Search results for: cell engineering

Authors: Suman Chaudhary, Rupinder K. Kanwar, Jagat R. Kanwar

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Azadirachta indica, also known as Neem belonging to the mahogany family is actively gaining interest in the era of modern day medicine due to its extensive applications in homeopathic medicine such as Ayurveda and Unani. More than 140 phytochemicals have been extracted from neem leaves, seed, bark and flowers for agro-medicinal applications. Among the various components, neem leaf protein (NLP) is currently the most investigated active ingredient, due to its immunomodulatory activities against tumor growth. However, these therapeutic ingredients of neem are susceptible to degradation and cannot withstand the drastic pH changes under physiological environment, and therefore, there is an urgent need of an alternative strategy such as a nano-delivery system to exploit its medicinal benefits. This study hypothesizes that guar gum (GG) derived biodegradable nano-carrier based encapsulation of NLP will improve its stability, specificity and sensitivity, thus facilitating targeted anti-cancer therapeutics. GG is a galactomannan derived from the endosperm of the guar beans seeds. Synthesis of guar nanocapsules (NCs) was performed using nanoprecipitation technique where the GG was encapsulated with NLP. Preliminary experiments conducted to characterize the NCs confirmed spherical morphology with a narrow size distribution of 30-40 nm. Differential scanning colorimetric analysis (DSC) validated the stability of these NCs even at a temperature range of 50-60°C which was well within the physiological and storage conditions. Thermogravimetric (TGA) analysis indicated high decomposition temperature of these NCs ranging upto 350°C. Additionally, Fourier Transform Infrared spectroscopy (FTIR) and the SDS-PAGE data acquired confirmed the successful encapsulation of NLP in the NCs. The anti-cancerous therapeutic property of this NC was tested on colon cancer cells (caco-2) as they are one of the most prevalent form of cancer. These NCs (both NLP loaded and void) were also tested on human intestinal epithelial cells (FHs 74) cells to evaluate their effect on normal cells. Cytotoxicity evaluation of the NCs in the cell lines confirmed that the IC50 for NLP in FHs 74 cells was ~2 fold higher than in caco-2 cells, indicating that this nanoformulation system possessed biocompatible anti-cancerous properties Immunoconfocal microscopy analysis confirmed the time dependent internalization of the NCs within 6h. Recent findings performed using Annexin V and PI staining indicated a significant increase (p ≤ 0.001) in the early and late apoptotic cell population when treated with the NCs signifying the role of NLP in inducing apoptosis in caco-2 cells. This was further validated using Western blot, Polymerase chain reaction (PCR) and Fluorescence activated cell sorter (FACS) aided protein expressional analysis which presented a downregulation of survivin, an anti-apoptotic cell marker and upregulation of Bax/Bcl-2 ratio (pro-apoptotic indicator). Further, both the NLP NC and unencapsulated NLP treatment destabilized the mitochondrial membrane potential subsequently facilitating the release of the pro-apoptotic caspase cascade initiator, cytochrome-c. Future studies will be focused towards granting specificity to these NCs towards cancer cells, along with a comprehensive analysis of the anti-cancer potential of this naturally occurring compound in different cancer and in vivo animal models, will validate the clinical application of this unprecedented protein therapeutic.

Keywords: anti-tumor, guar gum, nanocapsules, neem leaf protein

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Authors: Nitesh Kumar, Eoin Twohig, jasparl cheema, Sadiq mawji, Yousif al najjar

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Basal cell carcinoma (BCC) is the commonest cutaneous malignancy affecting humans. Despite this, distant spread is exceptionally rare. Metastatic BCC (mBCC) is estimated to occur in 0.0028 - 0.5%. it aim to illustrate with the aid of histological slides, a case of mBCC occurring in a fit and well 67-year-old. Initial diagnosis of desmoplastic BCC was made in 2006 from a scalp biopsy with the lesion then being excised. Re-excision of local recurrence was undertaken the following year. In 2014 the patient presented with an ipsilateral level 2a mass. Fine Needle Aspiration raised the suspicion of metastatic carcinoma. The patient had excision of two nodes from the left neck alongside pharyngeal tonsillectomy and tongue base biopsies. Histologically, the nodes closely resembled the immunophenotype of the initial scalp lesion. The patient subsequently had a modified radical neck dissection, and residual mBCC was excised from the left Sternocleidomastoid muscle. In 2023 the patient developed haematuria. On further investigation bilateral lung lesions on CT were noted with subsequent biopsy confirming mBCC. Spinal and renal lesions have also been found. Histopathology showed clear resemblance of the lung metastases to both those in the neck and the primary (scalp BCC) – with no squamous differentiation seen. The time span from primary to occurrence of lung metastasis (18 years) affirms the indolent and slow growing nature of BCC.  This case fulfils Lattes and Kessler diagnostic criteria. High risk cases are described as those with advanced local presentation, primary tumour on the Head and Neck and locally recurrent lesions.

Keywords: BCC, metastasis, rare, skin cancer

Procedia PDF Downloads 57

Authors: Sayem Zafar, Mahmood Rahi

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Rigorous international maritime regulations are in place to limit boat and ship hydrocarbon emissions. The global sustainability goals are reducing the fuel consumption and minimizing the emissions from the ships and boats. These maritime sustainability goals have attracted a lot of research interest. Energy harvesting and storage system is designed in this study based on hybrid renewable and conventional energy systems. This energy harvesting and storage system is designed for marine applications, such as, boats and small ships. These systems can be utilized for mobile use or off-grid remote electrification. This study analyzed the use of micro power generation for boats and small ships. The energy harvesting and storage system has two distinct systems i.e. dockside shore-based system and on-board system. The shore-based system consists of a small wind turbine, photovoltaic (PV) panels, small gas turbine, hydrogen generator and high-pressure hydrogen storage tank. This dockside system is to provide easy access to the boats and small ships for supply of hydrogen. The on-board system consists of hydrogen storage tanks and fuel cells. The wind turbine and PV panels generate electricity to operate electrolyzer. A small gas turbine is used as a supplementary power system to contribute in case the hybrid renewable energy system does not provide the required energy. The electrolyzer performs the electrolysis on distilled water to produce hydrogen. The hydrogen is stored in high-pressure tanks. The hydrogen from the high-pressure tank is filled in the low-pressure tanks on-board seagoing vessels to operate the fuel cell. The boats and small ships use the hydrogen fuel cell to provide power to electric propulsion motors and for on-board auxiliary use. For shore-based system, a small wind turbine with the total length of 4.5 m and the disk diameter of 1.8 m is used. The small wind turbine dimensions make it big enough to be used to charge batteries yet small enough to be installed on the rooftops of dockside facility. The small dimensions also make the wind turbine easily transportable. In this paper, PV, sizing and solar flux are studied parametrically. System performance is evaluated under different operating and environmental conditions. The parametric study is conducted to evaluate the energy output and storage capacity of energy storage system. Results are generated for a wide range of conditions to analyze the usability of hybrid energy harvesting and storage system. This energy harvesting method significantly improves the usability and output of the renewable energy sources. It also shows that small hybrid energy systems have promising practical applications.

Keywords: energy harvesting, fuel cell, hybrid energy system, hydrogen, wind turbine

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Authors: Swati Tomar, Sunil Kumar Gupta

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The start-up of anammox (anaerobic ammonium oxidation) process in hybrid reactor delineated four distinct phases i.e. cell lysis, lag phase, activity elevation and stationary phase. Cell lysis phase was marked by death and decay of heterotrophic denitrifiers resulting in breakdown of organic nitrogen into ammonium. Lag phase showed initiation of anammox activity with turnover of heterotrophic denitrifiers, which is evident from appearance of NO3-N in the effluent. In activity elevation phase, anammox became the dominant reaction, which can be attributed to consequent reduction of NH4-N into N2 with increased NO3-N in the effluent. Proper selection of mixed seed culture at influent NO2-/NH4+ ratio (1:1) and hydraulic retention time (HRT) of 1 day led to early startup of anammox within 70 days. Pseudo steady state removal efficiencies of NH4+ and NO2- were found as 94.3% and 96.4% respectively, at nitrogen loading rate (NLR) of 0.35 kg N/m3d at an HRT of 1 day. Analysis of the data indicated that attached growth system contributes an additional 11% increase in the ammonium removal and results in an average of 29% reduction in sludge washout rate. Mass balance study of nitrogen indicated that 74.1% of total input nitrogen is converted into N2 gas followed by 11.2% being utilized in biomass development. Scanning electron microscope (SEM) observation of the granular sludge clearly showed the presence of cocci and rod shaped microorganisms intermingled on the external surface of the granules. The average size of anammox granules (1.2-1.5 mm) with an average settling velocity of 45.6 m/h indicated a high degree of granulation resulting into formation of well compacted granules in the anammox process.

Keywords: anammox, hybrid reactor, startup, granulation, nitrogen removal, mixed seed culture

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Authors: Anupama Sahoo, Bongyong Lee, Katia Boniface, Julien Seneschal, Sanjaya K. Sahoo, Tatsuya Seki, Chunyan Wang, Soumen Das, Xianlin Han, Michael Steppie, Sudipta Seal, Alain Taieb, Ranjan J. Perera

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Vitiligo is a common, chronic skin disorder characterized by loss of epidermal melanocytes and progressive depigmentation. Vitiligo has a complex immune, genetic, environmental, and biochemical etiology, but the exact molecular mechanisms of vitiligo development and progression, particularly those related to metabolic control, are poorly understood. Here we characterized the human vitiligo cell line PIG3V and the normal human melanocytes, HEM-l by RNA-sequencing, targeted metabolomics, and shotgun lipidomics. Melanocyte-enriched miR-211, a known metabolic switch in non-pigmented melanoma cells, was severely downregulated in vitiligo cell line PIG3V and skin biopsies from vitiligo patients, while its novel predicted targets transcriptional co-activator PGC1-α (PPARGC1A), ribonucleotide reductase regulatory subunit M2 (RRM2), and serine-threonine protein kinase TAO1 (TAOK1) were reciprocally upregulated. miR-211 binds to PGC1-α 3’UTR locus and represses it. Although mitochondrial numbers were constant, mitochondrial complexes I, II, and IV and respiratory responses were defective in vitiligo cells. Nanoparticle-coated miR-211 partially augmented the oxygen consumption rate in PIG3V cells. The lower oxygen consumption rate, changes in lipid and metabolite profiles, and increased reactive oxygen species production observed in vitiligo cells appear to be partly due to abnormal regulation of miR-211 and its target genes. These genes represent potential biomarkers and therapeutic targets in human vitiligo.

Keywords: metabolism, microRNA, mitochondria, vitiligo

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Authors: Avoseh Funmilola, Osman Khalid, Wayne Nelson, Paramespri Naidoo, Deresh Ramjugernath

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The increasing global atmospheric temperature is of great concern and this has led to the development of technologies to reduce the emission of greenhouse gases into the atmosphere. Flue gas emissions from fossil fuel combustion are major sources of greenhouse gases. One of the ways to reduce the emission of CO₂ from flue gases is by post combustion capture process and this can be done by absorbing the gas into suitable chemical solvents before emitting the gas into the atmosphere. Alkanolamines are promising solvents for this capture process. Vapour liquid equilibrium of CO₂-alkanolamine systems is often represented by CO₂ loading and partial pressure of CO₂ without considering the liquid phase. The liquid phase of this system is a complex one comprising of 9 species. Online analysis of the process is important to monitor the concentrations of the liquid phase reacting and product species. Liquid phase analysis of CO₂-diethanolamine (DEA) solution was performed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. A robust Calibration was performed for the CO₂-aqueous DEA system prior to an online monitoring experiment. The partial least square regression method was used for the analysis of the calibration spectra obtained. The models obtained were used for prediction of DEA and CO₂ concentrations in the online monitoring experiment. The experiment was performed with a newly built recirculating experimental set up in the laboratory. The set up consist of a 750 ml equilibrium cell and ATR-FTIR liquid flow cell. Measurements were performed at 400°C. The results obtained indicated that the FTIR spectroscopy combined with Partial least square method is an effective tool for online monitoring of speciation.

Keywords: ATR-FTIR, CO₂ capture, online analysis, PLS regression

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Authors: Hye Kyung Kim, Myung-Gyou Kim, Kang-Hyun Leem

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Postmenopausal osteoporosis is characterized by low bone density which leads to increased bone fragility and greater susceptibility to fracture. Current treatments for osteoporosis are dominated by drugs that inhibit bone resorption although they also suppress bone formation that may contribute to pathogenesis of osteonecrosis. To restore the extensive bone loss, there is a great need for anabolic treatments that induce osteoblasts to build new bone. Pre-osteoblastic cells produce proteins of the extra-cellular matrix, including type I collagen at first, and then to successively produce alkaline phosphatase (ALP) and osteocalcin during differentiation to osteoblasts. Finally, osteoblasts deposit calcium. Present study investigated the effects of egg yolk peptide (EYP) on osteogenic activities and bone matrix gene expressions in human osteoblastic MG-63 cells. The effects of EYP on cell proliferation, alkaline phosphatase (ALP) activity, collagen synthesis, and mineralization were measured. The expression of osteogenic genes including COL1A1 (collagen, type I, alpha 1), ALP, BGLAP (osteocalcin), and SPP1 (secreted phosphoprotein 1, osteopontin) were measured by quantitative realtime PCR. EYP dose-dependently increased MG-63 cell proliferation, ALP activity, collagen synthesis, and calcium deposition. Furthermore, COL1A1, ALP, and SPP1 gene expressions were increased by EYP treatment. Present study suggested that EYP treatment enhanced osteogenic activities and increased bone matrix osteogenicgenes. These results could provide a mechanistic explanation for the bone-strengthening effects of EYP.

Keywords: egg yolk peptide, osteoblastic MG-63 cells, alkaline phosphatase, collagen synthesis, osteogenic genes, COL1A1, osteocalcin, osteopontin

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Authors: Kamyar Maleki Bagherabadi, Torstein Aarseth Bø, Truls Flatberg, Olve Mo

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Hydrogen fuel cells and batteries are one of the promising solutions aligned with carbon emission reduction goals for the marine sector. However, the higher installation and operation costs of hydrogen-based systems compared to conventional diesel gensets raise questions about the appropriate hydrogen tank size, energy, and fuel consumption estimations. Ship designers need methodologies and tools to calculate energy and fuel consumption for different component sizes to facilitate decision-making regarding feasibility and performance for retrofits and design cases. The aim of this work is to compare three alternative modeling approaches for the estimation of energy and fuel consumption with various hydrogen tank sizes, battery capacities, and load-sharing strategies. A fishery vessel is selected as an example, using logged load demand data over a year of operations. The modeled power system consists of a PEM fuel cell, a diesel genset, and a battery. The methodologies used are: first, an energy-based model; second, considering load variations during the time domain with a rule-based Power Management System (PMS); and third, a load variations model and dynamic PMS strategy based on optimization with perfect foresight. The errors and potentials of the methods are discussed, and design sensitivity studies for this case are conducted. The results show that the energy-based method can estimate fuel and energy consumption with acceptable accuracy. However, models that consider time variation of the load provide more realistic estimations of energy and fuel consumption regarding hydrogen tank and battery size, still within low computational time.

Keywords: fuel cell, battery, hydrogen, hybrid power system, power management system

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Authors: Scott A. Ochsner, Christopher M. Watkins, Apollo McOwiti, David L. Steffen Lauren B. Becnel, Neil J. McKenna

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Understanding signaling by nuclear receptors (NRs) requires an appreciation of their cognate ligand- and tissue-specific transcriptomes. While target gene regulation data are abundant in this field, they reside in hundreds of discrete publications in formats refractory to routine query and analysis and, accordingly, their full value to the NR signaling community has not been realized. One of the mandates of the Nuclear Receptor Signaling Atlas (NURSA) is to facilitate access of the community to existing public datasets. Pursuant to this mandate we are developing a freely-accessible community web resource, Transcriptomine, to bring together the sum total of available expression array and RNA-Seq data points generated by the field in a single location. Transcriptomine currently contains over 25,000,000 gene fold change datapoints from over 1200 contrasts relevant to over 100 NRs, ligands and coregulators in over 200 tissues and cell lines. Transcriptomine is designed to accommodate a spectrum of end users ranging from the bench researcher to those with advanced bioinformatic training. Visualization tools allow users to build custom charts to compare and contrast patterns of gene regulation across different tissues and in response to different ligands. Our resource affords an entirely new paradigm for leveraging gene expression data in the NR signaling field, empowering users to query gene fold changes across diverse regulatory molecules, tissues and cell lines, target genes, biological functions and disease associations, and that would otherwise be prohibitive in terms of time and effort. Transcriptomine will be regularly updated with gene lists from future genome-wide expression array and expression-sequencing datasets in the NR signaling field.

Keywords: target gene database, informatics, gene expression, transcriptomics

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Authors: Karolis Leonavičius, Dalius Kučiauskas, Dangiras Lukošius, Arnoldas Jasiūnas, Kostas Zdanys, Rokas Stanislovas, Emilis Gegevičius, Žana Kapustina, Juozas Nainys

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Screening throughput is a common bottleneck in many research areas, including functional genomics, drug discovery, and directed evolution. High-throughput screening techniques can be classified into two main categories: (i) affinity-based screening and (ii) functional screening. The first one relies on binding assays that provide information about the affinity of a test molecule for a target binding site. Binding assays are relatively easy to establish; however, they reveal no functional activity. In contrast, functional assays show an effect triggered by the interaction of a ligand at a target binding site. Functional assays might be based on a broad range of readouts, such as cell proliferation, reporter gene expression, downstream signaling, and other effects that are a consequence of ligand binding. Screening of large cell or gene libraries based on direct activity rather than binding affinity is now a preferred strategy in many areas of research as functional assays more closely resemble the context where entities of interest are anticipated to act. Droplet sorting is the basis of high-throughput functional biological screening, yet its applicability is limited due to the technical complexity of integrating high-performance droplet analysis and manipulation systems. As a solution, the Droplet Genomics Styx platform enables custom droplet sorting workflows, which are necessary for the development of early-stage or complex biological therapeutics or industrially important biocatalysts. The poster will focus on the technical design considerations of Styx in the context of its application spectra.

Keywords: functional screening, droplet microfluidics, droplet sorting, dielectrophoresis

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Authors: Amandeep Singh Oberoi, John Andrews, Alan L. Chaffee, Lachlan Ciddor

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Electrochemical storage of hydrogen in activated carbon electrodes as part of a reversible fuel cell offers a potentially attractive option for storing surplus electrical energy from inherently variable solar and wind energy resources. Such a system – which we have called a proton flow battery – promises to have roundtrip energy efficiency comparable to lithium ion batteries, while having higher gravimetric and volumetric energy densities. Activated carbons with high internal surface area, high pore volume, light weight and easy availability have attracted considerable research interest as a solid-state hydrogen storage medium. This paper compares the physical characteristics and hydrogen storage capacities of four activated carbon electrodes made by different methods from brown coal. The fabrication methods for these samples are explained. Their proton conductivity was measured using electrochemical impedance spectroscopy, and their hydrogen storage capacity by galvanostatic charging and discharging in a three-electrode electrolytic cell with 1 mol sulphuric acid as electrolyte. The highest hydrogen storage capacity obtained was 1.29 wt%, which compares favourably with metal hydrides used in commercially available solid-state hydrogen storages. The hydrogen storage capacity of the samples increased monotonically with increasing BET surface area (calculated from CO2 adsorption method). The results point the way towards selecting high-performing electrodes for proton flow batteries that the competitiveness of this energy storage technology.

Keywords: activated carbon, electrochemical hydrogen storage, proton flow battery, proton conductivity

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Authors: Ismail Borazan, Ayse Celik Bedeloglu, Ali Demir, David Carroll

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In this project, PEDOT:PSS layer was treated with formic acid, sulphuric acid, and hydrochloric acid, methanol, acetone, and dichlorobenzene:methanol. The resistivity measurements with 2-probes were carried out and the best-chosen method was employed to make an organic solar cell device.

Keywords: organic solar cells, PEDOT:PSS, polymer electrodes, resistivity

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Authors: Naser Shagerdi Esmaeli, Mohsen Hamidpour

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Background and Objective: Hematopoietic stem cell transplantation (HSCT) has been widely used for treating oncological and hematological diseases. Although HSCT has helped to improve patient survival, the risk of developing an infection during hospitalization is an important cause of morbidity and mortality. This study aimed to analyze the infection profile during hospitalization and the associated risk factors among patients undergoing autologous HSCT at the University Hospital, Shahid Ghazi Tabatabaei Hospital, Tabriz, Iran. Subjects and Methods: This was a cross-sectional study on patients undergoing autologous HSCT at a public university hospital. Methods: Patients with febrile neutropenia between 2015 and 2018 were retrospectively evaluated regarding their infection profile and associated risk factors. This survey included: bacterial culture and blood culture on specific media. Results: Infection occurred in 57.2% of 56 patients with febrile neutropenia. The main source of infection was the central venous catheter (25.9%). Infection was chiefly due to Gram-positive bacteria, although Gram-negative-related infections were more severe and caused a higher death rate. Sex, age, skin color, nutritional status, and underlying disease were not associated with the development of infection. Patients with severe mucositis (Grades III and IV) had a higher infection rate (P < 0.001). Patients who developed pulmonary complications during hospitalization had higher infection rates (P = 0.002). Infection was the main cause of death (57.1%) in the study sample. Conclusion: Strategies aimed at reducing infection-related mortality rates among patients undergoing autologous HSCT are necessary.

Keywords: hematopoietic stem cell, autologous bone marrow transplantation, infection profile, tabriz, Iran

Procedia PDF Downloads 119

Authors: Sudeshna Mukherjee, Leena Fageria, R. Venkataramana Dilip, Rajdeep Chowdhury, Jitendra Panwar

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Metal nanoparticles in recent years have gained importance in cancer therapy due to their enhanced permeability retention effect. Among various nanomaterials, silver nanoparticles (AgNPs) have received considerable attention due to their unique properties like conductivity, chemical stability, relative lower toxicity and outstanding therapeutic potential, such as anti-inflammatory, antimicrobial and anti-cancerous activities. In this study, we took a greener approach to synthesize silver nanoparticle from fungus and analyze its effects on both epithelial and mesenchymal derived cancer cells. Much research has been done on nanoparticle-induced apoptosis, but little is known about its role in autophagy. In our study, the silver nanoparticles were seen to induce autophagy which was analyzed by studying the expression of several autophagy markers like, LC3B-II and ATG genes. Monodansylcadaverine (MDC) assay also revealed the induction of autophagy upon treatment with AgNPs. Inhibition of autophagy by chloroquine resulted in increased cell death suggesting autophagy as a survival strategy adopted by the cells. In parallel to autophagy induction, silver nanoparticles induced ROS accumulation. Interestingly, autophagy inhibition by chloroquine increased ROS level, resulting in enhanced cell death. We further analyzed MAPK signaling upon AgNP treatment. It was observed that along with autophagy, activation of JNK signaling served as pro-survival while ERK signaling served as a pro-death signal. Our results provide valuable insights into the role of autophagy upon AgNP exposure and provide cues to probabilistic strategies to effectively sensitize cancer cells.

Keywords: autophagy, JNK signalling, reactive oxygen species, silver nanoparticles

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Authors: Angel Champion, Sadia Kanwal, Rafat Siddiqui

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Harnessing phytochemicals from plant sources presents a novel opportunity to prevent or treat malignant diseases, including breast cancer. Chemotherapy lacks precision in targeting cancerous cells while sparing normal cells, but a phytopharmaceutical approach may offer a solution. Dandelion, a common weed plant, is rich in phytochemicals and provides a safer, more cost-effective alternative with lower toxicity than traditional pharmaceuticals for conditions such as breast cancer. In this study, an in-vitro experiment will be conducted using the ethanol extract of Dandelion on triple-negative MDA-231 breast cancer cell lines. The polyphenolic analysis revealed that the Dandelion extract, particularly from the root and leaf (both cut and sifted), had the most potent antioxidant properties and exhibited the most potent antioxidation activity from the powdered leaf extract. The extract exhibits prospective promising effects for inducing cell proliferation and apoptosis in breast cancer cells, highlighting its potential for targeted therapeutic interventions. Standardizing methods for Dandelion use is crucial for future clinical applications in cancer treatment. Combining plant-derived compounds with cancer nanotechnology holds the potential for effective strategies in battling malignant diseases. Utilizing liposomes as carriers for phytoconstituent anti-cancer agents offers improved solubility, bioavailability, immunoregulatory effects, advancing anticancer immune function, and reducing toxicity. This integrated approach of natural products and nanotechnology has significant potential to revolutionize healthcare globally, especially in underserved communities where herbal medicine is prevalent.

Keywords: apoptosis, antioxidant activity, cancer nanotechnology, phytopharmaceutical

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Authors: Hassan Mohammadi Khujin

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Tissue engineering is the science of tissues and complex organs creation using scaffolds, cells and biologically active components. Most cells require scaffolds to grow and proliferate. These temporary support structures for tissue regeneration are later replaced with extracellular matrix produced inside the body. Recent advances in additive manufacturing methods allow production of highly porous, complex three dimensional scaffolds suitable for cell growth and proliferation. The current paper investigates the mechanical properties, including elastic modulus and compressive strength, as well as fluid flow dynamics, including permeability and flow-induced shear stress of scaffolds with four triply periodic minimal surface (TPMS) configurations, namely the Schwarz primitive, the Schwarz diamond, the gyroid, and the Neovius structures. Higher porosity in all scaffold types resulted in lower mechanical properties. The permeability of the scaffolds was determined using Darcy's law with reference to geometrical parameters and the pressure drop derived from the computational fluid dynamics (CFD) analysis. Higher porosity enhanced permeability and reduced wall shear stress in all scaffold designs.

Keywords: highly porous scaffolds, tissue engineering, finite elements analysis, CFD analysis

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Authors: Abu Salim Mustafa

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Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: mycobacterium tuberculosis, PPE68, peptides, vaccine

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Authors: Mayuva Youngsabanant-Areekijseree, Chanikarn Srinark, S. Sengsai, Mayuree Pumipaiboon

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Our project was aimed at morphology of oocytes, follicle cells and follicular fluid proteins study of Large White pig (at local slaughter house in Nakhon Pathom Province). The porcine oocytes and follicular fluid of healthy small follicles (1-2 mm), medium follicles (3-6 mm in diameters) and large follicles (7-8 mm and 10 mm in diameter) were aspirated and collected from the ovary by sterile technique. Then, the oocytes and the follicle cells were separated from the fluid. The oocytes were round shape and surrounded by zona pellucida with numerous layers of cumulus cells. Based on the number of cumulus cell layers surrounding oocytes, the oocytes were classified into 5 types, which were intact-, multi-, partial-cumulus layer oocyte, completely denuded oocyte and degenerative oocyte. The collected oocytes showed high percentages of intact- and multi- cumulus cell layers in the small follicles (53.48%) medium follicles (56.94%) and large follicles (56.52%) which have high potential to develop into mature oocytes in vitro. Proteins from follicular fluid of 3 size follicles were separated by SDS-PAGE and LC/MS/MS. The molecular weight of follicular fluid proteins from the small follicles were 24, 60-65, 79, 110, 140, 160, and > 220 kDa. Meanwhile, the follicular fluid protein from medium and large follicle contained 52, 65, 79, 90, 110, 120, 160, 190 and > 220 kDa. Almost all proteins played important roles in promoting and regulating growth and development of oocytes and ovulation. This finding was an initial tool for in vitro testing and applied biotechnology research. Acknowledgements: The project was funded by a grant from Silpakorn University Research & Development Institute (SURDI) and Faculty of Science, Silpakorn University, Thailand.

Keywords: follicular fluid protein, LC/MS/MS, porcine oocyte, SDS-PAGE, reproductive biology

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Authors: Sharmin Ferdewsi Rakhi, A. H. M. Mohsinul Reza, Brynley Davies, Jianzhong Wang, Youhong Tang, Jian Qin

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Mass production of microalgae has become a focus of research owing to their promising aspects for sustainable food, biofunctional compounds, and biofuel feedstock. However, low lipid content with optimum algal biomass is still a challenge that must be resolved for commercial use. This research aims to determine the effects of light spectral shift and reactive oxygen species (ROS) on growth and lipid biosynthesis in a green microalga, Chlamydomonas reinhardtii. Aggregation Induced Emission (AIE)-based photosensitisers, CN-TPAQ-PF6 ([C₃₂H₂₃N₄]+) with high ROS productivity, was introduced into the algal culture media separately for effective conversion of the green-yellow-light to the red spectra. The intense photon energy and high-photon flux density in the photosystems and ROS supplementation induced photosynthesis and lipid biogenesis. In comparison to the control, maximum algal growth (0.15 g/l) was achieved at 2 µM CN-TPAQ-PF6 exposure. A significant increase in total lipid accumulation (146.87 mg/g dry biomass) with high proportion of 10-Heptadecanoic acid (C17:1) linolenic acid (C18:2), α-linolenic acid (C18:3) was observed. The elevated level of cellular NADP/NADPH triggered the Acetyl-Co-A production in lipid biogenesis cascade. Furthermore, MTT analysis suggested that this nanomaterial is highly biocompatible on HaCat cell lines with 100% cell viability. This study reveals that the AIE-based approach can strongly impact algal biofactory development for sustainable food, healthy lipids and eco-friendly biofuel.

Keywords: microalgae, photosensitiser, lipid, biomass, aggregation-induced-emission, reactive oxygen species

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Authors: Maria Luiza D. Ramiento, Maria Lissette D. Lucas

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Electricity is said to serve as the backbone of modern technology. Considering this, electricity consumption has dynamically grown due to the continuous demand. An alternative producer of energy concerning electricity must therefore be given focus. Microbial fuel cell wholly characterizes a new method of renewable energy recovery: the direct conversion of organic matter to electricity using bacteria. Electricity is produced as fuel or new food is given to the bacteria. The study concentrated in determining the feasibility of electricity production from local benthic zones. Microbial fuel cells were constructed to harvest the possible electricity and to test the presence of electricity producing microorganisms. Soil samples were gathered from Calumpang River, Palawan Mangrove Forest, Rosario River and Batangas Port. Eleven modules were constructed for the different trials of the soil samples. These modules were made of cathode and anode chambers connected by a salt bridge. For 85 days, the harvested voltage was measured daily. No parameter is added for the first 24 days. For the next 61 days, acetic acid was included in the first and second trials of the modules. Each of the trials of the soil samples gave a positive result in electricity production.There were electricity producing microbes in local benthic zones. It is observed that the higher the organic content of the soil sample, the higher the electricity harvested from it. It is recommended to identify the specific species of the electricity-producing microorganism present in the local benthic zone. Complement experiments are encouraged like determining the kind of soil particles to test its effect on the amount electricity that can be harvested. To pursue the development of microbial fuel cells by building a closed circuit in it is also suggested.

Keywords: microbial fuel cell, benthic zone, electricity, reduction-oxidation reaction, bacteria

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Authors: Qing Zhang, Janak L. Pathak, Macro N. Helder, Richard T. Jaspers, Yin Xiao

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Introduction: Nanomaterial-based bone regeneration is greatly influenced by the immune microenvironment. Tissue-engineered nanomaterials mediate the inflammatory response of macrophages to regulate bone regeneration. Silica nanoparticles have been widely used in tissue engineering-related preclinical studies. However, the effect of topological features on the surface of silica nanoparticles on the immune response of macrophages remains unknown. Purposes: The aims of this research are to compare the influences of normal and pollen-like silica nano-surface topography on macrophage immune responses and to obtain insight into their potential regulatory mechanisms. Method: Macrophages (RAW 264.7 cells) were exposed to mesoporous silica nanoparticles with normal morphology (MSNs) and pollen-like morphology (PMSNs). RNA-seq, RT-qPCR, and LSCM were used to assess the changes in expression levels of immune response-related genes and proteins. SEM and TEM were executed to evaluate the contact and adherence of silica nanoparticles by macrophages. For the assessment of the immunomodulation-mediated osteogenic potential, BMSCs were cultured with conditioned medium (CM) from LPS pre-stimulated macrophage cultures treated with MSNs or PMSNs. Osteoimmunomodulatory potential of MSNs and PMSNs in vivo was tested in a mouse cranial bone osteolysis model. Results: The results of the RNA-seq, RT-qPCR, and LSCM assays showed that PMSNs inhibited the expression of pro-inflammatory genes and proteins in macrophages. SEM images showed distinct macrophage membrane surface binding patterns of MSNs and PMSNs. MSNs were more evenly dispersed across the macrophage cell membrane, while PMSNs were aggregated. PMSNs-induced macrophage anti-inflammatory response was associated with upregulation of the cell surface receptor CD28 and inhibition of ERK phosphorylation. TEM images showed that both MSNs and PMSNs could be phagocytosed by macrophages, and inhibiting nanoparticle phagocytosis did not affect the expression of anti-inflammatory genes and proteins. Moreover, PMSNs-induced conditioned medium from macrophages enhanced BMP-2 expression and osteogenic differentiation mBMSCs. Similarly, PMSNs prevented LPS-induced bone resorption via downregulation of inflammatory reaction. Conclusions: PMSNs can promote bone regeneration by modulating osteoimmunological processes through surface topography. The study offers insights into how surface physical contact cues can modulate the regulation of osteoimmunology and provides a basis for the application of nanoparticles with pollen-like morphology to affect immunomodulation in bone tissue engineering and regeneration.

Keywords: physical contact, osteoimmunology, macrophages, silica nanoparticles, surface morphology, membrane receptor, osteogenesis, inflammation

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Authors: Tekle Olbamo, Tegegn Tesfaye, Dikaso Unbushe, Belete Jorga

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Bovine trypanosomosis is a haemoprotozoan parasitic disease, mostly transmitted by the tsetse fly (Glossina species) and poses significant losses to the livestock industry in pastoral and agro-pastoral areas. Therefore, the current study was aimed to determine the prevalence of bovine trypanosomosis and its vectorial density in some selected tsetse suppression and non-tsetse suppression areas of South Omo Zonefrom December 2018- November 2019. Dark phase contrast buffy coat, hematocrit techniques, and thin blood smear method were used for determination of prevalence and packed cell volume of trypanosomosis infection, respectively. For entomological investigation, 96 NGU traps were deployed (64 traps in tsetse suppression areas, 32 traps in tsetse non-suppression areas) in vector breeding areas. The overall prevalence of bovine trypanosomosis was 11.05% (142/1284), and overall seasonal prevalence of disease was 14.33% (92/642) and 7.78% (50/642) for dry and wet seasons, respectively. There was a statistically significant difference (P <0.05) in disease prevalence between the two seasons. Trypanosomacongolensewas the dominant parasite species; 80% and 71.64%, followed by Trypanosomavivax. Overall mean packed cell volume indicated parasitaemic animals (23.57±3.13) had significantly lower PCV than aparasitaemic animals (27.80±4.95), and animals examined during dry season (26.22±4.37) had lower mean PCV than animals examined during wet season with the significant association. Entomological study result revealed a total of 2.64 F/T/D and 2.03 F/T/D respectively from tsetse suppression areas and tsetse non-suppression areas during dry season and 0.42 F/T/D and 0.56 F/T/D during the wet season. Glossinapallidipes was the only cyclical vectors collected and identified from current study areas along with numerous mechanical vectors of genus Tabanus, Stomoxys, and Haematopota. Therefore integrated and safe control and prevention effort should be engaged to uphold cattle production and productivity in the area.

Keywords: bovine trypanosomiasis, South Omo, tsetse fly density, epidemiological study

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Authors: Ivan A. Sandoval Salazar, Silvia F. Valderrama

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The microalgae oil emerges as a promising source of raw material for many industrial applications. Thus, this study had as a main focus on the cultivation of the microalgae species Desmodesmus sp. in laboratory scale with a view to maximizing biomass production and triglyceride content in the lipid fraction. Initially, culture conditions were selected to optimize biomass production, which was subsequently subjected to nutritional stress by varying nitrate and phosphate concentrations in order to increase the content and productivity of fatty acids. The culture medium BOLD 3N, nitrate and phosphate, light intensity 250,500 and 1000 μmol photons.m².s⁻¹, photoperiod of 12:12 were evaluated. Under the best conditions of the tests, a maximum cell division of 1.13 div.dia⁻¹ was obtained on the sixth day of culture, beginning of the exponential phase, and a maximum concentration of 8.42x107 cell.mL⁻¹ and dry biomass of 3.49 gL⁻¹ on the 20th day, in the stationary phase. The lipid content in the first stage of culture was approximately 8% after 12 days and at the end of the culture in the stationary phase ranged from 12% to 16% (20 days). In the microalgae grown at 250 μmol fotons.m2.s-1 the fatty acid profile was mostly polyunsaturated (52%). The total of unsaturated fatty acids, identified in this species of microalga, reached values between 70 and 75%, being qualified for use in the food and pharmaceutical industry. In addition, this study showed that the cultivation conditions influenced mainly the production of polyunsaturated fatty acids, with the predominance of γ-linolenic acid. However, in the cultures submitted to the highest the intensity of light (1000 μmol photons.m².s⁻¹) and low concentrations of nitrate and phosphate, saturated and monounsaturated fatty acids, which present greater oxidative stability, were identified mainly (60 to 70 %) being qualified for the production of biodiesel and for oleochemistry.

Keywords: microalgae, Desmodesmus sp, fatty acids, biodiesel

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Authors: Ajay Kumar, Satwinderjeet Kaur

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Onosma bracteata Wall. (Boraginaceae), is known to be a medicinal plant, useful in the treatment of body swellings, abdominal pain and urinary calculi, etc. The present study focused on the radical scavenging and cancer growth inhibitory properties of isolates from O. bracteata. Obea fraction demonstrated noticeable free radical scavenging ability along with antiproliferative activity in human osteosarcoma MG-63, human neuroblastoma IMR-32, and human lung cancer A549 cell lines using MTT assay with GI50 values of 88.56, 101.61 and 112.7 μg/ml, respectively. The scanning electron and confocal microscopy studies showed morphological alterations including nuclear condensation and formation of apoptotic bodies in osteosarcoma MG-63 cells. Obea fraction in osteosarcoma MG-63 cells augmented the reactive oxygen species (ROS) level and decreased the mitochondrial membrane potential. Flow cytometry analysis revealed the Obea treated cells to be arrested in the G0/G1 phase in a dose dependent manner supported by the observed increase in the early apoptotic cell population. Western blotting analysis showed that the expression of p-NF-kB, COX-2, p-Akt, and Bcl-xL decreased whereas, the expression of GSK-3β, p53, caspase-3 and caspase-9 proteins increased. The downregulation of Bcl-2, Cyclin E, CDK2 and mortalin gene expression and upregulation of p53 genes was unfolded in RT-qPCR studies. The presence of catechin, kaempferol, Onosmin A and epicatechin, as revealed in high-performance liquid chromatography (HPLC) studies, contributes towards the chemopreventive potential of O. bracteata which can be tapped for chemotherapeutic use.

Keywords: apoptosis, confocal microscopy, HPLC, mitochondria membrane potential, reactive oxygen species

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Authors: Marita Pigłowska, Beata Kurc, Paweł Daszkiewicz

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Railway vehicles are divided into two groups: traction (powered) vehicles and wagons. The traction vehicles include locomotives (line and shunting), railcars (sometimes referred to as railbuses), and multiple units (electric and diesel), consisting of several or a dozen carriages. In vehicles with diesel traction, fuel energy (petrol, diesel, or compressed gas) is converted into mechanical energy directly in the internal combustion engine or via electricity. In the latter case, the combustion engine generator produces electricity that is then used to drive the vehicle (diesel-electric drive or electric transmission). In Poland, such a solution dominates both in heavy linear and shunting locomotives. The classic diesel drive is available for the lightest shunting locomotives, railcars, and passenger diesel multiple units. Vehicles with electric traction do not have their own source of energy -they use pantographs to obtain electricity from the traction network. To determine the competitiveness of the hydrogen propulsion system, it is essential to understand how it works. The basic elements of the construction of a railway vehicle drive system that uses hydrogen as a source of traction force are fuel cells, batteries, fuel tanks, traction motors as well as main and auxiliary converters. The compressed hydrogen is stored in tanks usually located on the roof of the vehicle. This resource is supplemented with the use of specialized infrastructure while the vehicle is stationary. Hydrogen is supplied to the fuel cell, where it oxidizes. The effect of this chemical reaction is electricity and water (in two forms -liquid and water vapor). Electricity is stored in batteries (so far, lithium-ion batteries are used). Electricity stored in this way is used to drive traction motors and supply onboard equipment. The current generated by the fuel cell passes through the main converter, whose task is to adjust it to the values required by the consumers, i.e., batteries and the traction motor. The work will attempt to construct a fuel cell with unique electrodes. This research is a trend that connects industry with science. The first goal will be to obtain hydrogen on a large scale in tube furnaces, to thoroughly analyze the obtained structures (IR), and to apply the method in fuel cells. The second goal is to create low-energy energy storage and distribution station for hydrogen and electric vehicles. The scope of the research includes obtaining a carbon variety and obtaining oxide systems on a large scale using a tubular furnace and then supplying vehicles. Acknowledgments: This work is supported by the Polish Ministry of Science and Education, project "The best of the best! 4.0", number 0911/MNSW/4968 – M.P. and grant 0911/SBAD/2102—B.K.

Keywords: railway, hydrogen, fuel cells, hybrid vehicles

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Authors: Atef Y. Shenouda, Anton A. Momchilov

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Graphene and CdO with different stoichiometric ratios of Cd(CH₃COO)₂ and graphene samples were prepared by hydrothermal reaction. The crystalline phases of pure CdO and 3CdO:1graphene were identified by X-ray diffraction (XRD). The particle morphology was studied with SEM. Furthermore, impedance measurements were applied. Galvanostatic measurements for the cells were carried out using potential limits between 0.01 and 3 V vs. Li/Li⁺. The current cycling intensity was 10⁻⁴ A. The specific discharge capacity of 3CdO-1G cell was about 450 Ah.Kg⁻¹ up to more than 100 cycles.

Keywords: CdO, graphene, negative electrode, lithium battery

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Authors: Nusaiba Al-Nemrawi, Belal Al-Husein

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Methotrexate (MTX) is a stoichiometric inhibitor of dihydrofolate reductase, which is essential for DNA synthesis. MTX is a chemotherapeutic agent used for treating many types of cancer cells. However, cells’ resistant to MTX is very common and its pharmacokinetic behavior is highly problematic. of MTX within tumor cells, we propose encapsulation of antitumor drugs in nanoparticulated systems. Chitosan (CS) is a naturally occurring polymer that is biocompatibe, biodegradable, non-toxic, cationic and bioadhesive. CS nanoparticles (CS-NPs) have been used as drug carrier for targeted delivery. Titanium dioxide (TiO2), a natural mineral oxide, which is used in biomaterials due to its high stability and antimicrobial and anticorrosive properties. TiO2 showed a potential as a tumor suppressor. In this study a new formulation of MTX loaded in CS NPs (CS-MTX NPs) and coated with Titanium oxide (TiO2) was prepared. The mean particle size, zeta potential, polydispersity index were measured. The interaction between CS NPs and TiO2 NPs was confirmed using FTIR and XRD. CS-MTX NPs was studied in vitro using the tumor cell line MCF-7 (human breast cancer). The results showed that CS-MTX has a size around 169 nm and as they were coated with TiO2, the size ranged between and depending on the ratio of CS-MTX to TiO2 ratio used in the preparation. All NPs (uncoated and coated carried positive charges and were monodispersed. The entrapment efficacy was around 65%. Both FTIR and XRD proved that TiO2 interacted with CS-MTX NPs. The drug invitro release was controlled and sustained over days. Finally, the studied in vitro using the tumor cell line MCF-7 suggested that combining nanomaterials with anticancer drugs CS-MTX NPs may be more effective than free MTX for cancer treatment. In conclusion, the combination of CS-MTX NPs and TiO2 NPs showed excellent time-dependent in vitro antitumor behavior, therefore, can be employed as a promising anticancer agent to attain efficient results towards MCF-7 cells.

Keywords: Methotrexate, Titanium dioxide, Chitosan nanoparticles, cancer

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Authors: Patricia Jayshree Jacob, Mas Jaffri Masarudinb, Mohd Zobir Hussein, Raha Abdul Rahim

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Iron based ferromagnetic nanoparticles (IONP) and silver nanostructures (AgNP) have found a wide range of application in antimicrobial therapy, cell targeting, and environmental applications. As such, the design of well-defined monodisperse IONPs and AgNPs have become an essential tool in nanotechnology. Fabrication of these nanostructures using conventional methods is not environmentally conducive and weigh heavily on energy and outlays. Selected microorganisms possess the innate ability to reduce metallic ions in colloidal aqueous solution to generate nanoparticles. Hence, harnessing this potential is a way forward in constructing microbial nano-factories, capable of churning out high yields of well-defined IONP’s and AgNP's with physicochemical characteristics on par with the best synthetically produced nanostructures. In this paper, we report the isolation and characterization of bacterial strains isolated from the tropical marine and freshwater ecosystems of Malaysia that demonstrated facile and rapid generation of ferromagnetic nanoparticles and silver nanostructures when precursors such as FeCl₃.6H₂O and AgNO₃ were added to the cell-free bacterial lysate in colloidal solution. Characterization of these nanoparticles was carried out using FESEM, UV Spectrophotometer, XRD, DLS and FTIR. This aerobic bioprocess was carried out at ambient temperature and humidity and has the potential to be developed for environmental friendly, cost effective large scale production of IONP’s. A preliminary bioprocess study on the harvesting time, incubation temperature and pH was also carried out to determine pertinent abiotic parameters contributing to the optimal production of these nanostructures.

Keywords: iron oxide nanoparticles, silver nanoparticles, biosynthesis, aquatic bacteria

Procedia PDF Downloads 285

Authors: Anza-Vhudziki Mboyi, Ilunga Kamika, Maggy Momba

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The aim of this study was to ascertain the survival limit and capability of commonly found wastewater protozoan (Aspidisca sp, Trachelophyllum sp, and Peranema sp) and bacterial (Bacillus licheniformis, Brevibacillus laterosporus, and Pseudomonas putida) species to remove COD while exposed to commercial nanomaterials under varying pH conditions. The experimental study was carried out in modified mixed liquor media adjusted to various pH levels (pH 2, 7 and 10), and a comparative study was performed to determine the difference between the cytotoxicity effects of commercial zinc oxide (nZnO) and silver (nAg) nanomaterials (NMs) on the target wastewater microbial communities using standard methods. The selected microbial communities were exposed to lethal concentrations ranging from 0.015 g/L to 40 g/L for nZnO and from 0.015 g/L to 2 g/L for nAg for a period of 5 days of incubation at 30°C (100 r/min). Compared with the absence of NMs in wastewater mixed liquor, the relevant environmental concentration ranging between 10 µg/L and 100 µg/L, for both nZnO and nAg caused no adverse effects, but the presence of 20 g of nZnO/L and 0.65 g of nAg/L significantly inhibited microbial growth. Statistical evidence showed that nAg was significantly more toxic compared to nZnO, but there was an insignificant difference in toxicity between microbial communities and pH variations. A significant decrease in the removal of COD by microbial populations was observed in the presence of NMs with a moderate correlation of r = 0.3 to r = 0.7 at all pH levels. It was evident that there was a physical interaction between commercial NMs and target wastewater microbial communities; although not quantitatively assessed, cell morphology and cell death were observed. Such phenomena suggest the high resilience of the microbial community, but it is the accumulation of NMs that will have adverse effects on the performance in terms of COD removal.

Keywords: bacteria, biological treatment, chemical oxygen demand (COD) and nanomaterials, consortium, pH, protozoan

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Authors: Wenjiang Deng, Tian Mou, Yudi Pawitan, Trung Nghia Vu

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Estimation of isoform-level gene expression from RNA-seq data depends on simplifying assumptions, such as uniform reads distribution, that are easily violated in real data. Such violations typically lead to biased estimates. Most existing methods provide a bias correction step(s), which is based on biological considerations, such as GC content–and applied in single samples separately. The main problem is that not all biases are known. For example, new technologies such as single-cell RNA-seq (scRNA-seq) may introduce new sources of bias not seen in bulk-cell data. This study introduces a method called XAEM based on a more flexible and robust statistical model. Existing methods are essentially based on a linear model Xβ, where the design matrix X is known and derived based on the simplifying assumptions. In contrast, XAEM considers Xβ as a bilinear model with both X and β unknown. Joint estimation of X and β is made possible by simultaneous analysis of multi-sample RNA-seq data. Compared to existing methods, XAEM automatically performs empirical correction of potentially unknown biases. XAEM implements an alternating expectation-maximization (AEM) algorithm, alternating between estimation of X and β. For speed XAEM utilizes quasi-mapping for read alignment, thus leading to a fast algorithm. Overall XAEM performs favorably compared to other recent advanced methods. For simulated datasets, XAEM obtains higher accuracy for multiple-isoform genes, particularly for paralogs. In a differential-expression analysis of a real scRNA-seq dataset, XAEM achieves substantially greater rediscovery rates in an independent validation set.

Keywords: alternating EM algorithm, bias correction, bilinear model, gene expression, RNA-seq

Procedia PDF Downloads 142