Search results for: synthetic peptides

Authors: Abdulkareem M. Hamid, Yaseen Elhebshi, Adam Daïch

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Luotonins and its derivatives (Isoluotonins) are alkaloids from the aerial parts of Peganum nigellastrum Bunge that display three major skeleton types. Luotonins A, B, and E are pyrroloquinazolinoquinoline alkaloids. A few methods were known for the sysnthesis of Isoluotonin. All luotonins have shown promising cytotoxicities towards selected human cancer cell lines, especially against leukemia P-388 cells. Luotonin A is the most active one, with its activity stemming from topoisomerase I-dependent DNA-cleavage. Such intriguing biological activities and unique structures have led not only to the development of synthetic methods for the efficient synthesis of these compounds, but also to interest in structural modifications for improving the biological properties. Recent progress in the study of luotonins is covered.

Keywords: luotonin A, isoluotonin, pyrroloquiolines, alkaloids

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Authors: Babak Forouraghi

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A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of the flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on the spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts, as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with an attention mechanism. In previous works on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work, with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on the presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: machine learning, classification and regression, gene circuit design, bidirectional transformers

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Authors: Hanizam Awang, Muhammad Hafiz Ahmad

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An experimental study was conducted on foamed concrete with synthetic and natural fibres consisting of AR-glass, polypropylene, steel, kenaf and oil palm fibre. The foamed concrete mixtures produced had a target density of 1000 kg/m3 and a mix ratio of (1:1.5:0.45). The fibres were used as additives. The inclusion of fibre was maintained at a volumetric fraction of 0.25 and 0.4 %. The water absorption, thermal and shrinkage were determined to study the effect of the fibre on the durability properties of foamed concrete. The results showed that AR-glass fibre has the lowest percentage value of drying shrinkage compared to others.

Keywords: foamed concrete, fibres, durability, construction, geological engineering

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Authors: María Fernanda Quiceno Vallejo, Patricia del Portillo, María Mercedes Zambrano, Jeisson Alejandro Triana, Dayana Calderon, Juan Manuel Anzola

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Microorganisms from tropical ecosystems can be novel in terms of adaptations and conservation. Given the macrodiversity of Colombian ecosystems, it is possible that this diversity is also present in Colombian soils. Tropical soil bacteria could offer a potentially novel source of bioactive compounds. In this study we analyzed a metagenomic fosmid library constructed with tropical bacterial DNAs with the aim of understanding its underlying diversity and functional potential. 8640 clones from the fosmid library were sequenced by NANOPORE MiniOn technology, then analyzed with bioinformatic tools such as Prokka, AntiSMASH and Bagel4 in order to identify functional biosynthetic pathways in the sequences. The strains showed ample difference when it comes to biosynthetic pathways. In total we identified 4 pathways related to aryl polyene synthesis, 12 related to terpenes, 22 related to NRPs (Non ribosomal peptides), 11 related PKs (Polyketide synthases) and 7 related to RiPPs (bacteriocins). We designed primers for the metagenomic clones with the most BGCs (sample 6 and sample 2). Results show the biotechnological / pharmacological potential of tropical ecosystems. Overall, this work provides an overview of the genomic and functional potential of Colombian soil and sets the groundwork for additional exploration of tropical metagenomic sequencing.

Keywords: bioactives, biosyntethic pathways, bioinformatic, bacterial gene clusters, secondary metabolites

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Authors: Benyamina Imane, Benalioua Bahia, Mansour Meriem, Bentouami Abdelhadi

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The objective of this study is to use a synthetic route of the layered double hydroxide as a method of zinc oxide by doping a transition metal. The material is heat-treated at different temperatures then tested on the photo-fading of an acid dye indigo carmine under visible radiation compared with ZnO. The photo catalytic efficiency of Bi-ZnO in a visible light of 500 W was tested on photo-bleaching of an indigoid dye in comparison with the commercial ZnO. Indeed, a complete discoloration of indigo carmine solution of 16 mg / L was obtained after 40 and 120 minutes of irradiation in the presence of ZnO and ZnO-Bi respectively.

Keywords: LDH, POA, photo-catalysis, Bi-ZnO doping

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Authors: Rajesh Kumar, Anil Kamboj

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Inhibition of α- amylase play a vital role in the clinical management of postprandial hyperglycemia. Although, powerful synthetic inhibitors are available, natural inhibitors are potentially safer. The present study was carried out to evaluate α- amylase inhibition activity from hydroalcoholic extracts from aerial parts of Cestrum nocturnum. Hydroalcoholic extract was prepared by Soxhletation Method. The extract showed strong inhibition towards α- amylase activity and IC50 value were 45.9 µg. This In vitro studies indicate the potential of C. nocturnum in the development of effective anti-diabetic agents.

Keywords: α- amylase, cestrum nocturnum, hyperglycemia, hydroalcoholic extracts, diabetes

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Authors: Elmo Thiago Lins Cöuras Ford, Valentina Alessandra Carvalho do Vale

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Given the unquestionable need of environmental preservation, the natural fibers have been seen as a salutary alternative for production of composites in substitution to the synthetic fibers, vitreous and metallic. In this work, the behavior of a composite was analyzed done with fiber of the peel of the coconut as reinforcement and latex as head office, when submitted the source of heat. The temperature profiles were verified in the internal surfaces and it expresses of the composite as well as the temperature gradient in the same. It was also analyzed the behavior of this composite when submitted to a cold source. As consequence, in function of the answers of the system, conclusions were reached.

Keywords: natural fiber, composite, temperature, latex, gradient

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Authors: Inigo Beckett

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In forensic investigations, it is often the case that the most potentially useful recorded evidence derives from coincidental imagery, recorded immediately before or during an incident, and that during the incident (e.g. a ‘failure’ or fire event), the evidence is changed or destroyed. To an image analysis expert involved in photogrammetric analysis for Civil or Criminal Proceedings, traditional computer vision methods involving calibrated cameras is often not appropriate because image metadata cannot be relied upon. This paper presents an approach for resolving this problem, considering in particular and by way of a case study, the angle of a simple ladder shown in a photograph. The UK Health and Safety Executive (HSE) guidance document published in 2014 (INDG455) advises that a leaning ladder should be erected at 75 degrees to the horizontal axis. Personal injury cases can arise in the construction industry because a ladder is too steep or too shallow. Ad-hoc photographs of such ladders in their incident position provide a basis for analysis of their angle. This paper presents a direct approach for ascertaining the position of the camera and the angle of the ladder simultaneously from the photograph(s) by way of a workflow that encompasses a novel application of projective geometry and matrix analysis. Mathematical analysis shows that for a given pixel ratio of directly measured collinear points (i.e. features that lie on the same line segment) from the 2D digital photograph with respect to a given viewing point, we can constrain the 3D camera position to a surface of a sphere in the scene. Depending on what we know about the ladder, we can enforce another independent constraint on the possible camera positions which enables us to constrain the possible positions even further. Experiments were conducted using synthetic and real-world data. The synthetic data modeled a vertical plane with a ladder on a horizontally flat plane resting against a vertical wall. The real-world data was captured using an Apple iPhone 13 Pro and 3D laser scan survey data whereby a ladder was placed in a known location and angle to the vertical axis. For each case, we calculated camera positions and the ladder angles using this method and cross-compared them against their respective ‘true’ values.

Keywords: image analysis, projective geometry, homography, photogrammetry, ladders, Forensics, Mathematical modeling, planar geometry, matrix analysis, collinear, cameras, photographs

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Authors: A. Aslihan Gokaltun, Ali Tuncel

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The unique properties of capillary electrochromatography (CEC) such as high performance, high selectivity, low consumption of both reagents and analytes ensure this technique an attractive one for the separation of biomolecules including nucleosides and nucleotides, peptides, proteins, carbohydrates. Monoliths have become a well-established separation media for CEC in the format that can be compared to a single large 'particle' that does not include interparticular voids. Convective flow through the pores of monolith significantly accelerates the rate of mass transfer and enables a substantial increase in the speed of the separation. In this work, we propose a new approach for the preparation of cationic monolithic stationary phase for capillary electrochromatography. Instead of utilizing a charge bearing monomer during polymerization, the desired charge-bearing group is generated on the capillary monolith after polymerization by using the reactive moiety of the monolithic support via one-pot, simple reaction. Optimized monolithic column compensates the disadvantages of frequently used reversed phases, which are difficult for separation of polar solutes. Rapid separation and high column efficiencies are achieved for the separation of neutral analytes, nucleic acid bases and nucleosides in reversed phase mode. Capillary monolith showed satisfactory hydrodynamic permeability and mechanical stability with relative standard deviation (RSD) values below 2 %. A new promising, reactive support that has a 'ligand selection flexibility' due to its reactive functionality represent a new family of separation media for CEC.

Keywords: biomolecules, capillary electrochromatography, cationic monolith, neutral analytes

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Authors: Elad Arad, Raz Jelinek, Hanna Rapaport

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Amyloidoses are a family of diseases characterized by abnormal protein folding that leads to aggregation. They accumulate to form fibrillar plaques which are implicated in the pathogenesis of Alzheimer, prion, diabetes type II and other diseases. To the best of our knowledge, despite extensive research efforts devoted to plaque aggregates inhibition, there is yet no cure for this phenomenon. Titanium and its alloys are found in growing interest for biomedical applications. Variety of surface modifications enable porous, adhesive, bioactive coatings for its surface. Titanium oxides (titania) are also being developed for photothermal and photodynamic treatments. Inspired by this, we set to explore the effect of functionalized titania nanoparticles in combination with external stimuli, as potential photothermal ablating agents against amyloids. Titania nanoparticles were coated with bi-functional catechol derivatives (dihydroxy-phenylalanine propanoic acid, noted DPA) to gain targeting properties. In conjunction with UV-radiation, these nanoparticles may selectively destroy the vicinity of their target. Titania modified 5 nm nanoparticles coated with DPA were further conjugated to the amyloid-targeting Congo Red (CR). These Titania-DPA-CR nanoparticles were found to target mature amyloid fibril of both amyloid-β (Aβ 1-42 a.a). Moreover, irradiation of the peptides in presence of the modified nanoparticles decreased the aggregate content and oligomer fraction. This work provides insights into the use of modified titania nanoparticles for amyloid plaque targeting and photothermal destruction. It may shed light on future modifications and functionalization of titania nanoparticles for different applications.

Keywords: titanium dioxide, amyloids, photothermal treatment, catechol, Congo-red

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Authors: S. Gariani, I. Shyha

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Cutting titanium alloys are usually accompanied with low productivity, poor surface quality, short tool life and high machining costs. This is due to the excessive generation of heat at the cutting zone and difficulties in heat dissipation due to relatively low heat conductivity of this metal. The cooling applications in machining processes are crucial as many operations cannot be performed efficiently without cooling. Improving machinability, increasing productivity, enhancing surface integrity and part accuracy are the main advantages of cutting fluids. Conventional fluids such as mineral oil-based, synthetic and semi-synthetic are the most common cutting fluids in the machining industry. Although, these cutting fluids are beneficial in the industries, they pose a great threat to human health and ecosystem. Vegetable oils (VOs) are being investigated as a potential source of environmentally favourable lubricants, due to a combination of biodegradability, good lubricous properties, low toxicity, high flash points, low volatility, high viscosity indices and thermal stability. Fatty acids of vegetable oils are known to provide thick, strong, and durable lubricant films. These strong lubricating films give the vegetable oil base stock a greater capability to absorb pressure and high load carrying capacity. This paper details preliminary experimental results when turning Ti-6Al-4V. The impact of various VO-based cutting fluids, cutting tool materials, working conditions was investigated. The full factorial experimental design was employed involving 24 tests to evaluate the influence of process variables on average surface roughness (Ra), tool wear and chip formation. In general, Ra varied between 0.5 and 1.56 µm and Vasco1000 cutting fluid presented comparable performance with other fluids in terms of surface roughness while uncoated coarse grain WC carbide tool achieved lower flank wear at all cutting speeds. On the other hand, all tools tips were subjected to uniform flank wear during whole cutting trails. Additionally, formed chip thickness ranged between 0.1 and 0.14 mm with a noticeable decrease in chip size when higher cutting speed was used.

Keywords: cutting fluids, turning, Ti-6Al-4V, vegetable oils, working conditions

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Authors: Sofia Barbosa, Mariana Pinto, José António Almeida, Edgar Carvalho, Catarina Diamantino

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The aim of this work was to test a methodology able to generate spatial-temporal maps that can synthesize simultaneously the trends of distinct hydrochemical indicators in an old radium-uranium tailings dam deposit. Multidimensionality reduction derived from principal component analysis and subsequent data aggregation derived from clustering analysis allow to identify distinct hydrochemical behavioural profiles and to generate synthetic evolutionary hydrochemical maps.

Keywords: Contamination plume migration, K-means of PCA scores, groundwater and mine water monitoring, spatial-temporal hydrochemical trends

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Authors: Shalini Singh, Sanjay K. Srivastava, Govind, Mukhtar. A. Khan, P. K. Singh

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Nanotechnology is revolutionizing the development of biosensors. Nanomaterials and nanofabrication technologies are increasingly being used to design novel biosensors. Sensitivity and other attributes of biosensors can be improved by using nanomaterials with unique chemical, physical, and mechanical properties in their construction. Silicon is a promising biomaterial that is non-toxic and biodegradable and can be exploited in chemical and biological sensing. Present study demonstrated the streptavidin–biotin interaction on silicon surfaces with different topographies such as flat and nanostructured silicon (nanowires) surfaces. Silicon nanowires with wide range of surface to volume ratio were prepared by electrochemical etching of silicon wafer. The large specific surface of silicon nanowires can be chemically modified to link different molecular probes (DNA strands, enzymes, proteins and so on), which recognize the target analytes, in order to enhance the selectivity and specificity of the sensor device. The interaction of streptavidin with biotin was carried out on 3-aminopropyltriethoxysilane (APTS) functionalized silicon surfaces. Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Photoelectron Spectroscopy (XPS) studies have been performed to characterize the surface characteristics to ensure the protein attachment. Silicon nanowires showed the enhance protein attachment, as compared to flat silicon surface due to its large surface area and good molecular penetration to its surface. The methodology developed herein could be generalized to a wide range of protein-ligand interactions, since it is relatively easy to conjugate biotin with diverse biomolecules such as antibodies, enzymes, peptides, and nucleotides.

Keywords: FTIR, silicon nanowires, streptavidin-biotin, XPS

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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: Ali Moafi, Kourosh Kalantarzadeh, Richard Kaner, Parviz Parvin, Ebrahim Asl Soleimani, Dougal McCulloch

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In-situ Raman spectroscopy of flexible graphene-oxide films examined upon exposure to hydrogen gas, air, and synthetic air. The changes in D and G peaks are attributed to defects responding to atomic hydrogen spilled over from the catalytic behavior of Pt nanoparticles distributed all over the film. High-resolution transmission electron microscopy images (HRTEM) as well as electron energy loss spectroscopy (EELS) were carried out to define the density of the samples.

Keywords: in situ Raman Spectroscopy, EELS, TEM, graphene oxide, graphene, atomic hydrogen

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Authors: C.W. Kan

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Softening applied on textile products based on several reasons. First, the synthetic detergent removes natural oils and waxes, thus lose the softness. Second, compensate the harsh handle of resin finishing. Also, imitate natural fibres and improve the comfort of fabric are the reasons to apply softening. There are different types of softeners for softening finishing of textiles, nonionic softener, anionic softener, cationic softener and silicone softener. The aim of this study is to illustrate the proper application of different softeners and their final softening effect in textiles. The results could also provide guidance note to the students in learning this topic. Acknowledgment: Authors would like to thank the financial support from the Hong Kong Polytechnic University for this work.

Keywords: learning materials, softening, textiles, effect

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Authors: Shima Mahmoudi, Babak Pourakbari, Setareh Mamishi, Mostafa Teymuri, Majid Marjani

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Although cytokine analysis has greatly contributed to the understanding of tuberculosis (TB) pathogenesis, data on cytokine profiles that might distinguish progression from latency of TB infection are scarce. Since PE/PPE proteins are known to induce strong humoral and cellular immune responses, the aim of this study was to evaluate the diagnostic potential of interleukin-2 (IL-2) as biomarker after specific antigen stimulation with PE35 and PPE68 for the discrimination of active and latent tuberculosis infection (LTBI). The production of IL-2 was measured in the antigen-stimulated whole-blood supernatants following stimulation with recombinant PE35 and PPE68. All the patients with active TB and LTBI had positive QuantiFERON-TB Gold in Tube test. The level of IL-2 following stimulation with recombinant PE35 and PPE68 were significantly higher in LTBI group than in patients with active TB infection or control group. The discrimination performance (assessed by the area under ROC curve) for IL-2 following stimulation with recombinant PE35 and PPE68 between LTBI and patients with active TB were 0.837 (95%CI: 0.72-0.97) and 0.75 (95%CI: 0.63-0.89), respectively. Applying the 12.4 pg/mL cut-off for IL-2 induced by PE35 in the present study population resulted in sensitivity of 78%, specificity of 78%, PPV of 78% and NPV of 100%. In addition, a sensitivity of 81%, specificity of 70%, PPV of 67% and 87% of NPV was reported based on the 4.4 pg/mL cut-off for IL-2 induced by PPE68. In conclusion, peptides of the antigen PE35 and PPE68, absent from commonly used BCG strains, stimulated strong IL-2- positive T cell responses in patients with LTBI. This study confirms IL-2 induced by PE35 and PPE68 as a sensitive and specific biomarker and highlights IL-2 as new promising adjunct markers for discriminating of LTBI and Active TB infection.

Keywords: IL-2, PE35, PPE68, tuberculosis

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Authors: Nicholas Fletcher, Zachary Houston, Yongmei Zhao, Christopher Howard, Kristofer Thurecht

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One promising approach to enhance nanomedicine therapeutic efficacy is to include a targeting agent, such as an antibody, to increase accumulation at the tumor site. However, the application of such targeted nanomedicines remains limited, in part due to difficulties involved with biomolecule conjugation to synthetic nanomaterials. One approach recently developed to overcome this has been to engineer bispecific antibodies (BsAbs) with dual specificity, whereby one portion binds to methoxy polyethyleneglycol (mPEG) epitopes present on synthetic nanomedicines, while the other binds to molecular disease markers of interest. In this way, noncovalent complexes of nanomedicine core, comprising a hyperbranched polymer (HBP) of primarily mPEG, decorated with targeting ligands are able to be produced by simple mixing. Further work in this area has now demonstrated such complexes targeting the breast cancer marker epidermal growth factor receptor (EGFR) to show enhanced binding to tumor cells both in vitro and in vivo. Indeed the enhanced accumulation at the tumor site resulted in improved therapeutic outcomes compared to untargeted nanomedicines and free chemotherapeutics. The current work on these BsAb-HBP conjugates focuses on further probing antibody-nanomaterial interactions and demonstrating broad applicability to a range of cancer types. Herein are reported BsAb-HBP materials targeted towards prostate-specific membrane antigen (PSMA) and study of their behavior in vivo using ⁸⁹Zr positron emission tomography (PET) in a dual-tumor prostate cancer xenograft model. In this model mice bearing both PSMA+ and PSMA- tumors allow for PET imaging to discriminate between nonspecific and targeted uptake in tumors, and better quantify the increased accumulation following BsAb conjugation. Also examined is the potential for formation of these targeted complexes in situ following injection of individual components? The aim of this approach being to avoid undesirable clearance of proteinaceous complexes upon injection limiting available therapeutic. Ultimately these results demonstrate BsAb functionalized nanomaterials as a powerful and versatile approach for producing targeted nanomedicines for a variety of cancers.

Keywords: bioengineering, cancer, nanomedicine, polymer chemistry

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Authors: J. M. Cruz, X. Vecıno, L. Rodrıguez-López, J. M. Dominguez, A. B. Moldes

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The cosmetic and personal care industry are the fields where biosurfactants could have more possibilities of success because in this kind of products the replacement of synthetic detergents by natural surfactants will provide an additional added value to the product, at the same time that the harmful effects produced by some synthetic surfactants could be avoided or reduced. Therefore, nowadays, consumers are disposed to pay and additional cost if they obtain more natural products. In this work we provide data about the potential of biosurfactants in the cosmetic and personal care industry. Biosurfactants from corn steep liquor, that is a fermented and condensed stream, have showed good surface-active properties, reducing substantially the surface tension of water. The bacteria that usually growth in corn steep liquor comprises Lactobacillus species, generally recognize as safe. The biosurfactant extracted from CSL consists of a lipopeptide, composed by fatty acids, which can reduce the surface tension of water in more than 30 units. It is a yellow and viscous liquid with a density of 1.053 mg/mL and pH=4. By these properties, they could be introduced in the formulation of cosmetic creams, hair conditioners or shampoos. Moreover this biosurfactant extracted from corn steep liquor, have showed a potent antimicrobial effect on different strains of Streptococcus. Some species of Streptococcus are commonly found weakly living in the human respiratory and genitourinary systems, producing several diseases in humans, including skin diseases. For instance, Streptococcus pyogenes produces many toxins and enzymes that help to stabilize skin infections; probably biosurfactants from corn steep liquor can inhibit the mechanisms of the S. pyogenes enzymes. S. pyogenes is an important cause of pharyngitis, impetigo, cellulitis and necrotizing fasciitis. In this work it was observed that 50 mg/L of biosurfactant extract obtained from corn steep liquor is able to inhibit more than 50% the growth of S. pyogenes. Thus, cosmetic and personal care products, formulated with biosurfactants from corn steep liquor, could have prebiotic properties. The natural biosurfactant presented in this work and obtained from corn milling industry streams, have showed a high potential to provide an interesting and sustainable alternative to those, antibacterial and surfactant ingredients used in cosmetic and personal care manufacture, obtained by chemical synthesis, which can cause irritation, and often only show short time effects.

Keywords: antimicrobial activity, biosurfactants, cosmetic, personal care

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Authors: Karima Menad, Ahmed Feddag

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In this study, large crystals of the zeolite NaA were synthesized by hydrothermal way. By following this zeolite was used to recover two heavy metals that are allowing the most dangerous toxic, lead and cadmium. The synthesized zeolite was analyzed by XRD and SEM aims to verify its purity and its good morphology; after it was undergoing ion exchange operations by aqueous solution with lead and cadmium in two salts Pb(CH3COOH)2 and CdCl2 at different concentrations. The exchange was carried out under the effect of two temperatures (25 °C and 60 °C). The contents of Pb++, Cd++ and Na+ were analyzed by atomic absorption and the results are given in the form of exchange rates. At the end the samples are analyzed by XRD exchanged to confirm their conservation of their zeolite framework. It is found that the exchange rate increases with the increase of initial concentration and the best results are found for the temperature of 60 °C.

Keywords: exchange rate, ion exchange, LTA zeolite, zeolite NaA

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Authors: Tivani Phosa Mashamba-Thompson, Mahmoud E. S. Soliman

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To date, the cause of neurodegeneration is not well understood and diseases that stem from neurodegeneration currently have no known cures. Cathepsin B (CB) enzyme is known to be involved in the production of peptide neurotransmitters and toxic peptides in neurodegenerative diseases (NDs). CA-074Me is a membrane-permeable irreversible selective cathepsin B (CB) inhibitor as confirmed by in vivo studies. Due to the lack of the crystal structure, the binding mode of CA-074Me with the human CB at molecular level has not been previously reported. The main aim of this study is to gain an insight into the binding mode of CB CA-074Me to human CB using various computational tools. Herein, molecular dynamics simulations, binding free energy calculations and per-residue energy decomposition analysis were employed to accomplish the aim of the study. Another objective was to identify novel CB inhibitors based on the structure of CA-074Me using fragment based drug design using scaffold hoping drug design approach. Results showed that two of the designed ligands (hit 1 and hit 2) were found to have better binding affinities than the prototype inhibitor, CA-074Me, by ~2-3 kcal/mol. Per-residue energy decomposition showed that amino acid residues Cys29, Gly196, His197 and Val174 contributed the most towards the binding. The Van der Waals binding forces were found to be the major component of the binding interactions. The findings of this study should assist medicinal chemist towards the design of potential irreversible CB inhibitors.

Keywords: cathepsin B, scaffold hopping, docking, molecular dynamics, binding-free energy, neurodegerative diseases

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Authors: M. Bharath, Vasudevan Raghavan, B. V. S. S. S. Prasad, S. R. Chakravarthy

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In this experimental study, effects of addition of rice husk on coal gasification in a bubbling fluidized bed gasifier, operating at atmospheric pressure with air as gasifying agent, are reported. Rice husks comprising of 6.5% and 13% by mass are added to coal. Results show that, when rice husk is added the methane yield increases from volumetric percentage of 0.56% (with no rice husk) to 2.77% (with 13% rice husk). CO and H₂ remain almost unchanged and CO₂ decreases with addition of rice husk. The calorific value of the synthetic gas is around 2.73 MJ/Nm³. All performance indices, such as cold gas efficiency and carbon conversion, increase with addition of rice husk.

Keywords: bubbling fluidized bed reactor, calorific value, coal gasification, rice husk

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Authors: Ntalamagka N., Sanchis-Benlloch P. J., Mayoral-Serrano R., Tena-Medialdea J., García-March J. R.

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The pen shell Pinna nobilis population has declined dramatically since 2016 due to die-off events observed in the whole extent of the Mediterranean Sea associated with the protozoan Haplosporidium pinnae. As of 2019, it is considered a critically endangered species. Due to its ecological importance and its endangered status, several initiatives have been developed for its salvation and recovery. This research is an effort to understand and control its reproduction under captivity. As a limited number of Pinna nobilis individuals could be used for experimentation, the possibility of using the Pinna rudis as a model animal was explored. The molecular mechanism that regulates the reproduction of both species is unknown; consequently, transcriptomic analysis was performed to identify neuropeptides that are expressed in the key regulatory tissues of the visceral ganglia and gonads of both species. Neuropeptides form an important group of signaling peptides that regulate reproductive, behavioral and physiological functions in molluscs. In total, 17 neuropeptide precursors were identified in P. nobilis and 14 in P. rudis transcriptomes; 14 of them were identical in both species. This affinity verified the genetic similarity of these species at the reproduction level. APGWamide, buccalin, ELH and GnRH were tested in P. rudis and demonstrated their capacity to advance gonadal maturation and trigger spawning while spawning was recorded in P. nobilis after the usage of APGWamide and buccalin. The neuropeptides were administered using intramuscular injection and cholesterol implants following relative literature as well as a new method was developed for external administration without the use of anesthesia using a mathematical model. The know-how of this research will not only lead to the survival of the species but also will narrow the horizons of broodstock conditioning of other similar species.

Keywords: neuropeptides, Pinna nobilis, reproduction, transcriptomics

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

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Authors: Alireza Akbari, Gelareh Babaee Khou

Abstract:

Ground Penetrating Radar (GPR) is an important nondestructive remote sensing tool that has been used in both military and civilian fields. Recently, GPR imaging has attracted lots of attention in detection of subsurface shallow small targets such as landmines and unexploded ordnance and also imaging behind the wall for security applications. For the monostatic arrangement in the space-time GPR image, a single point target appears as a hyperbolic curve because of the different trip times of the EM wave when the radar moves along a synthetic aperture and collects reflectivity of the subsurface targets. With this hyperbolic curve, the resolution along the synthetic aperture direction shows undesired low resolution features owing to the tails of hyperbola. However, highly accurate information about the size, electromagnetic (EM) reflectivity, and depth of the buried objects is essential in most GPR applications. Therefore hyperbolic curve behavior in the space-time GPR image is often willing to be transformed to a focused pattern showing the object's true location and size together with its EM scattering. The common goal in a typical GPR image is to display the information of the spatial location and the reflectivity of an underground object. Therefore, the main challenge of GPR imaging technique is to devise an image reconstruction algorithm that provides high resolution and good suppression of strong artifacts and noise. In this paper, at first, the standard back-projection (BP) algorithm that was adapted to GPR imaging applications used for the image reconstruction. The standard BP algorithm was limited with against strong noise and a lot of artifacts, which have adverse effects on the following work like detection targets. Thus, an improved BP is based on cross-correlation between the receiving signals proposed for decreasing noises and suppression artifacts. To improve the quality of the results of proposed BP imaging algorithm, a weight factor was designed for each point in region imaging. Compared to a standard BP algorithm scheme, the improved algorithm produces images of higher quality and resolution. This proposed improved BP algorithm was applied on the simulation and the real GPR data and the results showed that the proposed improved BP imaging algorithm has a superior suppression artifacts and produces images with high quality and resolution. In order to quantitatively describe the imaging results on the effect of artifact suppression, focusing parameter was evaluated.

Keywords: algorithm, back-projection, GPR, remote sensing

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Authors: Maryam Ghamsari, Mitchell Nye-Wood, Kelvin Wang, Angela Juhasz, Michelle Colgrave, Don Otter, Jun Lu, Nazimah Hamid, Thao T. Le

Abstract:

Bee venom, a complex mixture of peptides, proteins, enzymes, and other bioactive compounds, has been widely studied for its therapeutic application. This study investigated the proteins present in New Zealand (NZ) honeybee venom (BV) using bottom-up proteomics. Two sample digestion techniques, in-solution digestion and filter-aided sample preparation (FASP), were employed to obtain the optimal method for protein digestion. Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH–MS) analysis was conducted to quantify the protein compositions of NZ BV and investigate variations in collection years. Our results revealed high protein content (158.12 µg/mL), with the FASP method yielding a larger number of identified proteins (125) than in-solution digestion (95). SWATH–MS indicated melittin and phospholipase A2 as the most abundant proteins. Significant variations in protein compositions across samples from different years (2018, 2019, 2021) were observed, with implications for venom's bioactivity. In vitro testing demonstrated immunomodulatory and antioxidant activities, with a viable range for cell growth established at 1.5-5 µg/mL. The study underscores the value of proteomic tools in characterizing bioactive compounds in bee venom, paving the way for deeper exploration into their therapeutic potentials. Further research is needed to fractionate the venom and elucidate the mechanisms of action for the identified bioactive components.

Keywords: honeybee venom, proteomics, bioactivity, fractionation, swath-ms, melittin, phospholipase a2, new zealand, immunomodulatory, antioxidant

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Authors: Dmitriy Yu. Korulkin, Raissa A. Muzychkina

Abstract:

The article represents the results of research of antitumor activity of different structural types of plant flavonoids extracted by authors from Polygonum L. plants in commercial reserves at the territory of the Republic of Kazakhstan. For the first time ever the results comparative research of antitumor activity of plant flavonoids of different structural groups and their synthetic derivatives have been represented. The results of determination of toxicity of flavonoids in single parenteral infusion conditions have been represented. Experimental substantiation of possible mechanisms of antiproliferative and cytotoxic action of flavonoids has been suggested. The perspectives of usage of plant flavonoids as medications and creation of effective dosage forms of antitumor medicines on their basis have been substantiated.

Keywords: antitumor activity, cytotoxicity, flavonoids, Polygonum L., secondary metabolites

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Authors: Norhaslina Mat Zian, Hasril Hasini, Nur Irmawati Om

Abstract:

This study focuses on the flow and combustion behavior inside gas turbine combustor used in thermal power plant. The combustion process takes place using synthetic gas and the baseline solution was made on gas turbine combustor firing natural gas (100% Methane) as the main source of fuel. Attention is given to the effect of the H2/CO ratio on the variation of the flame profile, temperature distribution, and emissions. The H2/CO ratio varies in the range of 10-80 % and the CH4 values are fixed 10% for each case. While keeping constant the mass flow rate and operating pressure, the preliminary result shows that the flow inside the can-combustor is highly swirling which indicates good mixing of fuel and air prior to the entrance of the mixture to the main combustion zone.

Keywords: cfd, combustion, flame, syngas

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Authors: Hiral D. Trivedi, Dinesh S. Patel, Sachin P. Shukla

Abstract:

We have immobilized alcohol dehydrogenase on k-carrageenan, which is a natural polysaccharide obtained from seaweeds by entrapment and on copolymer of acrylamide and 2-hydroxy ethylmethaacrylate by covalent coupling. We have optimized all the immobilization parameters and also carried the comparison studies of both. In case of copolymer of acrylamide and 2-hydroxy ethylmethaacrylate, we have activated both the amino and hydroxyl group individually and simultaneously using different activating agents and obtained some interesting results. We have found that covalently bound enzyme was found to be better under all tested conditions. The reaction on ethanol was carried out using these immobilized systems.

Keywords: alcohol dehydrogenase, acrylamide-co-2-hydroxy ethylmethaacrylate, ethanol, k-carrageenan

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Authors: Amarachi Delight Onyemachi, Gregory Ikechukwu Onwuka

Abstract:

The growing consumer trend for natural ingredients, functional foods with health benefits and the perceived risk of carcinogenesis associated with synthetic antioxidants have forced food manufacturers to look for alternatives for producing healthy and safe food. Herbs and spices are cheap, natural and harmless sources of antioxidants which can delay and prevent lipid oxidation of food products and also confer its unique organoleptic properties and health benefits to food products. The Nigerian climate has been proven to be conducive for the production of spices and herbs and is blessed bountifully with a wide range of them. Five selected Nigerian herbs and spices Piper guieense, Xylopia aethopica, Gongronema latifolium and Ocimum gratissimum were evaluated for their ability to act as radical scavengers. The spices were extracted with 80% ethanol and evaluated using total phenolic capacity (TPC), DPPH (1,1-diph diphenyl-2-picrylhydrazyl radical) ABTS (2,2’azinobis-(3-ethylbenzthiazoline-6-sulfonic acid)), total antioxidant capacity (TAC), reducing power (RP) assays. The TPC ranged from 5.33 µg GAE/mg (in Gongronema latifolium) to 15.55 µg GAE/mg (in Ocimum gratissimum). The DPPH and ABTS scavenging activity of the extracts ranged from 0.23-0.36 IC50 mg/ml and 2.32-7.25 Trolox equivalent % respectively. The TAC and RP of the extract ranged from 6.73-10.64 µg AAE/mg and 3.52-10.19 µg AAE/mg. The result of percentage yield of the extract ranged from as low as 9.94% in Gongronema latifolium and to as high as 23.85% in Xylopia aethopica. A very strong positive relationship existed between the total antioxidant capacity and total phenolic content of the tested herbs and spices (R2=0.96). All of the extracts exhibited different extent of strong antioxidant activity, high antioxidant activity was found in Ocimum gratissimum and Gongronema latifolium with the least. However, Gongronema latifolium possessed the highest total antioxidant capacity. These data confirm the appreciable antioxidant potentials and high phenolic content of Nigerian herbs and spices, thereby providing justification for their use in dishes and functional foods, prevention of cellular damage caused by free radicals and use as natural antioxidants in the food industry for prevention of lipid oxidation in food products. However, to utilize these natural antioxidants in food products, further analysis and studies of their behaviour in food systems at varying temperature, pH conditions and ionic concentrations should be carried out to displace the use of synthetic antioxidants like BHT and BHA.

Keywords: Antioxidant, free radicals, herbs, phenolic, spices

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