In silico allergenicity prediction of several lipid transfer proteins

Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of allergenicity of new molecules based on their homology with known allergens have been released, and guidelines to assess potential allergenicity of proteins through bioinformatics have been established. Even if such tools are only partially reliable yet, they can provide important indications when other kinds of molecular characterization are lacking. The potential allergenicity of 28 amino acid sequences of LTPs homologs, either retrieved from the UniProt database or in silico deduced from the corresponding EST coding sequence, was predicted using 7 publicly available web tools. Moreover, their similarity degree to their closest known LTP allergens was calculated, in order to evaluate their potential cross-reactivity. Finally, all sequences were studied for their identity degree with the peach allergen Pru p 3, considering the regions involved in the formation of its known conformational IgE-binding epitope. Most of the analyzed sequences displayed a high probability to be allergenic according to all the software employed. The analyzed LTPs from bell pepper, cassava, mango, mungbean and soybean showed high homology (>70%) with some known allergenic LTPs, suggesting a potential risk of cross-reactivity for sensitized individuals. Other LTPs, like for example those from canola, cassava, mango, mungbean, papaya or persimmon, displayed a high degree of identity with Pru p 3 within the consensus sequence responsible for the formation, at three-dimensional level, of its major conformational epitope. Since recent studies highlighted how in patients mono-sensitized to peach LTP the levels of IgE seem directly proportional to the chance of developing cross-reactivity to LTPs from non-Rosaceae foods, and these chances increase the more similar the protein is to Pru p 3, these proteins should be taken into special account for future studies aimed at evaluating the risk of cross-allergenicity in highly sensitized individuals.     

Immunopeptidome screening to design An immunogenic construct against PRAME positive breast cancer; An in silico study

BackgroundMetastasis is the main cause of breast cancer (BC) lethality, especially in early stages, led to improvements in therapeutic procedures. Lately, by improvements in our perception of biological processes and immune system new classes of vaccines are emerged that grant us the opportunity of designing resolute constructs against desired antigens. In the current study, we used a variety of immunoinformatics tools to design a novel cancer vaccine against Preferentially Expressed Antigen of Melanoma (PRAME), which counts as a cancer testis antigen for various human cancers including BC. The PRAME up-regulation leads to strengthen BC stem cells maintenance, drug resistance, cell survival, adaptation, and apoptosis evading in cancerous cells.Methods and resultsThe PRAME co-expressed genes were mined and validated through BC RNA-sequencing of TCGA data. The immunodominant T-cell predicted epitopes were fused and engineered to form the vaccine. The safety, allergenicity, and immunogenic capabilities of the vaccine were confirmed by promising immunoinformatics tools. The vaccine’s structure was verified to be hydrophilic in most areas through Kyte and Doolittle hydrophobicity plotting. The interactions between the designed vaccine and immune receptors of TLR4 and IL1R were confirmed by protein-protein docking after modeling its tertiary structure. Finally, codon optimization and in silico cloning were performed to guarantee better in-vivo results.ConclusionIn conclusion, concerning in silico assessments’ results in this study, the designed vaccine can potentially boost immune responses against PRAME, therefore may decrease BC development and metastasis. According to the mined PRAME co-expressed genes and their functional annotation, cell cycle regulation is the prime mechanism opted by this construct and its adjacent regulatory genes along boosting immune reactions.     

Variation in fat soluble vitamins (A,D, E,K) in in vitro and ex vitro germinated chickpea (Cicer arietinum L.) seedlings,as revealed by high performance liquid chromatography

In present communication, effect of in vitro and ex vitro culture conditions was investigated on the yield of fat soluble vitamins in chickpea (Cicer arietinum L.) seedlings analyzed by high performance liquid chromatography (HPLC). Amongst the tested culture conditions (in vitro and ex vitro); in vitro condition proved to be highly effective compared to ex vitro. We noticed a significant difference in vitamins D (ergocalciferol), E (α-tocopherol) and K (phylloquinone) yields in chickpea seedlings grown in two different conditions. Maximum yield with a linear increase in vitamins D and E was noticed upto 9 days old in vitro grown seedlings. Vitamin K yield was also high in in vitro grown seedlings with a linear increase upto 11 days. Although, vitamin A was not detected, the vitamin production in germinating seeds was, therefore, age and culture condition dependent. The study revealed that, in in vitro condition, the level of fat soluble vitamins enhanced in seedlings, which could be used for human consumption with value addition in the diet of vegetarians.     

Assessing hazelnut allergens by protein- and DNA-based approaches: LC-MS/MS,ELISA and real-time PCR

Hazelnut (Corylus avellana L.) is responsible for a significant part of the allergies related to nuts. Still, it is a very much appreciated nut and as consequence is widely used in all types of processed foods, such as chocolates. Correct food labelling is currently the most effective means of preventing the consumption of allergenic ingredients, namely hazelnut, by the sensitised/allergic individuals. Thus, to verify labelling compliance and to ensure allergic patient protection, the development of highly sensitive methodologies is of extreme importance. In this study, three major methodologies, namely enzyme-linked immunosorbent assays (ELISA), liquid chromatography coupled with mass spectrometry and real-time polymerase chain reaction, were evaluated for their performance regarding the detection of hazelnut allergens in model chocolates. The sandwich ELISA and respective antibodies were in-house developed and produced. With sensitivity levels of approximately 1 mg kg^?1 and limits of quantification of 50–100 mg kg^?1, all the performed methods were considered appropriate for the identification of hazelnut in complex foods such as chocolates. To our knowledge, this was the first successful attempt to develop and compare three independent approaches for the detection of allergens in foods.

Application of gamma irradiation for inhibition of food allergy

This study was carried out to evaluate the application of food irradiation technology as a method for reducing food allergy. Milk β-lactoglobulin, chicken egg albumin, and shrimp tropomyosin were used as model food allergens for experiments on allergenic and molecular properties by gamma irradiation. The amount of intact allergens in an irradiated solution was reduced by gamma irradiation depending upon the dose. These results showed that epitopes on the allergens were structurally altered by radiation treatment and that the irradiation technology can be applied to reduce allergenicity of allergic foods.     

Computational prediction and biochemical characterization of novel RNA aptamers to Rift Valley fever virus nucleocapsid protein

Rift Valley fever virus (RVFV) is a potent human and livestock pathogen endemic to sub-Saharan Africa and the Arabian Peninsula that has potential to spread to other parts of the world. Although there is no proven effective and safe treatment for RVFV infections, a potential therapeutic target is the virally encoded nucleocapsid protein (N). During the course of infection, N binds to viral RNA, and perturbation of this interaction can inhibit viral replication. To gain insight into how N recognizes viral RNA specifically, we designed an algorithm that uses a distance matrix and multidimensional scaling to compare the predicted secondary structures of known N-binding RNAs, or aptamers, that were isolated and characterized in previous in vitro evolution experiment. These aptamers did not exhibit overt sequence or predicted structure similarity, so we employed bioinformatic methods to propose novel aptamers based on analysis and clustering of secondary structures. We screened and scored the predicted secondary structures of novel randomly generated RNA sequences in silico and selected several of these putative N-binding RNAs whose secondary structures were similar to those of known N-binding RNAs. We found that overall the in silico generated RNA sequences bound well to N in vitro. Furthermore, introduction of these RNAs into cells prior to infection with RVFV inhibited viral replication in cell culture. This proof of concept study demonstrates how the predictive power of bioinformatics and the empirical power of biochemistry can be jointly harnessed to discover, synthesize, and test new RNA sequences that bind tightly to RVFV N protein. The approach would be easily generalizable to other applications.     

Application of current allergy assessment guidelines to next-generation biotechnology-derived crops

In any single day, our immune systems are exposed to thousands of different proteins from the environment and the food we eat. In a portion of the human population, some of those proteins will stimulate the immune systems to synthesize immunoglobulin E in an allergenic response. The discrepancy between the vast numbers of proteins we encounter and the limited number of proteins that actually become allergens have led scientists on a quest to discover what unique features exist that make proteins destined to be allergens. The information gained from these studies has led to an allergy assessment strategy that characterizes the potential allergenicity of biotechnology products prior to their commercialization. This testing strategy appears to be effective as shown by the fact that there have been no clinically documented food allergic reactions to any of the biotechnology proteins introduced into food crops, to date. The next generation of biotechnology products will most likely contain more complex traits, including nutritionally enhanced food crops, and the question arises as to whether the current allergy assessment strategy will be sufficient to protect the health of the consuming public. In this paper, we discuss general allergen characteristics in order to better understand how proteins become allergens, summarize the current allergy assessment process, evaluate the different aspects of this process for their adequacy in determining the allergenic potential of engineered functional foods, and, finally, we assess the possibility of new technologies having a positive impact on the allergy assessment of nutritionally enhanced crops.     

Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp.

The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences. The comparative modeling of protein was performed through Modeller 9v14 program and visualized by PyMOL tools. Validated protein models were deposited in the Protein Model Database (PMDB) (PMDB id: PM0080150 to PM0080159). Active sites of nirk encoding CuNiR enzyme were identified by Castp server. The PROCHECK showed significant scores for four protein models in the most favored regions of the Ramachandran plot. Active sites and cavities prediction exhibited that the amino acid, namely Glycine, Alanine, Histidine, Aspartic acid, Glutamic acid, Threonine, and Glutamine were common in four predicted protein models. The present in silico study anticipates that active site analyses result will pave the way for further research on the complex denitrification mechanism of the selected species in the experimental laboratory.     

A novel in silico minigene vaccine based on CD4+ T-helper and B-cell epitopes of EG95 isolates for vaccination against cystic echinococcosis

EG95 oncospheral antigen plays a crucial role in Echinococcus granulosus pathogenicity. Considering the diversity of antigen among different EG95 isolates, it seems to be an ideal antigen for designing a universal multivalent minigene vaccine, so-called multi-epitope vaccine. This is the first in silico study to design a construct for the development of global EG95-based hydatid vaccine against E. granulosus in intermediate hosts. After antigen sequence selection, the three-dimensional structure of EG95 was modeled and multilaterally validated. The preliminary parameters for B-cell epitope prediction were implemented such as the possible transmembrane helix, signal peptide, post-translational modifications and allergenicity. The high ranked linear and conformational B-cell epitopes derived from several online web-servers (e.g., ElliPro, BepiPred v1.0, BcePred, ABCpred, SVMTrip, IEDB algorithms, SEPPA v2.0 and Discotope v2.0) were utilized for multiple sequence alignment and then for engineering the vaccine construct. T-helper based epitopes were predicted by molecular docking between the high frequent ovar class II allele (Ovar-DRB1*1202) and hexadecamer fragments of the EG95 protein. Having used the immune-informatics tools, we formulated the first EG95-based minigene vaccine based on T-helper epitope with high-binding affinity to the ovar MHC allele. This designed construct was analyzed for different physicochemical properties. It was also codon-optimized for high-level expression in Escherichia coli k12. Taken all, we propose the present in silico vaccine constructs as a promising platform for the generation of broadly protective vaccines for species and genus-specific immunization of the natural hosts of the parasite.     

Assessing Heterologous Expression of Hyoscyamine 6β-Hydroxylase – A Feasibility Study

The protein sequence of the hyoscyamine 6β-hydroxylase gene from Hyoscyamusniger was analysed in silico for its potential of heterologous expression. Therefore different parameters determining the proteins properties and structure in prokaryotic or eukaryotic protein expression systems were taken into account. In silico prediction of co- and post-translational modifications revealed 25 putative glycosylation sites, one of which reported to be a co-factor stabilizing residue in 2-oxoglutarate dependent dioxygenases. Potential protein solubility and degradation (PEST) motifs were also evaluated. Together with the calculated physico-chemical properties the results indicated reasonable solubility but potential instability of the protein in Escherichia coli and Saccharomyces cerevisiae. Further a synthetic h6h-gene was introduced into the prokaryotic or eukaryotic hostsEscherichia coli and Saccharomyces cerevisiae to determine protein expression. The protein could be expressed in both organisms, though stability was confirmed to be an issue.     

Proteomics of cypress pollen allergens using double and triple one-dimensional electrophoresis

Italian cypress (Cupressus sempervirens, Cups) pollen causes allergic diseases in inhabitants of many of the cities surrounding the Mediterranean basin. However, allergens of Cups pollen are still poorly known. We introduce here a novel proteomic approach based on double one‐dimensional gel electrophoresis (D1‐DE) as an alternative to the 2‐DE immunoblot, for the specific IgE screening of allergenic proteins from pollen extracts. The sequential one‐dimensional combination of IEF and SDS‐PAGE associated with IgE immunoblotting allows a versatile multiplexed immunochemical analysis of selected groups of allergens by converting a single protein spot into an extended protein band. Moreover, the method appears to be valuable for MS/MS identification, without protein purification, of a new Cups pollen allergen at 43 kDa. D1‐DE immunoblotting revealed that the prevalence of IgE sensitization to this allergen belonging to the polygalacturonase (PG) family was 70% in tested French allergic patients. In subsequent triple one‐dimensional gel electrophoresis, the Cups pollen PG was shown to promote lectin‐based protein‐protein interactions. Therefore, D1‐DE could be used in routine work as a convenient alternative to 2‐DE immunoblotting for the simultaneous screening of allergenic components under identical experimental conditions, thereby saving considerable amounts of sera and allergen extracts.     

Reduction of allergenicity of irradiated ovalbumin in ovalbumin-allergic mice

Egg allergy is one of the most serious of the immediate hypersensitivity reactions to foods. Such an allergic disorder is mediated by IgE antibodies stimulated by T-helper type 2 (Th2) lymphocytes. This study was undertaken to evaluate changes of allergenicity and cytokine profiles by exposure of irradiated ovalbumin (OVA), a major allergen of egg white, in the OVA-allergic mice model. OVA solutions (2 mg/ml in 0.01 M phosphate buffered saline (PBS) were gamma-irradiated to 50 and 100 kGy. The allergenicity in the OVA-allergy-induced mice model was remarkably reduced when challenged with irradiated OVA. Cultures of spleen cells harvested from OVA-sensitized mice showed a significant decrease in Th2 cytokine levels of ILs-4 and -5 with a concomitant increase in Th1 cytokine levels of IL-12 when co-cultured with irradiated OVA. However, IFN-γ level decreased dependant on the radiation dose of co-cultured OVA. The levels of IgEs and Th2-cytokine were reduced dependant on the radiation dose. These data show that the irradiated OVA could downregulate the activity of Th2 lymphocytes in OVA-sensitized mice.     

Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs

High mobility group (HMG) proteins are the major architectural proteins. Among HMG proteins, High Mobility Group A (HMGA) is characterized by AT-hook (ATH) motifs, which have an affinity for AT-rich DNA. In this study, we characterized the plant HMGAs from the Poaceae family using in silico methods. The protein sequences for rice HMGAs were retrieved and the corresponding orthologs from grasses were extracted. The phylogenetic analysis identified three major evolutionary clades of grass HMGAs and their ATH motif analysis revealed that HMGAs from clade 1 and 2, except for clade 2 HMGAs, are devoid of high-affinity DNA-binding domain. The clade 2 HMGAs also displayed a highly conserved length of all the spacers and the length of the C-terminal tail following the last ATH. Moreover, the C-terminal tail in clade 2 HMGAs is smaller than HMGAs from any other clade. Unlike clade 2, other clades of Poaceae HMGAs displayed high variability in the length of spacers. Despite several differences among HMGAs of different clades in Poaceae, the H1/H5 domain was found to be highly conserved. This study has revealed the detailed analyses of Poaceae HMGAs and it will be useful for further investigation aiming at the determination of precise biological functions and molecular mechanisms of grass HMGAs.     

Identification of a microRNA encoded by Anticarsia gemmatalis multiple nucleopolyhedrovirus

MicroRNAs are regulatory RNAs that are scarcely described in Baculoviruses. In this work we predicted a microRNA in silico, denominated agmnpv-miR-4, encoded in the genome of Anticarsia gemmatalis Nucleopolyhedrovirus (AgMNPV), which is homologous to the already validated bmnpv-miR-4 from Bombyx mori Nucleopolyhedrovirus (BmNPV). Considering information known for bmnpv-miR-4 such as seed sequence, coding location in the genome and putative target binding, we searched for the coding sequence of agmnpv-miR-4 in AgMNPV genome. A precursor sequence of agmnpv-miR-4 was predicted, and we identified a putative 23 nt mature microRNA, agmnpv-miR-4, coded in the complementary strand of AgMNPV-2D between positions 49,450 and 49,472. We validated agmnpv-miR-4 by Northern blot from HighFive cells and A. gemmatalis larve extracts infected with AgMNPV.     

Comparison of green extraction methods with conventional extraction method for extract yield,L-DOPA concentration and antioxidant activity of Mucuna pruriens seed

ABSTRACT

Mucuna pruriens is a plant of Fabaceae family. Seed of M. pruriens is considered as a rich source of levo-3,4 dihydroxyphenylalanine (L-DOPA), a non-protein phenolic amino acid. In the present study, three different extraction methods were compared for extract yield, concentration of bioactive compounds such as total phenol, L-DOPA and antioxidant capacity. Extracts were prepared using water acidified with hydrochloric acid (0.1?N) by conventional method of refluxing as well as two green methods namely ultrasound and microwave assisted solvent extraction. A rapid and qualified high-performance liquid chromatography method was also developed for quantification of L-DOPA in different extracts. Among the three extraction methods, microwave assisted extraction provided the best results for yield and quality of M. pruriens extract in much shorter time in comparison to refluxing method of extraction.