Search results for: protein interaction network

Authors: Homayun Ghasemi, Mojtaba Yousefirad, Mozhgan Farzamisepehr

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Heavy metals are among soil pollutant resources that in case of accumulation in the soil and absorption by the plant, enter into the food chain and poison the plants or the people who consume those plants. This research was performed in order to examine the role of cadmium as a heavy metal in the activity of catalase and peroxidase as well as protein concentration in Trifolium resupinatum L. based on a randomized block design with three repetitions. The used treatments included consumption of Cd (NO3)2 at four levels, namely, 0, 100, 200, and 300 ppm. The plants under study were treated for 10 days. The results of the study showed that catalase activity decreased by the increase of cadmium. Moreover, peroxidase activity increased by an increase inthe consumption of cadmium. The analysis of protein level showed that plantlet protein decreased in high cadmium concentrations. The findings also demonstrated that cadmium concentration in roots was higher than in shoots.

Keywords: catalase, heavy metal, peroxidase, protein

Procedia PDF Downloads 219

Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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Authors: Ava Salmanpour, Hanieh Saeedi, Payam Rouhi, Elahe Hamzeil, Shima Alimohammadi, Siamak Hossein Khalaj, Mohammad Asadian

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Software-defined network (SDN) is a network architecture designed to control network using software application in a central manner. This ability enables remote control of the whole network regardless of the network technology. In fact, in this architecture network intelligence is separated from physical infrastructure, it means that required network components can be implemented virtually using software applications. Today, power networks are characterized by a high range of complexity with a large number of intelligent devices, processing both huge amounts of data and important information. Therefore, reliable and secure communication networks are required. SDNs are the best choice to meet this issue. In this paper, SDN networks capabilities and characteristics will be reviewed and different basic controllers will be compared. The importance of using SDNs to escalate efficiency and reliability in utility power networks is going to be discussed and the comparison between the SDN-based power networks and traditional networks will be explained.

Keywords: software-defined network, SDNs, utility network, open flow, communication, gas and electricity, controller

Procedia PDF Downloads 83

Authors: Simona Dostalova, Dita Munzova, Ana Maria Jimenez Jimenez, Marketa Vaculovicova, Vojtech Adam, Rene Kizek

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The boom of nanomedicine in recent years has led to the development of numerous new nanomaterials that can be used as nanocarriers in the drug delivery. These nanocarriers can either be synthetic or natural-based. The disadvantage of many synthetic nanocarriers is their toxicity in patient’s body. Protein cages that can naturally be found in human body do not exhibit such disadvantage. However, the release of cargo from some protein cages in target cells can be problematic. As a special type of protein cages can serve the capsid of many viruses, including phage. Phages infect bacterial cells; therefore they are not harmful to human cells. The targeting of phage particles to cancer cells can be solved by producing of empty phage capsids during which the targeting moieties (e.g. peptides) can be cloned into genes of phage capsid to decorate its surface. Moreover, the produced capsids do not contain viral nucleic acid and are therefore not infectious to beneficial bacteria in the patient’s body. The protein cage composed of viral capsid is larger than other frequently used apoferritin cage but its size is still small enough to benefit from passive targeting by Enhanced Permeability and Retention effect. In this work, bacteriophage λ was used, both whole and its empty capsid for delivery of different cytotoxic drugs (cisplatin, carboplatin, oxaliplatin, etoposide and doxorubicin). Large quantities of phage λ were obtained from phage λ-producing strain of E. coli cultivated in medium with 0.2 % maltose. After killing of E. coli with chloroform and its removal by centrifugation, the phage was concentrated by ultracentrifugation at 130 000 g and 4 °C for 3 h. The encapsulation of the drugs was performed by infusion method and four different concentrations of the drugs were encapsulated (200; 100; 50; 25 µg/ml). Free molecules of drugs were removed by dialysis. The encapsulation was verified using spectrophotometric and electrochemical methods. The amount of encapsulated drug linearly increased with the amount of applied drug (determination coefficient R2=0.8013). 76% of applied drug was encapsulated in phage λ particles (concentration of 10 µg/ml), even with the highest applied concentration of drugs, 200 µg/ml. Only 1% of encapsulated drug was detected in phage DNA. Similar results were obtained with encapsulation in phage empty capsid. Therefore, it can be concluded that the encapsulation of drugs into phage particles is efficient and mostly occurs by interaction of drugs with protein capsid.

Keywords: cytostatics, drug delivery, nanocarriers, phage capsid

Procedia PDF Downloads 465

Authors: Seyed Mohammad Ali Zahedi

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This field experiment was conducted in Isfahan in 2011 in order to study the effect of plant density and planting pattern on growth, yield and quality of silage corn (SC 704) using a randomized complete block design with split plot layout and four replications. The main plot consisted of three planting patterns (60 and 75 cm single planting row and 75 cm double planting row referred to as 60S, 75S and 75T, respectively). The subplots consisted of four levels of plant densities (65000, 80000, 95000 and 110000 plants per hectare). Each subplot consisted of 7 rows, each with 10m length. Vegetative and reproductive characteristics of plants at silking and hard dough stages (when the plants were harvested for silage) were evaluated. Results of variance analysis showed that the effects of planting pattern and plant density were significant on leaf area per plant, leaf area index (at silking), plant height, stem diameter, dry weights of leaf, stem and ear in silking and harvest stages and on fresh and dry yield, dry matter percentage and crude protein percentage at harvest. There was no planting pattern × plant density interaction for these parameters. As row space increased from 60 cm with single planting to 75 cm with single planting, leaf area index and plant height increased, but leaf area per plant, stem diameter, dry weight of leaf, stem and ear, dry matter percentage, dry matter yield and crude protein percentage decreased. Dry matter yield reduced from 24.9 to 18.5 t/ha and crude protein percentage decreased from 6.11 to 5.60 percent. When the plant density increased from 65000 to 110000 plant per hectare, leaf area index, plant height, dry weight of leaf, stem and ear and dry matter yield increased from 19.2 to 23.3 t/ha, whereas leaf area per plant, stem diameter, dry matter percentage and crude protein percentage decreased from 6.30 to 5.25. The best results were obtained with 60 cm row distance with single planting and 110000 plants per hectare.

Keywords: silage corn, plant density, planting pattern, yield

Procedia PDF Downloads 310

Authors: Umar Saeed

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Peptidyl-prolyl cis/trans isomerases Par14 and Par17 in humans play crucial roles in diverse cellular processes, including protein folding, chromatin remodeling, DNA binding, ribosome biogenesis, and cell cycle progression. However, the effects of Par14 and Par17 on viral replication have been explored to a limited extent. We first time discovered their influential roles in promoting Hepatitis B Virus replication. In this study, we observed that in the presence of HBx, either Par14 or Par17 could upregulate HBV replication. However, in the absence of HBx, neither Par14 nor Par17 had any effect on replication. Their mechanism of action involves binding to specific motifs within HBc and HBx proteins. Notably, they target the conserved 133Arg-Pro134 (RP) motif of HBc and the 19RP20-28RP29 motifs of HBx. This interaction is fundamental for the stability of HBx, core particles, and HBc. Par14 and Par17 exhibit versatility by binding both outside and inside core particles, thereby facilitating core particle assembly through their participation in HBc dimer-dimer interactions. NAGE and immunoblotting analyses unveiled the binding of Par14/Par17 to core particles. Co-immunoprecipitation experiments further demonstrated the interaction of Par14/Par17 with core particle assembly-defective and dimer-positive HBc-Y132A. It's essential to emphasize that R133 is the key residue in the HBc RP motif that governs their interaction with Par14/Par17. Chromatin immunoprecipitation conducted on HBV-infected cells elucidated the participation of residues S19 and E46/D74 in Par14 and S44 and E71/D99 in Par17 in the recruitment of 133RP134 motif-containing HBc into cccDNA. Depleting PIN4 in liver cell lines results in a significant reduction in cccDNA levels, pgRNA, sgRNAs, HBc, core particle assembly, and HBV DNA synthesis. Notably, parvulin inhibitors like juglone and PiB have proven to be effective in substantially reducing HBV replication. These inhibitors weaken the interaction between HBV core particles and Par14/Par17, underscoring the dynamic nature of this interaction. It's also worth noting that specific Par14/Par17 inhibitors hold promise as potential therapeutic options for chronic hepatitis B.

Keywords: Par14Par17, HBx, HBc, cccDNA, HBV

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Authors: Friday A. Ogori, Ojotu M. Eke, Oneh J. Abu, Abraham T. Girgih

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B.aeqygtiaca del (Balanites aegyptiaca del) seed protein concentrate (APC) was hydrolyzed using different enzymes such as pepsin+pancreatin (PP), Alcalase (Alca), and Flavourzyme (Flav). The Alca has higher yield (100%) when compared to PP (83.23%) and Flav (62.90%). The hydrophobic amino acid and Sulphur containing amino acid (40.19%, 7.04%) in PP hydrolysate were higher compared to Alcalase (38.92%, 6.69%), Flavourenzyme (37.43%,6.35%), and APC (39.97%, 6.95%) samples. The PP has stronger DPPH, Hydroxyl radical quenching, Ferric reducing activity, and linoleic acid peroxidation activity, followed by the protein concentrate (APC) and Alcalase (Alca), while Flavourenzyme (Flav) derived hydrolysate was least in scavenging and inhibiting radical peroxidation properties. Flavourenzyme derived hydrolysate had stronger Ferric reducing antioxidant potential and metal chelating property. The result showed that the Alcalase hydrolysate has promising peptide yield, and PP hydrolysate had excellent amino acid residues and good in-vitro antioxidant potentials and could be a preferred ingredients in the nutraceutical and functional food emerging industries.

Keywords: balanites aegyptiaca del, protein concentrate, protein hydrolysates, enzymatic hydrolysis, antioxidants

Procedia PDF Downloads 48

Authors: Jonas Colin

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Standing at the vanguard of AI development, Alpha represents an unprecedented synthesis of logical rigor and human abstraction, meticulously crafted to mirror the user's unique persona and personality, a feat previously unattainable in AI development. Alpha, an avant-garde artefact in the realm of artificial intelligence, epitomizes a paradigmatic shift in personalized digital interaction, amalgamating user-specific dialogic patterns with the sophisticated algorithmic prowess of OpenAI's GPT-3.5 to engender a platform for enhanced metacognitive engagement and individualized user experience. Underpinned by a sophisticated algorithmic framework, Alpha integrates vast datasets through a complex interplay of neural network models and symbolic AI, facilitating a dynamic, adaptive learning process. This integration enables the system to construct a detailed user profile, encompassing linguistic preferences, emotional tendencies, and cognitive styles, tailoring interactions to align with individual characteristics and conversational contexts. Furthermore, Alpha incorporates advanced metacognitive elements, enabling real-time reflection and adaptation in communication strategies. This self-reflective capability ensures continuous refinement of its interaction model, positioning Alpha not just as a technological marvel but as a harbinger of a new era in human-computer interaction, where machines engage with us on a deeply personal and cognitive level, transforming our interaction with the digital world.

Keywords: chatbot, GPT 3.5, metacognition, symbiose

Procedia PDF Downloads 33

Authors: Krishan Kumar, Mohit Mittal, Pramod Kumar

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Wireless sensor network is one of the most promising communication networks for monitoring remote environmental areas. In this network, all the sensor nodes are communicated with each other via radio signals. The sensor nodes have capability of sensing, data storage and processing. The sensor nodes collect the information through neighboring nodes to particular node. The data collection and processing is done by data aggregation techniques. For the data aggregation in sensor network, clustering technique is implemented in the sensor network by implementing self-organizing feature map (SOFM) neural network. Some of the sensor nodes are selected as cluster head nodes. The information aggregated to cluster head nodes from non-cluster head nodes and then this information is transferred to base station (or sink nodes). The aim of this paper is to manage the huge amount of data with the help of SOM neural network. Clustered data is selected to transfer to base station instead of whole information aggregated at cluster head nodes. This reduces the battery consumption over the huge data management. The network lifetime is enhanced at a greater extent.

Keywords: artificial neural network, data clustering, self organization feature map, wireless sensor network

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Authors: Mehrnaz Mostafavi

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Recent advances in single-molecule protein identification (ID) and quantification techniques are poised to revolutionize proteomics, enabling researchers to delve into single-cell proteomics and identify low-abundance proteins crucial for biomedical and clinical research. This paper introduces a different approach to single-molecule protein ID and quantification using tri-color amino acid tags and a plasmonic nanopore device. A comprehensive simulator incorporating various physical phenomena was designed to predict and model the device's behavior under diverse experimental conditions, providing insights into its feasibility and limitations. The study employs a whole-proteome single-molecule identification algorithm based on convolutional neural networks, achieving high accuracies (>90%), particularly in challenging conditions (95–97%). To address potential challenges in clinical samples, where post-translational modifications affecting labeling efficiency, the paper evaluates protein identification accuracy under partial labeling conditions. Solid-state nanopores, capable of processing tens of individual proteins per second, are explored as a platform for this method. Unlike techniques relying solely on ion-current measurements, this approach enables parallel readout using high-density nanopore arrays and multi-pixel single-photon sensors. Convolutional neural networks contribute to the method's versatility and robustness, simplifying calibration procedures and potentially allowing protein ID based on partial reads. The study also discusses the efficacy of the approach in real experimental conditions, resolving functionally similar proteins. The theoretical analysis, protein labeler program, finite difference time domain calculation of plasmonic fields, and simulation of nanopore-based optical sensing are detailed in the methods section. The study anticipates further exploration of temporal distributions of protein translocation dwell-times and the impact on convolutional neural network identification accuracy. Overall, the research presents a promising avenue for advancing single-molecule protein identification and quantification with broad applications in proteomics research. The contributions made in methodology, accuracy, robustness, and technological exploration collectively position this work at the forefront of transformative developments in the field.

Keywords: nano proteomics, nanopore-based optical sensing, deep learning, artificial intelligence

Procedia PDF Downloads 42

Authors: Thanusha D. Abeywickrama, Inoka C. Perera, Genji Kurisu

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Tuberculosis, considered being as the ninth leading cause of death worldwide, cause from a single infectious agent M. tuberculosis and the drug resistance nature of this bacterium is a continuing threat to the world. Therefore TB preventing treatment is expanding, where this study designed to analyze the regulatory mechanism of GntR transcriptional regulator gene Rv0792c, which lie between several genes codes for some hypothetical proteins, a monooxygenase and an oxidoreductase. The gene encoding Rv0792c was cloned into pET28a and expressed protein was purified to near homogeneity by Nickel affinity chromatography. It was previously reported that the protein binds within the intergenic region (BS region) between Rv0792c gene and monooxygenase (Rv0793). This resulted in binding of three protein molecules with the BS region suggesting tight control of monooxygenase as well as its own gene. Since monooxygenase plays a key role in metabolism, this gene may have a global regulatory role. The natural ligand for this regulator is still under investigation. In relation to the Rv0792 protein structure, a Circular Dichroism (CD) spectrum was carried out to determine its secondary structure elements. Percentage-wise, 17.4% Helix, 21.8% Antiparallel, 5.1% Parallel, 12.3% turn and 43.5% other were revealed from CD spectrum data under room temperature. Differential Scanning Calorimetry (DSC) was conducted to assess the thermal stability of Rv0792, which the melting temperature of protein is 57.2 ± 0.6 °C. The graph of heat capacity (Cp) versus temperature for the best fit was obtained for non-two-state model, which concludes the folding of Rv0792 protein occurs through stable intermediates. Peak area (∆HCal ) and Peak shape (∆HVant ) was calculated from the graph and ∆HCal / ∆HVant was close to 0.5, suggesting dimeric nature of the protein.

Keywords: CD spectrum, DSC analysis, GntR transcriptional regulator, protein structure

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Authors: Jaturong Matidtor, Krisna R. Torrissen, Saengtong Pongjareankit, Sudaporn Tongsiri, Jiraporn Rojtinnakorn

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Low survival rate has being particular problem in nursery of marble goby juvenile. The aim of this study was to investigate effect of garlic extract on protein digestive pancreatic enzymes, trypsin (T) and chymotrypsin (C). The marble goby were reared with commercial feed mixed garlic extract at concentration of 0 (control), 0.3, 0.5, 1.0, 3.0 and 5.0% (w/w) for 6 weeks. Analysis of the digestive enzymes at 2 and 6 weeks was performed. Growth parameters; weight gain (WG), specific growth rate (SGR) and feed efficiency (FE), were identified. For T, C and T/C at 2 weeks, values of T and T/C ratio of 0.3% (w/w) group showed significant difference (p < 0.05) with the highest values of 17685.64± 11981.77 U/mg protein and of 51.64 ± 27.46 U/mg protein, respectively. For C at 2 weeks, 0% (w/w) group showed the highest values of 16191.76± 2225.56 U/mg protein. Whereas value of T, C and T/C ratio at 6 weeks, there was no significant difference (p > 0.05). For growth performance, it significantly increased in all garlic extract fed groups (0.3-5.0%, w/w), both at 2 and 6 weeks. At 2 weeks, values of WG and SGR of 0.5% (w/w) group showed the highest values of 71.51 ± 1.60%, and 3.85 ± 0.07%, respectively. For FE, 0.3% (w/w) group showed the highest value of 60.21 ± 6.51%. At 6 weeks, it illustrated that all growth parameters of 5.0% (w/w) group were the highest values; WG = 35.06 ± 5.66%, SGR = 2.14 ± 0.30%, and FE = 5.86 ± 0.68%. We suggested that garlic extract could be available for protein digestive enzyme and growth enhancement in marble goby nursery with artificial feed. This result will be high benefit for commercial aquaculture of marble goby.

Keywords: marble goby, nursery, garlic extract, digestive enzyme, growth

Procedia PDF Downloads 295

Authors: Rizky Kusuma Cahyani

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Hepatitis B is a liver inflammatory disease caused by hepatitis B virus (HBV). This infection can be prevented by vaccination which contains HBV surface protein (sHBsAg). However, vaccine supply is limited. Several attempts have been conducted to produce local sHBsAg. However, the purity degree and protein yield are still inadequate. Therefore optimization of HBsAg purification steps is required to obtain high yield with better purification fold. In this study, optimization of purification was done in 2 steps, precipitation using variation of NaCl concentration (0,3 M; 0,5 M; 0,7 M) and PEG (3%, 5%, 7%); ion exchange chromatography (IEC) using NaCl 300-500 mM elution buffer concentration.To determine HBsAg protein, bicinchoninic acid assay (BCA) and enzyme-linked immunosorbent assay (ELISA) was used in this study. Visualization of HBsAg protein was done by SDS-PAGE analysis. Based on quantitative analysis, optimal condition at precipitation step was given 0,3 M NaCl and PEG 3%, while in ion exchange chromatography step, the optimum condition when protein eluted with NaCl 500 mM. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicates that the presence of protein HBsAg with a molecular weight of 25 kDa (monomer) and 50 kDa (dimer). The optimum condition for purification of sHBsAg produced in Pichia pastoris gave a yield of 47% and purification fold 17x so that it would increase the production of hepatitis B vaccine to be more optimal.

Keywords: hepatitis B virus, HBsAg, hepatitis B surface antigen, Pichia pastoris, purification

Procedia PDF Downloads 126

Authors: Zhiyong Shan, Preethi Santhanam, Vinod Namboodiri, Rajiv Bagai

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In recent years, the emerging network worms and attacks have distributive characteristics, which can spread globally in a very short time. Security management crossing networks to co-defense network-wide attacks and improve the efficiency of security administration is urgently needed. We propose a hierarchical distributed network security management system (HD-NSMS), which can integrate security management across multiple networks. First, we describe the system in macrostructure and microstructure; then discuss three key problems when building HD-NSMS: device model, alert mechanism, and emergency response mechanism; lastly, we describe the implementation of HD-NSMS. The paper is valuable for implementing NSMS in that it derives from a practical network security management system (NSMS).

Keywords: network security management, device organization, emergency response, cross-network

Procedia PDF Downloads 136

Authors: Christian H. Sanabria-Montaña, Rodrigo Huerta-Quintanilla

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A lattice network is a special type of network in which all nodes have the same number of links, and its boundary conditions are periodic. The most basic lattice network is the ring, a one-dimensional network with periodic border conditions. In contrast, the Cartesian product of d rings forms a d-dimensional lattice network. An analytical expression currently exists for the clustering coefficient in this type of network, but the theoretical value is valid only up to certain connectivity value; in other words, the analytical expression is incomplete. Here we obtain analytically the clustering coefficient expression in d-dimensional lattice networks for any link density. Our analytical results show that the clustering coefficient for a lattice network with density of links that tend to 1, leads to the value of the clustering coefficient of a fully connected network. We developed a model on criminology in which the generalized clustering coefficient expression is applied. The model states that delinquents learn the know-how of crime business by sharing knowledge, directly or indirectly, with their friends of the gang. This generalization shed light on the network properties, which is important to develop new models in different fields where network structure plays an important role in the system dynamic, such as criminology, evolutionary game theory, econophysics, among others.

Keywords: clustering coefficient, criminology, generalized, regular network d-dimensional

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Authors: Sasiphan Nitayaprapha

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A commercially-supported social network has become an emerging channel for an organization to communicate with and provide services to customers. The success of the commercially-supported social network depends on the ability of the organization to keep the customers in participating in the network. Drawing from the theories of information adoption, information systems continuance, and web usability, the author develops a model to explore how a commercially-supported social network can encourage customers to continue participating and using the information in the network. The theoretical model will be proved through an online survey of customers using the commercially-supported social networking sites of several high technology companies operating in the same sector. The result will be compared with previous studies to learn about the explanatory power of the research model, and to identify the main factors determining users’ intention to continue using a commercially-supported social network. Theoretical and practical implications, and limitations are discussed.

Keywords: social network, information adoption, information systems continuance, web usability, user satisfaction

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Authors: S. Bilal, S. A. Bhat, I. Hussain, J. D. Parrah, S. P. Ahmad, M. R. Mir

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Background: The wound healing involves a highly coordinated cascade of cellular and immunological response over a period including coagulation, inflammation, granulation tissue formation, epithelialization, collagen synthesis and tissue remodeling. Wounds in aged heal more slowly than those in younger, mainly because of comorbidities that occur as one age. The present study is about the influence of age on wound healing. 1x1cm^2 (100 mm) wounds were created on the back of the animal. The animals were divided into two groups; one group had animals in the age group of 3-9 months while another group had animals in the age group of 15-21 months. Materials and Methods: 24 clinically healthy rabbits in the age group of 3-21 months were used as experimental animals and divided into two groups viz A and B. All experimental parameters, i.e., Excision wound model, Measurement of wound area, Protein extraction and estimation, Protein extraction and estimation and DNA extraction and estimation were done by standard methods. Results: The parameters studied were wound contraction, hydroxyproline, glucosamine, protein, and DNA. A significant increase (p<0.005) in the hydroxyproline, glucosamine, protein and DNA and a significant decrease in wound area (p<0.005) was observed in the age group of 3-9 months when compared to animals of an age group of 15-21 months. Wound contraction together with hydroxyproline, glucosamine, protein and DNA estimations suggest that advanced age results in retarded wound healing. Conclusion: The decrease wound contraction and accumulation of hydroxyproline, glucosamine, protein and DNA in group B animals may be associated with the reduction or delay in growth factors because of the advancing age.

Keywords: age, wound healing, excision wound, hydroxyproline, glucosamine

Procedia PDF Downloads 631

Authors: Şevket Evci, Mehmet Akif Karsli

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The aim of this study is to determine nutrient contents, in situ ruminal degradation kinetics and protein fractions of screenings bean (B), chick pea (ChP), red lentil (RL) and green lentil (GL) that is used as residue in grain legume packing industry. For this purpose, four samples of each legumes species-a total of 16 samples, collected from different parts of our country were utilized. Feedstuffs used in the experiment were incubated for 0, 2 4, 8, 12, 24, and 48 hours in the rumen of 3 ruminally cannulated Akkaraman rams as duplicate. The nutrient contents, in situ ruminal dry matter (DM), organic matter (OM) and crude protein (CP) degradabilities and fractions, and escape protein contents were evaluated. The highest OM and CP contents were observed in RL (P<0.05). Chick pea had the highest ether extract (EE) content and EE values were 3.47, 6.72, 2.26, 8.66 % for RL, B, GL and ChP, respectively (P<0.05). Crude fiber (CF), ADF, and NDF contents were the highest in RL and the lowest in ChP. CF values were 24.03, 10.80, 4.09 and 3.57 % for RL, GL, B and ChP (P<0.05). Acid detergent insoluble nitrogen content of samples did not differ. Escape protein content was the highest in RL and the lowest in B (P<0.05). After 48 h incubation, the lowest OM and CP degradabilities were observed in RL. While the highest OM degradability was seen in ChP the highest CP degradability was observed in B (P<0.05). The lowest water soluble OM and CP contents were observed in RL whereas the highest potentially degradable OM and CP contents were seen in B and ChP (P<0.05). Both rate of OM and CP degradations (k-1) did not differ among samples (P>0.05). In conclusion, it was noted that feedstuffs (GL, ChP and B) used in the experiment except RL had a greater ruminal degradibilities of both OM and CP and moreover, had a higher escape protein contents, except B. It was thought that these feedstuffs can be substituted with some of common protein sources used in animal nutrition.

Keywords: in situ, nutrient contents, ruminant, subsieve

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Authors: O. P. Oladipo, O. A. Falode

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The determination of Recovery Factor is of great importance to the reservoir engineer since it relates reserves to the initial oil in place. Reserves are the producible portion of reservoirs and give an indication of the profitability of a field Development. The core objective of this project is to develop an artificial neural network model using selected reservoir data to predict Recovery Factors (RF) of hydrocarbon reservoirs and compare the model with a couple of the existing correlations. The type of Artificial Neural Network model developed was the Single Layer Feed Forward Network. MATLAB was used as the network simulator and the network was trained using the supervised learning method, Afterwards, the network was tested with input data never seen by the network. The results of the predicted values of the recovery factors of the Artificial Neural Network Model, API Correlation for water drive reservoirs (Sands and Sandstones) and Guthrie and Greenberger Correlation Equation were obtained and compared. It was noted that the coefficient of correlation of the Artificial Neural Network Model was higher than the coefficient of correlations of the other two correlation equations, thus making it a more accurate prediction tool. The Artificial Neural Network, because of its accurate prediction ability is helpful in the correct prediction of hydrocarbon reservoir factors. Artificial Neural Network could be applied in the prediction of other Petroleum Engineering parameters because it is able to recognise complex patterns of data set and establish a relationship between them.

Keywords: recovery factor, reservoir, reserves, artificial neural network, hydrocarbon, MATLAB, API, Guthrie, Greenberger

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Authors: Lavinia Ruta, Ileana Farcasanu

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The yeast surface display (YSD) technique enables the expression of proteins on yeast cell surfaces, facilitating the identification and isolation of proteins with targeted binding properties, such as nanobodies. Nanobodies, derived from camelid species, are single-domain antibody fragments renowned for their high affinity and specificity towards target proteins, making them valuable in research and potentially in therapeutics. Their advantages include a compact size (~15 kDa), robust stability, and the ability to target challenging epitopes. The project endeavors to establish and validate a platform for producing Green Fluorescent Protein (GFP) and mCherry nanobodies using the yeast surface display method. mCherry, a prevalent red fluorescent protein sourced from coral species, is commonly utilized as a genetic marker in biological studies due to its vibrant red fluorescence. The GFP-nanobody, a single variable domain of heavy-chain antibodies (VHH), exhibits specific binding to GFP, offering a potent means for isolating and engineering fluorescent protein fusions across various biological research domains. Both GFP and mCherry nanobodies find specific utility in cellular imaging and protein analysis applications.

Keywords: YSD, nanobodies, GFP, Saccharomyces cerevisiae

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Authors: Vineeta Kaushik, Manisha Goel

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Chaperones are proteins that help other proteins fold correctly, and are found in all domains of life i.e., prokaryotes, eukaryotes and archaea. Various comparative genomic studies have suggested that the archaeal protein folding machinery appears to be highly similar to that found in eukaryotes. In case of protein folding; slow rotation of peptide prolyl-imide bond is often the rate limiting step. Formation of the prolyl-imide bond during the folding of a protein requires the assistance of other proteins, termed as peptide prolyl cis-trans isomerases (PPIases). Cyclophilins constitute the class of peptide prolyl isomerases with a wide range of biological function like protein folding, signaling and chaperoning. Most of the cyclophilins exhibit PPIase enzymatic activity and play active role in substrate protein folding which classifies them as a category of molecular chaperones. Till date, there is not very much data available in the literature on archaeal cyclophilins. We aim to compare the structural and biochemical features of the cyclophilin protein from within the three domains to elucidate the features affecting their stability and enzyme activity. In the present study, we carry out in-silico analysis of the cyclophilin proteins to predict their conserved residues, sites under positive selection and compare these proteins to their bacterial and eukaryotic counterparts to predict functional divergence. We also aim to clone and express these proteins in heterologous system and study their biophysical characteristics in detail using techniques like CD and fluorescence spectroscopy. Overall we aim to understand the features contributing to the folding, stability and dynamics of the archaeal cyclophilin proteins.

Keywords: biophysical characterization, x-ray crystallography, chaperone-like activity, cyclophilin, PPIase activity

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Authors: Meenakshi Verma, Mandeep Singh Bakshi, Kultar Singh

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Magnetic nanoparticles have received incredible importance in view of their diverse applications, which arise primarily due to their response to the external magnetic field. The magnetic behaviour of magnetic nanoparticles (NPs) helps them in numerous different ways. The most important amongst them is the ease with which they can be purified and also can be separated from the media in which they are present merely by applying an external magnetic field. This exceptional ease of separation of the magnetic NPs from an aqueous media enables them to use for extracting/removing metal pollutants from complex aqueous medium. Functionalized magnetic NPs can be subjected for the metallic impurities extraction if are favourably adsorbed on the NPs surfaces. We have successfully used the magnetic NPs as vehicles for gold and silver NPs removal from the complex fluids. The NPs loaded with gold and silver NPs pollutant fractions has been easily removed from the aqueous media by using external magnetic field. Similarly, we have used the magnetic NPs for extraction of protein from complex media and then constantly washed with pure water to eliminate the unwanted surface adsorbed components for quantitative estimation. The purified and protein loaded magnetic NPs are best analyzed with SDS Page to not only for characterization but also for separating the protein fractions. A collective review of the results indicates that we have synthesized surfactant coated iron oxide NPs and then functionalized these with selected materials. These surface active magnetic NPs work very well for the extraction of metallic NPs from the aqueous bulk and make the whole process environmentally sustainable. Also, magnetic NPs-Au/Ag/Pd hybrids have excellent protein extracting properties. They are much easier to use in order to extract the magnetic impurities as well as protein fractions under the effect of external magnetic field without any complex conventional purification methods.

Keywords: magnetic nanoparticles, protein, functionalized, extraction

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Authors: Akhil Raj Pushparajan, Ranjit Ramachandran, Jijimole Gopi Reji, Ajay Kumar Ramakrishnan

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Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is one of the leading causes of death by an infectious disease. In spite of the availability of effective drugs and a vaccine, TB is a major health concern and was declared a global emergency by the World Health Organization (WHO). The success of intracellular pathogens like Mtb depends on its ability to overcome the challenging environment in the host. Gene regulation controlled by transcriptional regulators (TRs) plays a crucial role for the bacteria to adapt to the host environment. In vitro studies on gene regulatory mechanisms during dormancy and reactivation have provided insights into the adaptations employed by Mtb to survive in the host. Here we present our efforts to functionally characterize Rv1019, a putative TR of Mtb H37Rv which was found to be present at significantly varying levels during dormancy and reactivation in vitro. The expression of this protein in the dormancy-reactivation model was validated by qRT-PCR and western blot. By DNA- protein interaction studies and reporter assays we found that under normal laboratory conditions of growth this protein behaves as an auto-repressor and tetracycline was found to abrogate this repression by interfering with its ability to bind DNA. Further, by cDNA analysis, we found that this TR is co-transcribed with its downstream genes Rv1020 (mfd) and Rv1021 (mazG) which are involved in DNA damage response in Mtb. Constitutive expression of this regulator in the surrogate host M. smegmatis showed downregulation of the orthologues of downstream genes suggested that Rv1019 could negatively regulate these genes. Our finds also show that M. smegmatis expressing Rv1019 is sensitive to DNA damage suggests the role of this protein in regulating DNA damage response induced by oxidative stress. Because of its role in regulating DNA damage response which may help in the persistence of Mtb, Rv1019 could be used as a prospective target for therapeutic intervention to fight TB.

Keywords: auto-repressor, DNA repair, mycobacterium smegmatis, mycobacterium tuberculosis, tuberculosis

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Authors: O. A. Lawal, O. A Ojesanmi

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The demand for wireless cellular services continues to increase while the radio resources remain limited. Thus, network operators have to continuously manage the scarce radio resources in order to have an improved quality of service for mobile users. This paper proposes how to handle the problem of congestion in the mobile network by prioritizing handoff call, using the guard channel allocation scheme. The research uses specific threshold value for the time of allocation of the channel in the algorithm. The scheme would be simulated by generating various data for different traffics in the network as it would be in the real life. The result would be used to determine the probability of handoff call dropping and the probability of the new call blocking as a way of measuring the network performance.

Keywords: call block, channel, handoff, mobile cellular network

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Authors: Yasir Ali Arfat

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Composite films based on fish protein isolate (FPI) and fish skin gelatin (FSG) blend incorporated with 50 and 100% (w/w, protein) basil leaf essential oil (BEO) in the absence and presence of 3% (w/w, protein) ZnO nanoparticles (ZnONP) were prepared and characterised. Tensile strength (TS) decreased, whilst elongation at break (EAB) increased as BEO level increased (p < 0.05). However, ZnONP addition resulted in higher TS but lower EAB (p < 0.05). The lowest water vapour permeability (WVP) was observed for the film incorporated with 100% BEO and 3% ZnONP (p < 0.05). BEO and ZnONP incorporation decreased transparency of FPI/FSG films (p < 0.05). FTIR spectra indicated that films added with BEO exhibited higher hydrophobicity. Both BEO and ZnONP had a marked impact on thermal stability of the films. Microstructural study revealed that presence of ZnONP prevented bilayer formation of film containing 100% BEO. FPI/FSG films incorporated with 100% BEO, especially in combination with ZnONP, exhibited strong antibacterial activity against food pathogenic and spoilage bacteria and thus could be used as an active food packaging material to ensure safety and to extend the shelf-life of packaged foods.

Keywords: bionanocomposite, fish protein isolate, fish skin gelatin, basil essential oil, ZnO nanoparticles, antimicrobial packaging

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Authors: Mahani Razali, Nordin Mamat

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The purpose of the study is to explore how computer technology is integrated into pre-school activities and its relationship with children’s social interaction behaviour in pre-school classroom. The major question of interest in the present study is to investigate the social interaction behaviour of children when using computers in the Malaysian pre-school classroom. This research is based on three main objectives which are to identify children`s social interaction during computer play activities, teacher’s role and parent’s participation to develop children`s social interaction. This qualitative study was carried out among 25 pre-school children, three teachers and three parents as the research sample. On the other hand, parent’s support was obtained from their discussions, supervisions and communication at home. The data collection procedures involved structured observation which was to identify social interaction behaviour among pre-school children through computer play activities; as for semi-structured interviews, it was done to study the perception of the teachers and parents on the acquired social interaction behaviour among the children. Besides, documentation analysis method was used as to triangulate acquired information with observations and interviews. In this study, the qualitative data analysis was tabulated in descriptive manner with frequency and percentage format. This study primarily focused on social interaction behaviour elements among the pre-school children. Findings revealed that the children showed positive outcomes on the social interaction behaviour during their computer play. This research summarizes that teacher’s role and parent’s support can improve children`s social interaction behaviour through computer play activities. As a whole, this research highlighted the significance of computer play activities as to stimulate social interaction behavior among the pre-school children.

Keywords: early childhood, emotional development, parent support, play

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Authors: Sello Mokwena, Monyepao Thabang

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In this study, we propose a comprehensive approach to address the challenges in person re-identification models. By combining a centroid tracking algorithm with a Siamese convolutional neural network model, our method excels in detecting, tracking, and capturing robust person features across non-overlapping camera views. The algorithm efficiently identifies individuals in the camera network, while the neural network extracts fine-grained global features for precise cross-image comparisons. The approach's effectiveness is further accentuated by leveraging the camera network topology for guidance. Our empirical analysis on benchmark datasets highlights its competitive performance, particularly evident when background subtraction techniques are selectively applied, underscoring its potential in advancing person re-identification techniques.

Keywords: camera network, convolutional neural network topology, person tracking, person re-identification, siamese

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Authors: Muhammad Ajmal

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- Thermal processing and subsequent storage of ultra-heat treated (UHT) milk leads to alteration in protein profile, Maillard reaction and lipid oxidation. Concentration of carbohydrates in normal and flavored version of UHT milk is considerably different. Transition in protein profile, Maillard reaction and lipid oxidation in UHT flavored milk was determined for 90 days at ambient conditions and analyzed at 0, 45 and 90 days of storage. Protein profile, hydroxymethyl furfural, furosine, Nε-carboxymethyl-l-lysine, fatty acid profile, free fatty acids, peroxide value and sensory characteristics were determined. After 90 days of storage, fat, protein, total solids contents and pH were significantly less than the initial values determined at 0 day. As compared to protein profile normal UHT milk, more pronounced changes were recorded in different fractions of protein in UHT milk at 45 and 90 days of storage. Tyrosine content of flavored UHT milk at 0, 45 and 90 days of storage were 3.5, 6.9 and 15.2 µg tyrosine/ml. After 45 days of storage, the decline in αs1-casein, αs2-casein, β-casein, κ-casein, β-lactoglobulin, α-lactalbumin, immunoglobulin and bovine serum albumin were 3.35%, 10.5%, 7.89%, 18.8%, 53.6%, 20.1%, 26.9 and 37.5%. After 90 days of storage, the decline in αs1-casein, αs2-casein, β-casein, κ-casein, β-lactoglobulin, α-lactalbumin, immunoglobulin and bovine serum albumin were 11.2%, 34.8%, 14.3%, 33.9%, 56.9%, 24.8%, 36.5% and 43.1%. Hydroxy methyl furfural content of UHT milk at 0, 45 and 90 days of storage were 1.56, 4.18 and 7.61 (µmol/L). Furosine content of flavored UHT milk at 0, 45 and 90 days of storage intervals were 278, 392 and 561 mg/100g protein. Nε-carboxymethyl-l-lysine content of UHT flavored milk at 0, 45 and 90 days of storage were 67, 135 and 343mg/kg protein. After 90 days of storage of flavored UHT milk, the loss of unsaturated fatty acids 45.7% from the initial values. At 0, 45 and 90 days of storage, free fatty acids of flavored UHT milk were 0.08%, 0.11% and 0.16% (p<0.05). Peroxide value of flavored UHT milk at 0, 45 and 90 days of storage was 0.22, 0.65 and 2.88 (MeqO²/kg). Sensory analysis of flavored UHT milk after 90 days indicated that appearance, flavor and mouth feel score significantly decreased from the initial values recorded at 0 day. Findings of this investigation evidenced that in flavored UHT milk more pronounced changes take place in protein profile, Maillard reaction products and lipid oxidation as compared to normal UHT milk.

Keywords: UHT flavored milk , hydroxymethyl furfural, lipid oxidation, sensory properties

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Authors: Hwang Ahreum, Kang Taejoon, Kim Bongsoo

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Nanosensors for high sensitive detection of diseases have been widely studied to improve the quality of life. Here, we suggest robust nano-plasmonic diagnostic sensor using cysteine tagged protein G (Cys3-protein G) and ultraflat, ultraclean and single-crystalline Au nanoplates. Protein G formed on an ultraflat Au surface provides ideal background for dense and uniform immobilization of antibodies. The Au is highly stable in diverse biochemical environment and can immobilize antibodies easily through Au-S bonding, having been widely used for various biosensing applications. Especially, atomically smooth single-crystalline Au nanomaterials synthesized using chemical vapor transport (CVT) method are very suitable to fabricate reproducible sensitive sensors. As the C-reactive protein (CRP) is a nonspecific biomarker of inflammation and infection, it can be used as a predictive or prognostic marker for various cardiovascular diseases. Cys3-protein G immobilized uniformly on the Au nanoplate enable CRP antibody (anti-CRP) to be ordered in a correct orientation, making their binding capacity be maximized for CRP detection. Immobilization condition for the Cys3-protein G and anti-CRP on the Au nanoplate is optimized visually by AFM analysis. Au nanoparticle - Au nanoplate (NPs-on-Au nanoplate) assembly fabricated from sandwich immunoassay for CRP can reduce zero-signal extremely caused by nonspecific bindings, providing a distinct surface-enhanced Raman scattering (SERS) enhancement still in 10-18 M of CRP concentration. Moreover, the NP-on-Au nanoplate sensor shows an excellent selectivity against non-target proteins with high concentration. In addition, comparing with control experiments employing a Au film fabricated by e-beam assisted deposition and linker molecule, we validate clearly contribution of the Au nanoplate for the attomolar sensitive detection of CRP. We expect that the devised platform employing the complex of single-crystalline Au nanoplates and Cys3-protein G can be applied for detection of many other cancer biomarkers.

Keywords: Au nanoplate, biomarker, diagnostic sensor, protein G, SERS

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Authors: Debbarma Asis, Guha Chandan

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Tumor Protein-53 (P53) is one of the tumor suppressor proteins. P53 regulates the cell cycle that conserves stability by preventing genome mutation. It is named so as it runs as 53-kilodalton (kDa) protein on Polyacrylamide gel electrophoresis although the actual mass is 43.7 kDa. Experimental evidence has indicated that P53 cancer mutants loses tumor suppression activity and subsequently gain oncogenic activities to promote tumourigenesis. Tumor-specific DNA has recently been detected in the plasma of breast cancer patients. Detection of tumor-specific genetic materials in cancer patients may provide a unique and valuable tumor marker for diagnosis and prognosis. Commercially available MDA-468 breast cancer cell line was used for the proposed study.

Keywords: tumor protein (P53), cancer mutants, MDA-468, tumor suppressor gene

Procedia PDF Downloads 452