Optimization of Epigenetic Modifier Drug Combination for Synergistic Effect against Glioblastoma Multiform Cancer Cell Lines.

Glioblastoma multiforme (GBM), is a frequent class of malignant brain tumors. Epigenetic therapy, especially with synergistic combinations is highly paid attention for aggressive solid tumors like GBM. Here, RSM optimization has been used to increase the efficient arrest of U87 and U251 cell lines due to synergistic effects. Cell lines were treated with SAHA, 5-Azacytidine, GSK-126, and PTC-209 individually and then RSM was used to find most effective combinations. Results showed that optimized combinations significantly reduce cell survival and induce cell cycle arrest and apoptosis in both cell lines. Expression of cyclin B1 and cyclin D1 were decreased while caspase3 increased expression.

Maximization of uricase production in a column bioreactor through response surface methodology-based optimization.

Uricase (EC 1.7.3.3) is an oxidoreductase enzyme that is widely exploited for diagnostic and treatment purposes in medicine. This study focuses on producing recombinant uricase fromE. coliBL21 in a bubble column bioreactor (BCB) and finding the optimal conditions for maximum uricase activity. The three most effective variables on uricase activity were selected through the Plackett-Burman design from eight different variables and were further optimized by the central composite design of the response surface methodology (RSM). The selected variables included the inoculum size (%v/v), isopropylß-d-1-thiogalactopyranoside (IPTG) concentration (mM) and the initial pH of the culture medium. The activity of uricase, the final optical density at 600 nm wavelength (OD600) and the final pH were considered as the responses of this optimization and were modeled. As a result, activity of 5.84 U·ml-1and a final OD600of 3.42 were obtained at optimum conditions of 3% v/v inoculum size, an IPTG concentration of 0.54 mM and a pH of 6.0. By purifying the obtained enzyme using a Ni-NTA agarose affinity chromatography column, 165 ± 1.5 mg uricase was obtained from a 600 ml cell culture. The results of this study show that BCBs can be a highly effective option for large-scale uricase production.

Amyloid fibril cytotoxicity and associated disorders.

Misfolded proteins assemble into fibril structures that are called amyloids. Unlike usually folded proteins, misfolded fibrils are insoluble and deposit extracellularly or intracellularly. Misfolded proteins interrupt the function and structure of cells and cause amyloid disease. There is increasing evidence that the most pernicious species are oligomers. Misfolded proteins disrupt cell function and cause cytotoxicity by calcium imbalance, mitochondrial dysfunction, and intracellular reactive oxygen species. Despite profound impacts on health, social, and economic factors, amyloid diseases remain untreatable. To develop new therapeutics and to understand the pathological manifestations of amyloidosis, research into the origin and pathology of amyloidosis is urgently needed. This chapter describes the basic concept of amyloid disease and the function of atypical amyloid deposits in them.

Protein aggregation: An overview.

In order for an ordered protein to perform its specific function, it must have a specific molecular structure. Information about this structure is encoded in the protein's amino acid sequence. The unique functional state is achieved as a result of a specific process, known as protein folding. However, as a result of partial or complete unfolding of the polypeptide chain, proteins may misfold and aggregate, leading to the formation of various aggregated structures, such as like amyloid aggregates with the cross-ß structure. A variety of cellular biological processes can be affected by protein aggregates that consume essential factors necessary for maintaining proteostasis, which leads to the proteostasis imbalance and further accumulation of protein aggregates, often resulting in age-related neurodegenerative disease progression and aging. However, in addition to their well-established pathological effects, amyloids also play various physiological roles, and many important biological processes involve such 'functional amyloids'. This chapter represents a brief overview of the protein aggregation phenomenon outlines a timeline provides of some key discoveries in this exciting field.

Inhibitors of amyloid fibril formation.

Many diseases are caused by misfolded and denatured proteins, leading to neurodegenerative diseases. In recent decades researchers have developed a variety of compounds, including polymeric inhibitors and natural compounds, antibodies, and chaperones, to inhibit protein aggregation, decrease the toxic effects of amyloid fibrils, and facilitate refolding proteins. The causes and mechanisms of amyloid formation are still unclear, and there are no effective treatments for Amyloid diseases. This section describes research and achievements in the field of inhibiting amyloid accumulation and also discusses the importance of various strategies in facilitating the removal of aggregates species (refolding) in the treatment of neurological diseases such as chemical methods like as, small molecules, metal chelators, polymeric inhibitors, and nanomaterials, as well as the use of biomolecules (peptide and, protein, nucleic acid, and saccharide) as amyloid inhibitors, are also highlighted.

The hidden world of protein aggregation.

Though the book's journey into The Hidden World of Protein Aggregation has come to an end, the search for knowledge, the development of healthier lives, and the discovery of nature's mysteries continue, promising new horizons and discoveries yet to be discovered. The intricacies of protein misfolding and aggregation remain a mystery in cellular biology, despite advances made in unraveling them. In this chapter, we will summarize the specific conclusions from the previous chapters and explore the persistent obstacles and unanswered questions that motivate scientists to pursue exploration of protein misfolding and aggregation.

Factors influencing amyloid fibril formation.

Protein aggregation is a complex process with several stages that lead to the formation of complex structures and shapes with a broad variability in stability and toxicity. The aggregation process is affected by various factors and environmental conditions that disrupt the protein's original state, including internal factors like mutations, expression levels, and polypeptide chain truncation, as well as external factors, such as dense molecular surroundings, post-translation modifications, and interactions with other proteins, nucleic acids, small molecules, metal ions, chaperones, and lipid membranes. During the aggregation process, the biological activity of an aggregating protein may be reduced or eliminated, whereas the resulting aggregates may have the potential to be immunogenic, or they may have other undesirable properties. Finding the cause(s) of protein aggregation and controlling it to an acceptable level is among the most crucial topics of research in academia and biopharmaceutical companies. This chapter aims to review intrinsic pathways of protein aggregation and potential extrinsic variables that influence this process.

Prediction of protein aggregation.

The scientific community is very interested in protein aggregation because of its involvement in several neurodegenerative diseases and its significance in industry. Remarkably, fibrillar aggregates are utilized naturally for constructing structural scaffolds or creating biological switches and may be intentionally designed to construct versatile nanomaterials. Consequently, there is a significant need to rationalize and predict protein aggregation. Researchers have developed various computational methodologies and algorithms to predict protein aggregation and understand its underlying mechanics. This chapter aims to summarize the significant advancements in computational methods, accessible resources, and prospective developments in the field of in silico research. We assess the existing computational tools for predicting protein aggregation propensities, detecting areas that are prone to sequential and structural aggregation, analyzing the effects of mutations on protein aggregation, or identifying prion-like domains.

Biosynthesis Optimization of Antibacterial-Magnetic Iron Oxide Nanoparticles from Bacillus megaterium.

The occurrence of antibiotic resistance on common bacterial agents and the need to use new generations of antibiotics have led to the use of various strategies for production. Taking inspiration from nature, using bio-imitation patterns, in addition to the low cost of production, is advantageous and highly accurate. In this research, we were able to control the temperature, shake, and synthesis time of the synthesis conditions of Bacillus megaterium bacteria as a model for the synthesis of magnetic iron nanoparticles and optimize the ratio of reducing salt to bacterial regenerating agents as well as the concentration of salt to create iron oxide nanoparticles with more favorable properties and produced with more antibacterial properties. Bacterial growth was investigated by changing the incubation times of pre-culture and overnight culture in the range of the logarithmic phase. The synthesis time, salt ratio, and concentration were optimized to achieve the size, charge, colloidal stability, and magnetic and antibacterial properties of nanoparticles. The amount of the effective substance produced by the bacteria was selected by measuring the amount of the active substance synthesized using the free radical reduction (DPPH) method. With the help of DPPH, the duration of the synthesis was determined to be one week. Characterizations such as UV-vis spectroscopy, FTIR, FESEM, X-ray, and scattering optical dynamics were performed and showed that the nanoparticles synthesized with a salt concentration of 80 mM and a bacterial suspension to salt ratio of 2:1 are smaller in size and have a light scattering index, a PDI index close to 0.1, and a greater amount of reducing salt used in the reaction during one week compared to other samples. Moreover, they had more antibacterial properties than the concentration of 100 mM. As a result, better characteristics and more antibacterial properties than common antibiotics were created on E. coli and Bacillus cereus.

Performance of personalised prosthesis under static pressure: Numerical analysis and experimental validation.

This study investigates the performance of personalised middle ear prostheses under static pressure through a combined approach of numerical analysis and experimental validation. The sound transmission performances of both normal and reconstructed middle ears undergo changes under high positive or negative pressure within the middle ear cavity. This pressure fluctuation has the potential to result in prosthesis displacement/extrusion in patients. To optimise the design of middle ear prostheses, it is crucial to consider various factors, including the condition of the middle ear cavity in which the prosthesis is placed. The integration of computational modelling techniques with non-invasive imaging modalities has demonstrated significant promise and distinct prospects in middle ear surgery. In this study, we assessed the efficacy of Finite Element (FE) analysis in modelling the responses of both normal and reconstructed middle ears to elevated static pressure within the ear canal. The FE model underwent validation using experimental data derived from human cadaveric temporal bones before progressing to subsequent investigations. Afterwards, we assessed stapes and umbo displacements in the reconstructed middle ear under static pressure, with either a columella-type prosthesis or a prosthetic incus, closely resembling a healthy incus. Results indicated the superior performance of the prosthetic incus in terms of both sound transmission to the inner ear and stress distribution patterns on the TM, potentially lowering the risk of prosthesis displacement/extrusion. This study underscores the potential of computational analysis in middle ear surgery, encompassing aspects such as prosthesis design, predicting outcomes in ossicular chain reconstruction (OCR), and mitigating experimental costs.

Frequency dependence of ultrasonic effects on the kinetics of hen egg white lysozyme fibrillation.

Our study aimed to investigate the effects of ultrasound on the fibrillation kinetics of HEWL (hen egg white lysozyme) and its physicochemical properties. Ultrasound, a mechanical wave, can induce conformational changes in proteins. To achieve this, we developed an ultrasound exposure system and used various biophysical techniques, including ThT fluorescence spectroscopy, ATR-FTIR, Far-UV CD spectrophotometry, Fluorescence microscopy, UV-spectroscopy, and seeding experiments. Our results revealed that higher frequencies significantly accelerated the fibrillation of lysozyme by unfolding the native protein and promoting the fibrillation process, thereby reducing the lag time. We observed a change in the secondary structure of the sonicated protein change to the ß-structure, but there was no difference in the Tm of native and sonicated proteins. Furthermore, we found that higher ultrasound frequencies had a greater seeding effect. We propose that the effect of frequency can be explained by the impact of the Reynolds number, and for the Megahertz frequency range, we are almost at the transition regime of turbulence. Our results suggest that laminar flows may not induce any significant change in the fibrillation kinetics, while turbulent flows may affect the process.

Hippocampal tandem mass tag (TMT) proteomics analysis during kindling epileptogenesis in rat.

Epilepsy is a neurological disorder that remains difficult to treat due to the lack of a clear molecular mechanism and incomplete understanding of involved proteins. To identify potential therapeutic targets, it is important to gain insight into changes in protein expression patterns related to epileptogenesis. One promising approach is to analyze proteomic data, which can provide valuable information about these changes. In this study, to evaluate the changes in gene expression during epileptogenesis, LC-MC2 analysis was carried out on hippocampus during stages of electrical kindling in rat models. Subsequently, progressive changes in the expression of proteins were detected as a result of epileptogenesis development. In line with behavioral kindled seizure stages and according to the proteomics data, we described epileptogenesis phases by comparing Stage3 versus Control (S3/C0), Stage5 versus Stage3 (S5/S3), and Stage5 versus Control group (S5/C0). Gene ontology analysis on differentially expressed proteins (DEPs) showed significant changes of proteins involved in immune responses like Csf1R, Aif1 and Stat1 during S3/C0, regulation of synaptic plasticity like Bdnf, Rac1, CaMK, Cdc42 and P38 during S5/S3, and nervous system development throughout S5/C0 like Bdnd, Kcc2 and Slc1a3.There were also proteins like Cox2, which were altered commonly among all three phases. The pathway enrichment analysis of DEPs was also done to discover molecular connections between phases and we have found that the targets like Csf1R, Bdnf and Cox2 were analyzed throughout all three phases were highly involved in the PPI network analysis as hub nodes. Additionally, these same targets underwent changes which were confirmed through Western blotting. Our results have identified proteomic patterns that could shed light on the molecular mechanisms underlying epileptogenesis which may allow for novel targeted therapeutic strategies.

Targeted drug delivery into glial scar using CAQK peptide in a mouse model of multiple sclerosis.

In multiple sclerosis, lesions are formed in various areas of the CNS, which are characterized by reactive gliosis, immune cell infiltration, extracellular matrix changes and demyelination. CAQK peptide (peptide sequence: cysteine-alanine-glutamine-lysine) was previously introduced as a targeting peptide for the injured site of the brain. In the present study, we aimed to develop a multifunctional system using nanoparticles coated by CAQK peptide, to target the demyelinated lesions in animal model of multiple sclerosis. We investigated the binding of fluorescein amidite-labelled CAQK and fluorescein amidite-labelled CGGK (as control) on mouse brain sections. Then, the porous silicon nanoparticles were synthesized and coupled with fluorescein amidite-labelled CAQK. Five days after lysolecithin-induced demyelination, male mice were intravenously injected with methylprednisolone-loaded porous silicon nanoparticles conjugated to CAQK or the same amount of free methylprednisolone. Our results showed that fluorescein amidite-labelled CAQK recognizes demyelinated lesions in brain sections of animal brains injected with lysolecithin. In addition, intravenous application of methylprednisolone-loaded nanoparticle porous silicon conjugated to CAQK at a single dose of 0.24 mg reduced the levels of microglial activation and astrocyte reactivation in the lesions of mouse corpus callosum after 24 and 48 h. No significant effect was observed following the injection of the same dose of free methylprednisolone. CAQK seems a potential targeting peptide for delivering drugs or other biologically active chemicals/reagents to the CNS of patients with multiple sclerosis. Low-dose methylprednisolone in this targeted drug delivery system showed significant beneficial effect.

An emphatic study on the luciferin-luciferase bioluminescence system of Benthosema pterotum.

Approximately 80% of luminous organisms live in the oceans, and considerable diversity of life dependence on bioluminescence has been observed in marine organisms. Among vertebrates, luminous fish species are the only group of vertebrates that have the ability to emit bioluminescent light. Meanwhile, the lantern fish family (Myctophidae), with 33 genera all of which have the ability to emit light, is considered the most prominent family among the luminous fish of the deep oceans and seas. Lantern fish Benthosema pterotum has bioluminescence properties due to the presence of photophores scattered in its ventral-lateral region. However, no research has been performed on its bioluminescence system and light emission mechanism. The present research aimed to assess the type of bioluminescence, pigment, photoprotein, or luciferin-luciferase system in B. pterotum. In order to determine the type of light-emitting system in B. pterotum species, several specific experiments were designed and performed. It was shown that the light emission system in B. pterotum species is categorized into the luciferin-luciferase type. Conducting this research was not only innovative, but it also could be the beginning of further research in the field of marine biochemistry and production of the recombinant active forms of enzymes for industrial, commercial, medical, and pharmaceutical purposes.

Extracting Potential New Targets for Treatment of Adenoid Cystic Carcinoma using Bioinformatic Methods.

Background: Adenoid cystic carcinoma is a slow-growing malignancy that most often occurs in the salivary glands. Currently, no FDA-approved therapeutic target or diagnostic biomarker has been identified for this cancer. The aim of this study was to find new therapeutic and diagnostic targets using bioinformatics methods. Methods: We extracted the gene expression information from two GEO datasets (including GSE59701 and GSE88804). Different expression genes between adenoid cystic carcinoma (ACC) and normal samples were extracted using R software. The biochemical pathways involved in ACC were obtained by using the Enrichr database. PPI network was drawn by STRING, and important genes were extracted by Cytoscape. Real-time PCR and immunohistochemistry were used for biomarker verification. Results: After analyzing the PPI network, 20 hub genes were introduced to have potential as diagnostic and therapeutic targets. Among these genes, PLCG1 was presented as new biomarker in ACC. Furthermore, by studying the function of the hub genes in the enriched biochemical pathways, we found that insulin-like growth factor type 1 receptor and PPARG pathways most likely play a critical role in tumorigenesis and drug resistance in ACC and have a high potential for selection as therapeutic targets in future studies. Conclusion: In this study, we achieved the recognition of the pathways involving in ACC pathogenesis and also found potential targets for treatment and diagnosis of ACC. Further experimental studies are required to confirm the results of this study.

Improvement of thermal-stability of chondroitinase ABCI immobilized on graphene oxide for the repair of spinal cord injury.

Spinal cord injury healing has been shown to be aided by chondroitinase ABC I (cABCI) treatment. The transport of cABCI to target tissues is complicated by the enzyme's thermal instability; however, cABCI may be immobilized on nanosheets to boost stability and improve delivery efficiency. This investigation's goal was to assess the immobilization of cABC I on graphene oxide (GO). for this purpose, GO was produced from graphene using a modified version of Hummer's process. the immobilization of cABC I on GO was examined using SEM, XRD, and FTIR. The enzymatic activity of cABC I was evaluated in relation to substrate concentration. The enzyme was then surface-adsorption immobilized on GO, and its thermal stability was examined. As compared to the free enzyme, the results showed that the immobilized enzyme had a greater Km and a lower Vmax value. The stability of the enzyme was greatly improved by immobilization at 20, 4, 25, and 37 °C. For example, at 37 °C, the free enzyme retained 5% of its activity after 100 min, while the immobilized one retained 30% of its initial activity. The results showed, As a suitable surface for immobilizing cABC I, GO nano sheets boost the enzyme's stability, improving its capability to support axonal regeneration after CNC damage and guard against fast degradation.

Meniere's disease: Pathogenesis, treatments, and emerging approaches for an idiopathic bioenvironmental disorder.

Meniere's disease (MD) is a severe inner ear condition known by debilitating symptoms, including spontaneous vertigo, fluctuating and progressive hearing loss, tinnitus, and aural fullness or pressure within the affected ear. Prosper Meniere first described the origins of MD in the 1860s, but its underlying mechanisms remain largely elusive today. Nevertheless, researchers have identified a key histopathological feature called Endolymphatic Hydrops (ELH), which refers to the excessive buildup of endolymph fluid in the membranous labyrinth of the inner ear. The exact root of ELH is not fully understood. Still, it is believed to involve several biological and bioenvironmental etiological factors such as genetics, autoimmunity, infection, trauma, allergy, and new theories, such as saccular otoconia blocking the endolymphatic duct and sac. Regarding treatment, there are no reliable and definitive cures for MD. Most therapies focus on managing symptoms and improving the overall quality of patients' life. To make significant advancements in addressing MD, it is crucial to gain a fundamental understanding of the disease process, laying the groundwork for more effective therapeutic approaches. This paper provides a comprehensive review of the pathophysiology of MD with a focus on old and recent theories. Current treatment strategies and future translational approaches (with low-level evidence but promising results) related to MD are also discussed, including patents, drug delivery, and nanotechnology, that may provide future benefits to patients suffering from MD.

Peptide mediated targeted delivery of gold nanoparticles into the demyelination site ameliorates myelin impairment and gliosis.

Drug development for multiple sclerosis (MS) clinical management focuses on both neuroprotection and repair strategies, and is challenging due to low permeability of the blood-brain barrier, off-target distribution, and the need for high doses of drugs. The changes in the extracellular matrix have been documented in MS patients. It has been shown that the expression of nidogen-1 increases in MS lesions. Laminin forms a stable complex with nidogen-1 through a heptapeptide which was selected to target the lesion area in this study. Here we showed that the peptide binding was specific to the injured area following lysophosphatidylcholine (LPC) induced demyelination. In vivo data showed enhanced delivery of the peptide-functionalized gold nanoparticles (Pep-GNPs) to the lesion area. In addition, Pep-GNPs administration significantly enhanced myelin content and reduced astrocyte/microglia activation. Results demonstrated the possibility of using this peptide to target and treat lesions in patients suffering from MS.

Ferroptosis inhibition by deferiprone, attenuates myelin damage and promotes neuroprotection in demyelinated optic nerve.

Multiple sclerosis (MS) is a chronic inflammatory disease, which leads to focal demyelination in the brain and spinal cord. Studies showed that iron released during the course of myelin breakdown exacerbates tissue damage, which is in agreement with the features of iron-dependent cell death, ferroptosis. Here, we aimed to investigate the possible contribution of ferroptosis in the demyelinated optic nerve, and to explore the effectiveness of ferroptosis inhibitor, deferiprone (DFP), on the extent of demyelination, inflammation and axonal damage. For this purpose, focal demyelination was induced by injection of lysolecithin (LPC), into the optic nerve of male C57BL/6J mice. Afterward, optic nerves were harvested at different time points from as early as 6 h up to 7 days post-LPC injection. Next, to evaluate the effectiveness of DFP two groups of animals received daily intraperitoneal injection of DFP for 3 or 7 continuous days. Vehicle groups received saline. Iron deposition was observed at different time points post-LPC injection from 6 h to 7 days post injection. Examining ferroptosis markers showed a significant reduction in glutathione content along with increased level of malondialdehyde and upregulated ferroptosis marker genes at early time points after injection. Besides, DFP treatment during the inflammatory phase of the model resulted in decreased microgliosis and inflammation. Reduced demyelination, microgliosis and astrogliosis was shown in mice that received DFP for 7 days. Moreover, DFP protected against axonal damage and retinal ganglion cells loss. Our results suggest the possible contribution of ferroptosis pathway in the process of demyelination. The therapeutic strategies targeting iron deposition, e.g. DFP treatment might thus represent a promising therapeutic target for patients with MS.

Insulin fibrillation: Strategies for inhibition.

Insulin and its homologous are the most utilized protein drugs due to their role in diabetic patients' treatment. Insulin forms amyloid-like fibrils in vivo at the injection site. Therefore, the study of its fibrillation mechanism and designing efficient inhibitors have high importance in the pharmaceutical industry. Insulin fibrils are formed at both acidic and neutral pH in vitro. Overall, this process involves the dissociation of hexameric form to monomeric, partially dissociating the native monomeric form, nuclei formation, and finally converting oligomers to large ordered aggregates. Intermediate and terminal species are different pathologically. This review is focused on the research works dedicated to the inhibition of insulin fibril formation. The inhibitors include various polyphenols, natural compounds, nanoparticles, and synthetic chemicals/peptides, as well as the classification of inhibitors targets concerning protein fibrillation. Although most inhibitors stabilize the native structure of the protein and prevent the formation of partially folded species, there are other inhibitors that hinder other steps in the course of fibrillation. Also, several inhibitors were able to dissociate the pre-existing fibrils. Finding inhibition strategies could be beneficial for developing new inhibitors that are more efficient and can block the amyloid pathway in a specific desired stage.