Iranian Journal of Biotechnology
Volume:19 Issue: 3, Summer 2021

Polyhydroxybutyrate is a biodegradable plastic produced by some bacteria and can completely be replaced with petroleum based non-degradable plastics. This study was done to isolate and identify one local strain with a high-production ability for industrial purposes. The sampling from petrochemical wastewater was done. The existence of polyhydroxybutyrate in isolates was studied with Sudan Black staining. Using the Sudan Black B plate assay method and estimating produced PHB amount, the most potent isolate was chosen. This isolate was distinguished by morphological and biochemical methods and determining 16S rRNA gene sequencing. The final confirmation of polyhydroxybutyrate synthesis was done by FTIR and 1H NMR. To increase more production of polyhydroxybutyrate, the effect of different factors including carbon, nitrogen, pH, and temperature were assessed. Six bacterial isolates producing polyhydroxybutyrate were separated, which among them, one new strain of Bacillus megaterium named saba.zh was selected as better isolation. 16S rRNA nucleotide sequence of bacterium was assigned accession number: MN519999 in the NCBI database. The optimal conditions to increase the production of polyhydroxybutyrate, are using glucose as a carbon source, ammonium sulfate as the nitrogen source, in the condition with having pH 7 and temperature 30 °C. After optimizing, the production of PHB increased from 56.51% to 85.41%. This research indicated that Bacillus megaterium saba.zh, due to better polymer yield, is a potent PHB producer which can be used for PHB industrial production.

Antibiotic-resistant bacteria are a major threat to global health. Older antibiotics have become more or less ineffective as a result of widespread microbial resistance and an urgent need has emerged for the development of new antimicrobial strategies. Acidocin 4356 is a novel antimicrobial bacteriocin peptide produced by Lactobacillus acidophilus ATCC 4356 and capable of confronting the Pseudomonas aeruginosa ATCC 27853 infection challenges. According to our previous studies, the production of Acidocin 4356 is in parallel with cellular biomass production.

Given the costly production of Acidocin 4356, the development of a beneficial approach for increasing productivity of the cellular biomass has been targeted in the lab-scale fermenter for scale-up production of this bacteriocin. Therefore, in this study, we developed an inexpensive optimal culture medium based on the whey feedstock, evaluating this medium for scaling-up of the bacteriocin production from flask to fermenter.

In the first step, the optimization of the process parameters and medium components was carried out using the Plackett-Burman (PB) design and Response surface methodology (RSM) in flask culture. After optimization of the medium, bacteriocin production in the optimum culture medium was compared with de Man, Rogosa and Sharpe (MRS) medium by analyzing the intensity of the peptide band. Intensity analysis has been conducted on the PAGE band of the peptide using Image J software. Finally, the scale- up of bacteriocin production in the optimum culture medium was evaluated by batch fermentation in a 3-liter fermenter.

In this study, a medium containing whey (40 g.L-1) and sodium acetate (5 g.L-1) was used as basal medium, and the effect of other factors were then evaluated. According to the PB design, three factors of peptone concentration, yeast extract concentrations and cultivation temperature were selected as the most effective factors which improve the growth of L. acidophilus. The condition providing the highest growth capacity for bacteriocin production were predicted based on the results of RSM as following: temperature 40 ° C, yeast (4 g.L-1), and peptone (8 g.L-1). Finally, the dry cell weight was obtained after incubation for 12 h as 2.25 g.L-1. Comparison of cell growth and bacteriocin production between MRS medium and optimized medium confirmed the efficacy of these optimal conditions for the cost-effective production of Acidocin 4356 in the flask. Besides, the scale- up of bacteriocin production has made under optimal condition in the 3-L fermenter.

In this study, for the first time, scale- up production of Acidocin 4356 was presented by using a low-cost method based on whey feedstock to tackle P. aeruginosa infections.

Microorganisms play an important role in reducing harmful substances in flue-cured tobacco. Numerous studies have been conducted to degrade nicotine by microorganisms. The present research deals with the isolation of a potent bacterial strain able to efficiently degrade nicotine and tobacco-specific nitrosamines (TSNAs) in flue-cured tobacco. Bacterial strain J54, capable of efficiently degrading nicotine and tobacco-specific nitrosamines (TSNAs), was isolated from tobacco leaves and identified. The strain J54 can use nicotine as the sole carbon and nitrogen source and could effectively degrade nicotine while growing in a nicotine isolation medium (NIM) medium. Compared with the control (CK), the total TSNAs content in the tobacco flue-cured eaves after being sprayed with a solution of the J54 strain was found to decrease by 26.22%. Therein, the degradation rates of 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK), N’-nitrosonornicotine (NNN), N’-nitrosoanatabine (NAT), and N′-nitrosoanabasine (NAB) were 24.01%, 26.27%, 28.6%, and 1.83%, respectively. Bacterial strain J54, was isolated from tobacco leaves and identified as a bacterium, which is similar to Bacillus altitudinis based on its morphological and biochemical characteristics and by phylogenetic analysis based on 16S rRNA gene sequences. To our knowledge, this is the first report of the isolation and characterization of a Bacillus sp. strain that can efficiently degrade nicotine and TSNAs. The findings pave the way for the application of new biotechnologies for the degradation of nicotine and TSNAs by microorganisms.

Proteases play an important role in food, leather, detergent, and medical technologies. In the current study, an alkaliphilic solvent-stable thermotolerant metalloprotease was isolated from Bacillus sp. DEM05. For culture optimization, carbon, and nitrogen sources as well as incubation temperature, pH, and time were examined. Herein the highest outcome for bacterial growth and protease production was obtained after 72 h incubation (pH 7) at 37 °C. DEM05 protease was successfully purified and the specific activity of the protease was 1075 U.mg-1. The purity of the enzyme was verified by SDS-PAGE electrophoresis as a single band of 30 kDa. The optimal activity of the enzyme was at pH 10 and 50 °C. H2O2, SDS, Triton X-100, Zn2+, Co2+, and Cu2+ could increase the protease activity. EDTA inhibited the protease activity, revealed that it can be classified as a metalloprotease. The enzyme was compatible with the water-miscible and water-immiscible organic solvents and proteolyzed several substrates, implying the wide substrate specificity. The results brought convincing evidence that DEM05 protease could be recruited as a novel prevailing protease that can be earmarked on industrial and medical technologies.

Chronic wounds contribute to the majority of clinical cases, associated with significant morbidity, and place a massive financial burden on healthcare systems. Thus, various bandage mats have been designed to facilitate wound healing in clinical applications. Polylactic acid (PLA) nanofibers, as suitable drug carriers, are highly desirable to prepare a controlled environment for wound healing in dressing tissue. Zinc oxide (ZnO) nanoparticles as an effective antibacterial agent for wound treatment prevent bacterial invasion and wound infection.

In this project, for the first time, a new (PLA)/(ZnO) nanofibrous nanocomposite loaded with tranexamic acid (TXA) has been introduced as a useable dressing in wound healing. Furthermore, the antibacterial properties, coagulant assay, and wound healing assays of nanocomposite are evaluated.

PLA/ZnO nanofibrous nanocomposites were loaded with tranexamic acid fabricated by electrospinning method at distinct concentrations. The prepared structure was characterized using field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FTIR). Further, antimicrobial properties of tissue were investigated against Escherichia coli and Staphylococcus aureus bacteria. Also, the coagulation assays, in vitro cytotoxicity, and in vivo skin wound healing model in mice were evaluated.

Morphological analysis of the prepared nanofibrous nanocomposites showed uniform bead-free nanofibers with an average size of 90 nm diameter. The structure exhibited proper antibacterial activities against Escherichia coli and Staphylococcus aureus bacteria, and a good blood clotting effect. In vitro cytotoxicity assay of the structure approved that this mat has no cytotoxic effect on human dermal fibroblast cells. In vivo wound healing examination in mice observed over 7 and 14 days showed a faster rate of wound healing over the control.

Novel electrospun PLA/ZnO nanocomposites loaded with tranexamic acid can be prepared by the electrospinning method and used for wound treatment. This structure displayed the effect of two agents in wound healing, including antibacterial nanoparticles and antifibrinolytic drugs to accelerate wound closure.

Gene expression profiling and prediction of drug responses based on the molecular signature indicate new molecular biomarkers which help to find the most effective drugs according to the tumor characteristics. In this study two independent datasets, GSE28646 and GSE15372 were subjected to meta-analysis based on Affymetrix microarrays. In-silico methods were used to determine differentially expressed genes (DEGs) in the previously reported sensitive and resistant A2780 cell lines to Cisplatin. Gene Fuzzy Scoring (GFS) and Principle Component Analysis (PCA) were then used to eliminate batch effects and reduce data dimension, respectively. Moreover, SVM method was performed to classify sensitive and resistant data samples. Furthermore, Wilcoxon Rank sum test was performed to determine DEGs. Following the selection of drug resistance markers, several networks including transcription factor-target regulatory network and miRNA-target network were constructed and Differential correlation analysis was performed on these networks. The trained SVM successfully classified sensitive and resistant data samples. Moreover, Performing DiffCorr analysis on the sensitive and resistant samples resulted in detection of 27 and 25 significant (with correlation ≥|0.9|) pairs of genes that respectively correspond to newly constructed correlations and loss of correlations in the resistant samples. Our results indicated the functional genes and networks in Cisplatin resistance of ovarian cancer cells and support the importance of differential expression studies in ovarian cancer chemotherapeutic agent responsiveness.

Superoxide dismutases (SODs) are categorized as antioxidant enzymes that are involved in many processes such as stress signalling responses and cell protection against free radical species. The primary function of SOD is the removal of produced radical species like superoxide ions in different physiological processes. There are various isozymes of SODs which are classified according to the metal cofactor in their active sites into four general types of Fe-SOD, Mn-SOD, Cu/Zn-SOD and Ni-SOD. Among metal nanoparticles, gold nanoparticles (AuNPs) are useful for biological purposes as sensing probe for determining critical analysis based on surface plasmon resonance and colorimetric method. In this study, the human Cu-Zn SOD expressed, purified, and its interaction with AuNPs based on a new colorimetric method was investigated.

In this approach, a colorimetric detection method for SOD activity was developed based on the carboxylic stabilized AuNPs.

The Ni-NTA Sepharose affinity column was performed for the purification process of enzyme. Following SOD purification, the enzyme activity in presence of AuNPs due to the possible etching in the presence of free radicals which are produced by riboflavin, methionine, Na2CO3 and potassium phosphate buffer, have been performed. In addition, Fluorescence spectroscopy analysis toward SOD and gold nanoparticle were performed.

Superoxide radicals generated from the enzymatic reaction would preferentially etch AuNPs and resulted in remarkable changes of localized surface plasmon resonance of AuNPs, which is reduced in the presence of SOD. Under the optimized experimental conditions assay (pH~7.8 and 25 ˚C), better selectivity and sensitivity toward SOD activity was shown.

In this context, an indirect new colorimetric method for determining of SOD activity based on gold nanoparticles (AuNPs) was evaluated. According to the presented result, it may be concluded that by scavenging of free superoxide radicals in the presence of SOD, the amount of AuNP absorbance can be replenished.

Platycodon grandiflorus has long been used in Northeast Asia as a food and folk medicine to treat various diseases. The intense blue color of P. grandiflorus corolla is its characteristic feature. By comparing deep transcriptomic data of P. grandiflorus and its white cultivar, we intended to elucidate the molecular mechanisms concerning the biosynthesis of anthocyanins in this plant. We sampled blue mature flowers (PgB) and yellow young buds (PgY) of P. grandiflorus. Meanwhile, mature flowers (PgW) of P. grandiflorus white cultivar were also collected for RNA extraction and next-generation sequencing. After high-throughput sequencing, Trinity software was applied for de novo assembly and the resultant 49934 unigenes were subjected for expression analysis and annotation against NR, KEGG, UniProt, and Pfam databases. In all, 32.77 Gb raw data were generated and the gene expression profile for the flowers of P. grandiflorus was constructed. Pathway enrichment analysis demonstrated that genes involved in flavone and flavonol biosynthesis were differently expressed. The extremely low expression of flavonoid-3’,5’-hydroxylase in PgY and PgW was regarded as the reason for the formation of its white cultivar. Our findings provided useful information for further studies into the biosynthetic mechanism of anthocyanins.

Drought stress is a serious threat that limit maize growth and production. The assessment tolerance level of maize by measuring changes in the main biochemical and physiological indicators under drought stress. We performed a genome-wide association analysis of biochemical and physiological indicators using an elite association panel. The results revealed that eight significant SNPs (p<0.05/N) located in eight genes that are distributed on different chromosomes were associated with drought resistance indices under drought stress. Among these genes, four genes were linked via the associated SNPs with drought-resistance indices of the malondialdehyde activity (MDA), three genes were linked with drought resistance indexes of the superoxide dismutase activity (SOD), and one gene was linked with drought resistance indexes of relative conductivity (REC). The candidate genes functioned as transcription factors, enzymes, and transporters, which included trehalase, the AP2/EREB160 transcription factor, and glutathione S-transferase and also encoded a gene of unknown function. These genes may be directly or indirectly involved in drought resistance. The expression levels of ZmEREB160 responded to ABA and drought stress. These results provided good information to understand the genetic basis of variation in drought resistance indices of biochemical and physiological indicators during drought stress.

Sclerotinia sclerotiorum (Lib.) de Bary cause a deleterious disease on sunflower plants. Oxalic acid is the main pathogenicity factor of S. sclerotiorum. Two dimensional gel electrophoresis and mass spectrometry have been used in several studies to investigate molecular changes that occur in the plants in response to S. sclerotiorum infection. Comparing responses of resistant and susceptible lines upon pathogen infection provided novel information regarding defense mechanisms against this necrotrophic pathogen. The present study reports proteome changes of partially resistant and susceptible sunflower lines under pathogen’s culture filtrate treatment, resulting in the characterization of up- and down- regulated proteins. Sunflower partially resistant and susceptible lines with two true leaves were exposed to fungus culture filtrate. The stems of treated and untreated plants were sampled at 24, 48 and 72 hours after treatment for two-dimensional electrophoresis. Twenty spots showed more than 1.5-fold change in abundance were subjected to MALDI/TOF-TOF MS for further analysis. The identified proteins were categorized into several classes including carbohydrate and energy metabolism (25%), cellular metabolic process (15%), stress response (15%), plant cell wall biogenesis (10%), photosynthesis (10%), protein metabolism (10%), unknown function (10%) and redox homeostasis (5%). Our proteomic investigation demonstrates an increase in the expression of proteins only in partially resistant line, such as proteins involved in carbohydrate metabolism and plant defense responses (malate dehydrogenase and peroxidase), metabolic process (adenosine kinase), regulating cell redox homeostasis (disulfide isomerase) and lignin biosynthetic process (laccase). Moreover, the expression of pyrroline-5-carboxylate reductase, involved in proline biosynthesis, was significantly changed in both sunflower lines in response to pathogen culture filtrate. Proteins which were only up-regulated in the partially resistant lines might have a significant role in mediating the defense against Sclerotinia and could be considered for enhancing resistance against this devastating pathogen.