Journal of Applied Biotechnology Reports
Volume:11 Issue: 3, Summer 2024

Gastrointestinal (GI) tumors are a major public health problem worldwide, accounting for over one-third of global cancer-associated deaths. While the current therapies, such as traditional surgery, chemotherapy, and radiotherapy show little efficacy for GI cancers, studies suggest an increasing burden for these malignancies and emphasize the necessity of further studies to present an effective strategy for the treatment of GI tumors. Oncolytic virotherapy is a novel technology in which various oncolytic viruses are used for cancer therapy. Newcastle disease virus (NDV) is one such oncolytic virus that has been frequently investigated as an oncolytic agent in various pre-clinical and clinical studies. GI cancers, as a heterogeneous class of tumors originating from the stomach, liver, colorectum, esophagus, and pancreas, are one of the most studied malignancies with promising results, which have been evaluated for potential oncolytic activities of NDV. In this way, the present review aimed to focus on describing the pre-clinical and clinical studies about the use of oncolytic NDV therapy for GI cancers, including gastric cancer, hepatocellular carcinoma, pancreatic cancer, and colorectal cancer.

Cryopreservation is a critical enabling technology in stem cell-based therapies, tissue engineering and regenerative medicine that provides stable and long-term storage of organelles, cells, tissues, or any other biological constructs. However, this technology faces challenges, including decreasing cell survival rates and using dimethyl sulfoxide (DMSO), a cytotoxic agent. Moreover, cryopreserving methods are time-consuming and expensive. Various cells and tissues, due to some reasons, such as different metabolic and functional characteristics, respond differentially to the cryopreservation protocols which cause diversities in viability after thawing. This review discusses methods currently used for optimized cryopreservation of hematopoietic stem cells (HSCs), mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), adipose-derived stem cells (ASCs), and their advantages and disadvantages. Also, here we discuss about changing the DMSO, freezing rate, pre-freeze storage, and storage temperature that can improve the cryopreservation outcomes. Further studies are still needed to find better cryopreservation methods for stem cells.

Safflower (Carthamus tinctorius L.) is a medicinal and crop plant rich in phyto-compounds such as unsaturated fatty acids (UFAs) and flavonoids with a known pharmacological activity. Therefore, defining its activity pathways and functional genes involved in the main biological process during plant growth and development is of high importance. The objective of this study was to define the transcriptome profile and identification of genes, activity pathways, and important proteins/enzymes of safflower flower bract at the flowering stage. RNA was extracted from flower bracts for RNA-Seq assay, and the De novo assembly method was used to reconstruct the safflower transcriptome. Protein identification was run against the UniProt database. Gene ontology (GO) analysis was done for identified unigenes. 125,544 contigs were generated and 100,652 CDS coding for 12,941 proteins were identified. 8,113 proteins were selected for further downstream analyses. Functional annotation could identify 298 records for molecular function, 1,574 for biological process, 257 for cellular components, and 99 for KEGG pathways. Important pathways were metabolic pathways (991 genes), biosynthesis of secondary metabolites (496 genes), biosynthesis of cofactors (131 genes), endocytosis (93 genes), and glycerophospholipid metabolism (62 genes), respectively. In “biosynthesis of secondary metabolite” pathways, three activity sub-pathways related to biosynthesis/metabolism of vitamins (B2, B6, and D) were detected and the associated genes were identified. Five KEGG pathways related to fatty acids (FA) were identified including FA metabolism, FA degradation, FA biosynthesis, FA elongation and biosynthesis of UFAs. In this research, we didn’t identify any active pathway related to flavonoid biosynthesis in flower bract. Using De novo assembly, several GO terms and KEGG pathway were enriched for detected uingenes in safflower transcriptome in flower bract at flowering stage.

The main objective of this research was to study the chemical composition, as well as the antioxidant, anti-inflammatory, and hemolytic activities of the aerial part of the essential oil of Chrysanthemum coronarium and its isolated oxygenated fraction.
The oxygenated fraction was isolated from the oil by column chromatography. Analyses by GC coupled with mass spectrometry allowed for the characterization of these components. The antioxidant properties of the essential oil and its oxygenated fraction were evaluated using the DPPH and FRAP methods. The anti-inflammatory effect was characterized by the denaturation of proteins. In addition, the hemolytic impact was studied through a suspension of erythrocytes in human blood.
The essential oil studied was characterized by a composition dominated by oxygenated monoterpenes (39.3%), followed by hydrocarbon sesquiterpenes (21.1%) and oxygenated sesquiterpenes (16.5%). The oxygenated fraction consisted mainly of perillyl alcohol (14.3%) and lyratyl acetate (14.5%). The results of the DPPH and FRAP tests showed significant antioxidant activity of the essential oil (IC50 = 3 ml/L) and the oxygenated fraction (IC50 = 4.4 ml/L), surpassing that of the synthetic antioxidant BHT. Additionally, the oxygenated fraction exhibited perfect anti-inflammatory activity, compared to essential oil and diclofenac sodium. The toxicity assessment on human erythrocytes shows that both essential oil and oxygenated fraction of Chrysanthemum coronarium have a very low hemolysis rate even at high concentrations.
Tests on the essential oil and its oxygenated fraction have revealed promising properties. These results suggest promising opportunities for the development of new agents in the pharmaceutical field.

Nuclear factor κB (NF-κB) contributes to inflammation and cytokine storm in COVID-19 patients. The NF-κB activity is inhibited by p100 protein binding and downregulated using glutathione. Gamma Glutamyl Cysteine (GGC) is also a glutathione precursor. In this study, we aim to compare GGC binding stability to p100 and NF-κB to elucidate its effectiveness in reducing NF-κB activity. Tertiary structures were prepared by molecular graphics programs. Free binding energies of complexes were compared using molecular dynamics simulations and Auto Dock. Simulation outputs were analyzed using CMView. Analyzing RMSD values indicated quite stable binding of GGC to p100. Also, RMSD of the NF-κB-R complex was slightly lower than that of NF-κB at the simulation end. The Rg indicated less dense packing of p100 and its slight structural changes in the presence of GGC. Analyzing amino acid fluctuations using RMSF revealed an important role of Leu 450 and Phe 451 in interactions of p100 with GGC. Free binding energies of p100-GGC and NF-κB-GGC complexes were -6.972 kJ/mol and 25.857 kJ/mol respectively. These results showed that GGC attached stably to p100, whereas it did not bind to NF-κB. Contact maps of complexes and corresponding native structures were compared and slight structural changes were observed. The Interaction of P450 2C9 enzyme with GGC was more stable than that with Flurbiprophen. According to the findings, we suggest an antiviral effect for GGC through its stable binding to p100 and enhancing p100 activity for NF-κB inhibition. These results are useful for drug design against COVID-19.

Lipases are one of the most essential enzymes in biological systems and industries. The use of free lipase is not cost-effective because of its low half-life. Enzyme immobilization on different supports leads to enhanced stability, reusability, ease of product separation, and low cost. Lipases have been immobilized on various organic and inorganic supports, but recently, nanoparticles have been used because of their high surface-to-volume unit. The present study aims to green synthesize gold nanoparticles, covalently immobilize lipase, and compare the biochemical characteristics of free and immobilized enzymes. After synthesis of the nanoparticles and immobilization of lipase, nanoparticles and enzyme immobilization were characterized and confirmed by SEM microscopy, Raman spectroscopy, and DLS. The biochemical characteristics, such as optimal pH and temperature, thermal stability, and storage stability of free and immobilized enzymes, were then determined. The SEM results showed that the diameter of the synthesized nanoparticles was less than 50 nm. The Raman diagram of immobilized lipase showed two characterized peaks at 1468.44 cm-1 and 1639.61 cm-1 wavelength, confirming the immobilization process. Toward the free enzyme, the optimum pH of the immobilized enzyme shifted 0.5 units to the acidic range, whereas the optimum temperature did not change. Immobilized lipase showed higher thermal stability at 55 and 60 °C. Storage stability of the immobilized enzyme increased compared with the free enzyme. The immobilized enzyme could be used 10 times under optimum conditions. It appears that the immobilized lipase has improved characteristics for application in different industries.

The survival rate for oral tongue squamous cell carcinoma (OTSCC) is the lowest compared to other types of carcinomas in the oral cavity. This study aims to employ novel and robust methodologies based on bioinformatics techniques to identify differentially expressed genes in OTSCC tissues compared to normal tongue samples to shed light on the underlying causes of OTSCC. The dataset GSE13601 was obtained from the GEO, and the OPLS-DA method was applied to identify genes differentially expressed in OTSCC tissues compared to the normal healthy oral mucosa. A protein interaction map (PIM) was constructed, and hubs were identified. Survival analysis was performed to identify prognostic hub genes. The expression levels of the identified prognostic markers were evaluated at both mRNA and protein levels. Furthermore, bioinformatics web tools were used to perform pathway and GO annotation analyses. The study revealed 154 genes differentially expressed in OTSCC, with a statistically significant p<0.001 and a |Log2 fold change |>0.585. EIF2S1, EGF, NME1, NEDD8, EIF4A1, TOP1, and PSMA4 were found to have significant prognostic roles in OTSCC. The expression levels of all the identified prognostic markers were confirmed in HNSCC at the mRNA level and further validated the up-regulation of NME1, TOP1, and PSMA4 in HNSCC using immunohistochemical analysis. The FOXM1 was identified as the most important regulator of the hubs, while CDK2 was found to be the protein kinase acting on the transcription factors. The proteasome pathway and the regulation of ubiquitin-protein ligase activity were significantly enriched in OTSCC. This study provides valuable insights into the pathogenesis of OTSCC and may assist in improving the prognosis of OTSCC patients.

In this study, due to the importance of cholera as a water-borne infection, a new and appropriate multi-epitope polypeptide was designed against Vibrio cholerae O1 biovar ElTor using the reverse vaccinology method and immunoinformatic implements.

After identification of all ORFs of chromosome 1 bacterium, their outer membrane and secretory proteins were determined. Then, by removing the signal peptide and transmembrane domain, non-toxic, non-allergenic, and antigenic proteins were selected from the proteins of the previous step. Finally, high-score epitopes of the final antigenic proteins were identified using several specific software. To design the multi-epitope polypeptide, selected epitopes, and an appropriate adjuvant were connected using a flexible linker.

To validate the biochemical properties of the designed polypeptide, we implemented a range of servers to evaluate the biochemical and physicochemical properties of the designed polypeptide. Subsequently, we performed a molecular binding study to investigate the interaction of the designed polypeptide with the MHC I and MHC II molecules. The designed polypeptide contained 277 amino acids with a half-life of approximately 30 hours in mammalian cells. The results confirmed that this designed polypeptide not only has sufficient antigenic properties without toxicity and allergenicity but also has a good affinity for binding to MHC molecules.

After synthesis and appropriate immunological tests, the designed polypeptide can be considered as a new candidate vaccine against Vibrio cholera to prevent the spread of infection.