Search results for: fusion proteins

Authors: Tassia Batista Pessato, Francielli Pires Ribeiro Morais, Fernanda Guimaraes Drummond Silva, Flavia Maria Netto

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Proteins and phenolic compounds can interact mainly by hydrophobic interactions. Those interactions may lead to structural changes in both molecules, which in turn could affect positively or negatively their functional and nutritional properties. Here, the structural changes of whey proteins (WPI) due to interaction with caffeic acid (CA) were investigated by intrinsic and extrinsic fluorescence. The effects of protein-phenolic compounds interactions on the total phenolic content and antioxidant activity were also assessed. The WPI-CA complexes were obtained by mixture of WPI and CA stock solutions in deionized water. The complexation was carried out at room temperature during 60 min, using 0.1 M NaOH to adjust pH at 7.0. The WPI concentration was fixed at 5 mg/mL, whereas the CA concentration varied in order to obtain four different WPI:CA molar relations (1:1; 2:1; 5:1; 10:1). WPI and phenolic solutions were used as controls. Intrinsic fluorescence spectra of the complexes (mainly due to Trp fluorescence emission) were obtained at λex = 280 nm and the emission intensities were measured from 290 to 500 nm. Extrinsic fluorescence was obtained as the measure of protein surface hydrophobicity (S0) using ANS as a fluorescence probe. Total phenolic content was determined by Folin-Ciocalteau and the antioxidant activity by FRAP and ORAC methods. Increasing concentrations of CA resulted in decreasing of WPI intrinsic fluorescence. The emission band of WPI red shifted from 332 to 354 nm as the phenolic concentration increased, which is related to the exposure of Trp residue to the more hydrophilic environment and unfolding of protein structure. In general, the complexes presented lower S0 values than WPI, suggesting that CA hindered ANS binding to hydrophobic sites of WPI. The total phenolic content in the complexes was lower than the sum of two compounds isolated. WPI showed negligible AA measured by FRAP. However, as the relative concentration of CA increased in the complexes, the FRAP values enhanced, indicating that AA measure by this technique comes mainly from CA. In contrast, the WPI ORAC value (82.3 ± 1.5 µM TE/g) suggest that its AA is related to the capacity of H+ transfer. The complexes exhibited no important improvement of AA measured by ORAC in relation to the isolated components, suggesting complexation partially suppressed AA of the compounds. The results hereby presented indicate that interaction of WPI and CA occurred, and this interaction caused a structural change in the proteins. The complexation can either hide or expose antioxidant sites of both components. In conclusion, although the CA can undergo an AA suppression due to the interaction with proteins, the AA of WPI could be enhanced due to protein unfolding and exposure of antioxidant sites.

Keywords: bioactive properties, milk proteins, phenolic acids, protein-phenolic compounds complexation

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Authors: Alexandre Barbosa de Almeida, Telma Woerle de Lima Soares

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Protein structure prediction is a challenging task in the bioinformatics field. The biological function of all proteins majorly relies on the shape of their three-dimensional conformational structure, but less than 1% of all known proteins in the world have their structure solved. This work proposes a deep learning model to address this problem, attempting to predict some aspects of the protein conformations. Throughout a process of multiobjective dominance, a recurrent neural network was trained to abstract the particular bias of each individual multiobjective algorithm, generating a heuristic that could be useful to predict some of the relevant aspects of the three-dimensional conformation process formation, known as protein folding.

Keywords: Ab initio heuristic modeling, multiobjective optimization, protein structure prediction, recurrent neural network

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Authors: Nasser A. Al-Shabib

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Food allergens are most common non-native form when exposed to the immune system. Most food proteins undergo various treatments (e.g. thermal or proteolytic processing) during food manufacturing. Such treatments have the potential to impact the chemical structure of food allergens so as to convert them to more denatured or unfolded forms. The conformational changes in the proteins may affect the allergenicity of treated-allergens. However, most allergenic proteins possess high resistance against thermal modification or digestive enzymes. In the present study, ovomucoid (a major allergenic protein of egg white) was heated in phosphate-buffered saline (pH 7.4) at different temperatures, aqueous solutions and on different surfaces for various times. The results indicated that different antibody-based methods had different sensitivities in detecting the heated ovomucoid. When using one particular immunoassay‚ the immunoreactivity of ovomucoid increased rapidly after heating in water whereas immunoreactivity declined after heating in alkaline buffer (pH 10). Ovomucoid appeared more immunoreactive when dissolved in PBS (pH 7.4) and heated on a stainless steel surface. To the best of our knowledge‚ this is the first time that antibody-based methods have been applied for the detection of ovomucoid adsorbed onto different surfaces under various conditions. The results obtained suggest that use of antibodies to detect ovomucoid after food processing may be problematic. False assurance will be given with the use of inappropriate‚ non-validated immunoassays such as those available commercially as ‘Swab’ tests. A greater understanding of antibody-protein interaction after processing of a protein is required.

Keywords: ovomucoid, thermal treatment, solutions, surfaces

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Authors: Benito Minjarez, Jesse Haramati, Yury Rodriguez-Yanez, Florencio Recendiz-Hurtado, Juan-Pedro Luna-Arias, Salvador Mena-Munguia

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During the last decades, the world has experienced a rapid industrialization and an expanding economy favoring a demographic boom. As a consequence, countries around the world have focused on developing new strategies related to the production of different farm products in order to meet future demands. Consequently, different strategies have been developed seeking to improve the major food products for both humans and livestock. Corn, after wheat and rice, is the third most important crop globally and is the primary food source for both humans and livestock in many regions around the globe. In addition, maize (Zea mays) is an important source of protein accounting for up to 60% of the daily human protein supply. Generally, many of the cereal grains have proteins with relatively low nutritional value, when they are compared with proteins from meat. In the case of corn, much of the protein is found in the endosperm (75 to 85%) and is deficient in two essential amino acids, lysine, and tryptophan. This deficiency results in an imbalance of amino acids and low protein content; normal maize varieties have less than half of the recommended amino acids for human nutrition. In addition, studies have shown that this deficiency has been associated with symptoms of growth impairment, anemia, hypoproteinemia, and fatty liver. Due to the fact that most of the presently available maize varieties do not contain the quality and quantity of proteins necessary for a balanced diet, different countries have focused on the research of quality protein maize (QPM). Researchers have characterized QPM noting that these varieties may contain between 70 to 100% more residues of the amino acids essential for animal and human nutrition, lysine, and tryptophan, than common corn. Several countries in Africa, Latin America, as well as China, have incorporated QPM in their agricultural development plan. Large parts of these countries have chosen a specific QPM variety based on their local needs and climate. Reviews have described the breeding methods of maize and have revealed the lack of studies on genetic and proteomic diversity of proteins in QPM varieties, and their genetic relationships with normal maize varieties. Therefore, molecular marker identification using tools such as mass spectrometry may accelerate the selection of plants that carry the desired proteins with high lysine and tryptophan concentration. To date, QPM maize lines have played a very important role in alleviating the malnutrition, and better characterization of these lines would provide a valuable nutritional enhancement for use in the resource-poor regions of the world. Thus, the objectives of this study were to identify proteins in QPM maize in comparison with a common maize line as a control.

Keywords: corn, mass spectrometry, QPM, tryptophan

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Authors: I. Nyoman Mahayasa Adiputra

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Data in the field of health can be useful for the purposes of data analysis, one example of health data is disease data. Disease data is usually in a geographical plot in accordance with the area. Where the data was collected, in the city of Denpasar, Bali. Disease data report is still published in tabular form, disease information has not been mapped in GIS form. In this research, disease information in Denpasar city will be digitized in the form of a geographic information system with the smallest administrative area in the form of district. Denpasar City consists of 4 districts of North Denpasar, East Denpasar, West Denpasar and South Denpasar. In this research, we use Google fusion table technology for map digitization process, where this technology can facilitate from the administrator and from the recipient information. From the administrator side of the input disease, data can be done easily and quickly. From the receiving end of the information, the resulting GIS application can be published in a website-based application so that it can be accessed anywhere and anytime. In general, the results obtained in this study, divided into two, namely: (1) Geolocation of Denpasar and all of Denpasar districts, the process of digitizing the map of Denpasar city produces a polygon geolocation of each - district of Denpasar city. These results can be utilized in subsequent GIS studies if you want to use the same administrative area. (2) Dengue fever mapping in 2014 and 2015. Disease data used in this study is dengue fever case data taken in 2014 and 2015. Data taken from the profile report Denpasar Health Department 2015 and 2016. This mapping can be useful for the analysis of the spread of dengue hemorrhagic fever in the city of Denpasar.

Keywords: geographic information system, Google fusion table technology, delivery of disease data information, Denpasar city

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Authors: Syeda Kiran Shahzadi, Nasir Mahmood, Muhammad Abdul Qadir

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In the current research, three recombinant human interferon alpha-2b proteins (two modified and one normal form) were produced and Pegylated with an aim to produce more effective drugs against viral infections and cancers. The modified recombinant human interferon alpha-2b proteins were produced by site-directed modifications of interferon alpha 2b gene, targeting the amino acids at positions ‘R23’ and ‘H34’. The resulting chemically modified and unmodified forms of human interferon alpha 2b were conjugated with methoxy-polyethylene glycol propanealdehyde (400 KDa) and methoxy-polyethylene glycol succinimidyl succinate (400 KDa). Pegylation of normal and modified forms of Interferon alpha-2b prolong their release time and enhance their efficacy. The conjugation of PEG with modified and unmodified human interferon alpha 2b protein drugs was also characterized with 1H-NMR, HPLC, and SDS-PAGE. Antiproliferative assays of modified and unmodified forms of drugs were performed in cell based bioassays using MDBK cell lines. The results indicated that experimentally produced recombinant human interferon alpha-2b proteins were biologically active and resulted in significant inhibition of cell growth.

Keywords: protein refolding, antiproliferative activities, biomedical applications, human interferon alpha-2b, pegylation, mPEG-propionaldehyde, site directed mutagenesis, E. coli expression

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Authors: Ezzeddin Anawa, Abdol-Ghane Olabi

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The dissimilar joint between aluminum /titanium alloys (Al 6082 and Ti G2) alloys were successfully achieved by CO2 laser welding with a single pass and without filler material using the overlap joint design. Laser welding parameters ranges combinations were experimentally determined using Taguchi approach with the objective of producing welded joint with acceptable welding profile and high quality of mechanical properties. In this study a joining of dissimilar Al 6082 / Ti G2 was result in three distinct regions fusion area (FA), heat-affected zone (HAZ), and the unaffected base metal (BM) in the weldment. These regions are studied in terms of its microstructural characteristics and microhardness which are directly affecting the welding quality. The weld metal was mainly composed of martensite alpha prime. In two different metals in the two different sides of joint HAZ, grain growth was detected. The microhardness of the joint distribution also has shown microhardness increasing in the HAZ of two base metals and a varying microhardness in fusion zone.

Keywords: microharness , microstructure, laser welding and dissimilar jointed materials.

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Authors: Fadwa Alaskar, Fang-Chieh Chou, Carlos Flores, Xiao-Yun Lu, Alexandre M. Bayen

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This article proposes a perception model for enhancing the accuracy and stability of car-following control of a longitudinally automated truck. We applied a fusion-based tracking algorithm on measurements of a single preceding vehicle needed for car-following control. This algorithm fuses two types of data, radar and LiDAR data, to obtain more accurate and robust longitudinal perception of the subject vehicle in various weather conditions. The filter’s resulting signals are fed to the gap control algorithm at every tracking loop composed by a high-level gap control and lower acceleration tracking system. Several highway tests have been performed with two trucks. The tests show accurate and fast tracking of the target, which impacts on the gap control loop positively. The experiments also show the fulfilment of control design requirements, such as fast speed variations tracking and robust time gap following.

Keywords: object tracking, perception, sensor fusion, adaptive cruise control, cooperative adaptive cruise control

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Authors: Ozlem Oral, Emre Taskin, Aysel Yuce, Serap Dokmeci, Devrim Gozuacik

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Autophagy is an evolutionary conserved lysosome-dependent catabolic pathway, responsible for the degradation of long-lived proteins, abnormal aggregates and damaged organelles which cannot be degraded by the ubiquitin-proteasome system. Lysosomes degrade the substrates through the activity of lysosomal hydrolases and lysosomal membrane-bound proteins. Mutations in the coding region of these proteins cause malfunctional lysosomes, which contributes to the pathogenesis of lysosomal storage diseases. Gaucher disease is a lysosomal storage disease resulting from the mutation of a lysosomal membrane-associated glycoprotein called glucocerebrosidase and its cofactor saposin C. The disease leads to intracellular accumulation of glucosylceramide and other glycolipids. Because of the essential role of lysosomes in autophagic degradation, Gaucher disease may directly be linked to this pathway. In this study, we investigated the expression of autophagy and/or lysosome-related genes and proteins in fibroblast cells isolated from patients with different mutations. We carried out confocal microscopy analysis and examined autophagic flux by utilizing the differential pH sensitivities of RFP and GFP in mRFP-GFP-LC3 probe. We also evaluated lysosomal pH by active lysosome staining and lysosomal enzyme activity. Beside lysosomes, we also performed proteasomal activity and cell death analysis in patient samples. Our data showed significant attenuation in the expression of key autophagy-related genes and accumulation of their proteins in mutant cells. We found decreased the ability of autophagosomes to fuse with lysosomes, associated with elevated lysosomal pH and reduced lysosomal enzyme activity. Proteasomal degradation and cell death analysis showed reduced proteolytic activity of the proteasome, which consequently leads to increased susceptibility to cell death. Our data indicate that the major degradation pathways are affected by multifunctional lysosomes in mutant patient cells and may underlie in the mechanism of clinical severity of Gaucher patients. (This project is supported by TUBITAK-3501-National Young Researchers Career Development Program, Project No: 112T130).

Keywords: autophagy, Gaucher's disease, glucocerebrosidase, mutant fibroblasts

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility. Two groups are albumin and globulin dissolving in water and salt solutions possessing metabolic activities. Two other groups are inactive and non-dissolvable and contain glutelins or glutenins and prolamins or gliadins. Gliadins are major components of the storage proteins in wheat endosperm. Gliadin proteins are separated into three groups based on electrophoretic mobility: α/β-gliadin, γ-gliadin, and ω-gliadin. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, involving coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus, three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 37 of the 40 accessions (93%) carried 210 bp allele, and three accessions (8%) did not yield any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: diploied wheat, gliadin, Triticum boeoticum, Triticum urartu

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Authors: Daniela Manila Bianchi, Samantha Lupi, Elisa Barcucci, Sandra Fragassi, Clara Tramuta, Lucia Decastelli

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Introduction: The undeclared allergens detection in food products plays a fundamental role in the safety of the allergic consumer. The protection of allergic consumers is guaranteed, in Europe, by Regulation (EU) No 1169/2011 of the European Parliament, which governs the consumer's right to information and identifies 14 food allergens to be mandatorily indicated on food labels: among these, an egg is included. An egg can be present as an ingredient or as contamination in raw and cooked products. The main allergen egg proteins are ovomucoid, ovalbumin, lysozyme, and ovotransferrin. This study presents the results of a survey conducted in Northern Italy aimed at detecting the presence of undeclared egg proteins in food matrices in the latest ten years (2011-2021). Method: In the period January 2011 - October 2021, a total of 1205 different types of food matrices (ready-to-eat, meats, and meat products, bakery and pastry products, baby foods, food supplements, pasta, fish and fish products, preparations for soups and broths) were delivered to Food Control Laboratory of Istituto Zooprofilattico Sperimentale of Piemonte Liguria and Valle d’Aosta to be analyzed as official samples in the frame of Regional Monitoring Plan of Food Safety or in the contest of food poisoning. The laboratory is ISO 17025 accredited, and since 2019, it has represented the National Reference Centre for the detection in foods of substances causing food allergies or intolerances (CreNaRiA). All samples were stored in the laboratory according to food business operator instructions and analyzed within the expiry date for the detection of undeclared egg proteins. Analyses were performed with RIDASCREEN®FAST Ei/Egg (R-Biopharm ® Italia srl) kit: the method was internally validated and accredited with a Limit of Detection (LOD) equal to 2 ppm (mg/Kg). It is a sandwich enzyme immunoassay for the quantitative analysis of whole egg powder in foods. Results: The results obtained through this study showed that egg proteins were found in 2% (n. 28) of food matrices, including meats and meat products (n. 16), fish and fish products (n. 4), bakery and pastry products (n. 4), pasta (n. 2), preparations for soups and broths (n.1) and ready-to-eat (n. 1). In particular, in 2011 egg proteins were detected in 5% of samples, in 2012 in 4%, in 2013, 2016 and 2018 in 2%, in 2014, 2015 and 2019 in 3%. No egg protein traces were detected in 2017, 2020, and 2021. Discussion: Food allergies occur in the Western World in 2% of adults and up to 8% of children. Allergy to eggs is one of the most common food allergies in the pediatrics context. The percentage of positivity obtained from this study is, however, low. The trend over the ten years has been slightly variable, with comparable data.

Keywords: allergens, food, egg proteins, immunoassay

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Authors: Kerekoppa Puttaiah Bhatta Ramesha, Uday Kannegundla, Praseeda Mol, Lathika Gopalakrishnan, Jagish Kour Reen, Gourav Dey, Manish Kumar, Sakthivel Jeyakumar, Arumugam Kumaresan, Kiran Kumar M., Thottethodi Subrahmanya Keshava Prasad

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Spermatozoa are the highly specialized transcriptionally and translationally inactive haploid male gamete. The understanding of proteome of sperm is indispensable to explore the mechanism of sperm motility and fertility. Though there is a large number of human sperm proteomic studies, in-depth proteomic information on Bos indicus spermatozoa is not well established yet. Therefore, we illustrated the profile of sperm proteome in indigenous cattle, Malnad gidda (Bos Indicus), using high-resolution mass spectrometry. In the current study, two semen ejaculates from 3 breeding bulls were collected employing the artificial vaginal method. Using 45% percoll purification, spermatozoa cells were isolated. Protein was extracted using lysis buffer containing 2% Sodium Dodecyl Sulphate (SDS) and protein concentration was estimated. Fifty micrograms of protein from each individual were pooled for further downstream processing. Pooled sample was fractionated using SDS-Poly Acrylamide Gel Electrophoresis, which is followed by in-gel digestion. The peptides were subjected to C18 Stage Tip clean-up and analyzed in Orbitrap Fusion Tribrid mass spectrometer interfaced with Proxeon Easy-nano LC II system (Thermo Scientific, Bremen, Germany). We identified a total of 6773 peptides with 28426 peptide spectral matches, which belonged to 1081 proteins. Gene ontology analysis has been carried out to determine the biological processes, molecular functions and cellular components associated with sperm protein. The biological process chiefly represented our data is an oxidation-reduction process (5%), spermatogenesis (2.5%) and spermatid development (1.4%). The highlighted molecular functions are ATP, and GTP binding (14%) and the prominent cellular components most observed in our data were nuclear membrane (1.5%), acrosomal vesicle (1.4%), and motile cilium (1.3%). Seventeen percent of sperm proteins identified in this study were involved in metabolic pathways. To the best of our knowledge, this data represents the first total sperm proteome from indigenous cattle, Malnad Gidda. We believe that our preliminary findings could provide a strong base for the future understanding of bovine sperm proteomics.

Keywords: Bos indicus, Malnad Gidda, mass spectrometry, spermatozoa

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Authors: Anika Chebrolu

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Mono-targeted drugs can be of limited efficacy against complex diseases. Recently, multi-target drug design has been approached as a promising tool to fight against these challenging diseases. However, the scope of current computational approaches for multi-target drug design is limited. DeepLig presents a de-novo drug discovery platform that uses reinforcement learning to generate and optimize novel, potent, and multitargeted drug candidates against protein targets. DeepLig’s model consists of two networks in interplay: a generative network and a predictive network. The generative network, a Stack- Augmented Recurrent Neural Network, utilizes a stack memory unit to remember and recognize molecular patterns when generating novel ligands from scratch. The generative network passes each newly created ligand to the predictive network, which then uses multiple Graph Attention Networks simultaneously to forecast the average binding affinity of the generated ligand towards multiple target proteins. With each iteration, given feedback from the predictive network, the generative network learns to optimize itself to create molecules with a higher average binding affinity towards multiple proteins. DeepLig was evaluated based on its ability to generate multi-target ligands against two distinct proteins, multi-target ligands against three distinct proteins, and multi-target ligands against two distinct binding pockets on the same protein. With each test case, DeepLig was able to create a library of valid, synthetically accessible, and novel molecules with optimal and equipotent binding energies. We propose that DeepLig provides an effective approach to design multi-targeted drug therapies that can potentially show higher success rates during in-vitro trials.

Keywords: drug design, multitargeticity, de-novo, reinforcement learning

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Authors: Arifur Rahman, Ardeshir Amirkhani, Honghua Hu, Mark Molloy, Karen Vickery

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Introduction and Objectives: Staphylococcus aureus and coagulase-negative staphylococci comprises approximately 65% of infections associated with medical devices and are well known for their biofilm formatting ability. Biofilm-related infections are extremely difficult to eradicate owing to their high tolerance to antibiotics and host immune defences. Currently, there is no efficient method for early biofilm detection. A better understanding to enable detection of biofilm specific proteins in vitro and in vivo can be achieved by studying planktonic and different growth phases of biofilms using a proteome analysis approach. Our goal was to construct a reference map of planktonic and biofilm associated proteins of S. aureus. Methods: S. aureus reference strain (ATCC 25923) was used to grow 24 hours planktonic, 3-day wet biofilm (3DWB), and 12-day wet biofilm (12DWB). Bacteria were grown in tryptic soy broth (TSB) liquid medium. Planktonic growth was used late logarithmic bacteria, and the Centres for Disease Control (CDC) biofilm reactor was used to grow 3 days, and 12-day hydrated biofilms, respectively. Samples were subjected to reduction, alkylation and digestion steps prior to Multiplex labelling using Tandem Mass Tag (TMT) 10-plex reagent (Thermo Fisher Scientific). The labelled samples were pooled and fractionated by high pH RP-HPLC which followed by loading of the fractions on a nanoflow UPLC system (Eksigent UPLC system, AB SCIEX). Mass spectrometry (MS) data were collected on an Orbitrap Elite (Thermo Fisher Scientific) Mass Spectrometer. Protein identification and relative quantitation of protein levels were performed using Proteome Discoverer (version 1.3, Thermo Fisher Scientific). After the extraction of protein ratios with Proteome Discoverer, additional processing, and statistical analysis was done using the TMTPrePro R package. Results and Discussion: The present study showed that a considerable proteomic difference exists among planktonic and biofilms from S. aureus. We identified 1636 total extracellular secreted proteins, of which 350 and 137 proteins of 3DWB and 12DWB showed significant abundance variation from planktonic preparation, respectively. Of these, simultaneous up-regulation in between 3DWB and 12DWB proteins such as extracellular matrix-binding protein ebh, enolase, transketolase, triosephosphate isomerase, chaperonin, peptidase, pyruvate kinase, hydrolase, aminotransferase, ribosomal protein, acetyl-CoA acetyltransferase, DNA gyrase subunit A, glycine glycyltransferase and others we found in this biofilm producer. On the contrary, simultaneous down-regulation in between 3DWB and 12DWB proteins such as alpha and delta-hemolysin, lipoteichoic acid synthase, enterotoxin I, serine protease, lipase, clumping factor B, regulatory protein Spx, phosphoglucomutase, and others also we found in this biofilm producer. In addition, we also identified a big percentage of hypothetical proteins including unique proteins. Therefore, a comprehensive knowledge of planktonic and biofilm associated proteins identified by S. aureus will provide a basis for future studies on the development of vaccines and diagnostic biomarkers. Conclusions: In this study, we constructed an initial reference map of planktonic and various growth phase of biofilm associated proteins which might be helpful to diagnose biofilm associated infections.

Keywords: bacterial biofilms, CDC bioreactor, S. aureus, mass spectrometry, TMT

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Authors: Yahia Massinissa, Melakhessou Med Akram, Mezahdia Mehdi, Marref Salah Eddine

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Cytokines are natural proteins which act as true intercellular communication signals in immune and inflammatory responses. Reverse signaling pathways that activate cytokines help to regulate different functions at the target cell, causing its activation, its proliferation, the differentiation, its survival or death. It was shown that malfunctioning of the cytokine regulation, particularly over-expression, contributes to the onset and development of certain serious diseases such as chronic rheumatoid arthritis, Crohn's disease, psoriasis, lupus. The action mode of Kinoid® technology is based on the principle vaccine: The patient's immune system is activated so that it neutralizes itself and the factor responsible for the disease. When applied specifically to autoimmune diseases, therapeutic vaccination allows the body to neutralize cytokines (proteins) overproduced through a highly targeted stimulation of the immune system.

Keywords: cytokines, Kinoid tech, auto-immune diseases, vaccination

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Authors: Abderrahim Cheriguene, Fatiha Arioui

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The experimental study focuses on the extraction of pectin, whey protein and gelatin, and the study of their functional properties. Microbiological, physicochemical and sensory approach integrated has been implanted to study the effect of the incorporation of these natural food additives in the matrix of a fermented milk type set yogurt, to study the stability of the product during the periods of fermentation and post-acidification over a period of 21 days at 4°C. Pectin was extracted in hot HCl solution. Thermo-precipitation was carried out to obtain the whey proteins while the gelatin was extracted by hydrolysis of the collagen from bovine ossein. The fermented milk was prepared by varying the concentration of the incorporated additives. The measures and controls carried performed periodically on fermented milk experimental tests were carried out: pH, acidity, viscosity, the enumeration of Streptococcus thermophilus, cohesiveness, adhesiveness, taste, aftertaste, whey exudation, and odor. It appears that the acidity, viscosity, and number of Streptococcus thermophilus increased with increasing concentration of additive added in the experimental tests. Indeed, it seems clear that the quality of fermented milk and storability is more improved than the incorporation rate is high. The products showed a better test and a firmer texture limiting the whey exudation.

Keywords: fermented milk, pectin, gelatin, whey proteins, functional properties, quality, conservation, valorization

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Authors: Charbel Aoun, Loic Lagadec

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A Sensor Network (SN) is considered as an operation of two phases: (1) the observation/measuring, which means the accumulation of the gathered data at each sensor node; (2) transferring the collected data to some processing center (e.g., Fusion Servers) within the SN. Therefore, an underwater sensor network can be defined as a sensor network deployed underwater that monitors underwater activity. The deployed sensors, such as Hydrophones, are responsible for registering underwater activity and transferring it to more advanced components. The process of data exchange between the aforementioned components perfectly defines the Marine Observatory (MO) concept which provides information on ocean state, phenomena and processes. The first step towards the implementation of this concept is defining the environmental constraints and the required tools and components (Marine Cables, Smart Sensors, Data Fusion Server, etc). The logical and physical components that are used in these observatories perform some critical functions such as the localization of underwater moving objects. These functions can be orchestrated with other services (e.g. military or civilian reaction). In this paper, we present an extension to our MO meta-model that is used to generate a design tool (ArchiMO). We propose new constraints to be taken into consideration at design time. We illustrate our proposal with an example from the MO domain. Additionally, we generate the corresponding simulation code using our self-developed domain-specific model compiler. On the one hand, this illustrates our approach in relying on Enterprise Architecture (EA) framework that respects: multiple views, perspectives of stakeholders, and domain specificity. On the other hand, it helps reducing both complexity and time spent in design activity, while preventing from design modeling errors during porting this activity in the MO domain. As conclusion, this work aims to demonstrate that we can improve the design activity of complex system based on the use of MDE technologies and a domain-specific modeling language with the associated tooling. The major improvement is to provide an early validation step via models and simulation approach to consolidate the system design.

Keywords: smart sensors, data fusion, distributed fusion architecture, sensor networks, domain specific modeling language, enterprise architecture, underwater moving object, localization, marine observatory, NS-3, IMS

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Authors: Amal Khalifa, Nicolas Vana Santos

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Steganography has been known for centuries as an efficient approach for covert communication. Due to its popularity and ease of access, image steganography has attracted researchers to find secure techniques for hiding information within an innocent looking cover image. In this research, we propose a novel deep-learning approach to digital image steganography. The proposed method, DeepWaveletFusion, uses convolutional neural networks (CNN) to hide a secret image into a cover image of the same size. Two CNNs are trained back-to-back to merge the Discrete Wavelet Transform (DWT) of both colored images and eventually be able to blindly extract the hidden image. Based on two different image similarity metrics, a weighted gain function is used to guide the learning process and maximize the quality of the retrieved secret image and yet maintaining acceptable imperceptibility. Experimental results verified the high recoverability of DeepWaveletFusion which outperformed similar deep-learning-based methods.

Keywords: deep learning, steganography, image, discrete wavelet transform, fusion

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Authors: Jitendar Kumar Tiwari, Ajay Mandal, N. Sathish, A. K. Srivastava

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Since the last decade, graphene achieved great attention toward the progress of multifunction metal matrix composites, which are highly demanded in industries to develop energy-efficient systems. This study covers the two advanced aspects of the latest scientific endeavor, i.e., graphene as reinforcement in metallic materials and additive manufacturing (AM) as a processing technology. Herein, high-quality graphene and AlSi10Mg powder mechanically mixed by very low energy ball milling with 0.1 wt. % and 0.2 wt. % graphene. Mixed powder directly subjected to the powder bed fusion process, i.e., an AM technique to produce composite samples along with bare counterpart. The effects of graphene on porosity, microstructure, and mechanical properties were examined in this study. The volumetric distribution of pores was observed under X-ray computed tomography (CT). On the basis of relative density measurement by X-ray CT, it was observed that porosity increases after graphene addition, and pore morphology also transformed from spherical pores to enlarged flaky pores due to improper melting of composite powder. Furthermore, the microstructure suggests the grain refinement after graphene addition. The columnar grains were able to cross the melt pool boundaries in case of the bare sample, unlike composite samples. The smaller columnar grains were formed in composites due to heterogeneous nucleation by graphene platelets during solidification. The tensile properties get affected due to induced porosity irrespective of graphene reinforcement. The optimized tensile properties were achieved at 0.1 wt. % graphene. The increment in yield strength and ultimate tensile strength was 22% and 10%, respectively, for 0.1 wt. % graphene reinforced sample in comparison to bare counterpart while elongation decreases 20% for the same sample. The hardness indentations were taken mostly on the solid region in order to avoid the collapse of the pores. The hardness of the composite was increased progressively with graphene content. Around 30% of increment in hardness was achieved after the addition of 0.2 wt. % graphene. Therefore, it can be concluded that powder bed fusion can be adopted as a suitable technique to develop graphene reinforced AlSi10Mg composite. Though, some further process modification required to avoid the induced porosity after the addition of graphene, which can be addressed in future work.

Keywords: graphene, hardness, porosity, powder bed fusion, tensile properties

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Authors: John Hardy

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The expansion of special operations forces (SOF) in the twenty-first century is often discussed in terms of the size and disposition of SOF units. Research regarding the number SOF personnel, the equipment SOF units procure, and the variety of roles and mission that SOF fulfill in contemporary conflicts paints a fascinating picture of changing expectations for the use of force. A strong indicator of the changing nature of SOF in contemporary conflicts is the fusion of strike and intelligence functions in the SOF in many countries. What were once more distinct roles on the kind of battlefield generally associated with the concept of conventional warfare have become intermingled in the era of persistent conflict which SOF face. This study presents a historical analysis of the co-evolution of the intelligence and direct action functions carried out by SOF in counterterrorism, counterinsurgency, and training and mentoring missions between 2004 and 2016. The study focuses primarily on innovation in the US military and the diffusion of key concepts to US allies first, and then more broadly afterward. The findings show that there were three key phases of evolution throughout the period of study, each coinciding with a process of innovation and doctrinal adaptation. The first phase was characterized by the fusion of intelligence at the tactical and operational levels. The second phase was characterized by the industrial counterterrorism campaigns used by US SOF against irregular enemies in Iraq and Afghanistan. The third phase was characterized by increasing forward collection of actionable intelligence by SOF force elements in the course of direct action raids. The evolution of strike and intelligence functions in SOF operations between 2004 and 2016 was significantly influenced by reciprocity. Intelligence fusion led to more effective targeting, which then increased intelligence collection. Strike and intelligence functions were then enhanced by greater emphasis on intelligence exploitation during operations, which further increased the effectiveness of both strike and intelligence operations.

Keywords: counterinsurgency, counterterrorism, intelligence, irregular warfare, military operations, special operations forces

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Authors: Neha Bhadauria, Indu Gaur, Shilpi Shilpi, Susmita Goswami, Prabir K. Paul

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The aerial surface of plants colonized by Human Enteric Pathogens ()has been implicated in outbreaks of enteric diseases in humans. Practice of organic farming primarily using animal dung as manure and sewage water for irrigation are the most significant source of enteric pathogens on the surface of leaves, fruits and vegetables. The present work aims to have an insight into the molecular mechanism of interaction of Human Enteric Pathogens or their metabolites with cell wall receptors in plants. Tomato plants grown under aseptic conditions at 12 hours L/D photoperiod, 25±1°C and 75% RH were inoculated individually with S. fonticola and K. pneumonia. The leaves from treated plants were sampled after 24 and 48 hours of incubation. The cell wall and cytoplasmic proteins were extracted and isocratically separated on 1D SDS-PAGE. The sampled leaves were also subjected to formaldehyde treatment prior to isolation of cytoplasmic proteins to study protein-protein interactions induced by Human Enteric Pathogens. Protein bands extracted from the gel were subjected to MALDI-TOF-TOF MS analysis. The foremost interaction of Human Enteric Pathogens on the plant surface was found to be cell wall bound receptors which possibly set ups a wave a critical protein-protein interaction in cytoplasm. The study revealed the expression and suppression of specific cytoplasmic and cell wall-bound proteins, some of them being important components of signaling pathways. The results also demonstrated HEP induced rearrangement of signaling pathways which possibly are crucial for adaptation of these pathogens to plant surface. At the end of the study, it can be concluded that controlling the over-expression or suppression of these specific proteins rearrange the signaling pathway thus reduces the outbreaks of food-borne illness.

Keywords: cytoplasmic protein, cell wall-bound protein, Human Enteric Pathogen (HEP), protein-protein interaction

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Authors: Fadilah Aleanizy

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Colicins are a family of bacterial toxins that kill Escherichia coli and other closely related species. The mode of action of colicins involves binding to an outer membrane receptor and translocation across the cell envelope, leading to cytotoxicity through specific targets. The mechanism of colicin cytotoxicity includes a non-specific endonuclease activity or depolarization of the cytoplasmic membrane by pore-forming activity. For Group A colicins, translocation requires an interaction between the N-terminal domain of the colicin and a series of membrane- bound and periplasmic proteins known as the Tol system (TolB, TolR, TolA, TolQ, and Pal and the active domain must be translocated through the outer membranes. Protein-protein interactions are intrinsic to virtually every cellular process. The transient protein-protein interactions of the colicin include the interaction with much more complicated assemblies during colicin translocation across the cellular membrane to its target. The potassium release assay detects variation in the K+ content of bacterial cells (K+in). This assays is used to measure the effect of pore-forming colicins such as ColA on an indicator organism by measuring the changes of the K+ concentration in the external medium (K+out ) that are caused by cell killing with a K+ selective electrode. One of the goals of this work is to employ a quantifiable in-vivo method to spot which Tol protein are more implicated in the interaction with colicin A as it is translocated to its target.

Keywords: K+ efflux, Colicin A, Tol-proteins, E. coli

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Authors: Christopher Leung, Guillermo Becerril-Martinez

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Amyloidosis is a rare systemic disease where abnormal proteins invade various organs and impede their function. Occasionally, they can manifest in a solidary organ such as the heart, lung, and nervous systems; rarely do they manifest in the gallbladder. Diagnosis often requires biopsy of the affected area and histopathology shows deposition of abnormally folded globular proteins called amyloid proteins. This case presents a 69-year-old male with a 3-month history of RUQ pain, diarrhea and non-specific symptoms of tiredness, etc. On imaging, both his US and CT abdomen showed gallbladder wall thickening and pericholecystic fluid, which may represent acute cholecystitis with hypodense lesions around the gallbladder, possibly representing liver abscesses. Given his symptoms of abdominal pain and imaging findings, this gentleman eventually had a laparoscopic cholecystectomy showing a gangrenous gallbladder with a mass on the liver bed. On histopathology, it showed amorphous hyaline eosinophilic material, which Congo-stained confirmed amyloidosis. Amyloidosis explained his non-specific symptoms, he avoided further biopsy, and he was commenced immediately on Lenalidomide. Involvement of the gallbladder is extremely rare, with less than 30 cases around the world. Half of the cases are reported as primary amyloidosis. This case adds to the current literature regarding primary gallbladder amyloidosis. Importantly, this case highlights how laparoscopic cholecystectomy can help with the diagnosis of gallbladder amyloidosis.

Keywords: amyloidosis, cholecystitis, gangrenous cholecystitis, gallbladder, systemic amyloidosis

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Authors: Hosam El-Sayed, Amira Abou El-Kheir, Salwa Mowafi, Marwa Abou Taleb

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Two proteinic biopolymers; namely keratin and sericin, were extracted from their respective natural resources by simple appropriate methods. The said proteins were dissolved in the appropriate solvents followed by regeneration in a form of film polyvinyl alcohol. Proteinium thiocyanate (PTC) composite was prepared by reaction of a regenerated film with potassium thiocyanate in acid medium. In another experiment, the said acidified proteins were reacted with potassium thiocyante before dissolution and regeneration in a form of PTC composite. The possibility of using PTC composite for determination of the concentration of iron III ions in domestic as well as industrial water was examined. The concentration of iron III cations in water was determined spectrophotometrically by measuring the intensity of blood red colour of iron III thiocyanate obtained by interaction of PTC with iron III cation in the tested water sample.

Keywords: iron III cations, protein, sensor, thiocyanate, water

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Authors: Jae Young Song, In-Ohk Ouh, Seyeon Park, Byeong Sul Kang, Soo Dong Cho, In-Soo Cho

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Canine parvovirus (CPV) is a major pathogen of diarrhea disease in dogs. CPV type 2 has three of antigenic variants such as 2a, 2b, and 2c. CPV constructs a small non-enveloped, icosahedral capsid that contains single-stranded DNA. It has capsids that two largely overlapping virion proteins (VP), VP1 (82 kDa), and VP2 (65 kDa). Baculoviruses are insect pathogens that regulate insect populations in nature and are being successfully used to control insect pests. The proteins produced in the baculovirus-expression system are used for instance for functional studies, vaccine preparations, or diagnostics. The vaccines produced by baculovirus-expression system showed elicitation of antibodies. The recombinant baculovirus infected SF9 cells showed broken shape. The recombinant VP2 proteins from cell pellet or supernatant were confirmed by western blotting. The result showed that the recombinant VP2 protein bands were appeared at 65 kDa molecular weight in both cell pellet and supernatant of infected SF9 cell. These results indicated that the recombinant baculovirus infected SF9 cell express the recombinant VP2 protein successfully. In addition, the expressed recombinant VP2 protein is secreted from cell to supernatant. The baculovirus expression system can be used to produce the VP2 protein of CPV 2c. In addition, the secretion property of the expression of VP2 protein may decrease the cost of production, because it can be skipped the cell breaking step. The produced VP2 protein could be used for vaccine and the agent of diagnostic tests. This study provides the foundation of the production of CPV 2c vaccine and the diagnostic agent.

Keywords: baculovirus, canine parvovirus 2c, dog, Korea

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Authors: Tahra ElObeid, Omnya Ahmed, Reem Al-Sharshani, Doaa Dalloul, Jannat Alnattei

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Background: Camelus dormedarius camels are also called ‘the Arabian camels’ and are present in the desert area of North Africa and the Middle East. Recently, camel’s milk has a great attention globally because of their proteins and peptides that have been reported to be beneficial for the health and in the management of many diseases. Objectives: This study was designed to investigate the antioxidant, antimicrobial activity and to evaluate the total phenolic content of camel’s milk proteins in Qatar. Methods: Fresh two camel’s milk samples from Omani breed and called Muhajer (camel’s milk A and B) were collected on the 1st of the December. Both samples were from the same location Al- Shahaniyah, Doha, Qatar, but from different local private farms and feeding system. Camel’s milk A and B were defatted by centrifugation and their proteins were extracted by acid and thermal precipitation. The antioxidant activity was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. Total phenolic compound (TPC) was evaluated by Folin-Ciocalteu reagent (FCR). On the other hand, the antimicrobial activity against eight different type of pathogenic bacteria was evaluated by disc diffusion method and the zone of inhibition was measured. Results: The of the total phenolic content of whole milk in both camel’s milk A and B were significantly the highest among the protein extracts. The % of the DPPH radical inhibition of casein protein in both camel’s milk A and B were significantly the highest among the protein extracts. In this study, there were marked changes in the antibacterial activity in the different camel milk protein extracts. All extracts showed bacterial overgrowth. Conclusion: The antioxidant activity of the camel milk protein extracts correlated to their unique phenolic compounds and bioactive protein peptides. The antimicrobial activity was not detected perhaps due to the technique, the quality, or the extraction method. Overall, camel's milk exhibits a high antioxidant activity, which is responsible for many health benefits besides the nutritional values.

Keywords: camels milk, antioxidant content, antimicrobial activity, proteins, Qatar

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Authors: Navkiran Kaur, Apoorva Mathur, Abhishree Agarwal, Sakshi Gupta, Tuhin Rashmi

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Aim: Breast cancer is the most common cancer in women worldwide, and resistance to the current therapeutics, often concurrently, is an increasing clinical challenge. Glycosylation of proteins is one of the most important post-translational modifications. It is widely known that aberrant glycosylation has been implicated in many different diseases due to changes associated with biological function and protein folding. Alterations in cell surface glycosylation, can promote invasive behavior of tumor cells that ultimately lead to the progression of cancer. In breast cancer, there is an increasing evidence pertaining to the role of glycosylation in tumor formation and metastasis. In the present study, an attempt has been made to study the disease associated sialoglycoproteins in breast cancer by using bioinformatics tools. The sequence will be retrieved from UniProt database. A database in the form of a word document was made by a collection of FASTA sequences of breast cancer gene sequence. Glycosylation was studied using yinOyang tool on ExPASy and Differential genes expression and protein analysis was done in context of breast cancer metastasis. The number of residues predicted O-glc NAc threshold containing 50 aberrant glycosylation sites or more was detected and recorded for individual sequence. We found that the there is a significant change in the expression profiling of glycosylation patterns of various proteins associated with breast cancer. Differential aberrant glycosylated proteins in breast cancer cells with respect to non-neoplastic cells are an important factor for the overall progression and development of cancer.

Keywords: breast cancer, bioinformatics, cancer, metastasis, glycosylation

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Authors: Ozlem Oral, Seval Kilic, Ozlem Yedier, Serap Dokmeci, Devrim Gozuacik

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Autophagy is a degradation pathway, activating under stress conditions. It digests macromolecules, such as abnormal proteins and long-lived organelles by engulfing them and by subsequent delivery of the cargo to lysosomes. The members of the phospholipid-dependent serine/threonine kinases, involved in many signaling pathways, which are necessary for the regulation of cellular metabolic activation. Previous studies implicate that, serine/threonine kinases have crucial roles in the mechanism of many diseases depend on the activated and/or inactivated signaling pathway. Data indicates, the signaling pathways activated by serine/threonine kinases are also involved in activation of autophagy mechanism. However, the information about the effect of serine/threonine kinases on autophagy mechanism and the roles of these effects in disease formation is limited. In this study, we investigated the effect of activated serine/threonine kinases on autophagic pathway. We performed a commonly used autophagy technique, GFP-LC3 dot formation and by using microscopy analyses, we evaluated promotion and/or inhibition of autophagy in serine/threonine kinase-overexpressed fibroblasts as well as cancer cells. In addition, we carried out confocal microscopy analyses and examined autophagic flux by utilizing the differential pH sensitivities of RFP and GFP in mRFP-GFP-LC3 probe. Based on the shRNA-library based screening, we identified autophagy-related proteins affected by serine/threonine kinases. We further studied the involvement of serine/threonine kinases on the molecular mechanism of newly identified autophagy proteins and found that, autophagic pathway is indirectly controlled by serine/threonine kinases via specific autophagic proteins. Our data indicate the molecular connection between two critical cellular mechanisms, which have important roles in the formation of many disease pathologies, particularly cancer. This project is supported by TUBITAK-1001-Scientific and Technological Research Projects Funding Program, Project No: 114Z836.

Keywords: autophagy, GFP-LC3 dot formation assay, serine/threonine kinases, shRNA-library screening

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Authors: Yezli-Touiker Samira, Amrani-Kirane Leila, Soltani Mazouni Nadia

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Due to secondary effects of conventional insecticides on the environment, the agrochemical research has resulted in the discovery of novel molecules. That research work will help in the development of a new group of pesticides that may be cheaper and less hazardous to the environment and non-target organisms which is the main desired outcome of the present work. Angiotensin-converting enzyme as a target for the development of novel insect growth regulators. Captopril is an inhibitor of angiotensin converting enzyme (ACE) it was tested in vivo by topical application on reproduction of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae). The compound is diluted in acetone and applied topically to newly emerged pupae (10µg/ 2µl). The effects of this molecule was studied,on the biochemistry of ovary (on amounts nucleic acid, proteins, the qualitative analysis of the ovarian proteins and the reproductive potential (duration of the pre-oviposition, duration of the oviposition, number of eggs laid and hatching percentage). Captopril reduces significantly quantity of ovarian proteins and nucleic acid. The electrophoresis profile reveals the absence of tree bands at the treated series. This molecule reduced the duration of the oviposition period, the fecundity and the eggviability.

Keywords: environment, ephestia kuehniella, captopril, reproduction, the agrochemical research

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Authors: Abu Salim Mustafa

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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.

Keywords: genomic regions of differences, Mycobacterium tuberculossis, peptides, serodiagnosis

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