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Salt stress is a serious environmental threat reducing crop yield. Hence, developing any breeding plan requires an understanding of the basic physiology and cell molecular genetic regulation under salinity stress. In this study, we evaluated the effectiveness of gene expression changes on ion homeostasis comprising salt overly sensitive (SOS1) and vacuolar Na+/H+ antiporter (NHX1) along with ion content measurement and proline content in the rice mutants at Rice Research Institute of Iran in 2018-2019. To survey these realities, tolerant mutant genotypes (em₄hs290 and em₄hs84) along with Hashemi parent cultivar, IR28 (sensitive), and FL478 (tolerant) seedlings were treated with 100 mM NaCl. Based on the results of growth indices, the seedling length of Hashemi cultivar and IR28 decreased considerably about 44.7%, and 44.2% reduction to that of the control, and the leaves progressively yellowed. Results showed that proline content and K⁺ and K⁺/Na⁺ ratio increased about ~2–3-fold higher in the tolerant genotypes than in the susceptible ones. Also, the overall amount of the OsNHX1 and SOS1 expression increased in tolerant genotypes compared to the susceptible ones. Accordingly, the compatible solute accumulation significantly advanced resulting in improvement of ionic homeostasis and probably suppresses the stress. Moreover, the variable pattern of gene expression in the two salt-tolerant mutants (em₄hs290 and em₄hs84) and Hashemi parent showed that the induced mutation could increase the salt-tolerant in mutant genotypes through ionic and osmotic homeostasis. Generally, these tolerant mutant genotypes could be applied to develop salt-tolerant varieties in rice breeding programs which can bring on production sustainability.

 

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Background: Despite the genetic heterogeneity reported in familial ALS (FALS), SOD1 gene mutations are the most frequent cause of FALS, accounting for around 20% of familial cases (ALS1) and isolated sporadic cases. Mutant forms of SOD1 exhibit toxicity that promotes the death of motor neurons. It is well documented that FALS produces protein aggregates in the motor neurons of FALS patients, which have been found to be associated to mitochondria. Methods: In this study, we cloned the SOD1 gene, using reverse transcriptase-polymerase chain reaction (RT-PCR) method, from both a healthy control and a living 79 -year-old man with diagnosis of sporadic form of ALS who had shown unusual rapid progression of disease. RNA samples were available from lymphocytes of them. pET28a expression system and BL21 chemically competent Escherichia coli strain as host were used for protein expression. Results: DNA Sequencing data showed both heterozygosis C to G transition at nucleotide position 21 leading to a C6W changing at protein level and a deletion at nucleotides position 73 to 169 leading to complete deletion of exon two.

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Background: The kiss peptins and its receptor G protein coupled receptor (GPR54) or KISS1 receptor system are being described as key signaling molecules for reproductive function in animal models and humans. They play essential roles in regulation of the hypothalamic- pituitary- gonadal (HPG) axis and the onset of puberty and fertility. Objective: This study was performed to delineate the association of T305C (Leu 102 Pro) KISS1 receptor gene mutation with idiopathic female infertility in Iranian women. Methods: In this study, 140 healthy women with at least one child and no history of infertility and abortion and 130 idiopathic infertile women were recruited for this study.  By using allele specific PCR (AS-PCR) method, the allele and genotype frequencies among infertile and healthy women were determined. Results: The gene frequencies of the 305 T and C allele of the KISS1 receptor were 45% and 54% among infertile women and 50% and 50% among healthy controls, respectively. The distribution of genotype frequencies in the patients and controls was as follows: TT (Leu/Leu) was 15% and 0%, TC (Leu/Proline) was 60% and 100% and CC (Pro/Pro) was 24% and 0% respectively. Structural analysis was performed using the MedCalc program (version 12). Our results suggests that significant association were not observed in genotype (P=0.8) and allelic (P=0.6) distribution between cases and controls. Conclusions: The data presented show that mutant allele C  is not a risk factor for infertility, suggesting that the presence of KISS1 receptor T305C mutation is probably not associated with idiopathic female infertility in this population (P>0.05).

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In this paper, we show how to obtain suitable differential charactristics for block ciphers with neural networks. We represent the operations of a block cipher, regarding their differential characteristics, through a directed weighted graph. In this way, the problem of finding the best differential characteristic for a block cipher reduces to the problem of finding the minimum-weight multi-path way between two known nodes in the proposed graph. We applied Hopfield network to find the minimum-weight multi-path way. In this technique, the probability of convergence to a local minimum increases when the number of rounds of the cipher increases. We also applied Boltzmann machine to avoid local minima. We applied these techniques to find 3-round, 4-round and 5-round differential characteristics of Serpent block cipher, and repeated the optimization procedures for each characteristics 100 times. With Hopfield network, we obtained suitable results 100, 20 and 1 times for 3-round, 4-round and 5-round of the Serpent respectively. With Boltzmann machine, we obtained suitable results 100, 99 and 30 times for 3-round, 4-round and 5-round of the Serpent respectively. These results show that simulated annealing help avoiding the many local minima of energy function. We compare the probabilities of our obtained differential characteristics for Serpent with the probabilities of eight differential characteristics previously reported in other papers. The comparison shows that our proposed technique obtains better results in 6 cases, and the same results in 2 cases. We also found a 7-round differential characteristic with a probability of 2-125 with Boltzmann machine. Neglecting the reported Bommerang differential characteristics of Serpent, our obtained 7-round differential characteristic is the first report on a differential characteristic for more than 6 rounds of this cipher. The results of experiments indicate the efficiency of neural networks to find suitable differential characteristics of block ciphers.

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Figure turning is the change in the appearance of nature or the ability of Mythological heroes and legendary creatures that sometimes is demonstrated with apparent changes such as: turning inanimate objects to animals, human to animal or vice versa, human to angel and etc. It is sometimes without apparent change. For example, the Hero achieves a numinous power or maybe goes beyond his intrinsic abilities. However, it is important that these changes or figure turnings be considered as the most important factor to wonder in myths, legends and folk stories. The purpose of this study is to examine the written native legends in Sistan and Baluchistan province from the figure turning point of view. According to the diversity of types of tangible figure turning and the Breadth of the subject, the present article is assigned to the types of human transmutation in which human has been transformed in to animal, inanimate, plant, numinous creatures, nature, and human, or gains extraordinary abilities without a change in his nature. The results shows, there is human transmutation in 23 out of 157 myths in the province. The most human figure turnings are "transformation of human to animal" and "amazing trips", "transformation of human to human" and "human to numinous creatures" from the first kind of human transmutation which are not seen in any kind of these myths. The researchers try to demonstrate the obvious reasons of different figure turnings by interpreting mentioned legends and also, to show the role and function of these figure turnings in native legends.

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Introduction: Hypertrophic cardiomyopathy (HCM) is a rare cardiac disorder which can result in sudden death in young people. Molecular studies have been showed that mutations in the beta-myosin heavy chain (MYH7) gene are one of the most common genetic causes of HCM. The aim of this research was to study exons 8, 9, and 30 of MYH7 gene for possible mutation in HCM patients from Chahar Mahal va Bakhtyari Province.
Material and Methods: In this descriptive-laboratory study, DNA was extracted from 27 blood samples by phenol-chloroform method. DNA samples were then used for PCR-SSCP analysis for amplification and identification of mutation. The Suspected cases with possibility of having mutation were sequenced and the results were observed by Chromas software.
Results: 7 suspected cases recognized by PCR_SSCP were sequenced with forward and reverse primers to verify the presence of mutation.

Conclusion: Mutations in these exons do not have a role in establishment of disease in the studied population. However, study greater number of HCM cases and other exons of this gene are recommended to find the relationship between gene and HCM and to gain necessary information for treatment and management of disease.

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Colorectal cancer (CRC) is one of the most common cancers worldwide. Understanding of the tumor behavior, in a much closer look, at the molecular level, results in a more effective treatment and accurate prognosis of the disease. From among various genes altered in colorectal cancer K-ras is assumed to be of diagnostic and prognostic significance. K-ras mutations are believed to be a critical event in colorectal oncogenesis. Previous studies have demonstrated that 40% (20-50%) of CRCs harbor a mutant allele of K-ras oncogene. The mutations are limited to codons 12, 13, and 61 of the gene, with a great incidence at codon 12. The localization of mutations has given mutated K-ras an advantage of sensitive and simple detection over APC or p53 in which mutations are spread in their whole DNA sequence. To determine the incidence of K-ras mutations in CRC in Iran, compared with other countries, DNA was isolated from a random collection of 55 colorectal carcinoma samples, and codon 12 K-ras mutations were detected by RFLP. K-ras mutations in sporadic colorectal cancer in Iran are relatively frequent, with an incidence of 65%. This may be attributed to variation in methodology and to characteristics of the population studied such as differences in genetic background and variability in environmental factors and epidemiologic parameters such as diet, social lifestyle status, and other parameters that could be specific to the Iranian population. Correlation between the presence of codon 12 mutation and various clincopathological parameters was also investigated. A significant correlation was found with poor tumor differentiation of tumor samples. This places much emphasis on the role of promotion of differentiation as the most prominent effect of Ras.

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Trichoderma is very important as a bio control agent and probably a good alternative for chemical fungicides. Fusarium oxysporum is a plant pathogen that causes wilt in a wide range of plants. The use of gamma irradiation can be employed to increase Trichoderma efficiency against F. oxysporum. The induced mutation provides genetic changes in Trichoderma and in some of the mutated isolates the efficiency of bio control may be improved. In this study the efficiency of mutated T. harzianum CS5 against the F. oxysporum f.sp. radicis-cucumerinum was evaluated. Among 16 wild isolates of Trichoderma, CS5 isolate was chosen based on synchronous and nonsynchronous mutual cultivation with pathogen. The spore suspensions of T. harzianum CS5 were irradiated in a cobalt- 60 γ- irradiator at a dose rate of 0.23 Gy/Sec in Nuclear Agriculture Research School, (NSTRI, AEOI). Then antagonist screening of 76 mutants was investigated in the experiments of synchronous and nonsynchronous dual culture with pathogen. The results showed that only 17 mutants were able to control the pathogen better than wild type, and YFTM80 isolate had the most prevention. Using the ERIC-PCR marker, the distinction was investigated between the wild type and the 17 selected mutants. The results showed that the gamma ray is able to improve biocontrol efficiency of Trichoderma and the ERIC-PCR marker can differentiate among derived mutants, but it does not have the ability to distinguish mutants from wild type. In terms of antagonistic superiority, mutations might have occurred in antagonistic sites, which have led to improved antagonistic efficiency. Probably the ERIC-PCR marker has failed to replicate these areas.

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Abstracts This paper presents how the genetic algorithm (GA) can be applied to design of cascade stilling basins. Genetic Algorithm is adaptive method, which can be used to solve search and optimization problems over a period of generations, based upon the principles of natural selection and survival of the fittest ones. The objective of this research is to minimize total cost of construction effectively which is a function of height of falls and length of stilling basins, while fulfilling the hydraulic and topographical criteria. The efficiency of GA discussed here has been tested for a benchmark example and the result for this algorithm is compared with the other method introduced by Vittal and Porey. The results clearly reveal superiority of the GA algorithm

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Background: Despite the passage of more than two years since the coronavirus disease 2019 (COVID-19) pandemic, the persistence of the coronavirus and its circulation at varying levels globally necessitates a deeper understanding of the factors influencing its transmission and impact. This study aimed to investigate the relationship between environmental factors, population density, and genetic variations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a specific focus on elucidating their implications for public health measures and vaccine development.
Materials & Methods: This observational analysis was conducted utilizing daily reported SARS-CoV-2 cases in various countries. Additionally, monthly changes in ultraviolet (UV) radiation index, population density per km², and viral genetic variations were assessed. Comparative analysis was performed to examine correlations between these variables. Data analysis was conducted using SAS 9.3 software with a generalized linear model (GLM) approach.
Findings: This study revealed significant correlations between UV index and key epidemiological parameters, including mortality rate, average case number, and transmission rate. Population density per square kilometer did not exhibit any substantial relationship with these variables. Analysis of viral clades suggests potential immunological insights, indicating varying degrees of immunity conferred by certain genetic variants.
Conclusion: These findings underscore the importance of environmental and genetic factors in shaping the trajectory of the COVID-19 pandemic. By elucidating the role of UV radiation and viral genetic diversity, this study informs public health strategies and underscores the necessity of ongoing surveillance and vaccine development efforts tailored to the evolving SARS-CoV-2 landscape.

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Abstract - In this paper, an optimal trajectory planning method is presented for robot manipulators with multiple degrees of freedom in 3D space using a new analytical technique for collision avoidance in the presence of ellipsoidal obstacles. To generate the robot’s trajectory, a genetic algorithm with a fuzzy mutation rate is introduced to have a quick access to optimal solutions in a complex workspace. A cubic spline interpolation polynomial is applied to approximate trajectories in the joint space. In order to optimize the objective function, the genetic algorithm determines a number of interior points for curve fitting using interpolation polynomials. The performance of the proposed technique is demonstrated by simulations.

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The CD80 protein, a member of the super-family of immunoglobulin, is a transmembrane protein expressed on the surface of the antigen-presenting cells (APC). This protein has two receptors on the surface of T cells (CTLA-4 and CD28), due to the binding of this protein to these receptors, the inhibitory and stimulatory pathway in the T cells begin, respectively. Naturally, CD80 proteins tend to have more binding affinity to CTLA-4 than CD28, and this is a factor in the extinction of T cells in the immune system in order to prevent autoimmunity. The aim of the present study is to create a variant of the CD80 protein that has an increased binding affinity to CD28 to bind to this receptor more strongly and induce more simulate pathways than the wild type of this protein (primary CD80 protein) in T cells. To identify this variant, first, the ancestral sequence was mutated by R software at positions 31 and 92 with amino acids that play an important role in the formation of hydrogen bonds. The R software output sequences were modeled with the SWISS-MODEL server. Then, each output model was docked with the HADDOCK server, and finally, the electrostatic and van der Waals energies between the receptors and the ligands were calculated. Among all the built-in models, the mutated K31Y, R92F has the best electrostatic and van der Waals energies and has the ability to have a much better connection to its CD28 receptor compared to the ancestral type of CD80.

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Objective: The Brucella melitensis virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The product of the second gene of the virB operon, virB2, is predicted to be localized at the bacterial surface, where they could potentially interact with host cells. Studies to date have focused on characterization of transposon mutations in this gene, which is expected to exert polar effects on downstream genes. We researched on the evaluation of relation between virB2 mutant with immunogenicity in mouse model and intracellular replication in macrophages J774. Materials and Methods: In order to determine whether VirB2 is required for the function of the T4SS apparatus, we constructed and characterized deletion mutation of virB2 and kanamycin resistance gene replaced instead of virB2. For demonstration of intracellular replication, macrophages J774 and BALB/c mices were infected with wild type Brucella melitensis and mutated. Results: After 48 h, number of mutated Brucella severe decreased severly compaired to wild type in macrophages J774, and Brucella with virB2 deletion decreased from 1×106 CFU/spleen less than 1000 CFU/spleen during 8 weeks, also total IgG increased in both but IL-12 and IFN-γ increased only in wild type. Conclusion: VirB2 was essential for intracellular replication in mouse models and J774 macrophages. The virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus

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Nowadays, aromatic componds are widely used in food, pharmaceutical, cosmetic and chemical industries. Due to the growing tendency of consumers to use natural products, biotransformation by microorganisms is an interesting method for the production of aromatic compounds. Gamma-decalactone is a cyclic aroma with a peach-like flavor. The non-conventional yeast Yarrowia lipolytica can bioconversion the inexpensive castor oil substrate into the valuable gamma-decalactone. The process begins with the hydrolysis of castor oil by the lipase to ricinoleic acid, then continues by shortening the chain by beta-oxidation, and finally ends by lactonization. In this study, gamma-decalactone production was optimized via Response surface methodology (RSM) by a mutant strain of this yeast with the ability to produce high amounts of lipase. For this purpose, castor oil, yeast extract, peptone and pH were studied as factors at five levels. Based on statistical analysis of the relationships between the experimental variables, a mathematical model was obtained for the governing relationships between the experimental variables. Based on the results, the best values were obtained for castor oil 35 ml/l, yeast extract 6 g/l, peptone 8.5 g/l and pH 4. To validate the mathematical model, the proposed values were tested and 126 mg/L of gamma-decalactone was produced by the yeast strain, which shows a 46% increase compared to non-optimal conditions. The results of this study can be used to make cost-effective production of gamma-decalactone from castor oil by microbial biotransformation process.

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Mutation in microbial strains to increase coenzyme Q₁₀ production is one of the successful strategies for strain development. Therefore, in this study, the production of coenzyme Q₁₀ by Gluconobacter oxydans H621 was investigated through chemical mutation with nitrosoguanidine using the response surface methodology. Nitrosoguanidine was used to induce mutations at different concentrations (2.79 - 4.21 mg/mL) and treatment times (11.89 – 33.12 minutes), which was designed by a central composite design. The detection of mutant strains was investigated through their ability to grow in medium containing 160 μg/mL of menadione. The mutant strains were then examined for coenzyme Q₁₀ and dry cell weight production. The results showed that no mutant strains were obtained at a concentration of 4 mg/ml and above. The highest number of mutant colonies was obtained at a concentration of 2.79 mg/mL of nitrosoguanidine and treatment time of 22.5 minutes. It was also found that the concentration of nitrosoguanidine was effective on mutagenesis but the treatment time had a little effect. The mutant strain that was able to produce the highest amount of coenzyme Q₁₀ produced 5.2 mg/L, which was twice as much as the parent strain. According to the results of this study, it is concluded that by inducing mutation using nitrosoguanidine, mutant strains can be generated in Gluconobacter oxydans H621 that are able to produce more coenzyme Q₁₀ than the parent strain.

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Microbial oil has lots of similarity to the plant’s oil; the only difference between them is that microbial oil is rich in unsaturated fatty acids. This oil can be used in pharmaceutical industry for technical purposes or as edible oil in food industry. The purpose of this study was to increase lipid production and the amount of unsaturated fatty acids in oleaginous yeasts by mutagenesis. In this study, optimization of lipid production in the yeast ,Yarrowia lipolytica, was done using ultraviolet random mutation and screening was done with the inhibitory effect of cerulenin on lipid synthesis. Mutants that had normal growth in the presence of cerulenin were selected as superior strains for further investigations. Lipid production in mutants and wild strains were compared after incubation period. Then, the mutant with significant increase in lipid production was selected. The best mutant had increasing of 50% and 30% in lipid production and growth yield, respectively. Also, Linoleic acid was increased after mutation. The composition of fatty acids in the lipid profile of the evaluated yeast did not change a lot after mutation. Of course, unsaturated fatty acids were increased, so this technique was very effective to improve lipid production. Cerulenin used as an effective screening technique in this study and paved the way for the isolation of superior mutants.

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Objective: The use of antiretroviral drugs has proven remarkably effective in controlling the progression of human immunodeficiency virus (HIV) disease, but these benefits can be compromised by the development of drug resistance. This study aims to assess the drug resistance profile of the Pr gene in highly active antiretroviral therapy (HAART)-treated and naïve HIV-1 infected patients. Methods: A total of 30 samples from naïve and 16 samples of highly active antiretroviral therapy (HAART)-treated patients were collected and divided into two groups. After RNA extraction, RT nested PCR was performed. The final products were sequenced and then analyzed for drug-resistant mutations and subtypes. Results: No drug resistant mutations were noted in group one that have never used drug, but 40% of group two samples which are under treatment contained drug resistant mutations. According to the results, the following subtypes were seen among patients: A (50%), B (40.6%), D (6.2%), and C (3.2%). Conclusion: Transmission of drug-resistant viruses and their detection are very important epidemiologically. However our data and other studies suggest that other PIs should be replaced by LPV in the HAART regime.

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 Hepatitis C virus (HCV) NS3/4A Serine protease is an important drug target for treating patients with hepatitis C virus. However, its amino acid mutations, particularly A156G, commonly lead to the rapid emergence of drug resistance. Bosiprevir, simiprevir, and viniprevir drugs approved by the FDA show distinct resistance profiles against the HCV NS3/4A protease. In order to show the behavior of each of these drugs in the interaction with the protease in the wild type and A156G mutant, molecular dynamics simulation and binding free energy calculations were performed. MMPBSA-based binding free energy calculations showed that the binding affinity of each of the drugs in the interaction with NS3/4A protease in the wild type is significantly more than the interaction with the protease in the A156G mutant state. Free energy landscape (FEL) calculations revealed that in the presence of each of the drugs, more basins of conformations are formed. We hope that our data can provide useful insights for the design of a new effective inhibitory drug for the treatment of patients with the hepatitis C virus.
 

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In statistics, Entropy is a measure of disorder of time series. Entropy is used in physiologic for signal analysis. In physiologic science, Entropy is used for performance analysis of body organs such as heart and brain. Epileptic patients have been diagnosed by this technique. In this paper for the first time, Entropy is used to determine the health condition of mechanical systems. A special kind of Entropy, namely Permutation Entropy is used for this purpose.To perform the experiment an apparatus consisting of a motor coupled with a shaft has been designed and manufactured. Vibration signals from supporting bearing of this system in different shaft states namely healthy shaft, and shafts with 3, 5 and 7 mm crack were gathered with a vibration data analyzer. The vibration were taken from sensors mounted on bearing supports of the shaft. Shaft was subjected to a constant bending moment. The vibration signals were preprocessed by permutation Entropy method. Nine different features were extracted from the Entropy signals which are fed to an Adaptive Neuro Fuzzy Inference System (ANFIS). The designed ANFIS was capable of classifying different shaft states with an overall %96 percision.

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Computer-aided process planning (CAPP) is a bridge for integrating computer-aided design (CAD) and computer-aided manufacturing (CAM). One of the basic computer-aided process planning tasks is sequencing of machining features. Sequencing of machining features is determined based on technical and geometrical rules. In this paper, the technical rules, geometrical rules and sequencing of machining features method were discussed. At first, some of the technical rules were pointed. Then, the geometrical interactions were studied and two new geometrical rules were introduced for sequencing the machining features having geometrical interaction. These rules can yield unique results and they are identified easily by the computer systems. Also, an algorithm was introduced for automated application of these geometrical rules in computer systems. The conflict between the technical and geometrical rules that may occur in some cases was studied. This conflict must be considered in the sequencing of machining features methods. Finally, an algorithm was introduced for sequencing of machining features based on permutation. In this algorithm the technical and geometric rules were applied separately and step by step. If there is any conflict between technical and geometrical rules, this conflict could detect automatically in this algorithm. Algorithms were programmed and verified in PythonOCC.