Journal of Genetic Resources
Volume:8 Issue: 1, Winter -Spring 2022

Breast cancer is a major cause of cancer-associated death among Iranian women with an increasing trend in breast cancer incidence in recent years. However, few data about genetic determinants associated with breast cancer among Iranian females are available. According to the literature, the genetic variants at the non-coding region of 5q12 play a critical role in breast cancer susceptibility. Therefore, this study aims to determine the association of rs4415084 (T>C) and rs10941679 (A>G) with breast cancer risk in an Iranian sample population. Peripheral blood samples, taken from 72 patients and 65 controls, were subjected to DNA extraction and genotyping of the mentioned polymorphism by Tetra-primer amplification refractory mutation system PCR (Tetra-ARMS-PCR) assay. Also, the demographic characteristics of the participants were obtained. The results show that the majority of patients had estrogen-receptor (ER) and progesterone-receptor (PR) positive tumors (75% for either receptor) and 36 % were human epidermal growth factor receptor-2 (HER2) positive. Also, the majority of the tumors were at T2 (59.7 %), N0 (41.6 %), and M0 (86.1 %) grade. Moreover, a considerable association between the rs10941679 polymorphism and breast cancer was noticed (p=0.01) with significantly increased susceptibility of AG genotype. Genotyping of rs4415084 also revealed that TC and CC genotypes significantly increased breast cancer risk. This work revealed that the rs4415084 and rs10941679 at 5q12 might be risk-conferring factors for breast cancer among Iranian women, which could be employed in breast cancer screening and prognosis approaches.

Cancer Stem Cell (CSC) is known as a minor percentage of tumor cells inside various malignancies with shared common features with embryonic stem cells such as self-renewal capability and pluripotency. It is believed that not only stemness transcription factors but also pluripotent lncRNAs regulate various aspects of CSCs. It was demonstrated that the embryonic lncRNAs regulate the main features of these cells through interacting with ESC-associated transcription factors. LncRNA ES3 is a pluripotent lncRNA that was demonstrated to sustain the stemness status of human embryonic stem cells. However, there is little evidence for its contributory role in tumorigenesis. Therefore, in the present study, the possible expression of ES3 transcript in collected Colorectal Cancer (CRC) tissues and their non-tumor marginal samples were explored by employing the RT-qPCR strategy. Then, we accomplished a survival analysis of ES3 based on the TCGA database. Inconsistent with metadata, our results revealed that the ES3 expression markedly increased in CRC tissues rather than non-tumor marginal specimens. Furthermore, we detected that the ES3 expression meaningfully increased in high-grade and high-stage CRC tissues compared to low-grade and low-stage ones, respectively. Moreover, ES3 was significantly upregulated in tumor tissues along with increasing tumor size of CRC samples. Our findings, for the first time, demonstrated that lncRNA ES3 is expressed in CRC and its expression may contribute to the tumorigenesis process and progression of CRC. Hence, lncRNA ES3 can be regarded as a new cancer biomarker with possible utility in the diagnosis, prognosis, and therapy of colorectal cancer.

The emergence and outbreak of the deadly novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, become a global health problem in the last two years. SARS-CoV-2 is an enveloped virus with a non-segmented single-strand positive-sense RNA. It has some similarities with other coronaviruses, especially the SARS-CoV. However, the specific features of this virus have changed its pathogenicity and transmissibility compared to other coronaviruses. The distinctive structural differences of the SARS-CoV-2 spike protein have a key role in the kinetics of viral load and a broad range of virus tissue tropism. Because of these differences, SARS-CoV-2 has a greater affinity for binding host cell receptor angiotensin-converting enzyme 2 than SARS-CoV. Since its emergence, the SARS-CoV-2 genome has undergone several mutations. However, a small number can alter the virus antigenicity and clinical features of the disease, leading to the formation of different SARS-CoV-2 variants. Some of these variants have higher transmissibility, severity, and impact on host immunity than the original SARS-CoV-2. Although there are currently no specific therapeutic interventions for coronavirus disease 2019 (COVID-19), manufacturers are working to make and update vaccines by continuously monitoring antigenic and genetic changes in the SARS-CoV-2 population worldwide. Some of these vaccines are very effective against different variants of the virus, therefore in some countries, with widespread vaccination and compliance with health protocols, people have largely returned to normal living conditions. To better understand SARS-CoV-2, in this article, we reviewed its classification, genome organization, structure, and life cycle. In addition, an overview of the mutations occurring in the spike protein and the characteristics of the different variants is given here. Finally, vaccines produced against this coronavirus were briefly introduced.

Medicinal plants are stores of active and valuable secondary metabolites that have been economically beneficial for pharmacy and medicine. However, it is challenging to start large-scale and commercial cultivation of these plants since most of the arable land is mainly used to produce strategically essential crops. Other uncultivable lands are often affected by various abiotic stresses, one of the most important of which is salinity. Germination of plants is one of the critical stages during their growth period that is often affected by environmental stresses, especially salinity. In the present study, the seeds of medicinal plants such as Lavender (Lavandula angustifolia), Hyssop (Hyssopus officinalis), Black cumin (Nigella sativa L.), and Scrophularia (Scrophularia striata) were subjected to salinity stress at 20, 25, and 30 °C to determine the germination characteristics of their seeds. At each temperature, to create salinity stress, five levels of salinity potential, including 0, 50, 100, 150, and 200 mM NaCl were applied, prepared using sodium chloride salt with the required amounts. The results of this experiment generally showed that with increasing salinity concentration at different temperatures, all germination characteristics, including germination percentage, germination rate, shoot length, root length, shoot dry weight, dry root weight, and seed vigor index, decreased. Salinity stress is one of the most important abiotic stresses in areas with saline soil and water, which reduces the quality and yield of plants, especially medicinal plants, and weakens them against other environmental stresses. It seems that low salinity soil and water are needed to get the best yield for the commercial growth of plants.

Microbial alpha-amylases demonstrate more compatibility with industrial demands. These industrial enzymes have potential applications in various industrial parts, e.g., starch processing, brewing, baking bread, pharmaceuticals, and detergents. In this study, a mesophyll bacterium, Bacillus mojavensis strain UMF29, has been identified based on the 16S rDNA sequence and phylogenetic tree. After 72 h of incubation at 37 °C, the plates were inoculated with Lugol’s iodine, and the alpha-amylase-producing isolates were distinguished by clear zones in the blue background of starch agar plate around the colonies. Biochemical characterization of this enzyme was also investigated. Results showed that the optimal activity of this enzyme was at 50 °C, and pH of 7.0. In addition, the alpha-amylase exhibited optimum stability at 40 °C, and pH of 7.0. Some metal ions including Mn2+, Cu2+, Ca2+, Fe2+, Zn2+, Hg2+, and Mg2+ stimulated the alpha-amylase activity by about 122, 105, 61, 47, 46, 23 and 16%, respectively. The best activity of this enzyme was achieved in 0.5 M of KCl (81% enhancement), and 1.5 M of NaCl (9% enhancement). This alpha-amylase hydrolyzed a wide range of raw-starch granules (1.0 %, w/v) including potato, corn, grain, rice, and wheat and optimally was effective on wheat starch (16%, w/v) at 45 °C for 6 h with relative hydrolyses of ~10 U/ml. To our knowledge, it was also found that the alpha-amylase was a Ca2+-dependent enzyme for hydrolyzing higher concentrations of raw wheat starch (90-180 mg/ml) after 6 h of incubation at 45 ℃. Finally, these results indicated that UMF29 alpha-amylase showed high capacity in the degradation of the raw starch.

Lactuca undulata Ledeb. (Asteraceae) is an annual plant that has valuable compounds such as caffeic acid and its derivatives. This study aims to understand if there is detectable genetic diversity in the Iranian populations of L. undulata. For this purpose, the diversity of five L. undulata populations collected from different regions of Iran was evaluated based on the morphological characteristics and ISSR markers. A common garden experiment was conducted to assess the morphological variation of five L. undulata populations. The results of the study of morphological features showed that most of the studied traits have a high diversity among populations. In the PCoA performed, five populations of L. undulata were identified based on their morphological characteristics. In genetic analyses, using ISSR markers, a total of 60 bands were produced using four primers. The percentage of total polymorphism was 100% and no monomorphic band was obtained. The Nei gene diversity index (H) and Shannon diversity index (I) indicated high genetic diversity (0.24) in the populations. Analysis of molecular variance (AMOVA) showed that 73% of the genetic diversity was within the populations and another 27% was among the populations. The highest and the lowest genetic diversity were observed in Cheshmeh Ali and Qom populations, respectively. PCoA nearly separated genetically different populations into distinct groups. Five L. undulata populations were found to differ significantly in their morphological and genetic polymorphism. The studied populations were found in highly degraded habitats with a limited number of individuals. Degradation and loss of habitats are the major concerns in determining the conservation status of the species in general and at the population level in particular.

Carpinus is a genus of the family Betulaceae that comprises 42 species worldwide. Moreover, more than a third of total Caspian forests are occupied by C. betulus and it has an important role in slope stabilizing. C. orientalis, commonly known as oriental hornbeam, is a small tree or often shrub, rarely over 10 m tall, and a major pioneer species on slopes in shallow humus-poor or rocky soils. This species is distributed from southeastern Europe to the north of Iran, from west to easternmost of the Hyrcanian forest. Due to their peculiar and beautiful fruit cluster, some hornbeams are used as important ornamental plants. Taxonomy of this genus has always been problematic in Iran and the number of species ranges from 2 to 4 in different taxonomic literature. In the current study, we applied morphometric (PCA and cluster analyses) and molecular (ITS region) approaches to delineate the species boundary of the genus in Iran. Thirty-six quantitative and qualitative characters were used for morphological analyses. The PCA plot of morphological data divided the studied population into three groups. However, the cluster analysis revealed two major groups. Moreover, Iranian species of the genus Carpinus formed two distinct clades in the molecular analyses. The results of the present study showed that there are two Carpinus species in Iran, including C. betulus and C. orientalis with two subspecies and C. schuschaensis is introduced as a synonym for C. orientalis subsp. macrocarpa. In addition, the intraspecific morphological diversity has blurred species boundaries.

Squalene synthase (SQS, EC.2.5.1.21) is a key enzyme involved in the biosynthesis pathway of triterpenoid and steroidal saponins. The present study aimed to collect molecular information about the SQS gene in Achillea species, the medicinal plants rich in saponins. For this reason, genomic DNA was isolated from leaves of three Achillea species, including A. millefolium, A. wilhelmsii, and A. vermicularis in Iran, then partial SQS gene was amplified through PCR and sequenced (NCBI accession numbers: AmSQS KX589055, AwSQS KX685330, and AvSQS KX685331). AmSQS was 800 bp, containing four exons and three introns; AwSQS and AvSQS were 510 bp and 500 bp, respectively, containing three exons and two introns. Phylogenetic analysis demonstrated that the isolated SQS sequences were significantly similar to each other, and to Artemisia annua, another species of the genus Achillea. Furthermore, in the phylogeny tree, the SQS gene sequences of dicots and monocots were located in separate clades. The deduced amino acid sequences obtained from the isolated SQS gene had also a high similarity to each other and other organisms SQSs (>73% similarity to higher plants and more than 57% and 47% to the yeast and human). The deduced amino acid sequences included two regions overlapping with domains B and C of SQS, comprising an important motif of aspartate-rich (DYLED) for substrate binding via Mg2+-bridge. Data resulting from this study was the first report of SQS gene isolation and characterization in Achillea species, which also showed the ability of this gene in taxonomic classification.

Genus Lonicera has members that have opposite, narrowly elliptic to obovate leaves and yellow-white, red, or purple-red corollas together with capitate stigmas and undulated calyxes. According to Wendelbo (1965) in Flora Iranica, the 19 members of Lonicera are classified into two subgenera, i.e., Lonicera and Chamaecerasus, and three sections, i.e., Isika, Isoxylosteum, and Coeloxylosteum. The four studied species belong to subgenus Chamae cerasus and sections Isika and Coeloxylosteum. The taxonomy and phylogeny of this genus is highly complicated and controversial. The present study was done by the use of phenetic analyses of morphology together with Bayesian analyses of molecular data (ITS sequences) to illustrate the species relationships, taxonomic classification, and monophyly versus paraphyly of the species in genus Lonicera. We used seven Lonicera species for molecular studies, for which nrDNA-ITS sequences were newly obtained. Successive reweighting with rescaled consistency index was used to conduct the molecular examination, which showed close similarities among the results of maximum likelihood, maximum parsimony, and Bayesian methods based on the ITS dataset were observed. This study showed that in general, it is possible to differentiate the species via morphological features. Phylogenetic relationships within Lonicera were revealed, and ITS-based phylogenetic trees and morphological characters were in agreement.

Life-history traits and biometrics of plant development are greatly influenced by their changing environment. To survive under various stressful environments, plants develop a multifaceted regulatory network that is mainly governed by transcription factors, including the dehydration responsive element binding (DREB) family. The roles of DREB1A have been investigated in responses of plants to various abiotic stresses, however, its effects on plant growth and development over the whole life cycle has not yet been fully described. Here, we studied detailed developmental characterizations of dreb1a T-DNA insertional mutant alongside a previously reported DREB1A over-expressing plants (OX28) in Arabidopsis thaliana. Seed germination, vegetative and reproductive growth stages and plant yield were also investigated. Under normal growth conditions, both dreb1a and OX28 plants exhibited reduced seed germination and delayed early development. In addition, both dreb1a and OX28 plants showed prolonged vegetative growth and delayed transition from vegetative to reproductive development. At the reproductive phase, the time between the emergence of flower stem bolting and opening of the first flower in dreb1a was 15% shorter in comparison to wild type (WT-Col0). In contrast, the OX28 plant had a prolonged reproductive development with a remarkably increased number of flowers per plant. Interestingly, lateral branches on the main inflorescence stem showed a lower number in dreb1a, as opposed to the OX28 plant. Despite these observations, in both dreb1a and OX28 plants the total seed weight was decreased significantly. Our findings proposed that there was a relationship between a high expression level of the DREB1A gene with the development and seed yield of A. thaliana.

Lack of improved rice varieties has been identified as one of the challenges of rice research and development in Ethiopia, hindering the national production and productivity of the crop. Hence, the national rice research program of the country has tried to introduce and evaluate the diverse upland rice genotypes under the rainfed cropping season. In this experiment, 100 upland rice genotypes were introduced and evaluated with three locally well-adapted upland rice varieties as the standard checks using the augmented randomized complete block design/RCBD experimental design with a plot size of 1.5m2 and 3 rows per plot. The seeds were drilled in rows with a seed rate of 60 kilograms per hectare (kgh-1). The Nanoparticles/NPS (124 kgh-1) and urea (100 kgh-1) fertilizers were applied. The days to 50% heading, days to 85% maturity, plant height, panicle length, number of filled grains per panicle, number of unfilled grains per panicle, grain yield, and 1000 seed weight in gram were collected and subjected to a statistical analysis using SAS statistical software with 9.4 version from which a significant variation for all the traits was observed showing the presence of genetic variability among the rice genotypes. The genotypes were highly and significantly varied on their grain yield (coefficient of variation/CV= 7.86***), 1000 seed weight (CV= 9.97**), and days to 85% maturity (CV= 2.38**). A lower genotypic coefficient of variance and a higher phenotypic coefficient of variance among the genotypes were obtained, indicating that the variation was more due to environmental effects.

CRISPR-Cas9 is the most important tool in genome engineering in recent years. The efficiency of this instrument on active and non-active genes is variable. Programmed cell death protein 1(PD-1) is a surface acceptor on T cells, B cells, and dendritic cells. This protein has an important role in the production of inducing tolerance in lymphocytes. Nowadays, this characteristic is used in cell therapy and immunotherapy of cancer. In the present study, the peripheral blood mononuclear cells and HEK293 cells were selected as expression and non-expression cells of the PD-1 gene. Six pairs of sgRNA were designed for the PD-1 gene. The transfected cells were sorted by the FACS machine. A common pair of primers were used for amplification of cute regions. Px458 was used as an expressional vector for the transfection of PBMCs and HEK293. Transfection was done using lipofectamine and electroporation methods. In PBMCs, 2 guides, sgRNA (3+1) and sgRNA (3+5) were able to disrupt the PD-1 gene. In contrast, in HEK293, none of the 6 guides were able to disrupt it. According to the results obtained, the PD-1 gene cutting in HEK293 cells was failed. However, it was successful in PBMCs. Therefore, it can be told that the heterochromatin region or other genome remodeling mechanisms such as epigenetic remodeling inhibit the PD-1 gene cutting by CRISPR-Cas9 in HEK293 cells.