مجله پژوهش های سلولی مولکولی (زیست شناسی ایران)
سال سی و دوم شماره 4 (زمستان 1398)

Heat stress is one of the most significant problems which has negative effect on feed intake, growth rate, neural network, immune function and mortality. In heat stress, the synthesis of proteins delayed but the heat stress proteins quickly are synthesized. They have important role in survival cell in stress conditions. Hsp70 is one of most important hsps, Because of crystallographic structure of this protein is not determined in honey bee, modeling of honey bee hsp70 can identify the mechanism of action of this protein against environmental stresses and help to reduce costs associated with environmental stresses. HSP40 is as a regulator of the mechanism of HSP70. So, in the present study, 3d structure of two proteins and interaction of HSP70 and HSP40 was studied using simulation methods in two states: 1- To investigate the interaction between the two proteins in blind (whole 3d structure of proteins were used),this results show interaction between these proteins mainly is restricted to two regions. HSP70 is bound to the HSP40 from the amino acid region of 400-430 and 620-640, with the amino acid region of 330-350 and 165-175, respectively. 2- According to previous studies, docking is only possible in likely regions of the proteins. So, the interaction between Jdomain of HSP40 to HSP70 was investigated, in which the amino acids 28-41 of Jdomain are interacting to an acid groove in the ATPase domain of HSP70. The results could help to better understand the function of two proteins and to design new anti stress drugs.

The screening of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene groups is a quick way to show the potential for antibacterial agent production and novel drugs discovery. With regard to this matter, the presence and the phylogenetic relationship of these gene clusters were studied in three Streptomyces strains.

 Materials & Methods:

PCR amplification of PKS types I, PKS type II, and NRPS genes was performed using three degenerate primer sets in Streptomyces strains Iz8, F9 and F6, respectively. To separate the same-sized DNA fragments with different sequences, PCR products cloned to pTG19-T vector and then transformed to Escherichia coli TOP10. Polyacrylamide gel was used for the sequences variation. The purified plasmids were sequenced and phylogenetic trees were constructed using Bayesian inference, implemented in the MrBayes.

PKS I clone 3 and 8, PKS II clone 4 and NRPS clone 5 were deposited in the NCBI GenBank database. Phylogenetic tree from aligned nucletotide or amino acide sequences of PKS I and II contained several differential clades. PKS I clone 8 and PKS II clone 4 were one of these clades. This could raise the production possibility of new antimicrobial agents.

Construction of phylogenetic tree and determination of evolutionary relationships confirmed possibility of the presence of gene clusters with new compositions and therefore new products in strains Iz8 and F9.

Osteoarthritis is a common joint disease for which there are currently no disease-modifying drugs available. Osteoarthritis (OA) affects most of the elderly population, the main features of which are cartilage damage. Degradation of the cartilage extracellular matrix is a central feature of the disease and is widely thought to be mediated by proteinases that degrade structural components of the matrix. The matrix metalloproteinases (MMPs) are a family of human zinc endopeptidases that play significant roles in inflammatory diseases such as osteoarthritis.

In this experiential laboratory study. punicic acid of pomegranate seed oil was purchased from Clarodan Kerman Co,. THP-1 cells (Pasteur Institute of Iran) were cultured and administered with concentration of 8 to 100 μg/ml (in 24h, 48h, and 72h). Cellular toxicity of punicic acid against THP-1 was estimated using the MTT assay and to measure the inhibitory effects of PA on Matrix metalloproteinase proteinase activity, ELISA and Western blot, migration and invasion tests were performed. Data were analyzed using T.student and ANOVA.

Western blotting and ELISA showed inhibitory effect of punicic acid on the expression of MMP-1 but not in MMP-3. Punicic acid of pomegranate seed oil shows the most cellular toxicity effect at lc50=50 micrograms per milliliters and 72 hours after treatment.

According to effect of Punicic Acid on MMP-1 expression, this material can be used as a potential candidate for further studies on the other MMPS and its replacing the chemical drugs.

Among different kinds of edible mushrooms, white button mushroom is the most cultivated in the majority parts of the world. Pseudomonas tolaasii is the important causal agent of brown blotch bacterial disease of mushroom that reduces its marketing. To consider the fact that by applying mutations, open reading frame of genes will change and important virulence factors cannot be produced as before. The aim of this investigation was further study on the role of these factors and compare the characteristics of phenotypic and genotypic alterations in mutants with the wild type strain. In this research, one isolate with intense pathogenicity factors was selected and the genome of that was altered by the use of spontaneous and transposon (mini Tn5) mutagenesis procedure. Among virulence factors in this bacteria, the effect of mutations on the production of pyoverdine, tolaasin, white line inducing principle and the motility of isolates were studied. The results of this investigation suggest the direct correlation between the production of pyoverdine, Tolaasin and white line inducing principle with the bacterial pathogenesis. On the other hand, no logical correlation was found in motility of the mutants with their pathogenicity. Further studies to identify the genes that are related to this process, are carrying out.

Histone acetylation is one of the most important epigenetic processes that regulate gene expression. In other words, chromatin exposes DNA to transcription factors and gene regulators by histone tail acetylation in nucleosomes. There are some studies to show the relation between gene regulation and histone acetylation. In this paper, our main goal is to propose a computational method for transcription factor binding site prediction based on a pattern of 18 types of histone acetylations. In this regard, we analyze 18 types of histone acetylations near SP1 binding sites on Chromosome 1 in human CD4+T cells. The results show that 12 out of 18 marks are strongly correlated with transcription factor binding sites. Then, we implement a multilayer perceptron neural network with supervised training. This network is trained using binding sites of various transcription factors of SP1 in chromosome 1 and 18 types of histone acetylations near them. Finally, this network is applied for predicting binding sites of various transcription factors on chromosomes 1 and 2.

Cytochrome oxidase is one of a superfamily of proteins which act as the terminal enzymes of respiratory chains. The two main classes are cytochrome c oxidases, and quinol oxidases. There are two catalytic subunits, I and II. Subunit I contains two heme centers. In this study we have isolated the cytochrom oxidase (COX) gene from orange by PCR and clone it by ligation of this product to pGEM-T vector transformed E. coli bacteria. Sequencing analysis shows that open reading frame for this gene that encode a protein with 217 amino acids. Results of phylogenetic analysis showed that this gene in orange has related to Chondrostoma cytochrom oxidase gene (COX). cytochrom oxidase gene protein secrete in membrane and it’s extracellular secretion is little. The aim of this study was isolation and cloning of cytochrom oxidase gene genes from citrus genome and determining of it’s characterizations to practical use in the plants.

Recently, the application of nanoparticles has been extended in areas such as medicine, drug, agriculture, industry and environment. In medicine, different types of these nanoparticles have been applied in therapy of cancers, wounds, infections, and also drug delivery. Among these, graphene is a new 2-dimensional material with special properties like high surface area, high electrical and thermal conductivity, mechanical, biocompatibility and low cost in large scale production. For example, today, graphene nanoparticles are used for drug delivery, photothermal cancer therapy, biosensors, biocompatible scaffolds, bioimaging, and anti-microbial components. Graphene oxide was synthesized from natural graphite powder according to Hammer’s modified method. Then, bacterial toxicity of synthesized graphene was evaluated in 1, 10 and 100 µg/ml of E.coli and staphylococcus aureus. The AFM analysis showed that thickness of graphene sheets was 0.5 nm and after reduction reached to 1.4 nm. Our result showed that, antibacterial properties of graphene and reduced graphene were highly concentration depended and in 10 and 100 µg/ml significantly decreased bacterial growth rate.

The widespread use and misuse of antibiotics in recent years, has led to selection and spread of resistant strains to antibiotics. Ciprofloxacin is a fluoroquinolone effective against Gram-negative bacteria such as Escherichia coli. In Escherichia coli exposure to ciprofloxacin resulted in mutagenesis and antibiotic resistance. In addition, exposure to UV radiation induces the transcription of umuC by ciprofloxacin. UmuC is required for mutagenesis caused by UV rays. The aim of this study was to study the dependence of ciprofloxacin-induced mutagenesis on UmuC in Escherichia coli.

In this research, Escherichia coli UmuC- strain was used and resistance to ciprofloxacin was generated stepwise. To determine the MIC of ciprofloxacin serial dilution method in broth medium was used. The mutation frequency was determined in the presence of ciprofloxacin and UV ray.

The results showed that clones with low and medium resistance can be produced from umuC- mutant and the mutation frequency was low. Discussion and

In conclusion, UmuC is required to generate mutants with high resistance to ciprofloxacin and plays an important role in the mutagenesis. The low frequency of mutation accounts for creation of mutants with low and medium resistance to ciprofloxacin and at the same time suggests that in the absence of UmuC, other factors might be effective that needs to be investigated.

Acinetobacter is a kind of non-fermentative gram-negative cocobacilli which is considered as the second major cause of hospitalized infections after Pseudomonas aeruginosa. The Beta lactamase enzymes of these bacteria are very diverse and their constantly point mutations have led to the emergence of Extended-spectrum Beta lactamases ( ESBLs). In this study, which took place in a period of eight months, after confirmation of the identity of Acinetobacter strains by bacteriological tests, the pattern of drug resistance of the isolates and the production of ESBLs by them was investigated by Agar disk diffusion method. In this study, 50 strains of Acinetobacter baumannii and 15 strains of other Acinetobacter species were isolated from patients. The highest frequency of drug resistance in Acinetobacter baumannii isolates was related to Cefipime (100%), and the lowest was related to Cefixime-Clavulanic acid (50%). Acinetobacter with Multiple Resistance Patterns are a growing problem for medical centers around the world and the most important reason for this is the unnecessary and over-consumption of drugs, especially Beta lactam antibiotics.

Actinomycetes, Gram positive bacteria, are rich sources of bioactive compounds. Secondary metabolites of these bacteria are used as pharmaceutical compounds Enzymes are one of the most important secondary metabolites which act as bio-catalysts to perform reactions in bio-processes in an economical and environmentally-friendly manner. Enzyme production from actinomycetes makes significant facility in industrial and world economic. So, that it is becoming one of the economic indexes of developed countries. The goal of this research is isolation of actinomycetes from Shadegan estuary, optimization of bacterial growth and amylase production. Molecular identification was done by amplification of 16S rRNA gene using R1492 and F27 primers. Optimum growth condition was found at 6% NaCl concentration, 35˚C temperature and pH 8 . Maximum amylase activity in optimum condition was 80150 Unit (one Unit is amount of enzyme that release one microgram of glucose in a minute). The results showed that enzyme production is related to growth of bacteria conditions.

MicroRNAs (miRNAs) are endogenous, noncoding, small RNA molecules consisting of 18-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. Also, this group of RNAs play a crucial role in development of plant, biological processes, cell proliferation and stress response. To date, no miRNAs have been identified in the lentil species although there are several reports on miRNAs in other legume species. Therefore, in this study, in order to identify and analysis of potential miRNAs and their target genes in lentil, total RNA from leaf tissue was extracted using with TRIzol method and was sequenced. Non-protein coding unigenes were identified and considered for candidates of miRNA precursor. Finally five miRNAs belonging to 5 highly conserved families were identified following a range of strict filtering criteria, designated as, lcu-miR156, lcu-miR166, lcu-miR167, lcu-miR171 and lcu-miR391. In addition, we predicted target mRNA genes form complementary base pair in seed region of miRNAs. Totally, due to the regulatory role of the identified miRNA on changing the range of downstream genes in the gene networks, it may be possible to use the identified microRNA as candidate genes in breeding programs aimed at improving the quality and quantity of lentil.

Probiotics are live microorganisms with helpful effects on digestive system of human and animals. Isolation of novel bacteria with probiotic potentials from less investigated sources, expand the application of these microorganisms in human and animals health. Isolation and exploring the probiotic potentials of resident bacteria from a native cheese in south khorasan was the aim of the current study. In order to isolating the bacteria from Qaeni cheese, samples were inoculated on NA and MRS culture media after prepared suitable dilution. In order to assay their probiotic activity characteristics including acid and bile resistance, antibiotic susceptibility, antimicrobial activity, hydrophobicity, self-aggregation and anti-oxidant activity were analyzed among the selected strains. A total of 90 isolates were obtained in this study. Of them 30 isolates were selected as different ones base on colony pigmentation, microscopic morphology and Gram staining. A total of 5 isolated could survive in acidic and presence of bile conditions and selected for further analysis. All of the strains were susceptible to erythromycin, tetracycline, methicillin and chloramphenicol, rifampicin and ampicillin. Only one isolate was resistant to chloramphenicol. The most antibacterial activity was observed against E. coli and B. subtilis. Based on the results from all probiotic traits, strain 7C37 which belonged to the genus Enterococcus represent the highest probiotic potential. The novel strains from indigenous fermented cheese are good candidate for complementary analysis for selection as probiotic bacteria.