Search results for: fusion proteins

Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

Abstract:

Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

Procedia PDF Downloads 409

Authors: Fawzyah Albaldi

Abstract:

Urinary tract infections (UTIs) are the most prevalent of infectious diseases and > 80% are caused by uropathogenic E. coli (UPEC). Infection occurs following adhesion to urothelial plaques on bladder epithelial cells, whose major protein constituent are the uroplakins (UPs). Two of the four uroplakins (UPIa and UPIb) are members of the tetraspanin superfamily. The UPEC adhesin FimH is known to interact directly with UPIa. Tetraspanins are a diverse family of transmembrane proteins that generally act as “molecular organizers” by binding different proteins and lipids to form tetraspanin enriched microdomains (TEMs). Previous work by our group has shown that TEMs are involved in the adhesion of many pathogenic bacteria to human cells. Adhesion can be blocked by tetraspanin-derived synthetic peptides, suggesting that tetraspanins may be valuable drug targets. In this study, we investigate the role of tetraspanins in UPEC adherence to bladder epithelial cells. Human bladder cancer cell lines (T24, 5637, RT4), commonly used as in-vitro models to investigate UPEC infection, along with primary human bladder cells, were used in this project. The aim was to establish a model for UPEC adhesion/infection with the objective of evaluating the impact of tetraspanin-derived reagents on this process. Such reagents could reduce the progression of UTI, particularly in patients with indwelling catheters. Tetraspanin expression on the bladder cells was investigated by q-PCR and flow cytometry, with CD9 and CD81 generally highly expressed. Interestingly, despite these cell lines being used by other groups to investigate FimH antagonists, uroplakin proteins (UPIa, UPIb and UPIII) were poorly expressed at the cell surface, although some were present intracellularly. Attempts were made to differentiate the cell lines, to induce cell surface expression of these UPs, but these were largely unsuccessful. Pre-treatment of bladder epithelial cells with anti-CD9 monoclonal antibody significantly decreased UPEC infection, whilst anti-CD81 had no effects. A short (15aa) synthetic peptide corresponding to the large extracellular region (EC2) of CD9 also significantly reduced UPEC adherence. Furthermore, we demonstrated specific binding of that fluorescently tagged peptide to the cells. CD9 is known to associate with a number of heparan sulphate proteoglycans (HSPGs) that have also been implicated in bacterial adhesion. Here, we demonstrated that unfractionated heparin (UFH)and heparin analogs significantly inhibited UPEC adhesion to RT4 cells, as did pre-treatment of the cells with heparinases. Pre-treatment with chondroitin sulphate (CS) and chondroitinase also significantly decreased UPEC adherence to RT4 cells. This study may shed light on a common pathogenicity mechanism involving the organisation of HSPGs by tetraspanins. In summary, although we determined that the bladder cell lines were not suitable to investigate the role of uroplakins in UPEC adhesion, we demonstrated roles for CD9 and cell surface proteoglycans in this interaction. Agents that target these may be useful in treating/preventing UTIs.

Keywords: UTIs, tspan, uroplakins, CD9

Procedia PDF Downloads 100

Authors: Qimin Shi, Yi Sun, Constantinus Politis, Shoufeng Yang

Abstract:

In-situ preparation of particle-reinforced aluminium matrix composites (PRAMCs) by laser powder bed fusion (LPBF) additive manufacturing is a promising strategy to strengthen traditional Al-based alloys. The laser-driven thermite reaction can be a practical mechanism to in-situ synthesize PRAMCs. However, introducing oxygen elements through adding Fe₂O₃ makes the powder mixture highly sensitive to form porosity and Al₂O₃ film during LPBF, bringing challenges to producing dense Al-based materials. Therefore, this work develops a processing strategy combined with consecutive high-energy laser melting scanning and low-energy laser remelting scanning to prepare PRAMCs from a Fe₂O₃/AlSi12 powder mixture. The powder mixture consists of 5 wt% Fe₂O₃ and the remainder AlSi12 powder. The addition of 5 wt% Fe₂O₃ aims to achieve balanced strength and ductility. A high relative density (98.2 ± 0.55 %) was successfully obtained by optimizing laser melting (Emelting) and laser remelting surface energy density (Eremelting) to Emelting = 35 J/mm² and Eremelting = 5 J/mm². Results further reveal the necessity of increasing Emelting, to improve metal liquid’s spreading/wetting by breaking up the Al₂O₃ films surrounding the molten pools; however, the high-energy laser melting produced much porosity, including H₂₋, O₂₋ and keyhole-induced pores. The subsequent low-energy laser remelting could close the resulting internal pores, backfill open gaps and smoothen solidified surfaces. As a result, the material was densified by repeating laser melting and laser remelting layer by layer. Although with two-times laser scanning, the microstructure still shows fine cellular Si networks with Al grains inside (grain size of about 370 nm) and in-situ nano-precipitates (Al₂O₃, Si, and Al-Fe(-Si) intermetallics). Finally, the fine microstructure, nano-structured dispersion strengthening, and high-level densification strengthened the in-situ PRAMCs, reaching yield strength of 426 ± 4 MPa and tensile strength of 473 ± 6 MPa. Furthermore, the results can expect to provide valuable information to process other powder mixtures with severe porosity/oxide-film formation potential, considering the evidenced contribution of laser melting/remelting strategy to densify material and obtain good mechanical properties during LPBF.

Keywords: densification, laser powder bed fusion, metal matrix composites, microstructures, mechanical properties

Procedia PDF Downloads 150

Authors: Yasser Ahmed Mahmoud Ali Helal

Abstract:

The use of CAD (Computer Aided Design) technology is ubiquitous in the architecture, engineering and construction (AEC) industry. This has led to its inclusion in the curriculum of architecture schools in Nigeria as an important part of the training module. This article examines the ethical issues involved in implementing CAD (Computer Aided Design) content into the architectural education curriculum. Using existing literature, this study begins with the benefits of integrating CAD into architectural education and the responsibilities of different stakeholders in the implementation process. It also examines issues related to the negative use of information technology and the perceived negative impact of CAD use on design creativity. Using a survey method, data from the architecture department of University was collected to serve as a case study on how the issues raised were being addressed. The article draws conclusions on what ensures successful ethical implementation. Millions of people around the world suffer from hepatitis C, one of the world's deadliest diseases. Interferon (IFN) is treatment options for patients with hepatitis C, but these treatments have their side effects. Our research focused on developing an oral small molecule drug that targets hepatitis C virus (HCV) proteins and has fewer side effects. Our current study aims to develop a drug based on a small molecule antiviral drug specific for the hepatitis C virus (HCV). Drug development using laboratory experiments is not only expensive, but also time-consuming to conduct these experiments. Instead, in this in silicon study, we used computational techniques to propose a specific antiviral drug for the protein domains of found in the hepatitis C virus. This study used homology modeling and abs initio modeling to generate the 3D structure of the proteins, then identifying pockets in the proteins. Acceptable lagans for pocket drugs have been developed using the de novo drug design method. Pocket geometry is taken into account when designing ligands. Among the various lagans generated, a new specific for each of the HCV protein domains has been proposed.

Keywords: drug design, anti-viral drug, in-silicon drug design, hepatitis C virus (HCV) CAD (Computer Aided Design), CAD education, education improvement, small-size contractor automatic pharmacy, PLC, control system, management system, communication

Procedia PDF Downloads 68

Authors: Othman Maklouf, Ahmed Adwaib

Abstract:

This paper introduces a comparative study between the main GPS/INS coupling schemes, this will include the loosely coupled and tightly coupled configurations, several types of situations and operational conditions, in which the data fusion process is done using Kalman filtering. This will include the importance of sensors calibration as well as the alignment of the strap down inertial navigation system. The limitations of the inertial navigation systems are investigated.

Keywords: GPS, INS, Kalman filter, sensor calibration, navigation system

Procedia PDF Downloads 583

Authors: Dinara Ikramova, Karin A. Hing, Simon C. F. Rawlinson

Abstract:

Silicate-substituted hydroxyapatite (SiHA) has been shown to enhance bone regeneration in vivo compared with phase pure stoichiometric hydroxyapatite. Evidence suggests that substrate chemistry dependent formation of a permissive protein layer on the surface of synthetic bone graft substitute materials is key for bioactivity and cell attachment. However, little information is available on whether the substrate chemistry may affect cell migration and recruitment. The aim of this study is to investigate whether or not human Mesenchymal Stem Cells (hMSCs) exhibit a chemotactic response to SiHA porous granules and if it can be linked to either the ion exchange or protein sequestering and enrichment on the surface of the material. 150mg of SiHA granules with 80% total porosity and 20% strut porosity were incubated in 1ml of either Serum Free Media (SFM) or 10% Serum Containing Media (SCM) under static cell culture conditions (37°C, 5% CO2) in absence of cells. Protein sequestering and exchange of calcium, phosphate and silicate ions were analysed at 0.5, 1, 2, 4, 8, 16 and 24 hours with n=12 per time point. Migration of hMSCs in the presence of 150mg of SiHA granules was assessed over 24 hours using a modified transwell migration system in either SFM or SCM (n=6) with 30% serum containing media acting as a positive control. At 24 hours protein sequestering and ionic exchange were analysed, and the number of cells was quantified using a high throughput confocal microscope (IN Cell Analyser 6000). In acellular condition, both calcium and phosphate ion concentrations in media showed a decrease at 24 hours which was greater in SFM than in SCM. This suggests possible formation and precipitation of a bone like apatite on the surface of SiHA. Reduction in this activity observed in SCM indicates that the presence of serum proteins is interfering with the ion exchange at the material and media interface. Adsorbed protein levels showed fluctuation over time followed by sharp decrease at 24 hours, suggesting a possible protein rearrangement on the surface of the material. The ion analysis performed on SFM and SCM after 24-hour incubation with cells in the presence of granules showed a greater reduction in phosphate concentration in both SFM and SCM compared to phosphate levels in acellular condition. Silicate concentration in SCM increased from 1.6mM (absence of cells) to 5.1mM (presence of cells). This indicates that the cells are promoting the uptake of phosphate and release of silicate ions. No significant change was seen in levels of adsorbed proteins in the presence and absence of cells. Further analysis is required to determine whether the species of these proteins change over time. The analysis of cell migration after 24-hour incubation showed more cells migrating towards the granules, 12.7% in SFM and 8.3% in SCM, than in positive control, 4.5% in SFM and 3.6% in SCM respectively. These results suggest that SiHA has a chemotactic activity independent of serum proteins. A property which has not previously been demonstrated for a synthetic bone graft material.

Keywords: cell migration, hMSCs, SiHA, transwell migration system

Procedia PDF Downloads 127

Authors: Muhasin Koyiloth, Sathyanarayana N. Gummadi

Abstract:

Biological membranes are ordered association of lipids, proteins, and carbohydrates. Lipids except sterols possess asymmetric distribution across the bilayer. Eukaryotic membranes possess a group of lipid translocators called scramblases that disrupt phospholipid asymmetry. Their action is implicated in cell activation during wound healing and phagocytic clearance of apoptotic cells. Cholesterol is one of the major membrane lipids distributed evenly on both the leaflet and can directly influence the membrane fluidity through the ordering effect. The fluidity has an impact on the activity of several membrane proteins. The palmitoylated phospholipid scramblases localized to the lipid raft which is characterized by a higher number of sterols. Here we propose that cholesterol can interact with scramblases through putative CRAC motif and can modulate their activity. To prove this, we reconstituted phospholipid scramblase 1 of C. elegans (SCRM-1) in proteoliposomes containing different amounts of cholesterol (Liquid ordered/Lo). We noted that the presence of cholesterol reduced the scramblase activity of wild-type SCRM-1. The interaction between SCRM-1 and cholesterol was confirmed by fluorescence spectroscopy using NBD-Chol. Also, we observed loss of such interaction when one of I273 in the CRAC motif mutated to Asp. Interestingly, the point mutant has partially retained scramblase activity in Lo vesicles. The current study elucidated the important interaction between cholesterol and SCRM-1 to fine-tune its activity in artificial membranes.

Keywords: artificial membranes, CRAC motif, plasma membrane, PL scramblase

Procedia PDF Downloads 172

Authors: Peter Edwar Mortada Nasif

Abstract:

The use of CAD (Computer Aided Design) technology is ubiquitous in the architecture, engineering and construction (AEC) industry. This has led to its inclusion in the curriculum of architecture schools in Nigeria as an important part of the training module. This article examines the ethical issues involved in implementing CAD (Computer Aided Design) content into the architectural education curriculum. Using existing literature, this study begins with the benefits of integrating CAD into architectural education and the responsibilities of different stakeholders in the implementation process. It also examines issues related to the negative use of information technology and the perceived negative impact of CAD use on design creativity. Using a survey method, data from the architecture department of Chukwuemeka Odumegwu Ojukwu Uli University was collected to serve as a case study on how the issues raised were being addressed. The article draws conclusions on what ensures successful ethical implementation. Millions of people around the world suffer from hepatitis C, one of the world's deadliest diseases. Interferon (IFN) is treatment options for patients with hepatitis C, but these treatments have their side effects. Our research focused on developing an oral small molecule drug that targets hepatitis C virus (HCV) proteins and has fewer side effects. Our current study aims to develop a drug based on a small molecule antiviral drug specific for the hepatitis C virus (HCV). Drug development using laboratory experiments is not only expensive, but also time-consuming to conduct these experiments. Instead, in this in silicon study, we used computational techniques to propose a specific antiviral drug for the protein domains of found in the hepatitis C virus. This study used homology modeling and abs initio modeling to generate the 3D structure of the proteins, then identifying pockets in the proteins. Acceptable lagans for pocket drugs have been developed using the de novo drug design method. Pocket geometry is taken into account when designing ligands. Among the various lagans generated, a new specific for each of the HCV protein domains has been proposed.

Keywords: drug design, anti-viral drug, in-silicon drug design, hepatitis C virus, computer aided design, CAD education, education improvement, small-size contractor automatic pharmacy, PLC, control system, management system, communication

Procedia PDF Downloads 11

Authors: Kevin Kellner, Nga Lao, Orla Coleman, Paula Meleady, Niall Barron

Abstract:

Chinese Hamster Ovary (CHO) cells are the prominent cell line used in biopharmaceutical production. To improve yields and find beneficial bioprocess phenotypes genetic engineering plays an essential role in recent research. The miR-23 cluster, specifically miR-24 and miR-27, was first identified as differentially expressed during hypothermic conditions suggesting a role in proliferation and productivity in CHO cells. In this study, we used sponge decoy technology to stably deplete the miRNA expression of the cluster. Furthermore, we implemented the CRISPR/Cas9 system to knockdown miRNA expression. Sponge constructs were designed for an imperfect binding of the miRNA target, protecting from RISC mediated cleavage. GuideRNAs for the CRISPR/Cas9 system were designed to target the seed region of the miRNA. The expression of mature miRNA and precursor were confirmed using RT-qPCR. For both approaches stable expressing mixed populations were generated and characterised in batch cultures. It was shown, that CRISPR/Cas9 can be implemented in CHO cells with achieving high knockdown efficacy of every single member of the cluster. Targeting of one miRNA member showed that its genomic paralog is successfully targeted as well. The stable depletion of miR-24 using CRISPR/Cas9 showed increased growth and specific productivity in a CHO-K1 mAb expressing cell line. This phenotype was further characterized using quantitative label-free LC-MS/MS showing 186 proteins differently expressed with 19 involved in proliferation and 26 involved in protein folding/translation. Targeting miR-27 in the same cell line showed increased viability in late stages of the culture compared to the control. To evaluate the phenotype in an industry relevant cell line; the miR-23 cluster, miR-24 and miR-27 were stably depleted in a Fc fusion CHO-S cell line which showed increased batch titers up to 1.5-fold. In this work, we highlighted that the stable depletion of the miR-23 cluster and its members can improve the bioprocess phenotype concerning growth and productivity in two different cell lines. Furthermore, we showed that using CRISPR/Cas9 is comparable to the traditional sponge decoy technology.

Keywords: Chinese Hamster ovary cells, CRISPR/Cas9, microRNAs, sponge decoy technology

Procedia PDF Downloads 192

Authors: Srishti Sinha, Deepti Tikariha, Kallol K. Ghosh

Abstract:

Over the past few decades protein-surfactant interactions have been a subject of extensive studies as they are of great importance in wide variety of industries, biological, pharmaceutical and cosmetic systems. Protein-surfactant interactions have been explored the effect of surfactants on structure of protein in the form of solubilization and denaturing or renaturing of protein. Globular proteins are frequently used as functional ingredients in healthcare and pharmaceutical products, due to their ability to catalyze biochemical reactions, to be adsorbed on the surface of some substance and to bind other moieties and form molecular aggregates. One of the most widely used globular protein is bovine serum albumin (BSA), since it has a well-known primary structure and been associated with the binding of many different categories of molecules, such as dyes, drugs and toxic chemicals. Protein−surfactant interactions are usually dependent on the surfactant features. Most of the research has been focused on single-chain surfactants. More recently, the binding between proteins and dimeric surfactants has been discussed. In present study interactions of one dimeric surfactant Butanediyl-1,4-bis (dimethylhexadecylammonium bromide) (16-4-16, 2Br-) and the corresponding single-chain surfactant cetyl trimethylammonium bromide (CTAB) with bovine serum albumin (BSA) have been investigated by surface tension and spectrofluoremetric methods. It has been found that the bindings of all gemini surfactant to BSA were cooperatively driven by electrostatic and hydrophobic interactions. The gemini surfactant carrying more charges and hydrophobic tails, showed stronger interactions with BSA than the single-chain surfactant.

Keywords: bovine serum albumin, gemini surfactants, hydrophobic interactions, protein surfactant interaction

Procedia PDF Downloads 504

Authors: Ilya B. Tsyrlov, Dmitry Y. Oshchepkov

Abstract:

A computational search for dioxin response elements (DREs) in genes of proteins comprising the Ah receptor (AhR) cytosolic core complex was performed by highly efficient tool SITECON. Eventually, the following number of new DREs in 5’flanking region was detected by SITECON: one in AHR gene, five in XAP2, eight in HSP90AA1, and three in HSP90AB1 genes. Numerous DREs found in genes of AhR and AhR cytosolic complex members would shed a light on potential mechanisms of expression, the stoichiometry of unliganded AhR core complex, and its degradation vs biosynthesis dynamics resulted from treatment of target cells with the AhR most potent ligand, 2,3,7,8-TCDD. With human viruses, reduced susceptibility to TCDD of geneencoding HIV-1 P247 was justified by the only potential DRE determined in gag gene encoding HIV-1 P24 protein, whereas the regulatory region of CMV genes encoding IE gp/UL37 has five potent DRE, 1.65 kb/UL36 – six DRE, pp65 and pp71 – each has seven DRE, and pp150 – ten DRE. Also, from six to eight DRE were determined with SITECON in the regulatory region of HSV-1 IE genes encoding tegument proteins, UL36 and UL37, and of UL19 gene encoding bindingglycoprotein C (gC). So, TCDD in the low picomolar range may activate in human cells AhR: Arnt transcription pathway that triggers CMV and HSV-1 reactivation by binding to numerous promoter DRE within immediate-early (IE) genes UL37 and UL36, thus committing virus to the lytic cycle.

Keywords: dioxin response elements, Ah receptor, AhR: Arnt transcription pathway, human and viral genes

Procedia PDF Downloads 102

Authors: Marjan Javanmard

Abstract:

The rheological properties of dairy products critically depend on the underlying organisation of proteins at multiple length scales. When heated and acidified, milk proteins form particle gel that is viscoelastic, solvent rich, ‘soft’ material. In this work recent developments on the rheology of soft particles suspensions were used to interpret and potentially define the properties of dairy gel structures. It is discovered that at volume fractions below random close packing (RCP), the Maron-Pierce-Quemada (MPQ) model accurately predicts the viscosity of the dairy gel suspensions without fitting parameters; the MPQ model has been shown previously to provide reasonable predictions of the viscosity of hard sphere suspensions from the volume fraction, solvent viscosity and RCP. This surprising finding demonstrates that up to RCP, the dairy gel system behaves as a hard sphere suspension and that the structural aggregates behave as discrete particulates akin to what is observed for microgel suspensions. At effective phase volumes well above RCP, the system is a soft solid. In this region, it is discovered that the storage modulus of the sheared AMG scales with the storage modulus of the set gel. The storage modulus in this regime is reasonably well described as a function of effective phase volume by the Evans and Lips model. Findings of this work has potential to aid in rational design and control of dairy food structure-properties.

Keywords: dairy suspensions, rheology-structure, Maron-Pierce-Quemada Model, Evans and Lips Model

Procedia PDF Downloads 215

Authors: Angela U. Makolo, Temitayo A. Olagunju

Abstract:

The knowledge of signaling pathways is central to understanding the biological mechanisms of organisms since it has been identified that in eukaryotic organisms, the number of signaling pathways determines the number of ways the organism will react to external stimuli. Signaling pathways are studied using protein interaction networks constructed from protein-protein interaction data obtained using high throughput experimental procedures. However, these high throughput methods are known to produce very high rates of false positive and negative interactions. In order to construct a useful protein interaction network from this noisy data, computational methods are applied to validate the protein-protein interactions. In this study, a computational technique to identify signaling pathways from a protein interaction network constructed using validated protein-protein interaction data was designed. A weighted interaction graph of the Saccharomyces cerevisiae (Baker’s Yeast) organism using the proteins as the nodes and interactions between them as edges was constructed. The weights were obtained using Bayesian probabilistic network to estimate the posterior probability of interaction between two proteins given the gene expression measurement as biological evidence. Only interactions above a threshold were accepted for the network model. A pathway was formalized as a simple path in the interaction network from a starting protein and an ending protein of interest. We were able to identify some pathway segments, one of which is a segment of the pathway that signals the start of the process of meiosis in S. cerevisiae.

Keywords: Bayesian networks, protein interaction networks, Saccharomyces cerevisiae, signalling pathways

Procedia PDF Downloads 534

Authors: Javed Mohammed

Abstract:

Right now, bio-medical infrastructure lags well behind the curve. Our healthcare system is dispersed and disjointed; medical records are a bit of a mess; and we do not yet have the capacity to store and process the crazy amounts of data coming our way from widespread whole-genome sequencing. And then there are privacy issues. Despite these infrastructure challenges, some researchers are plunging into bio medical Big Data now, in hopes of extracting new and actionable knowledge. They are doing delving into molecular-level data to discover bio markers that help classify patients based on their response to existing treatments; and pushing their results out to physicians in novel and creative ways. Computer scientists and bio medical researchers are able to transform data into models and simulations that will enable scientists for the first time to gain a profound under-standing of the deepest biological functions. Solving biological problems may require High-Performance Computing HPC due either to the massive parallel computation required to solve a particular problem or to algorithmic complexity that may range from difficult to intractable. Many problems involve seemingly well-behaved polynomial time algorithms (such as all-to-all comparisons) but have massive computational requirements due to the large data sets that must be analyzed. High-throughput techniques for DNA sequencing and analysis of gene expression have led to exponential growth in the amount of publicly available genomic data. With the increased availability of genomic data traditional database approaches are no longer sufficient for rapidly performing life science queries involving the fusion of data types. Computing systems are now so powerful it is possible for researchers to consider modeling the folding of a protein or even the simulation of an entire human body. This research paper emphasizes the computational biology's growing need for high-performance computing and Big Data. It illustrates this article’s indispensability in meeting the scientific and engineering challenges of the twenty-first century, and how Protein Folding (the structure and function of proteins) and Phylogeny Reconstruction (evolutionary history of a group of genes) can use HPC that provides sufficient capability for evaluating or solving more limited but meaningful instances. This article also indicates solutions to optimization problems, and benefits Big Data and Computational Biology. The article illustrates the Current State-of-the-Art and Future-Generation Biology of HPC Computing with Big Data.

Keywords: high performance, big data, parallel computation, molecular data, computational biology

Procedia PDF Downloads 359

Authors: Amtul Jamil Sami

Abstract:

Apis mellifera is an insect of immense economic importance lives on rich carbohydrate diet including cellulose, nectar, honey and pollen. The carbohydrate metabolism in A mellifera has not been understood fully, as there are no data available, on the functional expression of cellulase gene. The cellulose hydrolyzing enzyme is required for the digestion of pollen cellulose wall, to release the important nutrients (amino acids, minerals, vitamins etc.) from the pollen. A dissection of Apis genome had revealed that there is one gene present for the expression of endo-beta-1,4-glucanase, for cellulose hydrolysis. In the presented work, functional expression of endo-beta-1,4 glucanase gene is reported. Total soluble proteins of the honey bee were isolated and were tested cellulose hydrolyzing enzyme activity, using carboxy-methyl cellulose, as a substrate. A mellifera proteins were able to hydrolyze carboxy-methyl cellulose, confirming its endo- type mode of action. Endo beta-1,4 glucanase enzyme was only present in the gut tissues, no activity was detected in the salivary glands. The pH optima of the enzyme were in the acidic pH range of 4-5-5-0, indicating its metabolic role in the acidic stomach of A mellifera. The reported enzyme is unique, as endo-beta- 1,4 glucanase was able to generate non reducing sugar, as an end product. The results presented, are supportive to the information that the honey bee is capable of producing its novel endo-beta-1,4 glucanase. Further it could be helpful, in understanding, the carbohydrate metabolism in A mellifera.

Keywords: honey bees, Endo-beta 1, 4- glucanase, Apis mellifera, functional expression

Procedia PDF Downloads 395

Authors: Thi Thao Ninh, Yuri Trusov, José Ramón Botella

Abstract:

Heterotrimeric G proteins, comprised of three subunits, α, β and γ, are involved in signal transduction pathways that mediate a vast number of processes across the eukaryotic kingdom. 23 Gα subunits are present in humans whereas most plant genomes encode for only one canonical Gα. The disparity observed between Arabidopsis, rice, and maize Gα-deficient mutant phenotypes suggest that Gα functions have diversified between eudicots and monocots during evolution. Alternatively, since the only Gα mutations available in dicots have been produced in Arabidopsis, the possibility exists that this species might be an exception to the rule. In order to test this hypothesis, we studied the G protein α subunit (TGA1) in tomato. Four tga1 knockout lines were generated in tomato cultivar Moneymaker using CRISPR/Cas9. The tga1 mutants exhibit a number of auxin-related phenotypes including changes in leaf shape, reduced plant height, fruit size and number of seeds per fruit. In addition, tga1 mutants have increased sensitivity to abscisic acid during seed germination, reduced sensitivity to exogenous auxin during adventitious root formation from cotyledons and excised hypocotyl explants. Our results suggest that Gα mutant phenotypes in tomato are very similar to those observed in monocots, i.e. rice and maize, and cast doubts about the validity of using Arabidopsis as a model system for plant G protein studies.

Keywords: auxin-related phenotypes, CRISPR/Cas9, G protein α subunit, heterotrimeric G proteins, tomato

Procedia PDF Downloads 127

Authors: Gadiri Sabiha

Abstract:

Introduction: Current allergy diagnostic tools using Multiplex technology have made it possible to increase the efficiency of the search for specific IgE. This opportunity is provided by the newly developed “Alex Biochip”, consisting of a panel of 282 allergens in native and molecular form, a CCD inhibitor, and the potential for detecting cross-reactive allergens. We evaluated the performance of this technology in detecting cross-reactivity in previously explored patients. Material/Method: The sera of 39 patients presenting sensitization and polysensitization profiles were explored. The search for specific IgE is carried out by the Alex ® IgE Biochip, and the results are analyzed by nature and by molecular family of allergens using specific software. Results/Discussion: The analysis gave a particular profile of cross-reactivity allergens: 33% for the Ole e1 family, 31% for NPC2, 26% for storage proteins, 20% for Tropomyosin, 10% for LTPs, 10% for Arginine Kinase and 10% for Uteroglobin CCDs were absent in all patients. The “Ole e1” allergen is responsible for a pollen-pollen cross allergy. The storage proteins found and LTP are not species-specific, causing cross-pollen-food allergy. The nDer p2 of the NPC2 family is responsible for cross-reactivity between mite species. Conclusion: The cross-reactivities responsible for mixed syndromes at diagnosis in our patients were dominated by pollen-pollen and pollen-food syndromes. They allow the identification of severity factors linked to the prognosis and the best-adapted immunotherapy.

Keywords: specific IgE, allergy, cross reactivity, molecular allergens

Procedia PDF Downloads 62

Authors: Mario Hanna Louis Hanna

Abstract:

The use of CAD (pc Aided layout) generation is ubiquitous inside the structure, engineering and construction (AEC) industry. This has led to its inclusion in the curriculum of structure faculties in Nigeria as an important part of the training module. This newsletter examines the moral troubles involved in implementing CAD (pc Aided layout) content into the architectural training curriculum. Using current literature, this study begins with the advantages of integrating CAD into architectural education and the responsibilities of various stakeholders in the implementation process. It also examines issues related to the terrible use of records generation and the perceived bad effect of CAD use on design creativity. The use of a survey technique, information from the architecture department of Chukwuemeka Odumegwu Ojukwu Uli college changed into accumulated to serve as a case observe on how the problems raised have been being addressed. The object draws conclusions on what guarantees a hit moral implementation. Tens of millions of human beings around the sector suffer from hepatitis C, one of the international's deadliest sicknesses. Interferon (IFN) is a remedy alternative for patients with hepatitis C, but these treatments have their aspect outcomes. Our research targeted growing an oral small molecule drug that goals hepatitis C virus (HCV) proteins and has fewer facet effects. Our contemporary study targets to broaden a drug primarily based on a small molecule antiviral drug precise for the hepatitis C virus (HCV). Drug improvement and the use of laboratory experiments isn't always best high-priced, however also time-eating to behavior those experiments. instead, on this in silicon have a look at, we used computational strategies to recommend a particular antiviral drug for the protein domain names of discovered in the hepatitis C virus. This examines used homology modeling and abs initio modeling to generate the 3-D shape of the proteins, then figuring out pockets within the proteins. Proper lagans for pocket pills were advanced the usage of the de novo drug design method. Pocket geometry is taken into consideration while designing ligands. A few of the various lagans generated, a different for each of the HCV protein domains has been proposed.

Keywords: drug design, anti-viral drug, in-silicon drug design, Hepatitis C virus (HCV) CAD (Computer Aided Design), CAD education, education improvement, small-size contractor automatic pharmacy, PLC, control system, management system, communication.

Procedia PDF Downloads 12

Authors: Renata Masarova, Bohuslava Juhasova, Martin Juhas, Zuzana Sutova

Abstract:

In dynamic system theory a mathematical model is often used to describe their properties. In order to find a transfer matrix of a dynamic system we need to calculate an inverse matrix. The paper contains the fusion of the classical theory and the procedures used in the theory of automated control for calculating the inverse matrix. The final part of the paper models the given problem by the Matlab.

Keywords: dynamic system, transfer matrix, inverse matrix, modeling

Procedia PDF Downloads 506

Authors: Harshita Raj, Joydeep Ghosh, Rakesh L. Tanna, Prabal K. Chattopadhyay, K. A. Jadeja, Sharvil Patel, Kaushal M. Patel, Narendra C. Patel, S. B. Bhatt, V. K. Panchal, Chhaya Chavda, C. N. Gupta, D. Raju, S. K. Jha, J. Raval, S. Joisa, S. Purohit, C. V. S. Rao, P. K. Atrey, Umesh Nagora, R. Manchanda, M. B. Chowdhuri, Nilam Ramaiya, S. Banerjee, Y. C. Saxena

Abstract:

Efficient gas fueling is a critical aspect that needs to be mastered in order to maintain plasma density, to carry out fusion. This requires a fair understanding of fuel recycling in order to optimize the gas fueling. In Aditya tokamak, multiple gas puffs are used in a precise and controlled manner, for hydrogen fueling during the flat top of plasma discharge which has been instrumental in achieving discharges with enhanced density as well as energy confinement time. Following each gas puff, we observe peaks in temporal profile of Hα emission, Soft X-ray (SXR) and chord averaged electron density in a number of discharges, indicating efficient gas fueling. Interestingly, Hα temporal profile exhibited an additional peak following the peak corresponding to each gas puff. These additional peak Hα appeared in between the two gas puffs, indicating the presence of a secondary hydrogen source apart from the gas puffs. A thorough investigation revealed that these secondary Hα peaks coincide with Hard X- ray bursts which come from the interaction of runaway electrons with vessel limiters. This leads to consider that the runaway electrons (REs), which hit the wall, in turn, bring out the absorbed hydrogen and oxygen from the wall and makes the interaction of REs with limiter a secondary hydrogen source. These observations suggest that runaway electron induced recycling should also be included in recycling particle source in the particle balance calculations in tokamaks. Observation of two Hα peaks associated with one gas puff and their roles in enhancing and maintaining plasma density in Aditya tokamak will be discussed in this paper.

Keywords: fusion, gas fueling, recycling, Tokamak, Aditya

Procedia PDF Downloads 395

Authors: Wissam Saliba, Mandy Nicholson

Abstract:

Secretory carcinoma (SC) is a rare type of salivary gland cancer. It was first realized as a distinct type of malignancy in 2010and wasinitially termed “mammary analogue secretory carcinoma” because of similarities with secretory breast cancer. The name was later changed to SC. Most SCs originate in parotid glands, and most harbour a rare gene mutation: ETV6-NTRK3. This mutation is rare in common cancers and common in rare cancers; it is present in most secretory carcinomas. Disease outcomes for SC are usually described as favourable as many cases of SC are lowgrade (LG), and cancer growth is slow. In early stages, localized therapy is usually indicated (surgery and/or radiation). Despitea favourable prognosis, a sub-set of casescan be much more aggressive.These cases tend to be of high-grade(HG).HG casesare associated with a poorer prognosis.Management of such cases can be challenging due to limited evidence for effective systemic therapy options. This case report describes the clinical management of a 46-year-oldmale patient with a unique case of SC. He was initially diagnosed with a low/intermediate grade carcinoma of the left parotid gland in 2009; he was treated with surgery and adjuvant radiation. Surgical pathology favoured primary salivary adenocarcinoma, and 2 lymph nodes were positive for malignancy. SC was not yet realized as a distinct type of cancerat the time of diagnosis, and the pathology reportvalidated this gap by stating that the specimen lacked features of the defined types of salivary carcinoma.Slow-growing pulmonary nodules were identified in 2017. In 2020, approximately 11 years after the initial diagnosis, the patient presented with malignant pleural effusion. Pathology from a pleural biopsy was consistent with metastatic poorly differentiated cancer of likely parotid origin, likely mammary analogue secretory carcinoma. The specimen was sent for Next Generation Sequencing (NGS); ETV6-NTRK3 gene fusion was confirmed, and systemic therapy was initiated.One cycle ofcarboplatin/paclitaxel was given in June 2020. He was switched to Larotrectinib (NTRK inhibitor (NTRKi)) later that month. Larotrectinib continued for approximately 9 months, with discontinuation in March 2021 due to disease progression. A second-generation NTRKi (Selitrectinib) was accessed and prescribedthrough a single patient study. Selitrectinib was well tolerated. The patient experienced a complete radiological response within~4 months. Disease progression occurred once again in October 2021. Progression was slow, and Selitrectinib continuedwhile the medical team performed a thorough search for additional treatment options. In January 2022, a liver lesion biopsy was performed, and NGS showed an NTRKG623R solvent-front resistance mutation. Various treatment pathways were considered. The patient pursuedanother investigational NTRKi through a clinical trial, and Selitrectinib was discontinued in July 2022. Excellent performance status was maintained throughout the entire course of treatment.It can be concluded that NTRK inhibitors provided satisfactory treatment efficacy and tolerance for this patient with high-grade transformation and NTRK gene fusion cancer. In the future, more clinical research is needed on systemic treatment options for high-grade transformations in NTRK gene fusion SCs.

Keywords: secretory carcinoma, high-grade transformations, NTRK gene fusion, NTRK inhibitor

Procedia PDF Downloads 106

Authors: Tyler Palma, Praveen Damasus, Michael Munther, Mehrdad Mohsenizadeh, Keivan Davami

Abstract:

The advancement of additive manufacturing, in both research and commercial realms, is highly dependent upon continuing innovations and creativity in materials and designs. Additive manufacturing shows great promise towards revolutionizing various industries, due largely to the fact that design data can be used to create complex products and components, on demand and from the raw materials, for the end user at the point of use. However, it will be critical that the material properties of additively-made parts for engineering purposes be fully understood. As it is a relatively new additive manufacturing method, the response of properties of Multi Jet Fusion (MJF) produced parts to different printing parameters has not been well studied. In this work, testing of mechanical and tribological properties MJF-printed Polyamide 12 parts was performed to determine whether printing orientation in this method results in significantly different part performances. Material properties were studied at macro- and nanoscales. Tensile tests, in combination with tribology tests including steady-state wear, were performed. Results showed a significant difference in resultant part characteristics based on whether they were printed in a vertical or horizontal orientation. Tensile performance of vertically and horizontally printed samples varied, both in ultimate strength and strain. Tribology tests showed that printing orientation has notable effects on the resulting mechanical and wear properties of tested surfaces, due largely to layer orientation and the presence of unfused fused powder grain inclusions. This research advances the understanding of how print orientation affects the mechanical properties of additively manufactured structures, and also how print orientation can be exploited in future engineering design.

Keywords: additive manufacturing, indentation, nano mechanical characterization, print orientation

Procedia PDF Downloads 134

Authors: Rahul Madathiparambil Visalakshan, Alex Cavallaro, John Hayball, Krasimir Vasilev

Abstract:

The role of biomaterial surface nanotopograhy on fibrinogen adsorption and unfolding, and the subsequent immune response were studied. Inconsistent topography and varying chemical functionalities along with a lack of reproducibility pose a challenge in determining the specific effects of nanotopography or chemistry on proteins and cells. It is important to have a well-defined nanotopography with a homogeneous chemistry to study the real effect of nanotopography on biological systems. Therefore, we developed a technique that can produce well-defined and highly reproducible topography to identify the role of specific roughness, size, height and density with the presence of homogeneous chemical functionality. Using plasma polymerisation of oxazoline monomers and immobilized gold nanoparticles we created surfaces with an equal number density of nanoparticles of different sizes. This surface was used to study the role of surface nanotopography and the interplay of surface chemistry on proteins and immune cells. The effect of nanotopography on fibrinogen adsorption was investigated using Quartz Cristal Microbalance with Dissipation and micro BCA. The mass of fibrinogen adsorbed on the surface increased with increasing size of nano-topography. Protein structural changes up on adsorption to the nano rough surface was studied using circular dichroism spectroscopy. Fibrinogen unfolding varied depending on the specific nanotopography of the surfaces. It was revealed that the in vitro immune response to the nanotopography surfaces changed due to this protein unfolding.

Keywords: biomaterial inflammation, protein and cell responses, protein unfolding, surface nanotopography

Procedia PDF Downloads 167

Authors: Silvia Gastaldello, Maria Grillo, Luca Tassoni, Claudio Maran, Stefano Balbo

Abstract:

Antioxidants are nowadays attractive not only for the countless benefits to the human and animal health, but also for the perspective of use as food preservative instead of synthetic chemical molecules. In this study, the radical scavenging activity of six protein extracts from pulse and oleaginous seeds was evaluated. The selected matrices are Pisum sativum (yellow pea from two different origins), Carthamus tinctorius (safflower), Helianthus annuus (sunflower), Lupinus luteus cv Mister (lupin) and Glycine max (soybean), since they are economically interesting for both human and animal nutrition. The seeds were grinded and proteins extracted from 20mg powder with a specific vegetal-extraction kit. Proteins have been quantified through Bradford protocol and scavenging activity was revealed using DPPH assay, based on radical DPPH (2,2-diphenyl-1-picrylhydrazyl) absorbance decrease in the presence of antioxidants molecules. Different concentrations of the protein extract (1, 5, 10, 50, 100, 500 µg/ml) were mixed with DPPH solution (DPPH 0,004% in ethanol 70% v/v). Ascorbic acid was used as a scavenging activity standard reference, at the same six concentrations of protein extracts, while DPPH solution was used as control. Samples and standard were prepared in triplicate and incubated for 30 minutes in dark at room temperature, the absorbance was read at 517nm (ABS30). Average and standard deviation of absorbance values were calculated for each concentration of samples and standard. Statistical analysis using t-students and p-value were performed to assess the statistical significance of the scavenging activity difference between the samples (or standard) and control (ABSctrl). The percentage of antioxidant activity has been calculated using the formula [(ABSctrl-ABS30)/ABSctrl]*100. The obtained results demonstrate that all matrices showed antioxidant activity. Ascorbic acid, used as standard, exhibits a 96% scavenging activity at the concentration of 500 µg/ml. At the same conditions, sunflower, safflower and yellow peas revealed the highest antioxidant performance among the matrices analyzed, with an activity of 74%, 68% and 70% respectively (p < 0.005). Although lupin and soybean exhibit a lower antioxidant activity compared to the other matrices, they showed a percentage of 46 and 36 respectively. All these data suggest the possibility to use undervalued edible matrices as antioxidants source. However, further studies are necessary to investigate a possible synergic effect of several matrices as well as the impact of industrial processes for a large-scale approach.

Keywords: antioxidants, DPPH assay, natural matrices, vegetal proteins

Procedia PDF Downloads 422

Authors: M. Latha, Achintya K. Dolui, P. Vijayaraj

Abstract:

Vegetable oils mainly triacylglycerol (TAG) are an essential nutrient in the human diet as well as one of the major global commodity. There is a pressing need to enhance the yield of oil production to meet the world’s growing demand. Oil content is controlled by the balance between synthesis and breakdown in the cells. Several studies have established to increase the oil content by the overexpression of oil biosynthetic enzymes. Interestingly the significant oil accumulation was observed with impaired TAG hydrolysis. Unfortunately, the structural, as well as the biochemical properties of the lipase enzymes, is widely unknown, and so far, no candidate gene was identified in seeds except sugar-dependent1 (SDP1). Evidence has shown that SDP1directly responsible for initiation of oil breakdown in the seeds during germination. The present study is the identification of seed-specific acyl-hydrolases by activity based proteome profiling (ABPP) using Arabidopsis thaliana as a model system. The ABPP reveals that around 8 to 10 proteins having the serine hydrolase domain and are expressed during germination of Arabidopsis seed. The N-term sequencing, as well as LC-MS/MS analysis, was performed for the differentially expressed protein during germination. The coding region of the identified proteins was cloned, and lipases activity was assessed with purified recombinant protein. The enzyme assay was performed against various lipid substrates, and we have observed the acylhydrolase activity towards lysophosphatidylcholine and monoacylglycerol. Further, the functional characteristic of the identified protein will reveal the physiological significance the enzyme in oil accumulation.

Keywords: lipase, lipids, vegetable oil, triacylglycerol

Procedia PDF Downloads 179

Authors: Kanchan Yadav, Ai-Chuan Chou, Rajesh Kumar Ulaganathan, Hua-De Gao, Hsien-Ming Lee, Chien-Yuan Pan, Yit-Tsong Chen

Abstract:

Optogenetics is an innovative technology now widely adopted by researchers in different fields of the biological sciences. However, due to the weak tissue penetration capability of the short wavelengths used to activate light-sensitive proteins, an invasive light guide has been used in animal studies for photoexcitation of target tissues. Upconverting nanoparticles (UCNPs), which transform near-infrared (NIR) light to short-wavelength emissions, can help address this issue. To improve optogenetic performance, we enhance the target selectivity for optogenetic controls by specifically conjugating the UCNPs with light-sensitive proteins at a molecular level, which shortens the distance as well as enhances the efficiency of energy transfer. We tagged V5 and Lumio epitopes to the extracellular N-terminal of channelrhodopsin-2 with an mCherry conjugated at the intracellular C-terminal (VL-ChR2m) and then bound NeutrAvidin-functionalized UCNPs (NAv-UCNPs) to the VL-ChR2m via a biotinylated antibody against V5 (bV5-Ab). We observed an apparent energy transfer from the excited UCNP (donor) to the bound VL-ChR2m (receptor) by measuring emission-intensity changes at the donor-receptor complex. The successful patch-clamp electrophysiological test and an intracellular Ca2+ elevation observed in the designed UCNP-ChR2 system under optogenetic manipulation confirmed the practical employment of UCNP-assisted NIR-optogenetic functionality. This work represents a significant step toward improving therapeutic optogenetics.

Keywords: Channelrhodopsin-2, near infrared, optogenetics, upconverting nanoparticles

Procedia PDF Downloads 272

Authors: Albina V. Moskvicheva, Gevorg G. Kazarian, Anna R. Valeeva, Marina A. Efimova, Malik N. Mukminov, Eduard A. Shuralev, Rustam Kh. Ravilov, Kamil S. Khaertynov

Abstract:

Improving the early diagnosis of tuberculosis and solving a number of problems associated with the differential diagnosis of Mycobacterium bovis infection, nonspecific tuberculin reactions caused by sensitization of the body by non-tuberculosis mycobacteria, is urgent. The filtrates and extracts of M. bovis cell surface components are promising antigens with diagnostic potential. The purpose of this study was to isolate and characterize antigenic proteins and determine the dominant M. bovis antigens recognized by the humoral immune system. The mycobacterial cells were homogenized on FastPrep-24. Gel-filtration chromatography was used to fractionate the lysates of cell surface component extracts and proteins isolated from M. bovis culture supernatant. The separated fractions were analyzed using two-dimensional gel electrophoresis followed by determination of antigen serological activity using immunoblot with specific hyperimmune rabbit blood serum. As a result of electrophoretic separation of components by molecular weight, 23 antigen fractions were obtained. Analysis of densitograms showed that the fractions contained two zones of antigens with pronounced serological activity, corresponding to molecular weights of 28 and 21 kDa. The high serological activity of the 28 kDa antigen was established by immunoblot using hyperimmune blood sera. Separated and characterized by M. bovis specific antigen with a molecular weight of 28 kDa was added to the collection of specific marker antigens for M. bovis.

Keywords: antigen, gel-filtration chromatography, immunoblot, Mycobacterium bovis

Procedia PDF Downloads 132

Authors: Zoe Goldberger, Priscilla S. Briquez, Jeffrey A. Hubbell

Abstract:

Tumor cells have mutations resulting from genetic instability that the immune system can actively recognize. Immune checkpoint immunotherapy (ICI) is commonly used in the clinic to re-activate immune reactions against mutated proteins, called neoantigens, resulting in tumor remission in cancer patients. However, only around 20% of patients show durable response to ICI. While tumor mutational burden (TMB) has been approved by the Food and Drug Administration (FDA) as a criterion for ICI therapy, the relevance of the subcellular localizations of the mutated proteins within the tumor cell has not been investigated. Here, we hypothesized that localization of mutations impacts the effect of immune responsiveness to ICI. We analyzed publicly available tumor mutation sequencing data of ICI treated patients from 3 independent datasets. We extracted the subcellular localization from the UniProtKB/Swiss-Prot database and quantified the proportion of membrane, cytoplasmic, nuclear, or secreted mutations per patient. We analyzed this information in relation to response to ICI treatment and overall survival of patients showing with 1722 ICI-treated patients that high mutational burden localized at the membrane (mTMB), correlate with ICI responsiveness, and improved overall survival in multiple cancer types. We anticipate that our results will ameliorate predictability of cancer patient response to ICI with potential implications in clinical guidelines to tailor ICI treatment. This would not only increase patient survival for those receiving ICI, but also patients’ quality of life by reducing the number of patients enduring non-effective ICI treatments.

Keywords: cancer, immunotherapy, membrane neoantigens, efficacy prediction, biomarkers

Procedia PDF Downloads 105

Authors: Mohammed Sabbah, Prospero Di Pierro, Raffaele Porta

Abstract:

Protein-based edible films and coatings have attracted an increasing interest in recent years since they might be used to protect pharmaceuticals or improve the shelf life of different food products. Among them, several plant proteins represent an abundant, inexpensive and renewable raw source. These natural biopolymers are used as film forming agents, being able to form intermolecular linkages by various interactions. However, without the addition of a plasticizing agent, many biomaterials are brittle and, consequently, very difficult to be manipulated. Plasticizers are generally small and non-volatile organic additives used to increase film extensibility and reduce its crystallinity, brittleness and water vapor permeability. Plasticizers normally act by decreasing the intermolecular forces along the polymer chains, thus reducing the relative number of polymer-polymer contacts, producing a decrease in cohesion and tensile strength and thereby increasing film flexibility allowing its deformation without rupture. The most commonly studied plasticizers are polyols, like glycerol (GLY) and some mono or oligosaccharides. In particular, GLY not only increases film extensibility but also migrates inside the film network often causing the loss of desirable mechanical properties of the material. Therefore, replacing GLY with a different plasticizer might help to improve film characteristics allowing potential industrial applications. To improve film properties, it seemed of interest to test as plasticizers some cationic small molecules like polyamines (PAs). Putrescine, spermidine (SPD), and spermine are PAs widely distributed in nature and of particular interest for their biological activities that may have some beneficial health effects. Since PAs contains amino instead of hydroxyl functional groups, they are able to trigger ionic interactions with negatively charged proteins. Bitter vetch (Vicia ervilia; BV) is an ancient grain legume crop, originated in the Mediterranean region, which can be found today in many countries around the world. This annual Vicia genus shows several favorable features, being their seeds a cheap and abundant protein source. The main objectives of this study were to investigate the effect of different concentrations of SPD on the mechanical and permeability properties of films prepared with native or heat denatured BV proteins in the presence of different concentrations of SPD and/or GLY. Therefore, a BV seed protein concentrate (BVPC), containing about 77% proteins, was used to prepare film forming solutions (FFSs), whereas GLY and SPD were added as film plasticizers, either singly or in combination, at various concentrations. Since a primary plasticizer is generally defined as a molecule that when added to a material makes it softer, more flexible and easier to be processed, our findings lead to consider SPD as a possible primary plasticizer of protein-based films. In fact, the addition of millimolar concentrations of SPD to BVPC FFS allowed obtaining handleable biomaterials with improved properties. Moreover, SPD can be also considered as a secondary plasticizer, namely an 'extender', because of its ability even to enhance the plasticizing performance of GLY. In conclusion, our studies indicate that innovative edible protein-based films and coatings can be obtained by using PAs as new plasticizers.

Keywords: edible films, glycerol, plasticizers, polyamines, spermidine

Procedia PDF Downloads 192

Authors: Hafiza Javaria Ashraf, Xinghong Wang, Zhanghong Shi, Youming Hou

Abstract:

Insect’s innate immunity depends on a variety of defense responses for the recognition of invading pathogens. Pathogen recognition involves particular proteins known as pattern recognition receptors (PRRs). These PRRs interact with pathogen-associated molecular patterns (PAMPs) present on the surface of pathogens to distinguish between self and non-self. C-type lectins (CTLs) belong to a superfamily of PPRs which involved in insect immunity and defense mechanism. Rhynchophorus ferrugineus Olivier is a devastating pest of Palm cultivations in China. Although studies on R. ferrugineus immune mechanism and host defense have conducted, however, the role of CTL in immune responses of R. ferrugineus remains elusive. Here, we report RfCTL, which is a secreted protein containing a single-CRD domain. The open reading frame (ORF) of CTL is 226 bp, which encodes a putative protein of 168 amino acids. Transcript expression analysis revealed that RfCTL highly expressed in immune-related tissues, i.e., hemolymph and fat body. The abundance of RfCTL in the gut and fat body dramatically increased upon Staphylococcus aureus and Escherichia coli bacterial challenges, suggesting a role in defense against gram-positive and gram-negative bacterial infection. Taken together, we inferred that RfCTL might be involved in the immune defense of R. ferrugineus and established a solid foundation for future studies on R. ferrugineus CTL domain proteins for better understanding of insect immunity.

Keywords: biological invasion, c-type lectin, insect immunity, Rhynchophorus ferrugineus Oliver

Procedia PDF Downloads 150