems. Our method differs from the existing since it is applicable to an assembled system, uses few microlitres of reagents and it is based on the use of microbeads. The microbeads have specific surface moieties to link the biomolecules and couple cell receptors. Furthermore, the microbeads serve as arm spacer and offer the benefit of the multi‐valent interaction. Microfluidics was adapted together with topology and biochemistry surface modifications to offer the microenvironment for cellomic studies. Based on this principle, we exploit the streptavidin–biotin interaction to couple antibodies to the biofunctionalised microfluidic environment within 5 h using 200 μL of reagents and biomolecules. We selected the antibodies able to form complexes with the MHC class I (MHC‐I) molecules present on the cell membrane and involved in the immune surveillance. To test the microfluidic system, tumour cell lines (RMA) were rolled across the coupled antibodies to recognise and strip MHC‐I molecules. As result, we show that cell rolling performed inside a microfluidic chamber functionalised with beads and the opportune antibody facilitate the removal of MHC class I molecules. We showed that the level of median fluorescent intensity of the MHC‐I molecules is 300 for cells treated in a not biofunctionalised surface. It decreased to 275 for cells treated in a flat biofunctionalised surface and to 250 for cells treated on a surface where biofunctionalised microbeads were immobilised. The cells with reduced expression of MHC‐I molecules showed, after cytotoxicity tests, susceptibility 3.5 times higher than normal cells.     

Simultaneous analysis of multiple PCR amplicons enhances capillary SSCP discrimination of MHC alleles

Major histocompatibility complex (MHC) genotyping still remains one of the most challenging issues for evolutionary ecologists. To date, none of the proposed methods have proven to be perfect, and all provide both important pros and cons. Although denaturing capillary electrophoresis has become a popular alternative, allele identification commonly relies upon conformational polymorphisms of two single‐stranded DNA molecules at the most. Using the MHC class II (β chain, exon 2) of the black kite (Aves: Accipitridae) as our model system, we show that the simultaneous analysis of overlapping PCR amplicons from the same target region substantially enhances allele discrimination. To cover this aim, we designed a multiplex PCR capable to generate four differentially sized and labeled amplicons from the same allele. Informative peaks to assist allele calling then fourfold those generated by the analysis of single PCR amplicons. Our approach proved successful to differentiate all the alleles (N=13) isolated from eight unrelated birds at a single optimal run temperature and electrophoretic conditions. In particular, we emphasize that this approach may constitute a straightforward and cost‐effective alternative for the genotyping of single or duplicated MHC genes displaying low to moderate sets of divergent alleles.     

Fabrication of graphene‐silver/polyurethane nanofibrous scaffolds for cardiac tissue engineering

The graphene‐based nanocomposites are considered as great candidates for enhancing electrical and mechanical properties of nonconductive scaffolds in cardiac tissue engineering. In this study, reduced graphene oxide‐silver (rGO‐Ag) nanocomposites (1 and 2 wt%) were synthesized and incorporated into polyurethane (PU) nanofibers via electrospinning technique. Next, the human cardiac progenitor cells (hCPCs) were seed on these scaffolds for in vitro studies. The rGO‐Ag nanocomposites were studied by X‐ray diffraction (XRD), Raman spectroscopy, and transmission electron microscope (TEM). After incorporation of rGO‐Ag into PU nanofibers, the related characterizations were carried out including scanning electron microscope (SEM), TEM, water contact angle, and mechanical properties. Furthermore, PU and PU/nanocomposites scaffolds were used for in vitro studies, wherein hCPCs showed good cytocompatibility via 3‐(4, 5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide (MTT) assay and considerable attachment on the scaffold using SEM studies. Real‐time polymerase chain reaction (PCR) and immunostaining studies confirmed the upregulation of cardiac specific genes including GATA‐4, T‐box 18 (TBX 18), cardiac troponin T (cTnT), and alpha‐myosin heavy chain (α‐MHC) in the PU/rGO‐Ag scaffolds in comparison with neat PU ones. Therefore, these nanofibrous rGO‐Ag–reinforced PU scaffolds can be considered as suitable candidates in cardiac tissue engineering.     

In silico identification of outer membrane protein (Omp) and subunit vaccine design against pathogenic Vibrio cholerae

Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26 mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31 mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds. Further, the selected antigenic sequences (having B-cell epitopes) were analyzed for T-cell epitopes (MHC I and MHC II alleles binding sequence) by using ProPred 1 and ProPred respectively. The epitope (9 mer: YKSISPQDA) that binds to both the MHC classes (MHC I and MHC II) and covers maximum MHC alleles were identified. The identified epitopes can be useful in designing comprehensive peptide vaccine development against V. cholerae by inducing optimal immune response.     

In silico designing breast cancer peptide vaccine for binding to MHC class I and II: A molecular docking study

Antigenic peptides or cancer peptide vaccines can be directly delivered to cancer patients to produce immunologic responses against cancer cells. Specifically, designed peptides can associate with Major Histocompatibility Complex (MHC) class I or II molecules on the cell surface of antigen presenting cells activating anti-tumor effector mechanisms by triggering helper T cell (Th) or cytotoxic T cells (CTL). In general, high binding to MHCs approximately correlates with in vivo immunogenicity. Consequently, a molecular docking technique was run on a library of novel discontinuous peptides predicted by PEPOP from Human epidermal growth factor receptor 2 (HER2 ECD) subdomain III. This technique is expected to improve the prediction accuracy in order to identify the best MHC class I and II binder peptides. Molecular docking analysis through GOLD identified the peptide 1412 as the best MHC binder peptide to both MHC class I and II molecules used in the study. The GOLD results predicted HLA-DR4, HLA-DP2 and TCR as the most often targeted receptors by the peptide 1412. These findings, based on bioinformatics analyses, can be exploited in further experimental analyses in vaccine design and cancer therapy to find possible proper approaches providing beneficial effects.     

Bioorthogonal Deprotection on the Dendritic Cell Surface for Chemical Control of Antigen Cross‐Presentation

The activation of CD8⁺ T‐cells requires the uptake of exogenous polypeptide antigens and proteolytic processing of these antigens to octamer or nonamer peptides, which are loaded on MHC‐I complexes and presented to the T‐cell. By using an azide as a bioorthogonal protecting group rather than as a ligation handle, masked antigens were generated—antigens that are not recognized by their cognate T‐cell unless they are deprotected on the cell using a Staudinger reduction.     

Recovery of known T-cell epitopes by computational scanning of a viral genome

A new computational method (EpiDock) is proposed for predicting peptide binding to class I MHC proteins, from the amino acid sequence of any protein of immunological interest. Starting from the primary structure of the target protein, individual three-dimensional structures of all possible MHC-peptide (8-, 9- and 10-mers) complexes are obtained by homology modelling. A free energy scoring function (Fresno) is then used to predict the absolute binding free energy of all possible peptides to the class I MHC restriction protein. Assuming that immunodominant epitopes are usually found among the top MHC binders, the method can thus be applied to predict the location of immunogenic peptides on the sequence of the protein target. When applied to the prediction of HLA-A^*0201-restricted T-cell epitopes from the Hepatitis B virus, EpiDock was able to recover 92% of known high affinity binders and 80% of known epitopes within a filtered subset of all possible nonapeptides corresponding to about one tenth of the full theoretical list.The proposed method is fully automated and fast enough to scan a viral genome in less than an hour on a parallel computing architecture. As it requires very few starting experimental data, EpiDock can be used: (i) to predict potential T-cell epitopes from viral genomes (ii) to roughly predict still unknown peptide binding motifs for novel class I MHC alleles.     

Incorporation of two‐dimensional nanomaterials into silk fibroin nanofibers for cardiac tissue engineering

Mimicking the extracellular matrix to have a similar nanofibrous structure regarding electrical conductivity and mechanical properties would be highly beneficial for cardiac tissue engineering. The molybdenum disulfide, MoS₂, and reduced graphene oxide, rGO, nanosheets are two‐dimensional nanomaterials which can be considered as great candidates for enhancing the electrical and mechanical properties of biological scaffolds for cardiac tissue engineering applications. In this study, MoS₂ and rGO nanosheets were synthesized and incorporated into silk fibroin nanofibers, SF, via electrospinning method. Then, the human iPSCs transfected with TBX‐18 gene, TBX18‐hiPSCs, were seeded on these scaffolds for in vitro studies. The MoS₂ and rGO nanosheets were studied by Raman spectroscopy. After incorporation of the nanosheets into SF nanofibers, the associated characterizations were carried out including scanning electron microscopy, transmission electron microscopy, water contact angle, and mechanical test. Furthermore, SF, SF/MoS₂, and SF/rGO scaffolds were used for in vitro studies. Herein, the scaffolds exhibited acceptable biocompatibility and considerable attachment to TBX18‐hiPSCs confirmed by 3‐(4, 5‐dimethylthiazol‐2‐yl)‐2, 5‐diphenyl tetrazolium bromide, MTT, assay, and scanning electron microscopy. Also, the real‐time PCR and immunostaining studies confirmed the maturity and upregulation of cardiac functional genes, including GATA‐4, c‐TnT, and α‐MHC in the SF/MoS₂ and SF/rGO scaffolds compared with the bare SF one. Therefore, the reinforcement of these SF‐based scaffolds with MoS₂ and rGO endues them as a suitable candidate for cardiac tissue engineering.     

Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach

Peptides bound to MHC molecules on the surface of cells convey critical information about the cellular milieu to immune system T cells. Predicting which peptides can bind an MHC molecule, and understanding their modes of binding, are important in order to design better diagnostic and therapeutic agents for infectious and autoimmune diseases. Due to the difficulty of obtaining sufficient experimental binding data for each human MHC molecule, computational modeling of MHC peptide-binding properties is necessary. This paper describes a computational combinatorial design approach to the prediction of peptides that bind an MHC molecule of known X-ray crystallographic or NMR-determined structure. The procedure uses chemical fragments as models for amino acid residues and produces a set of sequences for peptides predicted to bind in the MHC peptide-binding groove. The probabilities for specific amino acids occurring at each position of the peptide are calculated based on these sequences, and these probabilities show a good agreement with amino acid distributions derived from a MHC-binding peptide database. The method also enables prediction of the three-dimensional structure of MHC-peptide complexes. Docking, linking, and optimization procedures were performed with the XPLOR program [1].     

Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse‐grained molecular dynamics simulations with a weighted histogram analysis method

We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with the weighted histogram analysis method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse‐grained (CG) force field (MARTINI) is less prone to significant error induced by inadequate‐sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3–4 residue peptide segments while leaving the remaining peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and reliably estimate the binding free energy between an arbitrary peptide and an MHC class II molecule. © 2017 Wiley Periodicals, Inc.     

Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles

Major Histocompatibility Complex (MHC) is a cell surface glycoprotein that binds to foreign antigens and presents them to T lymphocyte cells on the surface of Antigen Presenting Cells (APCs) for appropriate immune recognition. Recently, studies focusing on peptide-based vaccine design have allowed a better understanding of peptide immunogenicity mechanisms, which is defined as the ability of a peptide to stimulate CTL-mediated immune response. Peptide immunogenicity is also known to be related to the stability of peptide-loaded MHC (pMHC) complex. In this study, ENCoM server was used for structure-based estimation of the impact of single point mutations on pMHC complex stabilities. For this purpose, two human MHC molecules from the HLA-B*27 group (HLA-B*27:05 and HLA-B*27:09) in complex with four different peptides (GRFAAAIAK, RRKWRRWHL, RRRWRRLTV and IRAAPPPLF) and three HLA-B*44 molecules (HLA-B*44:02, HLA-B*44:03 and HLA-B*44:05) in complex with two different peptides (EEYLQAFTY and EEYLKAWTF) were analyzed. We found that the stability of pMHC complexes is dependent on both peptide sequence and MHC allele. Furthermore, we demonstrate that allele-specific peptide-binding preferences can be accurately revealed using structure-based computational methods predicting the effect of mutations on protein stability.     

Discrete Arrays of Liquid‐Crystal‐Supported Proteolipid Monolayers as Phantom Cell Surfaces

The phospholipid bilayers of living cell membranes exist almost universally in a liquid state. This enables motion and spatial reorganization of membrane components on multiple length scales, which is an essential feature of many biological processes. There is great interest in the development of molecularly defined interfaces between synthetic materials and living cells. To this end, there is a need for solid substrate materials that can be derivatized with fluid, membrane‐like interfaces. Herein, we describe array fabrication of discrete liquid‐crystal areas supporting phospholipid monolayer membranes, and characterize the interactions with several different membrane surface proteins [avidin series, cholera toxin, green fluorescent protein (GFP), intercellular adhesion molecule (ICAM) and major histocompatibility complex (MHC)]. Three different linkage strategies (biotin, nickel chelating lipids complexing with histidine, and the choleratoxin binding unit (CTB) associating with G_M1 are evaluated. Additionally, experiments with live immunological T cells forming active synapses at the interface exhibit the specific nature of the surface.     

Structurally Defined αMHC‐II Nanobody–Drug Conjugates: A Therapeutic and Imaging System for B‐Cell Lymphoma

Antibody–drug conjugates (ADCs) of defined structure hold great promise for cancer therapies, but further advances are constrained by the complex structures of full‐sized antibodies. Camelid‐derived single‐domain antibody fragments (VHHs or nanobodies) offer a possible solution to this challenge by providing expedited target screening and validation through switching between imaging and therapeutic activities. We used a nanobody (VHH7) specific for murine MHC‐II and rendered “sortase‐ready” for the introduction of oligoglycine‐modified cytotoxic payloads or NIR fluorophores. The VHH7 conjugates outcompeted commercial monoclonal antibodies (mAbs) for internalization and exhibited high specificity and cytotoxicity against A20 murine B‐cell lymphoma. Non‐invasive NIR imaging with a VHH7–fluorophore conjugate showed rapid tumor targeting on both localized and metastatic lymphoma models. Subsequent treatment with the nanobody–drug conjugate efficiently controlled tumor growth and metastasis without obvious systemic toxicity.     

Guinea Pig Skin,a Model for Epidermal Cellular and Molecular Changes Induced by UVR in vivo and in vitro: Effects on Mycobacterium bovis Bacillus Calmette–Guérin Vaccination

Previously, we reported that ultraviolet B‐radiation (UVR) suppressed Bacillus Calmette–Guérin (BCG) vaccine‐induced resistance to Mycobacterium tuberculosis in guinea pigs (GP). Herein, we investigated the cellular and molecular changes within the irradiated GP epidermis and the in vivo effect of supernatants from UV‐irradiated (200 J m^?2) epidermal cells (UV‐sup) on M. bovis BCG vaccination. UVR increased the number of nucleated keratinocytes in the skin, but caused a decrease in the proportions of CD25⁺T cells. In the spleen, UVR resulted in a decrease in the proportions of T‐cell subsets including CD25⁺T cells, and major histocompatibility complex (MHC) class II⁺ and CD14⁺ cells. Similarly, significant up‐regulation of several cytokine mRNAs including IL‐10 was also observed. Furthermore, UV‐sup significantly reduced the MHC class II expression in peritoneal cells and reduced T‐cell proliferation to ConA. The proliferation to purified protein derivative (PPD) was restored to normal levels by anti‐IL‐10 antibody. The UV‐sup when injected into BCG‐vaccinated GP significantly diminished the skin test response and T‐cell proliferation to PPD and up‐regulated the expression of IL‐10, IL‐4, IL‐1β and Foxp3 mRNAs in the lymph node or spleen. Thus, whole body UVR induces profound cellular and molecular changes and injection of UV‐sup from epidermal cells mimics the effect of whole body UVR in BCG‐vaccinated GP.     

Removal of phosphate from solution by adsorption and precipitation of calcium phosphate onto monohydrocalcite

The sorption behavior and mechanism of phosphate on monohydrocalcite (CaCO₃?H₂O: MHC) were examined using batch sorption experiments as a function of phosphate concentrations, ionic strengths, temperatures, and reaction times. The mode of PO₄ sorption is divisible into three processes depending on the phosphate loading. At low phosphate concentrations, phosphate is removed by coprecipitation of phosphate during the transformation of MHC to calcite. The sorption mode at the low-to-moderate phosphate concentrations is most likely an adsorption process because the sorption isotherm at the conditions can be fitted reasonably with the Langmuir equation. The rapid sorption kinetics at the conditions is also consistent with the adsorption reaction. The adsorption of phosphate on MHC depends strongly on ionic strength, but slightly on temperature. The maximum adsorption capacities of MHC obtained from the regression of the experimental data to the Langmuir equation are higher than those reported for stable calcium carbonate (calcite or aragonite) in any conditions. At high phosphate concentrations, the amount of sorption deviates from the Langmuir isotherm, which can fit the low-to-moderate phosphate concentrations. Speciation–saturation analyses of the reacted solutions at the conditions indicated that the solution compositions which deviate from the Langmuir equation are supersaturated with respect to a certain calcium phosphate. The obtained calcium phosphate is most likely amorphous calcium phosphate (Ca₃(PO₄)₂?xH₂O). The formation of the calcium phosphate depends strongly on ionic strength, temperature, and reaction times. The solubility of MHC is higher than calcite and aragonite because of its metastability. Therefore, the higher solubility of MHC facilitates the formation of the calcium phosphates more than with calcite and aragonite.     

Substrate specificity of the human proteasome

BACKGROUND: Regulated proteolysis by the proteasome is crucial for a broad array of cellular processes, from control of the cell cycle to production of antigens. RESULTS: The rules governing the N-terminal primary and extended substrate specificity of the human 20S proteasome in the presence or absence of 11S proteasome activators (REGalpha/beta and REGgamma) have been elaborated using activity-based proteomic library tools. CONCLUSIONS: The 11S proteasome activators are shown to be important for both increasing the activity of the 20S proteasome and for altering its cleavage pattern and substrate specificity. These data also establish that the extended substrate specificity is an important factor for proteasomal cleavage. The specificities observed have features in common with major histocompatibility complex (MHC) class I ligands and can be used to improve the prediction of MHC class I restricted cytotoxic T-cell responses.     

Immunology of O-glycosylated proteins: approaches to the design of a MUC1 glycopeptide-based tumor vaccine

Until about 1990 there was general consent about the assumption that only protein and peptide antigens have the capacity of CD4(+) or CD8(+) T-cell stimulation. Since about ten years evidence is now accumulating that carbohydrate-peptide epitopes do play a role in classical MHC-mediated immune responses. This holds true for glycopeptides, where the glycan chain is short and not located at an "anchor residue" needed for MHC interaction. T-cell recognition of O-glycosylated peptides is potentially of high biomedical significance, because it can mediate the immune protection against microorganisms, the vaccination in anti-tumor therapies, but also some aspects of autoimmunity. The epithelial type 1 transmembrane mucin MUC1 is established as a marker for monitoring recurrence of breast cancer and is a promising target for immunotherapeutic strategies to treat cancer by active specific immunization. Natural human immune responses to the tumor-associated glycoforms of the mucin indicate that antibody reactivities are more directed to glycopeptide than to non-glycosylated peptide epitopes. To overcome the weak immunogenicity of the natural target, heavily O-glycosylated MUC1, the question was addressed whether O-linked glycans remain intact during processing in the MHC class II pathway and interfere with endosomal processing and peptide presentation. Attempts were made to define on a biochemical level the structural requirements for an efficient endosomal proteolysis catalyzed by cathepsin L in antigen-presenting cells. Evidence based on work with CD4(+) T-hybridomas confirms that O-glycopeptides can be effectively presented to T-cells and that glycans can form integral parts of the TCR defined epitopes. Similar approaches are currently followed in the MHC class I pathway which aim at the identification of immunogenic glycopeptides generated by immunoproteasomes.