Search results for: fusion proteins

Authors: Pengfei Meng, Shuangcheng Jia, Qian Li

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We proposed a real-time high-precision semantic segmentation network based on a multi-resolution feature fusion module, the auxiliary feature extracting module, upsampling module, and atrous spatial pyramid pooling (ASPP) module. We designed a feature fusion structure, which is integrated with sufficient features of different resolutions. We also studied the effect of side-branch structure on the network and made discoveries. Based on the discoveries about the side-branch of the network structure, we used a side-branch auxiliary feature extraction layer in the network to improve the effectiveness of the network. We also designed upsampling module, which has better results than the original upsampling module. In addition, we also re-considered the locations and number of atrous spatial pyramid pooling (ASPP) modules and modified the network structure according to the experimental results to further improve the effectiveness of the network. The network presented in this paper takes the backbone network of Bisenetv2 as a basic network, based on which we constructed a network structure on which we made improvements. We named this network deep multiple-resolution bilateral networks for real-time, referred to as DMBR-Net. After experimental testing, our proposed DMBR-Net network achieved 81.2% mIoU at 119FPS on the Cityscapes validation dataset, 80.7% mIoU at 109FPS on the CamVid test dataset, 29.9% mIoU at 78FPS on the COCOStuff test dataset. Compared with all lightweight real-time semantic segmentation networks, our network achieves the highest accuracy at an appropriate speed.

Keywords: multi-resolution feature fusion, atrous convolutional, bilateral networks, pyramid pooling

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

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An VP2 gene from the current prevalent CPV (Canine Parvovirus) strain (new CPV-2a) in the Republic of Korea was expressed in a baculovirus expression system. Genomic DNA was extracted from the isolate strain CPV-2a. The recombinant baculovirus, containing the coding sequences of VP2 with the histidine tag at the N-terminus, were generated by using the Bac-to-Bac system. For production of the recombinant VP2 proteins, SF9 cells were transfection into 6 wells. Propagation of recombinant baculoviruses and expression of the VP2 protein were performed in the Sf9 cell line maintained. The proteins were detected to Western blot anlaysis. CPV-2a VP2 was detected by Western blotting the monoclonal antibodies recognized 6x His and the band had a molecular weight of 65 KDa. We demonstrated that recombinant CPV-2a VP2 expression in baculovirus. The recombinant CPV-2a VP2 may able to development of specific diagnostic test and vaccination of against CPV2. This study provides a foundation for application of CPV2 on the development of new CPV2 subunit vaccine.

Keywords: baculovirus, canine parvovirus 2a, Dog, Korea

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Authors: Pedro M. Rodrigues, Claudia Raposo, Denise Schrama, Marco Cerqueira

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Farmed fish welfare is a very recent concept, widely discussed among the scientific community. Consumers’ interest regarding farmed animal welfare standards has significantly increased in the last years posing a huge challenge to producers in order to maintain an equilibrium between good welfare principles and productivity, while simultaneously achieve public acceptance. The major bottleneck of standard aquaculture is to impair considerably fish welfare throughout the production cycle and with this, the quality of fish protein. Welfare assessment in farmed fish is undertaken through the evaluation of fish stress responses. Primary and secondary stress responses include release of cortisol and glucose and lactate to the blood stream, respectively, which are currently the most commonly used indicators of stress exposure. However, the reliability of these indicators is highly dubious, due to a high variability of fish responses to an acute stress and the adaptation of the animal to a repetitive chronic stress. Our objective is to use comparative proteomics to identify and validate a fingerprint of proteins that can present an more reliable alternative to the already established welfare indicators. In this way, the culture conditions will improve and there will be a higher perception of mechanisms and metabolic pathway involved in the produced organism’s welfare. Due to its high economical importance in Portuguese aquaculture Gilthead seabream will be the elected species for this study. Protein extracts from Gilthead Seabream fish muscle, liver and plasma, reared for a 3 month period under optimized culture conditions (control) and induced stress conditions (Handling, high densities, and Hipoxia) are collected and used to identify a putative fish welfare protein markers fingerprint using a proteomics approach. Three tanks per condition and 3 biological replicates per tank are used for each analisys. Briefly, proteins from target tissue/fluid are extracted using standard established protocols. Protein extracts are then separated using 2D-DIGE (Difference gel electrophoresis). Proteins differentially expressed between control and induced stress conditions will be identified by mass spectrometry (LC-Ms/Ms) using NCBInr (taxonomic level - Actinopterygii) databank and Mascot search engine. The statistical analysis is performed using the R software environment, having used a one-tailed Mann-Whitney U-test (p < 0.05) to assess which proteins were differentially expressed in a statistically significant way. Validation of these proteins will be done by comparison of the RT-qPCR (Quantitative reverse transcription polymerase chain reaction) expressed genes pattern with the proteomic profile. Cortisol, glucose, and lactate are also measured in order to confirm or refute the reliability of these indicators. The identified liver proteins under handling and high densities induced stress conditions are responsible and involved in several metabolic pathways like primary metabolism (i.e. glycolysis, gluconeogenesis), ammonia metabolism, cytoskeleton proteins, signalizing proteins, lipid transport. Validition of these proteins as well as identical analysis in muscle and plasma are underway. Proteomics is a promising high-throughput technique that can be successfully applied to identify putative welfare protein biomarkers in farmed fish.

Keywords: aquaculture, fish welfare, proteomics, welfare biomarkers

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Authors: Nafees Ahmed, Nur Izyani Kamaruzman, Saralla Nathan, Mohd Ezharul Hoque Chowdhury, Anuar Zaini Md Zain, Iekhsan Othman, Sharifah Binti Syed Hassan

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Meat quality is always subject to consumer scrutiny when purchasing from retail markets on mislabeling as fresh meat. Various physiological and biochemical changes influence the quality of meat. As a major component of muscle tissue, proteins play a major role in muscle foods. In meat industry, freezing is the most common form of storage of meat products. Repeated cycles of freezing and thawing are common in restaurants, kitchen, and retail outlets and can also occur during transportation or storage. Temperature fluctuation is responsible for physical, chemical, and biochemical changes. Repeated cycles of ‘freeze-thaw’ degrade the quality of meat by stimulating the lipid oxidation and surface discoloration. The shelf life of meat is usually determined by its appearance, texture, color, flavor, microbial activity, and nutritive value and is influenced by frozen storage and subsequent thawing. The main deterioration of frozen meat during storage is due to protein. Due to the large price differences between fresh and frozen–thawed meat, it is of great interest to consumer to know whether a meat product is truly fresh or not. Researchers have mainly focused on the reduction of moisture loss due to freezing and thawing cycles of meat. The water holding capacity (WHC) of muscle proteins and reduced water content are key quality parameters of meat that ultimately changes color and texture. However, there has been limited progress towards understanding the actual mechanisms behind the meat quality changes under the freeze–thaw cycles. Furthermore, effect of freeze-thaw process on integrity of proteins is ignored. In this paper, we have studied the effect of ‘freeze-thawing’ on physicochemical changes of chicken meat protein. We have assessed the quality of meat by pH, spectroscopic measurements, Western Blot. Our results showed that increase in freeze-thaw cycles causes changes in pH. Measurements of absorbance (UV-visible and IR) indicated the degradation of proteins. The expression of various proteins (CREB, AKT, MAPK, GAPDH, and phosphorylated forms) were performed using Western Blot. These results indicated the repeated cycles of freeze-thaw is responsible for deterioration of protein, thus causing decrease in nutritious value of meat. It damges the use of these products in Islamic Sharia.

Keywords: chicken meat, freeze-thaw, halal, protein, western blot

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Authors: María José Bugueño, Natalia Jaime, Cristian Castro, Diego Naranjo, Guido Trautmann, Mario Pérez-Won, Vilbett Briones-Labarca

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Proteins play a crucial role in various prepared foods, including dairy products, drinks, emulsions, and ready meals. These food proteins are naturally present in food waste and byproducts. The alkaline extraction and acid precipitation method is commonly used to extract proteins from plants and animals due to its product stability, cost-effectiveness, and ease of use. This study aimed to investigate the impact of pH-shifting storage at two different pH levels on the conformational changes affecting the physicochemical and functional properties of quinoa protein isolate (QPI) and yellow shrimp byproduct protein isolate (YSPI). The QPI and YSPI were extracted using the alkaline extraction-isoelectric precipitation method. The dispersions were adjusted to pH 4 or 12, stirred for 2 hours at 20°C to achieve a uniform dispersion, and then freeze-dried. Various analyses were conducted, including flexibility (F), free sulfhydryl content (Ho), emulsifying activity (EA), emulsifying capacity (EC), water holding capacity (WHC), oil holding capacity (OHC), intrinsic fluorescence, ultraviolet spectroscopy, differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR) to assess the properties of the protein isolates. pH-shifting at pH 11 and 12 for QPI and YSPI, respectively, significantly improved protein properties, while property modification of the samples treated under acidic conditions was less pronounced. Additionally, the pH 11 and 12 treatments significantly improved F, Ho, EA, WHC, OHC, intrinsic fluorescence, ultraviolet spectroscopy, DSC, and FTIR. The increase in Ho was due to disulfide bond disruption, which produced more protein sub-units than other treatments for both proteins. This study provides theoretical support for comprehensively elucidating the functional properties of protein isolates, promoting the application of plant proteins and marine byproducts. The pH-shifting process effectively improves the emulsifying property and stability of QPI and YSPI, which can be considered potential plant-based or marine byproduct-based emulsifiers for use in the food industry.

Keywords: quinoa protein, yellow shrimp by-product protein, physicochemical properties, structural properties

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Authors: Yifan Hou, Haibo Liu, Le Jiang, Wandong Su, Binqing Wang

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Road defect detection is crucial for modern urban management and infrastructure maintenance. Traditional road defect detection methods mostly rely on manual labor, which is not only inefficient but also difficult to ensure their reliability. However, existing deep learning-based road defect detection models have poor detection performance in complex environments and lack robustness to multi-scale targets. To address this challenge, this paper proposes a distinct detection framework based on the one stage algorithm network structure. This article designs a deep feature extraction network based on RCSDarknet, which applies channel shuffling to enhance information fusion between tensors. Through repeated stacking of RCS modules, the information flow between different channels of adjacent layer features is enhanced to improve the model's ability to capture target spatial features. In addition, a multi-scale feature fusion mechanism with weighted dual flow paths was adopted to fuse spatial features of different scales, thereby further improving the detection performance of the model at different scales. To validate the performance of the proposed algorithm, we tested it using the RDD2022 dataset. The experimental results show that the enhancement algorithm achieved 84.14% mAP, which is 1.06% higher than the currently advanced YOLOv8 algorithm. Through visualization analysis of the results, it can also be seen that our proposed algorithm has good performance in detecting targets of different scales in complex scenes. The above experimental results demonstrate the effectiveness and superiority of the proposed algorithm, providing valuable insights for advancing real-time road defect detection methods.

Keywords: roads, defect detection, visualization, deep learning

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Authors: Mohit Wadhawan, Sushma Rathaur

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Lymphatic filariasis, also called elephantiasis is a tropical disease afflicting over 120 million people in 81 countries worldwide. Existing anti filarial drugs are effective against the larval stages of filarial parasites which call for an urgent need of drugs which are macrofilaricidal. Identification of molecular targets crucial for survival of filarial parasites is a prerequisite for drug designing. Prolyl oligopeptidase (POP) is one such crucial enzyme involved in the maturation and degradation of neuropeptides and peptide hormones. We have identified this peptidase in the bovine filarial parasite, Setaria cervi. Effect of inhibition of POP on the proteome profile of filarial parasite has been discussed in this study. Filarial parasites were exposed to Z-pro-prolinal (ZPP), a specific POP inhibitor for 8 h and the motility and viability of the parasites was observed. It significantly reduced the motility and viability of the parasites. To study the proteome profile, the cytosolic, endoplasmic reticulum (ER) and mitochondrial extracts of the adult female parasites were subjected to 2-dimensional electrophoresis. As analyzed by the PD-Quest software, the ZPP caused the alteration in the different subcellular proteins, and the significantly altered proteins were identified using MALDI-MS/MS spectrometry. The major proteins identified were found to play important role in diverse biological functions like signaling, redox regulation, energy metabolism, stress response, and cytoskeleton formation. Moreover, we found upregulation in the calcium binding proteins such as calreticulin, calponin, and calpain-6 suggesting that POP inhibition regulates calcium release. This relates to earlier reports that POP plays non-catalytic role in inositol 1,4,5-trisphosphate (IP3) signaling inducing release of calcium from ER. Taken together, the data demonstrated that inhibition of prolyl oligopeptidase alter the overall proteome signifying its role in survival of the filarial parasites. Thus this study provides a basis for the use of POP as a chemotherapeutic target for the treatment of lymphatic filariasis.

Keywords: lymphatic filariasis, setaria cervi, prolyl oligopeptidase, proteomics

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Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Niv Papo

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Characterizing the binding selectivity landscape of interacting proteins is crucial both for elucidating the underlying mechanisms of their interaction and for developing selective inhibitors. However, current mapping methods are laborious and cannot provide a sufficiently comprehensive description of the landscape. Here, we introduce a distinct and efficient strategy for comprehensively mapping the binding landscape of proteins using a combination of experimental multi-target selective library screening and in silico next-generation sequencing analysis. We map the binding landscape of a non-selective trypsin inhibitor, the amyloid protein precursor inhibitor (APPI), to each of four human serine proteases (kallikrein-6, mesotrypsin, and anionic and cationic trypsins). We then use this map to dissect and improve the affinity and selectivity of APPI variants toward each of the four proteases. Our strategy can be used as a platform for the development of a new generation of target-selective probes and therapeutic agents based on selective protein–protein interactions.

Keywords: drug design, directed evolution, protein engineering, protease inhibition.

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Authors: Javier Enciso-Benavides, Fredy Fabian, Carlos Castaneda, Luis Alfaro, Alex Choque, Aparicio Aguilar, Javier Enciso

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Background: The use of biomarkers in breast cancer diagnosis, therapy, and prognosis has gained increasing interest. Cancer stem cells (CSCs) are a subpopulation of tumor cells that can drive tumor initiation and may cause relapse. Therefore, due to the importance of diagnosis, therapy, and prognosis, several biomarkers that characterize CSCs have been identified; however, in treatment-naïve triple-negative breast tumors, there is an urgent need to identify new biomarkers and therapeutic targets. According to this, the aim of this study was to identify serum proteins associated with cancer stem cells and pluripotency in women with triple-negative breast tumors in order to subsequently identify a biomarker for this type of breast tumor. Material and Methods: Whole blood samples from 12 women with histopathologically diagnosed triple-negative breast tumors were used after obtaining informed consent from the patient. Blood serum was obtained by conventional procedure and frozen at -80ºC. Identification of cancer stem cell-associated proteins was performed by matrix-assisted laser desorption/ionisation-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS), protein analysis was obtained using the AB Sciex TOF/TOF™ 5800 system (AB Sciex, USA). Sequences not aligned by ProteinPilot™ software were analyzed by Protein BLAST. Results: The following proteins related to pluripotency and cancer stem cells were identified by MALDI TOF/TOF mass spectrometry: A-chain, Serpin A12 [Homo sapiens], AIEBP [Homo sapiens], Alpha-one antitrypsin, AT {internal fragment} [human, partial peptide, 20 aa] [Homo sapiens], collagen alpha 1 chain precursor variant [Homo sapiens], retinoblastoma-associated protein variant [Homo sapiens], insulin receptor, CRA_c isoform [Homo sapiens], Hydroxyisourate hydrolase [Streptomyces scopuliridis], MUCIN-6 [Macaca mulatta], Alpha-actinin-3 [Chrysochloris asiatica], Polyprotein M, CRA_d isoform, partial [Homo sapiens], Transcription factor SOX-12 [Homo sapiens]. Recommendations: The serum proteins identified in this study should be investigated in the exosome of triple-negative breast cancer stem cells and in the blood serum of women without breast cancer. Subsequently, proteins found only in the blood serum of women with triple-negative breast cancer should be identified in situ in triple-negative breast cancer tissue in order to identify a biomarker to study the evolution of this type of cancer, or that could be a therapeutic target. Conclusions: Eleven cancer stem cell-related serum proteins were identified in 12 women with triple-negative breast cancer, of which MUCIN-6, retinoblastoma-associated protein variant, transcription factor SOX-12, and collagen alpha 1 chain are the most representative and have not been studied so far in this type of breast tumor. Acknowledgement: This work was supported by Proyecto CONCYTEC–Banco Mundial “Mejoramiento y Ampliacion de los Servicios del Sistema Nacional de Ciencia Tecnología e Innovacion Tecnologica” 8682-PE (104-2018-FONDECYT-BM-IADT-AV).

Keywords: triple-negative breast cancer, MALDI TOF/TOF MS, serum proteins, cancer stem cells

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Authors: Hao Cheng, Yingzhou Ni, Amr M. Bakry, Li Liang

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Functional foods containing bioactive nutrients offer benefits beyond basic nutrition and hence the possibility of delaying and preventing chronic diseases. However, many bioactive nutrients degrade rapidly under food processing and storage conditions. Encapsulation can be used to overcome these limitations. Food proteins have been widely used as carrier materials for the preparation of nano/micro-particles because of their ability to form gels and emulsions and to interact with polysaccharides. The mechanisms of interaction between bioactive nutrients and proteins must be understood in order to develop protein-based lipid-free delivery systems. Beta-lactoglobulin, a small globular protein in milk whey, exhibits an affinity to a wide range of compounds. Alfa-tocopherol, resveratrol and folic acid were respectively bound to the central cavity, the outer surface near Trp19–Arg124 and the hydrophobic pocket in the groove between the alfa-helix and the beta-barrel of the protein. Beta-lactoglobulin could thus bind the three bioactive nutrients simultaneously to form protein-multi-ligand complexes. Beta-casein, an intrinsically unstructured but major milk protein, could also interact with resveratrol and folic acid to form complexes. These results suggest the potential to develop milk-protein-based complex carrier systems for encapsulation of multiple bioactive nutrients for functional food application and also pharmaceutical and medical uses.

Keywords: milk protein, bioactive nutrient, interaction, protection

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Authors: Duc Dong Do, Ngoc Ha Tran, Thanh Hai Dang, Cao Cuong Dang, Xuan Huan Hoang

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Global aligning two protein-protein interaction networks is an essentially important task in bioinformatics/computational biology field of study. It is a challenging and widely studied research topic in recent years. Accurately aligned networks allow us to identify functional modules of proteins and/ororthologous proteins from which unknown functions of a protein can be inferred. We here introduce a novel efficient heuristic global network alignment algorithm called FASTAn, including two phases: the first to construct an initial alignment and the second to improve such alignment by exerting a local optimization repeated procedure. The experimental results demonstrated that FASTAn outperformed the state-of-the-art global network alignment algorithm namely SPINAL in terms of both commonly used objective scores and the run-time.

Keywords: FASTAn, Heuristic algorithm, biological network alignment, protein-protein interaction networks

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Authors: Flaurence Benjamain, Michel Casperance

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We present in this paper, first, a comparative study of three mathematical theories to achieve the fusion of information sources. This study aims to identify the characteristics inherent in theories of possibilities, belief functions (DST) and plausible and paradoxical reasoning to establish a strategy of choice that allows us to adopt the most appropriate theory to solve a problem of fusion in order, taking into account the acquired information and imperfections that accompany them. Using the new theory of plausible and paradoxical reasoning, also called Dezert-Smarandache Theory (DSmT), to fuse information multi-sources needs, at first step, the generation of the composites events witch is, in general, difficult. Thus, we present in this paper a new approach to construct pertinent paradoxical classes based on gray levels histograms, which also allows to reduce the cardinality of the hyper-powerset. Secondly, we developed a new technique for order and coding generalized focal elements. This method is exploited, in particular, to calculate the cardinality of Dezert and Smarandache. Then, we give an experimentation of classification of a remote sensing image that illustrates the given methods and we compared the result obtained by the DSmT with that resulting from the use of the DST and theory of possibilities.

Keywords: segmentation, image, approach, vision computing

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Authors: Daniel Schimmelpfennig

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This paper attempts to delineate the idea to curate the leveling up for whole-systems change. Curation is the act fo select, organize, look after, or present information from a professional point of view through expert knowledge. The trans-paradigmatic, trans-contextual, trans-disciplinary, trans-perspective of trans-media futures studies hopes to enable a move from a monochrome intellectual pursuit towards breathing a higher dimensionality. Progressing to the next level to equip actors for whole-systems change is in consideration of the commonly known symptoms of our time as well as in anticipation of future challenges, both a necessity and desirability. Systems of collective intelligence could potentially scale regenerative, adaptive, and anticipatory capacities. How could such a curation then be enacted and implemented, to initiate the process of leveling-up? The suggestion here is to focus on the metasystem transition, the bio-digital fusion, namely, by merging neurosciences, the ontological design of money as our operating system, and our understanding of the billions of years of time-proven permutations in nature, biomimicry, and biological metaphors like symbiogenesis. Evolutionary cybernetics accompanies the process of whole-systems change.

Keywords: bio-digital fusion, evolutionary cybernetics, metasystem transition, symbiogenesis, transmedia futures studies

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Authors: A. Alem, Y. Dahmani, A. Hadjali, A. Boualem

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Managing the problem of the conflict, either by using the Dempster-Shafer theory, or by the application of the fusion process to push researchers in recent years to find ways to get to make best decisions especially; for information systems, vision, robotic and wireless sensor networks. In this paper we are interested to take account of the conflict in the combination step that took the conflict into account and tries to manage such a way that it does not influence the decision step, the conflict what from reliable sources. According to [1], the conflict lead to erroneous decisions in cases where was with strong degrees between sources of information, if the conflict is more than the maximum of the functions of belief mass K > max1...n (mi (A)), then the decision becomes impossible. We will demonstrate in this paper that the multiplication of mass functions by coefficients of reliability is a decreasing function; it leads to the reduction of conflict and a good decision. The definition of reliability coefficients accurately and multiply them by the mass functions of each information source to resolve the conflict and allow deciding whether the degree of conflict. The evaluation of this technique is done by a use case; a comparison of the combination of springs with a maximum conflict without, and with reliability coefficients.

Keywords: Dempster-Shafer theory, fusion process, conflict managing, reliability factors, decision

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Authors: Serap Pektas

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Ataxia telangiectasia mutated (ATM) is a serine-threonine kinase, which is the major regulator of the DNA damage response. ATM is activated upon the formation of DNA double-strand breaks (DSBs) in the cells. ATM phosphorylates the proteins involved in apoptotic responses, cell cycle checkpoint control, DNA repair, etc. Tumor protein p53, known as p53 is one of these proteins that phosphorylated by ATM. Phosphorylation of p53 at Ser15 residue leads to p53 stabilization in the cells. Often enzymes activity is affected by hydrogen ion concentration (pH). In order to find the optimal pH range for ATM activity, steady-state kinetic assays were performed at acidic and basic pH ranges. Ser15 phosphorylation of p53 is determined by using ELISA. The results indicated that the phosphorylation rate was better at basic pH range compared with the acidic pH range. This could be due to enzyme stability, or enzyme-substrate interaction is pH dependent.

Keywords: ataxia telangiectasia mutated, DNA double strand breaks, DNA repair, tumor protein p53

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Authors: Vinaya Kambappa, Chinnadurai Mani, Komaraiah Palle

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Non-small cell-lung cancer (NSCLC) cells have increased expression of EGFR, which makes them a potential target for cancer therapy. Based on molecular docking and previous reports, we designed and synthesized quinazoline derivatives as potent EGFR inhibitors. Among the derivatives, three compounds showed good antiproliferative activity against A-549 and H-1299 cells. Furthermore, these compounds inhibited EGFR signaling exhibiting diminishing p-EGFR and its downstream proteins like p-Akt, p-Erk1/2, and p-mTOR; however, it did not alter the levels of EGFR, Akt, Erk1/2 and mTOR proteins. Flow cytometric analysis indicated the accumulation of cells at G1 phase suggesting induction of apoptosis, which was further confirmed by annexin V/propidium iodide staining. Our study suggested that quinazoline scaffold can be developed as novel EGFR kinase inhibitors for cancer therapy.

Keywords: apoptosis, non-small cell-lung cancer cells, EGFR, quinazoline

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Authors: E. Obreque-Slier, V. Contreras-Cortez, R. López-Solís

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Astringency is a drying, roughing, and sometimes puckering sensation that is experienced on the various oral surfaces during or immediately after tasting foods. This sensation has been closely related to the interaction and precipitation between salivary proteins and polyphenols, specifically flavanols or proanthocyanidins. In addition, the type and concentration of proanthocyanidin influences significantly the intensity of the astringency and consequently the protein/proanthocyanidin interaction. However, most of the studies are based on the interaction between saliva and highly complex polyphenols, without considering the effect of monomeric proanthoancyanidins present in different foods. The aim of this study was to evaluate the effect of different monomeric proanthocyanidins on the diffusion and precipitation of salivary proteins. Thus, solutions of catechin, epicatechin, epigallocatechin and gallocatechin (0, 2.0, 4.0, 6.0, 8.0 and 10 mg/mL) were mixed with human saliva (1: 1 v/v). After incubation for 5 min at room temperature, 15 µL aliquots of each mix were dotted on a cellulose membrane and allowed to dry spontaneously at room temperature. The membrane was fixed, rinsed and stained for proteins with Coomassie blue. After exhaustive washing in 7% acetic acid, the membrane was rinsed once in distilled water and dried under a heat lamp. Both diffusion area and stain intensity of the protein spots were semiqualitative estimates for protein-tannin interaction (diffusion test). The rest of the whole saliva-phenol solution mixtures of the diffusion assay were centrifuged, and 15-μL aliquots from each of the supernatants were dotted on a cellulose membrane. The membrane was processed for protein staining as indicated above. The blue-stained area of protein distribution corresponding to each of the extract dilution-saliva mixtures was quantified by Image J 1.45 software. Each of the assays was performed at least three times. Initially, salivary proteins display a biphasic distribution on cellulose membranes, that is, when aliquots of saliva are placed on absorbing cellulose membranes, and free diffusion of saliva is allowed to occur, a non-diffusible protein fraction becomes surrounded by highly diffusible salivary proteins. In effect, once diffusion has ended, a protein-binding dye shows an intense blue-stained roughly circular area close to the spotting site (non-diffusible fraction) (NDF) which becomes surrounded by a weaker blue-stained outer band (diffusible fraction) (DF). Likewise, the diffusion test showed that epicatechin caused the complete disappearance of DF from saliva with 2 mg/mL. Also, epigallocatechin and gallocatechin caused a similar effect with 4 mg/mL, while catechin generated the same effect at 8 mg/mL. In the precipitation test, the use of epicatechin and gallocatechin generated evident precipitates at the bottom of the Eppendorf tubes. In summary, the flavanol type differentially affects the diffusion and precipitation of saliva, which would affect the sensation of astringency perceived by consumers.

Keywords: astringency, polyphenols, tannins, tannin-protein interaction

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Authors: Fatemeh Mirakhorli

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Porosity is the main issue during welding of aluminum alloys, and surface cleaning has a critical influence to reduce the porosity level by removing the oxidized surface layer before fusion welding. Developing an optimum and economical surface cleaning method has an enormous benefit for aluminum welding industries to reduce costs related to repairing and repeating welds as well as increasing the mechanical properties of the joints. In this study, several mechanical and chemical surface cleaning methods were examined for butt joint welding of 2 mm thick AA6xxx alloys using ER5556 filler metal. The effects of each method on porosity formation and tensile properties are evaluated. It has been found that, compared to the conventional mechanical cleaning method, the use of chemical cleaning leads to an important reduction in porosity level even after a significant delay between cleaning and welding. The effect of the higher porosity level in the fusion zone to reduce the tensile strength of the welds is shown.

Keywords: gas metal arc welding (GMAW), aluminum alloy, surface cleaning, porosity formation, mechanical property

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Authors: Suwattana Visetnan, Premruethai Supungul, Sureerat Tang, Ikuo Hirono, Anchalee Tassanakajon, Vichien Rimphanitchayakit

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In animals, infection by Gram-negative bacteria and certain viruses activates the Imd signaling pathway wherein the a NF-κB transcription factor, Relish, is a key regulatory protein for the synthesis of antimicrobial proteins. Infection by yellow head virus (YHV) activates the Imd pathway. To investigate the expression of genes involved in YHV infection and under the influence of PmRelish regulation, RNA interference and suppression subtractive hybridization (SSH) are employed. The genes in forward library expressed in shrimp after YHV infection and under the activity of PmRelish were obtained by subtracting the cDNAs from YHV-infected and PmRelish-knockdown shrimp with cDNAs from YHV-infected shrimp. Opposite subtraction gave a reverse library whereby an alternative set of genes under YHV infection and no PmRelish expression was obtained. Sequencing of 252 and 99 cDNA clones from the respective forward and reverse libraries were done and annotated through blast search against the GenBank sequences. Genes involved in defense and homeostasis were abundant in both libraries, 31% and 23% in the forward and reverse libraries, respectively. They were predominantly antimicrobial proteins, proteinases and proteinase inhibitors. The expression of antimicrobial protein genes, ALFPm3, crustinPm1, penaeidin3 and penaeidin5 were tested under PmRelish silencing and Gram-negative bacterium V. harveyi infection. Together with the results previously reported, the expression of penaeidin5 and also penaeidin3 but not ALFPm3 and crustinPm1 were under the regulation of PmRelish in the Imd pathway.

Keywords: relish, yellow head virus, penaeus monodon, antimicrobial proteins

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Authors: Yuting Wu, Faraz Choudhury, Daniel Benjamin, James Whalin, Joshua Blatz, Leon Shohet, Michael Sussman, Mark Richards

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Plasma-Induced Modification of Biomolecules (PLIMB) has been developed as a technology, which, together with mass spectrometry, measures three-dimensional structural characteristics of proteins. This technique uses hydroxyl radicals generated by atmospheric-pressure plasma discharge to react with the solvent-accessible side chains of protein in an aqueous solution. In this work, we investigate the three-dimensional structure of hemoglobin and myoglobin using PLIMB. Additional modifications to these proteins, such as oxidation, fragmentations, and conformational changes caused by PLIMB are also explored. These results show that PLIMB, coupled with mass spectrometry, is an effective way to determine solvent access to hemoproteins. Furthermore, we show that many factors, including pH and the electrical parameters used to generate the plasma, have a significant influence on solvent accessibility.

Keywords: plasma, hemoglobin, myoglobin, solvent access

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Authors: Han Xue, Zhang Lanyue

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In order to seek more effective feature extraction technology, feature extraction method based on MFCC combined with vector hydrophone is exposed in the paper. The sound pressure signal and particle velocity signal of two kinds of ships are extracted by using MFCC and its evolution form, and the extracted features are fused by using fisher-ratio and correlated distance criterion. The features are then identified by BP neural network. The results showed that MFCC, First-Order Differential MFCC and Second-Order Differential MFCC features can be used as effective features for recognition of underwater targets, and the fusion feature can improve the recognition rate. Moreover, the results also showed that the recognition rate of the particle velocity signal is higher than that of the sound pressure signal, and it reflects the superiority of vector signal processing.

Keywords: vector information, MFCC, differential MFCC, fusion feature, BP neural network

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Authors: Edmaritz Hernandez-Pagan, Kanjana Laosuntisuk, Alex Harris, Allison Haynes, David Buitrago, Michael Kudenov, Colleen Doherty

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Rare Earth Elements (REEs) are critical metals for modern electronics, green technologies, and defense systems. However, due to their dispersed nature in the Earth’s crust, frequent co-occurrence with radioactive materials, and similar chemical properties, acquiring and purifying REEs is costly and environmentally damaging, restricting access to these metals. Plants could serve as resources for bioengineering REE mining systems. Although there is limited information on how REEs affect plants at a cellular and molecular level, plants with high REE tolerance and hyperaccumulation have been identified. This dissertation aims to develop a plant-based system for harvesting REEs from industrial waste material with a focus on Acid Mine Drainage (AMD), a toxic coal mining product. The objectives are 1) to develop a non-destructive, in vivo detection method for REE detection in Phytolacca plants (REE hyperaccumulator) plants utilizing fluorescence spectroscopy and with a primary focus on dysprosium, 2) to characterize the uptake of REE and Heavy Metals in Phytolacca americana and Phytolacca acinosa (REE hyperaccumulator) in AMD for potential implementation in the plant-based system, 3) to implement the REE detection method to identify REE-binding proteins and peptides for potential enhancement of uptake and selectivity for targeted REEs in the plants implemented in the plant-based system. The candidates are known REE-binding peptides or proteins, orthologs of known metal-binding proteins from REE hyperaccumulator plants, and novel proteins and peptides identified by comparative plant transcriptomics. Lanmodulin, a high-affinity REE-binding protein from methylotrophic bacteria, is used as a benchmark for the REE-protein binding fluorescence assays and expression in A. thaliana to test for changes in REE plant tolerance and uptake.

Keywords: phytomining, agromining, rare earth elements, pokeweed, phytolacca

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Authors: Mouheb Mehdoui, Amel Fraisse, Mounir Zrigui

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This paper explores the potential of short texts through semantic enrichment and disambiguation techniques. By employing context fusion, we aim to enhance the comprehension and utility of concise textual information. The methodologies utilized are grounded in recent advancements in natural language processing, which allow for a deeper understanding of semantics within limited text formats. Specifically, topic classification is employed to understand the context of the sentence and assess the relevance of added expressions. Additionally, word sense disambiguation is used to clarify unclear words, replacing them with more precise terms. The implications of this research extend to various applications, including information retrieval and knowledge representation. Ultimately, this work highlights the importance of refining short text processing techniques to unlock their full potential in real-world applications.

Keywords: information traffic, text summarization, word-sense disambiguation, semantic enrichment, ambiguity resolution, short text enhancement, information retrieval, contextual understanding, natural language processing, ambiguity

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Authors: Ava Faridi, Pouya Faridi, Aleksandr Kakinen, Ibrahim Javed, Thomas P. Davis, Pu Chun Ke

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Human islet amyloid polypeptide (IAPP) is a hormone associated with glycemic control and type 2 diabetes. Biophysically, the chirality of IAPP fibrils has been little explored with respect to the aggregation and toxicity of the peptide. Biochemically, it remains unclear as for how protein expression in pancreatic beta cells may be altered by cell exposure to the peptide, and how such changes may be mitigated by nanoparticle inhibitors for IAPP aggregation. In this study, we first demonstrated the elimination of the IAPP nucleation phase and shortening of its elongation phase by silica nanoribbons. This accelerated IAPP fibrillization translated to reduced toxicity, especially for the right-handed silica nanoribbons, as revealed by cell viability, helium ion microscopy, as well as zebrafish embryo survival, developmental and behavioral assays. We then examined the proteomes of βTC6 pancreatic beta cells exposed to the three main aggregation states of monomeric, oligomeric and amyloid fibrillar IAPP, and compared that with cellular protein expression modulated by graphene quantum dots (GQDs). A total of 29 proteins were significantly regulated by different forms of IAPP, and the majority of these proteins were nucleotide-binding proteins. A regulatory capacity of GQDs against aberrant protein expression was confirmed. These studies have demonstrated the great potential of employing nanomaterials targeting the mesoscopic enantioselectivity and protein expression dysregulation in pancreatic beta cells.

Keywords: graphene quantum dots, IAPP, silica nanoribbons, protein expression, toxicity

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

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Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: M. Dehestani, F. Kamali, M. Klantari Pour, L. Zeidabadi-Nejad

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Chemical bonding between polyethylene glycol (PEG) with pharmaceutical proteins called pegylation is one of the most effective methods of improving the pharmacological properties. The covalent attachment of polyethylene glycol (PEG) to proteins will increase their pharmacologic properties. For the formation of a combination of pegylated protein should first be activated PEG and connected to the protein. Interferons(IFNs) are a family of cytokines which show antiviral effects in front of the biological and are responsible for setting safety system. In this study, the nature and properties of the interaction between active positions of IFNs and polyethylene glycol have been investigated using molecular dynamics simulation. The main aspect of this theoretical work focuses on the achievement of valuable data on the reaction pathways of PEG-IFNs and the transition state energy. Our results provide a new perspective on the interactions, chemical properties and reaction pathways between IFNs and PEG.

Keywords: interaction, interferons, molecular dynamics simulation, polyethylene glycol

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Authors: Mayuva Youngsabanant, Chanikarn Srinark, Supanyika Sengsai, Soratorn Kerdkriangkrai, Nongnuch Gumlungpat, Mayuree Pumipaiboon

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The follicular fluid proteins of healthy medium size follicles (4-6 mm in diameters) and large size follicles (7-8 mm in diameter) of large white pig ovaries were collected by using sterile technique. They were used for testing the effect on primary in vitro cell culture growth of porcine oviductal epithelial cells (pOEC). Porcine oviductal epithelial cells of luteal phase was culture in M199 and added with 10% fetal calf serum 2.2 mg/mL, NaHCO₃, 0.25 mM pyruvate, 15 µg/mL and 50 µg/mL, gentamycin sulfate at high humidified atmosphere with 5% CO₂ in 95% air atmosphere at 37°C for 96 h before testing. The optimized concentration of pFF of two follicle sizes (at concentration of 2, 4, 20, 40, 200, 400, 500, and 600 µg proteins) in culture medium was observed for 24 h using MTT assay. Results were analyzed with a one-way ANOVA in SPSS statistic. Moreover, pOEC was also studied in morphological characteristic on long-term culture. The results of long-term study revealed that pOEC showed 70-80 percentage of healthy morphology on epithelial-like character and contained 30 percentage of an elongated shape (fibroblast-like morphology) at 4 weeks of culture time. MTT assay reviewed an increase in the percentage of viability of pOEC in 2 treated of follicular fluid groups. Two treatment concentration groups were higher than control group (p < 0.05) but not in positive control group. Interestingly, at 200 µg protein of 2 treated follicular fluid groups were reached the highest cell viability which is higher than a positive control and it is significantly different form control group (P < 0.05). These cells are developed and had fibroblast elongate shape which is longer than the cells in control group and positive control group. This report implies that pFF of medium follicle size at 200 µg proteins and large follicle size at 200 and 500 µg proteins could be optimized concentration for using as a supplement in culture medium to promote cell growth and development instead of growth hormone from fetal calf serum. It could be applied in cell biotechnology researches. Acknowledgements: The project was funded by a grant from Silpakorn University Research and Development Institute (SURDI) and Faculty of Science, Silpakorn University, Thailand.

Keywords: in vitro, porcine follicular fluid protein (pFF), porcine oviductal epithelial cells (pOEC), MTT

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Authors: Bouchiha Hanene, Rouabhi Rachid, Bouchama Khaled, Djebar Berrebbah Houraya, Djebar Mohamed Reda

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Recently, some natural products such as essentials oils (EOs) have been used in the fields as alternative to synthetic compounds, to minimize the negative impacts to the environment. This fact has led to questions about the possible impact of EOs on ecosystems. Currently in toxicology, the use of alternative models can help to understand the mechanisms of toxic action, at different levels of organization of ecosystems. Algae, protozoa and bacteria form the base of the food chain and protozoan cells are used as bioindicators often of pollution in environment. Unicellular organisms offer the possibility of direct study of independent cells with specific characteristics of individual cells and whole organisms at the same time. This unicellular facilitates the study of physiological processes, and effects of pollutants at the cellular level, which makes it widely used to assess the toxic effects of various xenobiotics. This study aimed to verify the effects of EOs of one famous plant used tremendously in our folk medicine, namely Artemisia herba alba in causing acute toxicity (24 hours) and chronic (15 days) toxicity for model cellular (Paramecium sp). To this end, cellular’s of paramecium were exposed to various concentrations (Three doses were chosen) of EOs extracted from plant (Artemisia herba alba). In the first experiment, the cellular s cultures were exposed for 48 hours to different concentrations to determine the median lethal concentration (DL50). We followed the evolution of physiological parameters (growth), biochemical (total proteins, respiratory metabolism), as well as the variations of a bio marker the GSH. Our results highlighted a light inhibition of the growth of the protozoa as well as a disturbance of the contents of total proteins and a reduction in the reduced rate of glutathione. The polarographic study revealed a stimulation of the consumption of O2 and this at the treated cells.

Keywords: essential oils, protozoa, bio indicators, toxicity, Growth, bio marker, proteins, polarographic

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Authors: Sulhee Lee, Geon Kim, Young-Seo Park

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Unlike the traditional milk sterilization methods (LTLT, HTST, or UHT), pulsed electric field (PEF) technology is a non-thermal pasteurization process. This technology minimizes energy required for heat treatment in food processing, changes in sensory properties, and physical losses. In this study, structural changes of bovine milk proteins, the amount of immunoproteins such as IgG, and their storability by PEF treatment were examined. When the changes of protein content in PEF-treated milk were examined using HPLC, the amounts of α-casein and β-lactoglobulin were reduced over 40% each, whereas those of κ-casein and β-casein did not change. The amount of α-casein in HTST milk was reduced to 50%. When PEF was applied to milk at the energy level of 250 kJ, the amounts of IgG, IgA, β-lactoglobulin (β-LG), lactoferrin, and α-lactalbumin (α-LA) decreased by 43, 41, 35, 63, and 45%, respectively. When milk was sterilized by LTLT process followed by PEF process at the level of 150 kJ, the concentrations of IgG, IgA, β-LG, lactoferrin, and α-LA were 56.6, 10.6, 554, 2.8 and 660.1 μg/mL, respectively. When the bovine milk was sterilized by LTLT process followed by PEF process at the energy level of 180 kJ, storability of immunoproteins of milk was the highest and the concentrations of IgG, IgA, and β-LG decreased by 79.5, 6.5, and 134.5 μg/mL, respectively, when compared with the initial concentrations of those proteins. When bovine milk was stored at 4℃ after sterilization through HTST sterilizer followed by PEF process at the energy level of 200 kJ, the amount of lactoferrin decreased 7.3% after 36 days of storage, whereas that of lactoferrin of raw milk decreased 16.4%. Our results showed that PEF treatment did not change the protein structure nor induce protein denaturation in milk significantly when compared with LTLT or HTST sterilization. Also, LTLT or HTST process in combination with PEF were more effective than LTLT only or HTST only process in the conservation of immunoproteins in bovine milk.

Keywords: pulsed electric field, bovine milk, immunoproteins, sterilization

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