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Background: The COVID-19 pandemic is a red alarm for global health, so researchers around the world are working on it to design an effective vaccine against it. Protein is one of the candidates for vaccine development which plays an important role in virus pathogenesis. Accordingly, this study was done to evaluate the critical characteristic of this protein as a vaccine candidate using in-silico analysis.Methods: The sequence of SARS-CoV-2-associated E protein was recruited from NCBI and subjected to the IEDB software to evaluate the most potent epitopes. The capacity of the interactions of HLA-I and HLA-II molecules with selective peptides was studied using IEBD tool kit. The E protein sequence was subjected to B cell and T cell tests to realize the most promising peptides that could act as COVID-19 vaccine.Results: Among the tested peptides for the T cell-test, this study found two interesting epitopes: VSEETGTLI and LTALRLCAY that exhibit high binding affinity as a strong indicator to HLA-I and HLA-II alleles together. The results of the analysis demonstrated that some epitopes in the E protein have a relatively higher immunogenicity score based on interaction with HLA-II, such as SEETGTLIVNSVLLF, TLIVNSVLLFLAFVV, LAFVVFLLVTLAILT, LAILTALRLCAYCCN, and SVLLFLAFVVFLLVT. Furthermore, two sequences (FVSEET and PSFYVYSRVKNLNSSRVP) were reported as the selective linear epitopes for B cell, on the surface of SARS-CoV-2 E protein and being Immunogenic.Conclusion: Since E protein can stimulate favorable immune responses, T and B- cell responses, its evaluation in patients with COVID-19 is of a great importance.

Background: Nowadays, ovarian cancer is the most lethal gynecological cancer worldwide. Tumor debulking surgery followed by Cisplatin-based chemotherapy is the first line of ovarian cancer therapy. However, many patients experience a relapse of the disease due to chemotherapy resistance. Accordingly, this study aims to investigate the ability of microwave (MW) radiation to increase the susceptibility of ovarian cancer cells toward Cisplatin (Cis). Methods: Firstly we designed a hand-made electromagnetic field exposure system and CO2 incubator to irradiate cells with a frequency equal to 2450±30 MHz and a power density of 2.47 mW/cm2 at a distance of 30 cm from the antenna. Two ovarian cancer cell lines A2780 (Cisplatin-sensitive) and A2780CP (Cisplatin-resistant) were subjected to either Cis, MW alone or Cisplatin + microwave radiation (Cis+MW). Cell viability, apoptosis, and P53 gene expression were assessed following drug/radiation exposure. Results: After 48 hours of treatment the combination of Cis and MW radiation has significantly inhibited the growth of the A2780 and A2780CP cell lines in comparison with Cis-control groups. The percentages of early apoptosis induced by Cis+MW was significantly increased in comparison with Cis alone. P53 expression was significantly upregulated after treatment with Cis+MW. Conclusion: It can be concluded that MW radiation has been able to decrease the resistance of ovarian cancer cells to Cis and it may improve the chemotherapy protocol for ovarian cancer treatment.

Background: The objective of this study was to design and construct a CO2 incubator with nonmetallic walls and to investigate the viability of the cells and microwave irradiance inside this incubator. Methods: Because the walls of conventional incubators are made of metal, this causes scattering, reflection, and absorption of electromagnetic waves. We decided to build a nonmetallic wall incubator to examine cells under microwave radiation. Incubator walls were made using polyvinyl chloride and Plexiglas and then temperature, CO2 pressure, and humidity sensors were placed in it. Atmel® ATmega1284, a low-power CMOS 8-bit microcontroller, collects and analyzes the sensor information, and if the values are less or more than the specified limits, the command to cut off or connect the electric current to the heater or CO2 solenoid valve is sent. Using a fan inside the incubator chamber, temperature and CO2 are uniforms. The temperature of the points where the cell culture plates are placed was measured, and the temperature difference was compared. Ovarian cancer cells (A2780) were cultured in the hand-made and commercial incubators at different times, and cell viability was compared by the MTT method. Microwave radiation in the incubator was also investigated using a spectrum analyzer. The survival of cells after microwave irradiation in the incubator was measured and compared with control cells. Results: The data showed that there was no significant difference in temperature of different points in hand-made incubator and also there was no significant difference between the viability of cells cultured in the hand-made and commercial incubators. The survival of irradiated cells in the incubator was reduced compared to control cells, but this reduction was not significant. Conclusion: This incubator has the ability to maintain cells and study the effects of electromagnetic radiations on the desired cells, which becomes possible by using this device.

Objective(s): Helicobacter pylori is one of the most prevalent human infectious agents that is directly involved in various upper digestive tract diseases. Although antibiotics-based therapy and proton pump inhibitors eradicate the bacteria mostly, their effectiveness has been declined recently due to emergence of antibiotic-resistant strains. Development of a DNA vaccine is a promising approach against bacterial pathogens. Genes encoding motility factors are promising immunogens to develop a DNA vaccine against H. pylori infection due to critical role of these genes in bacterial attachment and colonization within the gastric lumen. The present study aimed to synthesize a DNA vaccine construct based on the Flagellin A gene (flaA), the predominant flagellin subunit in H. pylori flagella. Materials and Methods: The coding sequence of flaA was amplified through PCR and sub-cloned in the pBudCE4.1 vector. The recombinant vector was introduced into the human dermal fibroblast cells, and its potency to express the flaA protein was analyzed using SDS-PAGE. The recombinant construct was intramuscularly (IM) injected into the mice, and the profiles of cytokines and immunoglobulins were measured using ELISA. Results: It has been found that flaA was successfully expressed in cells. Recombinant-vector also increased the serum levels of evaluated cytokines and immunoglobulins in mice. Conclusion: These findings showed that the pBudCE4.1-flaA construct was able to activate the immune responses. This study is the first step towards synthesis of recombinant-construct based on the flaA gene. Immunization with such construct may inhibit the H. pylori-associated infection; however, further experiments are urgent.

BackgroundBiofilm is an accumulation of cells, which are formed on mucosal surfaces of the host as well as on medical devices. The inherent resistance of Candida strains producing biofilms to antimicrobial agents is an important and key feature for biofilm growth, which can lead to treatment failure. This resistance is due to the regulatory increase of the output pumps, the presence of extracellular matrix, and the existence of persister cells. Persister cells are phenotypic variants that have MICs similar to antibiotic-sensitive populations and are able to tolerate high doses of antibiotics. The current study investigated the possible role of EFG1, BCR1, and CAT1 in the establishment or maintenance of persister cells in Candida albicans strains that produce biofilms.MethodsAfter identifying Candida isolates by molecular methods, C. albicans isolates were confirmed by sequencing. Isolation of persister cells and determination of their MIC were performed by microdilution method. Then, RNA extraction and cDNA synthesis were performed from 60 C. albicans isolates under promoting and inducing conditions. Afterward, the mean expression of BCR1, EFG1, and CAT1 genes in both persister and non-persister groups was calculated using real-time qPCR. Phylogeny tree of persister and non-persister group isolates was drawn using ITS fragment.ResultsA total of 77 persister isolates were taken from the oral cavity of HIV patients as well as from patients undergoing chemotherapy. Biofilm intensity in persister isolates separated from HIV-infected patients was different from the non-persister group. The mean fold change of BCR1 (10.73), CAT1 (15.34), and EFG1 (2.41) genes in persister isolates was significantly higher than these genes in isolates without persister.ConclusionIt can be concluded that the most important factor in the production of persister cells is biofilm binding and production, not biofilm development or mature biofilm production, which was found in the expression of BCR1 gene without change in the expression of EFG1 gene in the persister group. Also, catalase plays an essential role in the production of persister in C. albicans biofilm producers with ROS detoxification.

Objective(s): Acinetobacter baumannii is one the most dangerous opportunistic pathogens in hospitalized infections. This bacterium is resistant to 90% of commercial antibiotics. Therefore, developing new strategies to cure A. baumannii-infections is urgent. The DNA vaccines new approach in which the immunogen can be directly expressed inside the target cells through cloning of immunogen into an expression vector. The outer membrane protein A(OmpA) is one the critical factors in pathogenicity of A. baumannii which has been repeatedly described as a powerful immunogen to trigger the immune responses. As the pure form of the OmpA is insoluble, vaccine delivery is very hard. Materials and Methods: We previously cloned the ompA gene from A. baumannii into the eukaryotic expression vector pBudCE4.1 and observed that the OmpA protein has been considerably expressed in eukaryotic cell model. In current study, the immunogenic potential of pBudCE4.1-ompA has been evaluated in mice model of experimental. The serum levels of IgM, IgG, IL-2, IL-4, IL-12 and INF-γ were measured by enzyme-linked immunosorbent assay (ELISA) after immunization with ompA-vaccine. The protective efficiency of the designed-DNA vaccine was evaluated following intranasal administration of mice with toxic dose of A. baumannii.Results: Obtained data showed the elevated levels of IgM, IgG, IL-2, IL-4, IL-12 and INF-γ in serum following the vaccine administration and mice who immunized with recombinant vector were survived more than control group.Conclusion: These findings indicate ompA-DNA vaccine is potent to trigger humoral and cellular immunity responses although further experiments are needed.

Objective(s): Charcot-Marie Tooth disease (CMT) is one of the main inherited causes of motor and sensory neuropathies with variable expressivity and age-of onset. Although more than 70 genes have been identified for CMT, more studies are needed to discover other genes involved in CMT. Introduction of whole exome sequencing (WES) to capture all the exons may help to find these genes.Materials and Methods: Here, we tried to find the genetic cause of the neuropathy in two Iranian brothers using WES. Blood sample was collected from probands and their family members to extract the genomic DNA. The extracted DNA from one of the affected case was subjected for WES. The variant calls were filtered to reveal the pathogenic variant. Presence of the candidate mutation was confirmed using Sanger sequencing. The pathogenic potential of the variant was examined using in silico software. Using ClustalW multiple alignment, the presence of variant in conserved domain of protein was investigated. The parent and another affected boy were also checked for presence of the variant using PCR-sequencing. Results: The obtained data presented a novel TTC del mutation in CDS 738 of dystrophin related protein 2 (DRP2) gene, which was validated by sequencing. The variant was located in a conserved domain of DRP2 protein and predicted as pathogenic. Two affected boys were hemizygous for the mutation and received the mutation from mother. Conclusion: Here, we provided the evidence for the contribution of DRP2 in CMT. Also, the symptoms shed light on molecular aspect of this genetically heterogeneous disease.

OBJECTIVES Oropharyngeal candidiasis is one of the most common opportunistic fungal infections among human immunodeficiency virus (HIV)-infected individuals. The most common cause is Candida albicans, followed by non-albicans Candida. This study aimed to identify colonized Candida species in HIV-infected patients from Ahvaz, Iran. Additionally, the relationships between immunity-related factors, lifestyle, and colonization of Candida spp. were studied. METHODS Oral swabs were taken from 201 HIV-positive patients referred for consultations at the Behavioral Modification Center. Oral Candida colonization was detected using culture-based and molecular assays. Data were assessed by descriptive statistics and analyzed to investigate the correlation between Candida colonization and various factors, including the CD4+ cell count and viral load. RESULTS It was found that 43.8% of patients were positive for Candida. The most common species was C. albicans (48.0%), followed by non-albicans Candida isolates, including C. dubliniensis, C. glabrata, C. tropicalis, C. parapsilosis, C. guilliermondii, C. kefyr, and C. krusei. Colonization of Candida spp. in patients was associated with a CD4 count ≤200 cells/mm3 (odds ratio [OR], 4.62; p

Bardet-Biedl syndrome (BBS) is a pleiotropic and multisystemic disorder characterized by rod-cone dystrophy, polydactyly, learning difficulties, renal abnormalities, obesity and hypogonadism. This disorder is genetically heterogeneous. Until now, a total of nineteen genes have been identified for BBS whose mutations explain more than 80% of diagnosed cases. Recently, the development of next generation sequencing (NGS) technology has accelerated mutation screening of target genes, resulting in lower cost and less time consumption. Here, we screened the most common BBS genes (BBS1-BBS13) using NGS in an Iranian family of a proposita displaying symptoms of BBS. Among the 18 mutations identified in the proposita, one (BBS12 c.56T>G and BBS12 c.1156C>T) was novel. This compound heterozygosity was confirmed by Sanger sequencing in the proposita and her parents. Although our data were presented as a case report, however, we suggest a new probable genetic mechanism other than the conventional autosomal recessive inheritance of BBS. Additionally, given that in some Iranian provinces, like Khuzestan, consanguineous marriages are common, designing mutational panels for genetic diseases is strongly recommended, especially for those with an autosomal recessive inheritance pattern.

Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer.

MicroRNA-155 (miR-155) has a critical role in pro-inflammatory activation and tumor progression. In addition, miR-155 has various oncogenic effects in the tumor microenvironment by targeting the suppressor gene of cytokine signaling-1(SOCS-1) and interleukin-6 (IL-6). This study investigated the association of inflammatory changes with the variations of miR-155 expression in newly diagnosed breast cancer (NDBC) patients. Seventy NDBC patients were categorized as lobular and ductal subgroups and forty healthy individuals participated in this study. The expression rate of miR-155 and its downstream target gene, SOCS-1, as well as the plasma levels of IL-6, were evaluated in peripheral blood mononuclear cells of NDBC patients; using real-time PCR and enzyme-linked immunosorbent assay, respectively. Our results indicated an over-expression of miR-155 in the PBMCs of NDBC patients which was significantly associated with the tumor grade and the type of ductal carcinoma. In contrast, a significant downregulation of SOCS-1 was observed in NDBC patients compared to control group, however, there was no significant difference between two subtypes of BC. Furthermore, a higher concentration of plasma IL-6 was detected in NDBC patients compared to the healthy control group which had an inverse correlation with the SOCS-1 levels. According to the potential effects of miR-155 on regulating the expression of SOCS-1 and IL-6, we suggest this small transcript as a promising diagnostic marker for various types of BC patients.

Abstract Background: Cytogenetics and association studies showed that folate gene polymorphisms can increase the risk of chromosomal nondisjunction and aneuploidies. The folate-metabolizing gene polymorphisms in Down syndrome mothers (DSM) have been assessed in a variety of populations. Reduced folate carrier 1 (RFC1) and cystathionine beta-synthase (CBS) are key enzymes in folate metabolism. Objective: 2 common polymorphisms, CBS 844ins68 and RFC1 A80G, were analyzed to determine their probable risk for having Down syndrome (DS) babies in young mothers of Khuzestan province, Iran. Materials and Methods: This study was conducted on 100 mothers who had trisomy 21 DS children. 100 age- and ethnic-matched mothers with at least 2 healthy children and no history of abnormal pregnancies were considered as control. The samples were collected from all the mothers from June 2019 to April 2021. Genomic DNA was extracted from peripheral blood. The CBS-844ins68 and RFC1-A80G were genotyped using polymerase chain reaction-electrophoresis and restriction fragment length polymorphism, respectively. Results: The frequency of RFC1 AG and GG genotypes in DSM was significantly higher than the control mothers (odds ratio [OR] of 2.38 and 3.07, respectively). The heterozygote genotype of CBS 844ins68 was significantly more prevalent among DSM than the control (OR: 2.419). The OR was significantly increased to 6.667 when the homozygote of both variants was found together. Conclusion: Studying polymorphisms possibly increases the susceptibility of having a DS child. However, ethnicity, nutrition, and epistatic interactions are considerable factors to be evaluated in future studies.

Background and purpose: Hyperlipidemia is one of the main risk factors for coronary artery disease and is defined as abnormal elevation of lipids or lipoproteins in the blood. Pcsk9 is the ninth member of the proprotein convertase family that binds to the LDLR on the surface of the hepatocyte, leading to degradation of LDLR in lysosomes which could cause hyperlipidemia. The present study aimed to analyze the methylation status of pcsk9 promoter in patients with hyperlipidemia. Materials and methods: This case-control study was conducted in 50 patients with hyperlipidemia and 50 healthy controls. DNA isolation from whole blood was performed using salting out procedure. Promoter methylation of the Pcsk9 gene was analyzed by methylation-specific PCR (MSP). Ten MSP products were sequenced to confirm the data obtained. Results: According to MSP results, methylation pattern of pcsk9 gene promoter displayed an unmethylated status among the patients and control individuals. In other words, no methylation was seen in case and control samples. Conclusion: The current study showed no significant association between PCSK9 methylation pattern and blood lipid profile level in case group and control group.

Abstract Background Hepatocellular carcinoma (HCC) is the most common type of liver cancer that occurs predominantly in patients with previous liver conditions. In the absence of an ideal screening modality, HCC is usually diagnosed at an advanced stage. Recent studies show that loss or gain of genomic materials can activate the oncogenes or inactivate the tumor suppressor genes to predispose cells toward carcinogenesis. Here, we evaluated both the copy number alteration (CNA) and RNA sequencing data of 361 HCC samples in order to locate the frequently altered chromosomal regions and identify the affected genes. Results Our data show that the chr1q and chr8p are two hotspot regions for genomic amplifications and deletions respectively. Among the amplified genes, YY1AP1 (chr1q22) possessed the largest correlation between CNA and gene expression. Moreover, it showed a positive correlation between CNA and tumor grade. Regarding deleted genes, CHMP 7 (chr8p21.3) possessed the largest correlation between CNA and gene expression. Protein products of both genes interact with other cellular proteins to carry out various functional roles. These include ASH1L, ZNF496, YY1, ZMYM4, CHMP4A, CHMP5, CHMP2A and CHMP3, some of which are well-known cancer-related genes. Conclusions Our in-silico analysis demonstrates the importance of copy number alterations in the pathology of HCC. These findings open a door for future studies that evaluate our results by performing additional experiments.

Background: MicroRNA-155 is a key player in inflammatory reactions, carcinogenesis, and tumor development. In this study, polymorphism of miRNA-155 rs767649 T>A and its gene and suppressor of cytokine signaling-1 (SOCS-1) expression were investigated in relation to cancer susceptibility and development in breast cancer (BC) patients. Materials and Methods: Polymorphism of miRNA-155 rs767649 T>A was evaluated between a population of 174 patients with BC and 129 controls using restriction fragment length polymorphism and the expression of miR-155 and SOCS-1 were examined in peripheral blood mononuclear cells (PBMCs) by real-time polymerase chain reaction. Results: TT genotype of miR-155 rs767649 T>A was associated with higher level of miR-155 in PBMCs of BC patients relative to AT and AA genotypes (21.76 ± 4.4, 4.046 ± 1.35, 2.56 ± 0.81, respectively; P < 0.001) and increased lymph node metastasis (r = 0.292, P = 0.001), not BC susceptibility (P = 0.402 and P = 0.535; respectively). TT genotype of miR-155 rs767649 T>A was associated with less gene expression of SOCS-1 in PBMCs of BC patients compared to AT and AA genotypes (1.173 ± 0.57, 0.92 ± 0.827, 5.512 ± 0.92, respectively; P = 0.003). Conclusion: This study demonstrated for the first time the association between the T allele of the rs767649 T>A polymorphism in the pre-MIR155 gene and higher expression of miR-155, lower expression of SOCS-1, and swift latent progression in newly diagnosed BC patients. Thus, miR-155 may play a critical role in BC pathogenesis.