Iranian Journal of Biotechnology
Volume:19 Issue: 2, Spring 2021

Polyethylene (PE) is one of the most abundant plastic wastes which accumulates in marine and terrestrial environments. As microbial degradation has been a promising approach for the bioremediation of polluted environments, identification of the microbial community profile where these pollutants accumulate, has recently been in focus. We have investigated the taxonomic and functional characteristics of polyethylene- degrading microorganisms in a plastic waste recycling site in Tehran, Iran. We have analyzed and compared a 16S rRNA dataset from this study with 15 datasets from 4 diverse plastic and oil polluted habitats to identify and evaluate bacterial communities involved in bioremediation. Our findings reveal that Proteobacteria, Actinobacteria, Acidobacteria and Cloroflexi were the dominant phyla and Actinobacteria, Alphaproteobacteria, Gammaproteobacteria and Acidimicrobia were dominant classes in these samples. The most dominant Kegg Orthology associated with PE bioremediation in these samples are related to peroxidases, alcohol dehydrogenases, monooxygenases and dioxygenases. Long-term presence of contaminants in soil could lead to changes in bacterial phyla abundance, resulting in metabolic adaptations to optimize biological activity and waste management in a diverse group of bacteria.

The native sponges of Persian Gulf are unique species facing difficult climate conditions and environmental contamination. It is necessary to investigate these native sponges because global warming most probably destroyed many of these creatures. Therefore, the study of the microorganisms associated with sponges will introduce new bacterial strains with various industrial and environmental applications and, in this way, a part of the Persian Gulf biodiversity will be preserved for posterity. The aim of this study was the isolation and molecular identification of bacteria associated with the ability of biodegrading crude oil from the native sponges of the Persian Gulf. Also, optimization of crude oil biodegradation was done for one of the most efficient bacterial strains. Isolated species were compared in terms of E24 index and growth rate in a culture medium containing at least 2% of oil as the sole carbon source. Molecular identification was done for five bacterial strains. Using the Taguchi experimental design, the effects of 4 factors, namely, carbon source auxiliary, organic and inorganic nitrogen sources, salinity and pH, were evaluated at 3 levels. GC-Mass analysis was performed on the remaining oil in the culture medium.. In the initial screening of two native species of sponges, 22 bacterial strains were isolated which were capable of decomposing oil. Five bacterial strains showed the best results and were recorded in NCBI with access numbers KY283126, KY283128, KY285290, KY285289, and KY285288. Brevibacterium sp. (KY283128) showed the highest level of oil degradation (about 97%) and growth rate. The results showed that the optimal oil degradation occurs in the absence of carbon source auxiliary, at 0.5% of salinity, with NH4 Cl as the nitrogen source and at a pH of 6.5. This bacterial strain can be used for biodegradation in oil-contaminated areas and oil refineries. By isolating the oil degrading gene in this bacterial strain and cloning it in other bacterial strains, the efficiency of eliminating oil contamination can be increased.

Fingerprints can serve to identify individuals, but fingerprint quality may be deteriorated, even to the point of eliminating fingerprints, due to the external environment. Poor fingerprint quality cannot be effectively used to identify individuals; hence, the need for other methods. We investigated the utility of bacterial communities and the only microorganisms present in the sample to identify internal and external factors in individuals. Samples included eight participants’ fingerprints and their mobile phone surfaces. Bacterial DNA in the samples was sequenced using next-generation sequencing to target the V3– V4 region in the 16S ribosomal RNA gene. The QIIME program was used to perform a taxonomic assignment and alpha diversity and beta diversity analyses based on the sequence data. Until now, personal identification has only relied on microbial communities. However, this study identified microbial differences according to Korean mobile phones, fingertips, or gender, and confirmed the possibility of characterization of samples when it was difficult to identify individuals by the microbial community. The biodiversity and composition of individual bacterial communities were affected by internal and external environments. Bacteria from individuals and mobile phones were shared due to contact between mobile phone surfaces and fingertips. Of the eight Koreans, six of the fingertips and mobile phone samples matched each other for personal identification. This study confirmed that the bacteria from an individual could be matched with the contact object and could be used as forensic evidence. Such bacterial profiling of individuals may confer forensic evidence and serve as a basis for improving the accuracy of forensic verification.

Septoria tritici blotch (STB) caused by fungus Zymoseptoria tritici, is one of the important wheat (Triticum aestivum L.) diseases difficult to control because of the lack of wheat resistant cultivars. The use of biological control agents is one possible way for triggering host plant resistance to biotic and abiotic stresses. In this study, we examined the ability of Serendipita indica and Pseudomonas protegens CHA0-mCherry in inducing the local wheat cultivar Tajan resistance to STB. The interaction between biological control agents and the roots of wheat was evaluated. The experiment was conducted in a completely randomized design by three replicates. Spore suspension was supplied at concentrations of 107 and 109 for S. indica and bacteria isolate (CHA0-mCherry) respectively. Five treatments were applied including S. indica, CHA0-mCherry, S. indica and CHA0-mCherry co-inoculation, positive and negative control. Twentyone days after inoculation, the interaction between biological agents and plant roots were evaluated through morphological traits and qPCR. The plant resistance, disease severity, and the correlation between resistance and disease severity were assessed. Pycnidial variation and agronomic traits were also evaluated. Twenty-one days after inoculation, both biological agents clearly colonized all treated roots of all treatments except in control plants as demonstrated by qPCR analysis. Chlamydospores were observed in the S. indica-treated hosts with the CHA0-mCherry colonizing assessment showing 5×109 CFU g-1 in the root. The asexual phase of the fungal pathogen, pycnidial diameter, was reduced in S. indica treated plants more considerably than in the other treatments. There was a positive correlation between resistance and disease severity mean when calculated by Pearson’s correlation. There was a significant difference between the root length, fresh, and dry weight of root. Spore density was inversely correlated to resistance and disease severity, when compared with control, with CHA0-mCherry being the most effective in reducing the spore density. S. indica was the most effective in promoting root growth and stem biomass, when compared with control. Serendipita indica and Pseudomonas protegens CHA0-mCherry colonies showed a potential biological control activity and efficiently enhanced the plant resistance to Z. tritici in the treated wheat roots. The microbial biological control agents are very practical in crop protection against plant disease and can be very useful in sustainable agriculture. Abbreviations: PLSN: percentage of leave surface necrosis, DPI: day past inoculation, PLACL: percentage of leaf area covered by lesions, PPMLA: pycnidia per millimeter in leaf area.

As a thermoacidophilic microalga, Galdieria sulphuraria has a unique biological function. MicroRNA (miRNA) plays an important regulating role in plant various stress responses. In this study, we identified lots of conserved and novel miRNAs in G. sulphuraria (gsu-miRNAs), and predicted their putative targets for the first time. Conserved and novel gsu-miRNAs were predicted via deep sequencing on the Illumina HiSeq 4000 platform combined with bioinformatics analysis with a series of filtration criteria. Characterization of gsu-miRNAs and their targets were searched by different bioinformatics software. Some gsu-miRNAs were validated by Northern blot and RT-PCR analysis. MiRNA target gene function was predicted via GO and KEGG analysis. The interrelationship between gsu-miRNAs and target genes was constructed via Cytoscape networks analysis. A total of 134 gsu-miRNAs belonging to 124 MIRNA families were identified. Characterization analysis and experimental validation revealed that most of them were credible. A few miRNAs showed conservatism between G. sulphuraria and 20 representative plants. 1,589 putative miRNA targets were predicted. GO analysis revealed that the genes targeted by gsu-miRNAs involved in some important physiological processes of this alga, such as the ETC, and KEGG pathway analysis revealed that RNA transport and the PPP were predicted to be the two most enriched pathways. Cytoscape networks between miRNAs and target genes indicated their various interactions. Research on gsu-miRNAs, which act as key regulators during gene expression in G. sulphuraria will open a new avenue for further developing this thermoacidophilic alga at the post-transcriptional level.

Cranberry (Vaccinium macrocarpon Ait.) has high developmental prospects and great research value. Cranberry has a narrow genetic base, however, its morphological characteristics are not easily distinguishable. Besides, traditional breeding methods are limited, and breeding progress on cranberry cultivars has been slow. The objective of this study was to assess polymorphic EST-SSR markers developed from a cranberry fruit transcriptomic sequencing library to provide candidate EST-SSR sequences for future research on stress resistance breeding of cranberry. Thirteen cranberry accessions were used for EST-SSR analysis, and 16 accessions of other Vaccinium species were used to test primer transferability. Genomic DNA was extracted from young leaves of 6-yearold cranberry plants and subjected to PCR amplification. A binary matrix was established and analyzed in NTSYS-pc v.2.10e for calculation of the genetic similarity of cranberry cultivars and construction of a cluster dendrogram. A total of 47 stress-resistance-related primer pairs were designed, of which 7 pairs showed polymorphism. The average number of effective alleles was 1.844, and the average expected heterozygosity was 0.455. The average transfer rate was 63.39%. Genetic similarity coefficients ranged from 0.28 to 1.00, with an average of 0.76. UPGMA clustering divided the 13 cranberry accessions into four groups at a genetic similarity of 0.74. The seven polymorphic EST-SSR markers were able to reveal genetic relationships among 13 cranberry accessions and can be used for future research on stress resistance breeding of cranberry.

Nanomaterials, e.g.carbon nanotubes (CNTs), have broad usage in medicine for diagnosis, treatment, and drug delivery. Prior to the widespread use of CNTs, any potential toxicity issues must be considered. Apoptosis is an important issue in toxicological studies, and tumor necrosis factor (TNF) family members execute crucial roles in apoptosis and inflammation. We examined the survival of Jurkat cells under the influence of single-walled CNTs (SWCNTs) and multiwalled CNTs (MWCNTs) as well as their impacts on the mRNA levels of TNF family transcripts in Jurkat cells and rats. To evaluate the toxicity or safety of a specific concentration and form of CNT on the expression of one of the gene families of the apoptotic pathway. Jurkat cells were exposed to SWCNTs and MWCNTs in carboxylated form (SWCNTS -COOH and MWCNTs-COOH). MTT assay assessed the cell survival, and using qRT-PCR, the expression levels of TNF, CD40LG, TNFSF10, TNFSF8, CD40, TNFRSF10A, TNFRSF10B, TNFRSF11B, TNFRSF1A, TNFRSF21, TNFRSF25, and TNFRSF9 were examined. The housekeeping genes β-actin and glyceraldehyde 3-phosphate dehydrogenase was utilized for normalization. We also evaluated the expression levels of TNF and TNFRSF10A in rats in vivo 30 and 60 days after being injected with CNTs. After 72 h of carboxylated CNTs at 100 µg. mL-1, no significant change was observed in the survival rate of treated Jurkat cells. The expression of two genes (TNF and TNFRSF10A) changed significantly. Examining the expression profiles of these two genes in rats demonstrated an insignificant change in the expression of any of these genes after 30 and 60 days. The qRT-PCR analysis exhibited the elevated levels of TNF and TNFRSF10A mRNA in the CNT-treated cells, while expression of other TNF family members did not significantly differ from control (untreated) Jurkat cells. There was also no significant change in the gene expression levels of TNF and TNFRSF10A in CNT-treated rats after 30 and 60 days. Administration of SWCNTs-COOH and MWCNTs-COOH could result in the up-regulation of TNF and TNFRSF10A but did not initiate apoptosis in Jurkat cells. Carboxylated SWCNTs showed more potent activity than MWCNTs in activating TNF gene expression and probably trigger cell death through external apoptotic pathways.

Hemophilia A is an X-linked bleeding disorder resulting in a deficiency of plasma clotting factor VIII and caused by mutations in the FVIII gene (F8 gene). MicroRNAs (miRNAs) in body fluids are promising biomarker candidates for Hemophilia A, due to their stability in body fluids and accessibility by non- or minimally-invasive procedures. Therefore; Advances in miRNA analysis methods resulted in a wide range of publications on miRNAs as putative biomarkers.

Here we tried to scan the F8 gene region to predict a novel miRNA and identify it as a regulator of the F8 gene.

To this aim, the ability to express novel miRNAs in F8 locus was assessed via reliable bioinformatics databases such as SSCprofiler, RNAfold, miREval, FOMmiR, MaturBayes, miRFIND, UCSC genome browser, Deep Sequencing, and miRBase.

Data analysis from the relevant databases offers one stem-loop structure that is predicted to express a novel miRNA.

The diagnosis of Hemophilia A with the help of these types of biomarkers is a non-invasive procedure that has been demonstrated to have a significant role in the early diagnosis of the disease. Hopefully, the proposed candidate sequence will be confirmed in vitro and become a non-invasive biomarker in the near future.

Effective treatment of acute myeloid leukemia (AML) is still controversial, therefore; a comprehensive understanding regarding the impaired cellular signaling pathways in AML can be useful in designing new therapeutic approaches. Among signaling pathways involved in AML, the mammalian target of rapamycin (mTOR) signaling pathway is of particular importance. While dysregulation of mTOR signaling has been reported in a wide range of patients with AML, but most studies have focused on mTOR downstream targets, and mTOR upstream targets have been overlooked.

In this study, expression of mTOR genes and three upstream targets (5' adenosine monophosphate-activated protein kinase (AMPK, adiponectin, and sestrin 2) involved in mTOR signaling was investigated.

In this study, expression of mTOR, AMPK, sestrin 2, and adiponectin genes in 60 patients with AML were evaluated compared to those of 30 healthy individuals as controls using the Real-Time polymerase chain reaction (Real-Time RT-PCR) method.

According to the results, there was a significant difference in the expression of all the studied genes in patients in comparison to the normal control group (P <0.05). Expression of the mTOR gene was increased, while expression of AMPK, sestrin 2, and adiponectin genes was decreased in the patients with AML. Mean expression of the genes (2-ΔCt) (AMPK, sestrin 2, adiponectin, and mTOR) was equal to 7.9, 3.2, 3.74, and 1.49 for controls and 6, 2.1, 2.83, and 2.64 for patients with AML, respectively.

Given the decreased expression levels of sestrin 2, adiponectin, and AMPK genes as tumor inhibitors and the increased expression level of the mTOR gene as an oncogene in the patients with AML in our study, it is thought that disruption of this pathway may be involved in leukemogenesis and can be considered as an effective factor in the progression of cancer.

The unique expression pattern of prostate stem cell antigen (PSCA) in a number of prevalent neoplasms has made the antigen a great target for cancer researches, and many clinical methods have been developed based on the application of this tumor marker. Hence, optimal PSCA laboratory production can be considered a hallmark for many researchers.

An analytical study was designed to improve the quality and quantity of PSCA production.

The effects of different compositions of lysis buffers and some ultrasound durations were assessed by calculation of the protein recovery followed by PSCA specific blotting experiments. Then, based on the results of the webbased characterization, interference removal, followed by re-solubilization of the protein in various buffers, was designed, applied, and assessed.

Since the selection of an appropriate methodology depends merely on the research purposes, we tried to discuss the pros and cons of the investigated methods according to the hydrophobic nature of PSCA as well as its dramatic tendency to aggregate in the form of inclusion bodies in the expression hosts.

We introduced a newly designed method to fit the delicate immunological surveys and overcome some limiting factors in PSCA production.

Atrazine (ATZ) is a triazine herbicide that is widely used in agriculture and has been detected in surface and underground water. Recently, laboratory and epidemiological research have found that the bioaccumulation of ATZ in the environment leads to biotoxicity in the human immune and endocrine systems and results in tumor development. To investigate the effects of ATZ exposure on epithelial ovarian cancer (EOC) cells and elucidate the potential mechanisms governing these effects. The human EOC cell lines Skov3 and A2780 were used in this study to explore the effects and mechanisms of ATZ exposure on EOC. The mouse embryonic osteoblastic precursor MC3T3-E1 cells served as the control cells to determine the effects of ATZ on cancer cell lines. After exposure to ATZ, the MTT assay, flow cytometry, the colony formation assay, immunohistochemical staining, the cell scratch assay, and the Transwell assay were used to evaluate the proliferative activity, invasion, and migration capabilities of EOC cell lines. Moreover, flow cytometry was also applied to detect the level of reactive oxygen species (ROS) in these two EOC cell lines, as well as the MC3T3-E1 cells. To further illustrate the underlying mechanisms governing the effect of ATZ on EOC, real-time PCR and Western blotting were employed to assess the transcription and the expression level of Stat3 signaling pathway-related genes in Skov3 and MC3T3-E1 cells. The results showed that following ATZ treatment, the cell proliferation, migration, and invasion potencies of Skov3 and A2780 cells were increased compared to those of the control group. Meanwhile, the ROS levels of EOC and MC3T3-E1 cells were notably elevated after ATZ treatment. In Skov3 cells, the expression levels of p53 and p21 were downregulated, while those of Cyclin E, vascular endothelial growth factor (VEGF), matrix metallopeptidase 2 (MMP2), MMP9, signal transducers and activators of transcription 3 (Stat3), and p-Stat3 were upregulated by ATZ treatment. In MC3T3-E1 cells, however, ATZ treatment did not affect the level of p53/p21 mRNA compared to the control groups. Moreover, there was no significant change in the expression levels of Stat3 and p-Stat3 in MC3T3-E1 cells exposed to ATZ. This phenomenon was observed while the proliferation rate was enhanced in MC3T3-E1 cells by ATZ. The results of this study suggest that ATZ effectively promotes the proliferation and metastasis of EOC cells through the Stat3 signaling pathway by inducing low levels of ROS. Additionally, although ATZ might also induce proliferative potential in normal cells, the mechanisms governing its effects in these cells might be different from those in EOC cells.