فصلنامه ژنتیک نوین
سال هفدهم شماره 1 (پیاپی 68، بهار 1401)

Today, the approach of many biologists and biotechnologists is to replace naturally evolved molecules with man-made mimetic molecules, so that they can take advantage of the intrinsic potential of diversity in the challenge of overcoming the limitations of natural evolution and reach for alternative molecules. These molecules, commonly called mimetic molecules, are originally and structurally different from natural types, but can have very similar capacities to natural molecules. So far, the diverse applications of antibodies in research, diagnosis, and treatment have been extensively developed, and their advantages and disadvantages have been elucidated. Small size, elimination of post-translational modifications, increased affinity for ligand binding, increased temperature stability, activity in the wide pH range and lack of structural disulfide bond, etc. are among the basic considerations in introducing a set of antibody mimetics. Since the primary scaffolds of these molecules are known domains of human proteins, they are free of immunological reactions. The antibody mimetics introduced so far include DARPins, Avimers, Aptameric peptides or Affimers, Atrimers, Affibodies, Adnectins, Anticalins, Konitz domains, Knottins, and Fynomers, which were designed and manufactured for the diagnostic and in vivo imaging, molecular detection in biological samples, treatment of cancer and inflammatory diseases, and drug delivery. In this article, first, the basis and applications of antibody mimetics are introduced, and then the origin, construction, and particular applications, along with their likely limitations and future prospects, will be discussed separately.

This study aimed to investigate the effect of zinc nano-chelate on vegetative characteristics and expression of genes affecting the synthesis of thymol and carvacrol in thyme. The experimental design was factorial in a completely randomized design with three replications. The first factor included two cultivars of thyme and the second factor was the foliar application of zinc nano-chelate at four levels (zero (control), 2.5, 3.5, and 4.5 mg/l). The results of the present study showed that the highest content of carotenoids was at the level of 4.5 mg /l and the highest content of caracrol essential oil was at the level of 2.5 mg /l nano-zinc chelate. The results of comparing the mean of interaction treatments also showed that both cultivars showed the highest plant dry yield, chlorophyll a and b content in response to spraying of 3.5 mg /l nano-zinc chelate. In this study, the highest thymol content of essential oil was recorded in the levels of 2.5 and 3.5 mg/l  for Thymus vulgaris cultivars and Thymus Dena cultivars at the levels of 2.5 and 4.5 mg / L. The results showed that the effect of nano-chelate zinc foliar application on the expression of CYP71D180 and CYP71D178 genes was significant at the level of 1% and on the expression of DXR and CYP71D180 genes at the level of 5% probability. In this study, the level of 2.5 mg / l nano-zinc chelate increased the expression of DXR gene by 27.36% compared to the control treatment. Also, foliar application of two levels of 2.5 and 3.5 mg / l increased the expression of gamaterpinene synthase genes by 51.13% and 2.38%, expression of CYP71D180 gene by 36.31% and 42.28, and the expression of CYP71D178 gene by 61.70% and 36.34%, respectively.

Effect of genetic markers to enhance response to selection for weekly body traits in Japanese quails were investigated using deterministic simulation. The QTL variance for body weight at 0, 1, 3, 4 weeks of age was 1.25, 1.63, 1.18 and 1.13 percent of whole variance, respectively. Due to QTL variance, increased response to selection was 3.16, 2.92, 3.10 and 4.05 g for body weight at 0, 1, 3, 4 weeks of age, respectively. The highest value was related to body weight at 4 weeks of age because of its low heritability. Inbreeding coefficient for breeding programs are decreased because the birds are selected based on own performance generally. Therefore, using genetic markers in breeding programs, is suitable because of enhanced response to selection and decreased inbreeding coefficient in all traits like those with difficult and easily measurement.

The biofilms production by Staphylococcus aureus is one of the problematic factors of these bacteria.One of the biofilm gene loci is icaD, which plays an important role in biofilm production. Many plants have medicinal and antimicrobial properties. In this study the antimicrobial properties and molecular effects of Mary thistle and ginseng extracts on the expression of icaD biofilm gene in S. aureus were studied. The extracts of Mary thistle and ginseng were prepared and after evaluation of bacterial growth inhibition zone under the influence of these extracts, the inhibitory effect of growth was assessed by MIC test. Following RNA extraction and cDNA synthesis from strains treated with Mary thistle and ginseng extracts and untreated strains, the expression levels of icaD biofilm gene in pathogen and standard strains of S. aureus were analyzed by Real time PCR. The diameter of growth inhibition zone in standard strain affected by 100 mg/ml of the Mary thistle and ginseng extracts were 10 and 8 mm, respectively. The diameter of the growth inhibition zone for the pathogen strain was 10 and 12 mm, respectively. A combination of equal use of Mary thistle and ginseng extracts also created a 15 mm growth inhibition zone in both studied strains. In different concentrations of plant extracts (39.6 g/ml to 5000 g/ml) used in MIC, all strains were grown. According to Real time PCR results, icaD biofilm gene expression increased 17-fold in the standard strain treatment with Mary thistle extract and 24-fold under the influence of ginseng extract. In the pathogenic strains, icaD gene expression was reduced to 0.3% under the influence of Mary thistle extract and the expression of this gene was almost inhibited. Ginseng extract also reduced the expression of this gene in the pathogen strain to about 49%. The combined use of Mary thistle and ginseng extracts also reduced icaD gene expression in the pathogen strain to about 6% of the control sample and led to a 94% reduction in the expression of this gene.

The ABC-transporter system is found in the three main domains of prokaryotes, eukaryotes, and fungi. Most of them mediate the active adsorption or release of specific molecules into biological membranes. So far, a comprehensive study on the expression pattern of ABC-transporter genes has not been done. The genes were selected based on biological function, and the pattern of relative gene expression in different stolon development stages in responses to heat (29°C), cold (4°C), ABA (50, 75 and 100 µM) and control (greenhouse conditions) were studied. In order to evaluate the relative changes in the expression of StABC transporter genes in response to abiotic stresses, real-time PCR was used. The effect of cold stress on the relative changes expression of StABC transporter genes in different stages of potato development showed that StABC-012 and StABC-002 genes have increased expression and StABC-001, StABC-024, StABC genes-002, StABC-124, StABC-138 had high expression level in response to heat stress and ABA all StABC transporter genes at different developmental stages had lower expression than control conditions. StABC-084 and StABC-138 genes in 50 μM treatment of ABA in the first developmental stage and StABC-084, StABC-001 and StABC-124 genes in 75 μM in the third developmental stage and StABC-024 in 100 μM ABA in the first stage have a higher expression relative to other developmental stages. The third development had a higher expression other developmental stages. Also, to ensure the effect of abiotic stresses on the potato plant, the amount of proline (mg/g FW) and ABA (ppm) in different stages of stolon development were measured and evaluated. The content of proline levels also increased at different developmental stages. In heat stress, the amount of proline in the first, second and third developmental stages were 41.24, 67.2 and 21.48 mg /g FW, respectively. Also, the amount of proline in different time levels of cold stress (temperature 4°C) showed a significant increase. so that, in the first developmental stage at the treatment level of 48 hours (76.92 mg / g fresh weight) the highest and third development stage had the lowest proline content at the treatment level of 48 hours (44.58 mg / g fresh weight). The results of ABA assay show a significant difference with control; in a concentration of 50 μM, showed the highest increase in the third developmental stage (0.777 ppm). Also, by increasing the hormone concentration to 75 μM, the amount of ABA in the second developmental stage compared to the control conditions by 0.0073 ppm shows an acceptable increase. The aim of this study was to investigate the relative changes in the expression pattern of ABC transporter genes at different stages of development stolon in response to cold, heat and ABA stresses. The findings of this study improve the understanding of the function of the ABC transporter gene family and facilitate further studies on the detailed molecular and biological function of potatoes.

To identify single nucleotide polymorphisms (SNP) in beta-cyclase (B-CYC) and phytoene synthase (PSY1) genes in 93 tomato genotypes and three commercial cultivars, fragments with a length of 409 and 1000 bp were amplified from the coding regions of these two genes. The amplified fragments of both genes were digested using Tru1I and PstI restriction enzymes to visualize polymorphisms among the studied genotypes, but no polymorphism was observed. Therefore, four individuals from different populations (Urmia, Sardasht, Turkey and Boukan for CYC-B; Urmia, Sardasht, Turkey and Piranshahr for PSY1) were selected and the amplified fragment of the genes were sequenced in these genotypes. After retrieval of the sequenced fragments of each gene, multiple alignment was used for the sequences of the genes to identify SNPs using Clustal omega software. Eight SNPs were identified in the CYC-B gene, 75% of which was transition with a frequency of 50% A/G, 25% T/C, and 25% of which was transversion with a frequency of 12.5% ​​C/A and 12.5% G/C. In PSY1 gene, eight SNPs were also identified in the PSY1 gene, with three and five SNPs in the exon and intron regions, respectively. 62.5% of these SNPs was transition with a frequency of 37.5% A/G, 25% T/C, and 37.5% of them was transversion with a frequency of 25% C/G and 12.5% ​​C/A. The average number of SNPs per 100 bp in the amplified fragment of CYC-B was 0.44, while taht was 1.26 and 0.71 for intron and exon of PSY1, respectively. The SNPs identified in this study can be used in the preparation of genetic maps as well as the identification of functional markers associated with fruit color in tomato.

Various species of genus Trigonella are important from medical and food aspects.Assessment of genetic diversity is an important principal for plant breeding, providing an opportunity to identify the novel genetic characters and new genes for breeders. In the current work, 90 fenugreek ecotypes were evaluated for genetic diversity using several start codon targeted polymorphism (SCoT) and universal rice primer (URP) markers. Ten SCoT and 10 URP primers amplified a total of 100 and 109 fragments, respectively, which out all fragments were polymorphic. The mean values of polymorphic information content (PIC) for both marker systems was 0.34. However, the highest means values for MI and Rp parameters were estimated for URP compared with SCoT markers. The results of the molecular analysis of variance (AMOVA) based on SCoT, URP, and SCoT+URP data showed that the genetic variation within populations is more than between them. Based on genetic variation parameters, the highest number of observed alleles (Na), Shannon’s information index (I), Nei’s genetic diversity (H) and the percentage of polymorphic loci (PPL) were found in T. foenum-graecum and T. monantha species. Cluster analysis based on each marker and pooled data clustered all investigated samples into three main clusters. Furthermore, our results indicated that the grouping pattern obtained by pooled data is in accordance to taxonomic structure of species. In conclusion, our results revealed the high rate of genetic diversity within fenugreek ecotypes. Hence, this germplasm can be used as a valuable gene source for breeding programs.

Yellow or strip rust, caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most important wheat diseases in Iran and all over the world. Genetic resistance is the best control method for this disease. So far, several resistance genes have been identified for this disease. Due to the rapid evolution of yellow rust, the resistances of these genes were not durable. According to the literatures, Yr5 and Yr15 are the most important resistance genes in the seedling stage. In the present study, Yr5 and Yr15 were transferred to Iranian cultivars, Roshan, Mahdavi and Shiraz, using marker assisted backcross (MAB). For this purpose, each of these cultivars was crossed with the standard lines carrying the mentioned genes, and then F1 progeny were crossed with their own recurrent parent (Iranian cultivars) to create backcross 1 (BC1F1) generation. In this generation, in each population, heterozygous genotypes carrying the resistance genes were identified using a specific marker, then backcrossed with their own recurrent parent to create second backcross (BC2F1) generation. Third backcross (BC3F1) generation was also created using the same method. In each backcross generation, two types of genotypes including susceptible homozygous and heterozygous were observed. The similarities of the created isogenic lines with their recurrent parents are 93.75%. After some next backcross and a selfing generation, yellow rust resistant isogenic lines would be created. If created resistant isogenic lines are significantly better than newly introduced cultivars, they could introduced to the farmer's to reduce pesticide consumption in addition to disease control. The created resistant lines will have a chance to be introduced as a new cultivar if they have better agronomic characteristics in comparison with newly introduced cultivars.

Litter size is one of the most important reproductive criteria in animals. Hence, the effect of this trait on the productivity of the flock has been addressed by its genetic enhancement through molecular technologies. Previous studies have shown that the major genes including GDF9, BMP15, ALK6, and B4GALNT2 (FecL) are associated with litter size. The effect of FecL mutation in homozygous states is additive and results in the release of three ovum for two copies of this gene. The aim of this study was to investigate polymorphism DLX3: c. * 803A> G in B4GALNT2 (FecL) gene on chromosome 11, using High Resolution Melting technique (HRM), and it is association with litter size in Zandi sheep. HRM analysis is a method that reduces the amount of fluorescence during the process of thermal melting of the DNA through color exhaust. The results of HRM were consistent with the sequencing results. No mutations were observed in the nucleotide sequence of the target studied in the Zandi sheep. Therefore, B4GALNT2 gene is monomorphic for this site length in 232bp fragment of this gene. We discovered many deletions, but there was no change in the resulting amino acid. Therefore, that did not result in structural alteration of the protein. In addition, two new mutations included A> G mutation at position 2242 in sample 7 and mutation C> G at position 2241 in sample 77 were detected. It seems necessary to investigate mutations in other major genes for this breed