مجله پژوهش های سلولی مولکولی (زیست شناسی ایران)
سال سی و پنجم شماره 1 (بهار 1401)

Nowadays, bioactive peptides are considered as suitable substitutes for chemical drugs due to diversity proliferation, easy synthesis, no side effects and no accumulation in the kidneys and liver. Insects with huge diversity and success in all habitats are an appropriate source for extracting bioactive peptides. The aim of current study was to extract and purify bioactive peptide from white grub larvae hydrolysate. Bioactive peptides from white grub larvae hydrolysate were produced using papain, pancreatin, proteinase-K and trypsin. The obtained results showed that 4-hour hydrolysate of papain had the most DPPH radical scavenging (21%). This papain hydrolysate was fractionized by reverse-phase high-performance liquid chromatography (RP-HPLC). The most antioxidant fraction with the sequence of YPQSLRWRAK (1304.6 Da, named Po-1) was identified by tandem mass spectrometry. DPPH scavenging activity of synthetic Po-1 peptide at 100 µM reached to 54.41%. The IC50 value for DPPH scavenging activity of peptide was 76.45-µM. while, IC50 values natural compounds of vitamin-C and reduced glutathione (GSH) were 3.27 and 9.96 µM. In conclusion, our results showed that Po-1 bioactive peptide possesses antioxidant activity that might be used for therapeutic purposes in the future.

Catechol 2,3-dioxygenases play a key role in the metabolism of aromatic molecules in the environment by soil bacteria. The aim of this study is to introduce the new catechol 2,3-dioxygenase and also to survey bioinformatics and biochemical characteristics in the presence of various substrates as well as to study its activity in various pH ranges for the widespread use of such enzymes in bioremediation industry.In this study, the DNA sequences of Catechol 2,3-dioxygenase were separated from Aneurinibacillus migulanus Znu12 and recorded with accession number MN197546.1 in NCBI, then it was cloned in plasmid pET28a. The accuracy of cloning and not changing the frame shift was confirmed by sequencing. After transferring of plasmid into E. coli BL21 (DE3) cells, protein expression was assessed by SDS-PAGE. Afterwards, the purification, assay and optimization of enzyme activity were evaluated.The results of PCR reaction on agarose gel indicated a sequence of 912 bp, an enzyme with 304 amino acid residues. Results of sequence alignment by ESPript3 server also confirmed highly conserved residues of His199 and Tyr 255 in the enzymes active site. Biochemical characterization of the enzyme showed that the enzyme had the highest (100%) activity at pH 7.2, while it had only 70% activity at pH 7.4. As compared with pyrogallol and phenol, catechol by optimal concentration of 0.032 was the most preferred substrate for the enzyme. Bioinformatics results confirmed also such substrate preference based on the type and position of amino acid residues in the enzyme active site.

The proteins that bind to the elements that respond to drought stress, have particular important in rising plant resistance to drought. In this study with the aim of evaluate different expression of TFs in different tissue, the expression of genes encoding NAC10 and NAC6 transcription factors in rice under drought stress in leaf and anther tissues were estimated. In this study, transgenic and non-transgenic rice seeds of Nipponbare variety were cultivated. Leaf and anther tissues on young microspore stage were sampled at several times after Stop irrigation. Promoter analysis for finding transcription binding sites has done by two web sites and two TF from NAC family were selected. RNA extraction was maintained at -80 ° C, RNA quality and quantity were evaluated. Expression comparison of genes encoding these transcription factors were performed by real-time PCR with Delta-Delta CT method. The results of this study showed that NAC10 and NAC6 are expressed in both anther and leaf tissues. Under drought stress, the highest expression of both transcription factors was in anther tissue after 24h stress, the highest expression of NAC10 was in non-transgenic plants, about 70 times more than control and the highest expression of NAC6 was in transgenic plant about 60 times more than control condition. These results indicate the important role of these factors in anther tissue of rice, response to drought stress.

The studies have shown that sex steroids affected cancer cells at the cellular and molecular level. The aim of this study was to investigate the anti-proliferation effects of testosterone on colorectal cancer (HCT) cell lines and caspase-3, -8 and -9 activity level.

In this laboratory-experimental study, cells were randomly divided into control group (no exposure to hormone) and groups exposed to 0.001, 0.01, 0.1, 1 and 10 mg/ml of testosterone. The cytotoxic effect of the extract was measured using MTT assay method. Caspase-3, -8 and -9 activity level was evaluated by ELISA method. The data were statistically analyzed between groups using student’s t-test and ANOVA (Tukey).

0.1, 1 and 10 mg/ml of testosterone significantly reduced the viability of HCT cells compared to the control group (P

Organophosphorus compounds, are widely used as pesticides in agriculture. Organophosphate Hydrolase (OPH) enzyme hydrolyses a wide variety of organophosphate esters. In the present study, by using both enrichment culture and maximum dilution frequency techniques, the diazinon degradation bacteria was isolated from treated samples and was identified by morphological and biochemical tests. The enzyme was extracted from its bacterial strain and then purified using ammonium sulfate and ion exchange chromatography. The purity of the enzyme was confirmed by electrophoresis (SDS-PAGE), then its molecular weight was determined by specific marker proteins and its kinetic properties was evaluated.Using enrichment culture technique and the increasing factor of the biodegradability diazinon, enzymatic hydrolysis time decreased significantly with less than 10 hours. The main metabolite produced from diazinon hydrolysis was identified as 2-isopropyl-6-methyl-4-Hydroxy pyrimidine (IMHP, with less toxicity) through both thin layer chromatography (TLC) and spectrophotometry techniques. Purified OPH enzyme specific activity was found to be 57.48 fold of 16.44 U/mg of protein with a yield of 11.4 percent and approximate molecular weight of 40 KD. Maximum activity enzyme was at optimum pH 8.5 and temperature of 37 ͦ C. Substrate concentration up to 0.05 M and Co+2, Ca+2 metal ions had positive effects on activity enzyme. Michaelis constant (Km) and maximal velocity (Vmax) values were calculated as 434.2 μM and 107.3 μM/min, respectively. The results showed that OPH enzyme with its activity gradual and effective in addition to detoxification, could be played a key role in recovery of phosphate for the production of biofertilizer.

Antimicrobial peptides are desirable targets as new antibiotics. Histatin peptides belong to a family of antimicrobial peptides that are rich in histidine amino acids. Human histatin 3 functionally has both antimicrobial and wound healing properties. In this study, the mutation design of histatin 3 peptide were performed. Then, in order to produce this peptide on a laboratory scale, its sequencing followed by Sumo fusion peptide in E.coli was cloned and expressed and then purified by Ni++ affinity chromatography technique and the results were analyzed by SDS-PAGE technique. The results of its microbiological tests (MIC) indicate the value of this peptide, which is effective on gram positive bacteria such as Staphylococcus aureus. According to this research, the antimicrobial activity of this peptide and the possibility of its production, it is hoped to use this peptide in the pharmaceutical and medical industries as new antibiotics or in addition to traditional antibiotics to increase their efficiency.

Cadmium is a heavy metal used in industry. This metal enters water and soil through factory effluents and causes environmental pollution and thus affects the growth of plants and microorganisms. Cadmium can disrupt metabolism by affecting cellular enzymes. Pseudomonas aeruginosa is a soil bacterium that is involved in the removal of hydrocarbon contaminants such as oil and industrial effluents. Infiltration of cadmium along with industrial effluents can affect the ability of this bacterium to remove contaminants. In this study, the effect of the presence of cadmium on the growth of P. aeruginosa and its effect on protease activity were studied. The results showed that the presence of cadmium in the culture medium reduced the biomass and decreased the activity of protease secreted in the medium. The effect of the presence of different sources of nitrogen to activate protease secretion in the culture medium was investigated and it was found that nutrient broth has the highest effect on activating protease. The effect of different concentrations of cadmium on the extracted protease showed that cadmium can reduce the activity of the extracted enzyme. The value of IC50 was estimated to be about 0.1 mM. The optimum pH and temperature of the enzyme were 9 and 40oC, respectively, which the presence of cadmium reduced the enzyme activity at this pH and temperature. Finally, the results showed that the presence of cadmium can not only affect the growth of bacteria, but also reduce the activity of protease

Genetic diversity and genetic relationships of 25 populations from five diploid Aelilops and Triticum were investigated using 15 SCoT primers, 12 primers with scalable bands. Based on the PIC, RP, EMR and MI markers, SC6, SC11, SC63 and SC20 primers showed high levels for the analysis of the germplasm collection of Aegilops and Triticum species in subsequent studies. The genetic distance of the populations studied using the Jaccard distance coefficient showed that the average distance between populations was 0.307 and the mean inter-species distance was 0.636. Also two species Ae. strangulata and Ae. tauschii, both of which have the genome D, have the smallest distance. The results of UPGMA cluster analysis based on Jaccard distance coefficient showed that the populations were divided into 5 groups, so that the species were 100% separated, indicating the high efficiency of the marker, these results corresponded to the results of the gap matrix and the decomposition to the original coordinates of 100 percent. The analysis of genetic indices for the species studied showed that the highest intra-population variation and genetic diversity were related to Ae. tauschii was the highest polymorphism was observed among the populations of this species.

Silver carp (Hypophthalmichthys molitrix) as the major species in total production of freshwater fish, has a special place in the aquaculture industry of Iran. The common method for breeding of this species in our country is semi-natural which provides the brooders opportunities for mate selection that is one of the most striking features in this method. Given the importance of MHC gene complex to sexual behaviors and its historical role in the process of evolution of living organisms especially in terms of safety issues, various patterns of mentioned loci between two generations of Silver carp were studied. 33 males and female silver carp were reproduced in two independent groups by semi-natural method after that larvae in each group were sampled. Using data in NCBI and designing the appropriate primer, MHC-DAB loci of the parents and their F1 were studied by SSCP method. Analysis of six different genotypes between the samples indicated an increased level of observed heterozygosity (1) compare to the expected value (0.660 -0.709). Deviation from Hardy-Weinberg equilibrium was observed in most groups and the main share of genetic diversity assigned to individual differences. The pattern of genetic diversity distributed in larvae and high variation of MHC-DAB loci meanwhile retaining number of the alleles, represents a positive selection.

The particular properties of nanoparticles and their interactions with biomolecules have attracted the attention of many scientists. Nanoparticles may affect the structure and function of biomolecules within the body. Proteins can easily attach to the surface of gold nanoparticles and form a protein corona around the nanoparticles. The formation of corona can affect the conformation of absorbed proteins and disrupt their physiological function. Therefore, understanding the interactions of gold nanoparticles and proteins can be considered as a starting point for studying the biological effects of nanoparticles. Considering the broad applications of gold nanoparticles and also the crucial role of acetylcholinesterase in the nervous system, this research used molecular dynamics simulations to study the effects of the gold nanoparticles on the structure of acetylcholinesterase. The results of RMSD, DSSP, and the radius of gyration indicate that the structure of AChE is stable in the presence of gold nanoparticles. Also, the results showed that gold nanoparticles do not cause any significant conformational changes in the protein structure.

The biological knowledge of different species can be transferred to the conserved sequence regions via genomic sequence alignment. Similarly, through biological network alignment, knowledge of the conserved regions of molecular networks can be transferred to different conserved regions of different species. Therefore, relying on biological network alignment, we can extend the traditional "sequence-based homology" concept to the new concept of "network-based homology". Discovery of networks alignment is especially important because of its applications, such as discovering new drugs, tracking disease progression, or predicting users' behavior on social networks. In this regard, the main challenge is that the problem of finding the alignments in two graphs is NP-hard. In situations like this, we can use the relatively fast meta-heuristic algorithms to find some acceptable approximate solutions. The main contribution of this research consists of conducting a comparison over the network alignment algorithms, based on the respective evaluation criteria, execution time, memory consumption and complexity of the testing networks. The experimental results are obtained from running the relevant algorithms on the well-known BioGRID dataset. Evaluations indicate that among other methods, using genetic algorithm, memetic, particle swarm optimization, simulated annealing and the ant colony, could yield more valuable results. The named methods apply appropriate heuristics to generate and investigate only a very small subset of the whole search space with the highest probability of holding a solution; therefore, they often can find the optimal solution or some acceptable solutions in a relatively short time.

In the present study, quantitative structure-activity relationship study of inhibition characteristic of pyrazoline derivatives as inflammatory cyclooxygenase-2 inhibitors were performed using different chemoinformatics methods. Selective inhibition of cyclooxygenase-2 is an important strategy in designing of potent anti-inflammatory compounds with significantly reduced side effects. Classification and regression tree and stepwise multiple linear regression were used to select the most important molecular descriptors. The final model was developed using adaptive neuro-fuzzy inference system and artificial neural network with selected molecular descriptors. Results of different validation techniques of leave one out, leave multiple out and prediction set show the validation of acquired model. In the next step, molecular docking studies was performed to obtain receptor-ligand binding pattern. Results of molecular docking revealed that the amino acids of Arg44, Glu46, Glu465 and Cys41 have important role in receptor-ligand interaction. In the present study, interpretable quantitative structure-activity relationship and molecular docking techniques were used to predict inhibitory concentration of pyrazoline derivatives. The present results can be used to predict inhibitory concentration of cyclooxygenase-2 inhibitors in drug design with consuming lower cost and time.