Modares Journal of Biotechnology

Abstract The number of microbial cells on the planet is much larger than the stars we know in the galaxies. However, the microbial diversity and their ecological network remain unknown, they have key roles on the Earth's ecosystems. Omics technologies such as metagenomics provide tools for recognizing a large part of these cryptic forms of life accurately, which are much higher than the uncultivated majority. One example is the diversity of the Vampyrellids from protista and micro-eukaryotes. Using meta-omics technologies, it found that the diversity within this one group equals that of the entire kingdom of fungi, and they are found in all corners of nature, from the oceans to terrestrial soils. It is noticeable that they are only one of the seven protista groups. In this article, in addition to introducing Omics technologies, some of big relevant projects and their results have also been discussed covering all of the Earth's environment. Metagenomics is the direct sequencing and characterization of genes and genomes present in complex microbial ecosystems (e.g. metagenomes). Viromics is the research of viral metagenome. In metatranscriptomics the mRNA is being analyzed which is due to its notoriously labile nature in environmental samples, its conservation and analyzing are the main challenges in this omics. Identification and measurement of various proteins that can directly measure microbial activity is performed in metaproteomics. Environmental metabolomics includes the study of low molecular weight metabolites generated from interactions between microorganisms, such as small eukaryotes, plants, animals, predators, abiotic stresses, and other stimulants.

Abstract Among the sources of oils (vegetable, animal, microorganism), microbial oil has attracted the attention of many researchers. Oily microorganisms are able to accumulate 20 to 80% of lipids in each dry biomass. Among various microorganisms (bacterias, microalgae, fungal species including yeasts), some yeasts are considered to be the superior source of oil production. Yarrowia lipolytica is an excellent example of oily microorganisms with high fat production efficiency. By using cheap, native and available pulp as a production medium, the cost of oil produced by yeasts can be reduced. The microbial oil produced is used for medicinal, food and cosmetic purposes. In this study, the pleomorphism of Yarrowia lipolytica (ATCC 18942) was examined microscopically in different culture media. After culturing the yeast in media containing olive, sesame and sunflower pulp, in semi-open culture conditions, the fatty acids produced were analyzed using GC-MS and FTIR techniques. After reviewing the results, the medium containing olive pulp was selected and the microbial lipid produced in this medium was extracted. Then dry weight of biomass and microbial fat were measured. The results showed that the fatty acids extracted from the medium containing olive oli cake included oleic acid, palmitic acid, linoleic acid and stearic acid, which had the best production of fatty acids among the pulp. The content of microbial fat and dry weight were 4.07 and 7.83 g/l, respectively, and microbial fat production efficiency was 51.97%.

Abstract In this article, the interaction between lysozyme and CdTe nanoparticles was investigated by UV-Vis spectroscopy, fluorescence, thermal stability, kinetics, and circular dichroism (CD) spectroscopic methods at pH 7.25. It was proved that the fluorescence quenching of lysozyme by CdTe NPs was mainly a result of the formation of the CdTe–lysozyme complex. By the fluorescence quenching results, the Stern–Volmer quenching constant (K_SV), binding constant (Ka), and binding sites (n) were calculated. Under pH 7.25 conditions, the level of binding constant is determined to be 2.33×10³ from fluorescence data. The hydrogen bond or van der Waals force is involved in the binding process. The blue shift of the fluorescence spectral peak of protein after the addition of CdTe nanoparticles reveals that the microenvironments around tryptophan residues are disturbed by CdTe nanoparticles. The effect of CdTe NPs on the conformation of lysozyme has been analyzed by means of UV-Vis spectra and CD spectra, which provided evidence that the secondary structure of lysozyme has been changed by the interaction of CdTe NPs with lysozyme.

Abstract Aim: Multiple sclerosis is important in Iran because of its high prevalence and low age of onset. It exerts a large burden on affected people and the health care system. Studies have shown that the genetic content of humans has a critical role in MS. The histocompatibility loci which their products present the foreign antigenic peptides for detection by lymphocytes are of MS associated genetic elements. In this study, the association of HLA-DQB1*03 with MS was studied in Tehran, using a PCR-based system.
Methods: In this case-control study, a total of 367 blood samples were collected from 172 patients and 195 healthy people. Both groups were similar in age and gender. Blood DNA was extracted, and PCR technique was used to identify the presence of the allele.
Results: In this study, the HLA-DQB1*03 allele in men was significantly higher than that of women (p = 0.002). Also, the allele was less frequent in patients than in healthy subjects (53% versus 67%), and this difference is significant (p = 0.02).
Conclusions: The DQB1*03 allele is significantly lower in patients with MS than in healthy people, and this relationship is more pronounced in male subjects. Therefore, it seems that this allele plays a protective role against MS disease.

Abstract Poly-γ-glutamic acid (γ-PGA) is a beneficial, biocompatible, and biodegradable biopolymer. These properties have been led to the development of the use of this compound in various industries such as bio-medicine, biopharmaceutical, biotechnology, and tissue engineering. The limitation of the industrial development of γ-PGA is the high cost of its production. To reduce γ-PGA production costs, various strategies are used, such as culture medium optimization using inexpensive compounds, the development of efficient cultivation processes of batch and fed-batch. In this research, first, an efficient batch culture medium was developed to produce γ-PGA of Bacillus licheniformis ATCC 9945^a. Then, the γ-PGA production increased by the pulsed feeding method and its optimization. By optimal culture medium development, the production of this product in batch culture was increased from 11 g/L to 47 g/L. Then, using the optimized pulsed feeding strategy of citrate (γ-PGA precursor), γ-PGA production was increased to 59.5 g/L, which is one of the highest production values reported with this strain. To optimize two-pulse feeding, the effect of feeding times, stock citrate solution concentration, and time of calcium and manganese solutions addition on γ-PGA production were investigated and optimized. Finally, FTIR confirmed the chemical structure of poly gamma glutamic acid, and the study of γ-PGA morphological properties with SEM showed a nanostructure ideal for biological applications.

Abstract Chemotherapy is one of the methods used in the treatment of cancer. Not being targeted has many side effects for the patient. The use of nano-carriers, including nano-liposomes, is a very effective way to target chemotherapy. In this study, a liposomal system containing doxorubicin was designed and evaluated for its effect on lung cancer cells.
In this in vitro study, two liposomal systems were prepared by the method of thin-film hydration and using different concentrations of phosphatidylcholine and cholesterol. Doxorubicin was then loaded into the systems. Finally, one of the systems was selected based on the drug loading rate and drug release pattern. At the end, the selected drug delivery system in terms of particle size, zeta potential, liposomal vesicle appearance, and the interaction between the drug and the system was investigated.
The selected liposomal system contains doxorubicin with an encapsulation efficiency of 58.89%, size of 273 nm, dispersion index of 0.458 and zeta potential of -35.7 mv. Doxorubicin release from liposomes was controlled and no chemical interaction was observed between liposomes and referees. Liposomal vesicles are also spherical and have a smooth surface.
The results of this study show that nano-liposomes can be prepared with appropriate formulation containing doxorubicin using nanotechnology. Which has good physicochemical properties. Therefore, this liposomal system can be recommended for further cancer-related research.

Abstract Moonlight proteins are a subset of multifunctional proteins in which more than one independent or usually distinct function occurs in a single polypeptide chain. Analyzing the interactive networks of proteins in the cell makes it possible to understand how complex processes cause disease. With the help of systems biology, larger and more complex systems can be studied, and the molecular basis of several diseases can be considered. The proteins of the human organism that are moonlight are mostly involved in cancer, anemia, and neurodegeneration. In this work, we created a subnet according to the human PPI network, in which the nodes, the proteins that cause the three selected diseases, and the edges, are the connection of these proteins with each other. We measured the power of the indirect effects of non-disease mediators between the three disease groups and identified key disease-binding intermediate proteins. The results show the relationship between mediator role and centrality and between mediator role and functional properties of these proteins. We have shown that a protein that plays a key indirect mediator between two diseases is not necessarily a hub in the PPI network. Therefore, as hub proteins are considered, intermediate proteins should be considered. We have observed that the mediators between anemia and neurodegeneration diseases are functionally important in the cell. The mediator proteins suggested herein should be experimentally tested as hypothetical disease-related proteins.

Abstract Methyl tertiary-butyl ether (MTBE) One of the gasoline additives used to increase octane and reduce greenhouse gas emissions, MTBE can enter the human blood flow through different ways including inhalation, oral and skin contact. Human carbonic anhydrase is one of the metalloenzymes that is found in almost all living organisms and has been extensively studied and many diseases are associated with carbonic anhydrase. In this study, the effect of MTBE proximity with human carbonic anhydrase II enzyme on enzyme activity was investigated by visible-ultraviolet spectroscopy and changes in enzyme Tm at different concentrations of MTBE were reported. In addition, the structural changes of the enzyme in the presence of MTBE were examined by intrinsic fluorescence spectroscopy. The results show that the enzyme activity in the presence of MTBE is inhibited by liner-complex mechanism. The results of intrinsic fluorescence spectroscopy of the enzyme show changes in the structure of the enzyme in the presence of MTBE. Also, following the binding of MTBE to the enzyme, the thermal stability of the enzyme is reduced and it becomes sensitive to temperature changes.

Abstract Background and Aim: Toxins produced by Clostridium botulinum are among the deadliest compounds known that cause botulism. Currently, the detection of BoNTs in food using bioassays on laboratory mice is a very sensitive method with a detection range of 7 to 20 pg.mL^-1. However, bioassay for mice is time consuming. This method is fast, highly specific, and sensitive to experiments on mice. The aim of this study was to use the modified Sandwich ELISA method to detect BoNT/B toxin.

Materials and Methods: Recombinant 370 amino acid protein was expressed from the carboxyl terminus of the binding moiety of BoNT / B toxin with a molecular weight of 45 kDa as antigen and purified by Ni-NTA affinity chromatography. IgG antibodies were isolated from mouse and rabbit sera byG protein affinity chromatography. The sensitivity and specificity of the method designed to detect recombinant BoNT/B-HcC antigen and botulinum toxin type B were evaluated.

Results: Purified rat and rabbit antibody concentrations were 3 and 4.5 mg / ml serum, respectively. The minimum concentrations of detectable protein were determined by indirect ELISA with purified mouse and rabbit antibodies at 475 and 118 pg. By optimizing the sandwich ELISA method, at least 30 ng of recombinant BoNT/B-HcC antigen and146 pg of highly specific BoNT/B were detected.

Conclusion: sandwich ELISA method can be used for accurate and sensitive identification of Clostridium botulinum toxin type B. It is necessary to evaluate the effectiveness of this method in the future to detect botulinum toxin in environmental and food samples.

Abstract In a marine environment, the biofilm formed on the submerged surfaces leads to fouling of larger organisms. This leads to many environmental and economic problems for the marine industries. Due to the harmful effects of chemical antifouling, the development of environmentally friendly anti-biofilm strategies can be an important step to control fouling.
Therefore, the present study was performed with the aim of isolation of biofilm-forming bacteria from Persian Gulf waters and investigating the antimicrobial effect of thymol against selected bacteria.82 bacterial were isolated and their ability to form biofilm was measured. Among these, 5 isolates were selected and identified using 16S rRNA sequences. The results showed that the 5 selected isolates belonged to the Proteobacteria (genus Vibrio, Kangiella and Psudoaltromonas). In the study of the antibacterial effect of thymol, K. spongicola (PH1) showed the highest sensitivity in disk diffusion method (with a growth inhibition zone diameter of 18 ± 0.57 mm). The minimum inhibitory concentration and minimum bactericidal concentration (at 31.5 and 62.5 μg /ml, respectively) were obtained against the same bacterium. The inhibitory thymol on biofilm formation and performed biofilm by Psudoaltromonas sp. (PH18) showed that thymol at concentrations sub-MIC is able to inhibit biofilm formation. The effect of thymol on the performed biofilm at concentrations higher than MIC is noticeable. Based on the results, due to the anti-biofilm activity of thymol against marine bacteria, its use as a natural compound in antifouling coatings can be suggested.

Abstract Reactive oxygen species (ROS) at low concentrations effectively regulates intracellular pathways such as gene expression. Whereas their high concentrations are involved in the pathogenesis of many diseases by causing oxidative stress and damaging vital macromolecules. Each cell is equipped with an antioxidant defense system to neutralize high levels of ROS. Peroxidase, as an essential antioxidant enzyme, catalyzes the oxidation of various substrates using hydrogen peroxide which is a reactive oxygen species. Since, the caffeine and theobromine are widely consumed daily in the world, and their concentrations affect the activity of many enzymes. Therefore, in the present study, the inhibitory effect of these methylxanthines on peroxidase activity has been examined. The peroxidase activity is measured by a spectrophotometer at 510 nm for 3 minutes with following absorption due to the oxidation of 4-aminoantipyrine in the presence and absence of caffeine and theobromine. In this study, it was observed that both compounds had an inhibitory effect on peroxidase activity. The values of IC₅₀ for theobromine and caffeine were obtained as 0.5 and 0.6 mmol, respectively. Moreover, the values of K_m and V_max showed that both inhibitors acted by an un-competitive mechanism of inhibition. Also, K_i values for theobromine and caffeine were calculated 0.03 and 0.08 mM, respectively. The values of K_i and IC₅₀ for theobromine was lower than those of caffeine indicating that theobromine has a higher inhibition strength and binding affinity to the enzyme-substrate complex. Therefore, it can be concluded that theobromine has a stronger inhibitory effect on peroxidase activity.

Abstract This study investigates the factors affecting the commercialization of products in medical biotechnology accelerators, it also demonstrates the priority of these factors. The research is applied and descriptive survey. It has been done in two phases, qualitative and quantitative. Based on the general purpose of this study, to provide a framework for the commercialization of products in medical biotechnology accelerators, we interviewed with informed experts. 62 sub-codes were obtained as effective factors in the commercialization of products in medical biotechnology accelerators, which were classified into 5 main dimensions including individual, organizational, industry and competition, institutional and product. These dimensions are presented as a framework. In the quantitative phase, the main dimensions as well as the sub-themes were ranked in the main dimension. Finally, the priority of the main dimensions was as follows: 1. Individual (personality, behavioral and mental characteristics of the mentor and manager) 2. Industry and competition (interaction with pharmaceutical companies as customers, investors, etc.) 3. Organizational (experience of startup teams, codified strategy, R&D, etc.) 4. Product (value added and high-tech) 5. Institutional (government is pragmatic to the country's slogans, interaction with government managers, etc.).