Tehran University Medical Journal

Background: Molecular detection has recently been proposed by nucleic acid amplification, known as polymerase chain reaction (PCR). The aim of this study was to compare the diagnostic method of smear and polymerase chain reaction with culture in terms of sensitivity, specificity, positive and negative predictive value in the diagnosis of pulmonary tuberculosis.
Methods: In this cross-sectional study, sputum samples were collected from 58 patients with suspected pulmonary tuberculosis referred to Ghaem Hospital in Mashhad from the beginning of April 2017 to the end of March 2018. The samples were delivered to the laboratory in less than 72 hours. Patients were sampled for three times. Bronchoscopy and Broncho alveolar lavage were performed in patients who were unable to produce sputum. The smear test was reported by Ghaem’s Laboratory after 24 hours. In our study, the culture method was considered as the gold standard and the sensitivity and specificity of the PCR methods and smear were compared with it.
Results: Patients ranged in age from 18 to 89 years. Among 58 suspected pulmonary tuberculosis, the method of cultivation confirmed the presence of the disease in 25 cases (43.1%). However, with smear, the presence of the disease has been proved in 27 patients (46.6%) and with the method of PCR in 24 patients was (41.4%). Sensitivity of smear in the diagnosis of pulmonary tuberculosis was (100%), and its specificity was 93.9%, the positive predictive value of this test was (92.6%) and the negative predictive value was (100.0%). The sensitivity of the PCR method in diagnosis of pulmonary tuberculosis was 88.0% and its specificity was 93.9%. The positive predictive value of this was (91.7%) and the negative predictive value was (91.2%).
Conclusion: In this study, between the two methods of smear and polymerase chain reaction, the acid fast smear method was more sensitive to the diagnosis of pulmonary tuberculosis than the polymerase chain reaction and the specificity of both methods were the same.

Background: Micro-Ribonocellic Acids (miRNA) are non-coding nucleic acids that are evolutionally protected and have a length of 24-20 nucleotides. MiRNAs control the expression of genes after transcription by mRNA degradation or translation inhibition. By blocking the oncogenic miRNAs and creating the necessary and functional miRNAs (tumor suppressor), these small regulatory RNAs can have therapeutic applications in cancer. The high mortality from lung cancer highlights the fact that the majority of patients are diagnosed at an advanced stage of the disease. The use of serum biomarkers can help early detection. MiRNA is more stable than mRNA. MiRNA expression in tissue, plasma, sputum, and urine samples can be detected by fixed formulation. In addition, miRNAs are important modulators of gene expression, diagnostic markers, and prognosis. Therefore, in the present study, the expression of miR-137 in the serum of patients with lung cancer was investigated.
Methods: In this descriptive and analytical study, 100 serum samples were collected from patients referring to Masih Daneshvari Hospital in Tehran from August 2017 to May 2018. Also, individual and clinical information were collected by a questionnaire and real-time polymerase chain reaction (RT-PCR) was used for the qualitative evaluation of changes in expression of miR-137.
Results: Data showed that there was no significant difference between the expression of miR-137 in serum samples of the first and second stages of the disease. While in the serum of patients with lung cancer who metastasized in the third and fourth stages, miR-137 expression decreased by 3.2 (P=0.42) and 6.8 times (P=0.003), respectively. Based on the results, it can be inferred that the measurement of miR-137 expression in lung cancer patients with concomitant reduction can be a sign of the progression of the disease.
Conclusion: Based on the results of this study, there was a significant relationship between miR-137 expression and lung cancer.

Background: Sepsis or blood stream infection is a clinical lethal syndrome with severe systemic inflammatory response to infection, if not treated quickly, is associated with dangerous consequences and high morbidity and mortality. The traditional and conventional method for identification of sepsis is blood culture method which is so time-consuming and long that it eliminates the possibility of rapid treatment. Although, new molecular methods, due to their high sensitivity, specificity, and speed, lead to the rapid and accurate and exact detection of bacterial sepsis within only a few hours. The aim of this study was diagnosis of bacteremia in patients with suspected sepsis using amplification of 23S rRNA gene by polymerase chain reaction (PCR).
Methods: This cross-sectional study was performed in two clinical and analytical steps at Shahid Beheshti University Hospital in Kashan City, Iran, in twelve months from November 2016 to December 2017. The blood samples of two hundred and fifty-six patients with suspected sepsis admitted to Shahid Beheshti Hospital were studied by PCR method using specific primers of 23S rRNA gene of the bacteria.
Results: The finding of molecular assays using PCR showed that of 256 blood samples that were collected from patients with clinical signs and symptoms of sepsis, 80 (30.2%) diagnosed with bacteremia. Of these patients diagnosed with sepsis, 46 out of 80 (57.5%) were male while 34 out of 80 (42.5%) were female. The most PCR positive results were obtained among patients with diabetes and bedsore as underlying diseases (21.3%). Statistical analysis showed that there was a significant correlation between results of molecular methods by PCR assays and history of antibiotic use. 
Conclusion: Overall, the results of the present study showed that the molecular methods such as polymerase chain reaction using universal 23S rRNA primers is an appropriated test for diagnosis of bacteremia in blood samples of patients with suspected sepsis.

Background: Skeletal muscle mass, which is regulated by a balance between muscle protein synthesis and degradation, is an important factor for movement to meet everyday needs, especially in pathological conditions and aging. The purpose of the present investigation was to compare the alterations of the gene expression involved in muscle protein synthesis and degradation signaling pathways induced by two exercise training protocols.
Methods: Eight weeks old Wistar rats have been assigned to the present experimental study, which was conducted from August 2018 to October 2018 at the animal laboratory of Tehran University. They were randomly divided into two resistance and endurance training groups and one control group, and run on a treadmill, 5 sessions per week for 8 weeks. 48 hours after the last exercise session, the rats in the two groups were anesthetized, and the dissected soleus muscles from euthanized animals were stored at -80° for RT-PCR and Western blot analysis later. Between-group differences were analyzed by the parametric and non-parametric tests for normally and non-normally distributed data respectively, at the significance level of α˂0.05.
Results: Compared with the control group, mTORC1 gene expression was increased significantly just in the endurance group (P=0.022), whereas both endurance and resistance exercise protocols caused a significant increase in Rps6kb1 (P˂0.001 and P=0.001 respectively). In protein degradation pathway, although, FOXO3a did not alter significantly (P=0.463), eIF4Ebp1 gene expression was inhibited by both endurance and resistance exercise training protocols (P˂0.001 and P=0.001 respectively). The alterations of Rps6kb1 and FOXO3a gene expression were confirmed by Western blot analysis.
Conclusion: The results showed that the exercise training protocols of the present study had approximately similar effects on alterations of gene expression involved in skeletal muscle protein synthesis and degradation pathways. Therefore, application of the protocols may be considered to prevent or reduce the muscle atrophy in pathological conditions such as motor neuron disease, aging, and/or muscle strength improvement in athletes.

Background: The H9N2 subtype of the influenza virus, which is endemic in many regions of Iran, is considered as a candidate for future pandemics. In the present study, excretion time of the Iranian endemic influenza virus (H9N2 subtype) from the feces and pharyngeal secretions of laying chicken breeds was evaluated.
Methods: This experimental study conducted at the Diagnostic Laboratory Sciences and Technology Research Center of Shiraz University of Medical Sciences, and the Department of Clinical Science in School of Veterinary Medicine of Shahid Bahonar University of Kerman, from June 2017 to September 2017. At first, the influenza virus A/Chicken/Iran/SH-110/99 (H9N2) was cultured in the allantoic fluid of the embryonated egg and the EID50 for virus was determined by Reed and Muench method. Afterward, the Hy-Line chicks were inoculated intranasally with 106 EID50/ml of influenza virus (H9N2 subtype) and samples were collected from the oropharynx and feces of the birds on days 2, 5, 10 and 17 after inoculation. The presence of the virus in the samples of challenged birds was assessed using the real-time polymerase chain reaction (PCR) method.
Results: The influenza virus was shed from the oro-pharyngeal secretion and feces of the birds 2 days post-infection, and continued until days 10 and 17, respectively. In comparison to the oro-pharynx, the virus was recovered in the feces for a longer time. The influenza virus was detected in 100% and 57.1% of oro-pharyngeal and feces samples of the infected birds on day 2, 85.7% and 100% on day 5, 28.6% and 71.4% on day 10, and 0% and 28.6% on day 17 post-inoculation, respectively. The maximum risk of infected chicken for humans is seen from 2 to 5 days post-infection.
Conclusion: Detection of virus in the samples of birds that challenged with the H9N2 influenza virus showed that the virus could shed from the feces to the surrounding environment longer than the pharyngeal secretions and could be hazardous to humans in contact.

Background: Trichosporon species are commonly known as causative agents of skin infections and also responsive in some other systemic and disseminated diseases, especially in immunocompromised patients and those with leukemia or lymphoma. Chronic cutaneous infections with Trichosporon have been reported in non-immunocompromised patients, too.
Case Presentation: This study is a case report of tinea pedis caused by Trichosporon asahii in an immunocompetent 39-year-old man who was a member of the military force with continuous wearing of army boots during his daytime work. In April of 2019, after visiting a dermatologist, he was referred to the Ghaem medical mycology laboratory of the Department of Health, Rescue and Treatment of Iran Police Force in Tehran. Clinical symptoms were scaling and erythematous patches on his left foot with intensive itching for four-months. In the laboratory, macroscopic and microscopic examination using direct 15% KOH wet mount was carried out as well as culture methods on fungal media (Sabouraud's dextrose agar with and without cycloheximide and chloramphenicol). According to microscopic observation and appearance of culture media colonies, the diagnosis was Trichosporon genus as the fungal agent of disorder. Molecular method analysis (PCR) using amplification of ITS region with universal primers (ITS1 and ITS4) and sequencing identified Trichosporon asahii as a causative species of the disease. The patient was treated with topical clotrimazole (twice/day) and oral fluconazole (150 mg/day) for four weeks, and recovered.

Background: Lung cancer has the highest incidence and mortality rate of all cancers worldwide. In Iran, it is one of the commonly diagnosed malignancies, and its frequency is increasing rapidly. Genetic variants in DNA repair genes are linked to differences in efficiency of repairing DNA damage, which can influence lung cancer susceptibility. EXO1 is a key gene involved in the mismatch repair pathway. The K589E polymorphism in EXO1 may alter the DNA repair activity of the encoded protein and impact lung cancer risk. The aim of this study was to investigate associations between the K589E polymorphism in EXO1 and lung cancer risk in the Iranian population, and evaluate its potential as a prognostic biomarker.
Methods: This case-control study was conducted to investigate EXO1 K589E variant with susceptibility to lung malignancy in the Iranian population. One hundred patients with lung cancer as a patient group and 100 healthy individuals from Khansari Hospital located in Markazi province were studied, from January 2020 to May 2022. DNA extraction from blood samples of participants was done using a kit.  Genotype determination of both patient and control groups was done using PCR-RFLP technique. Finally, statistical results were analyzed using SPSS software and the logistic regression method.

Results: Genotype and allele frequency  analysis showed the AA genotype (P=0.004, OR=5.391, 95% CI: 1.690-17.200) and A allele (P=0.010, OR=2.851, 95% CI: 1.291-6.300) were correlated with susceptibility to lung cancer. On the other hand, people carrying the G variant allele had a lower risk of lung cancer. Conclusion:  In summary, this study found the AA genotype and A allele of K589E in EXO1 are correlated with risk of lung cancer in Iranians, while the G allele has protective effects. The K589E polymorphism may serve as a prognostic biomarker for lung cancer susceptibility, but more studies with high population size are required.

Results: Staphylococcus aureus diagnostic tests including gram staining on colonies, catalase, coagulase, DNase tests were performed and it was found that all strains were Staphylococcus aureus. In the next step, all samples were resistant to Cloxacillin by disc diffusion method, and the presence of mec A gene in them was confirmed by PCR method, thus the presence of MRSA strains was confirmed from the genotypic point of view. Of the 43 Staphylococcus aureus strains, 26 samples were identified as having the nor A gene by PCR and electrophoresis. Conclusion: The results of the present research have shown that the prevalence of Staphylococcus aureus bacteria in hospital samples is significant and resistance to methicillin and ciprofloxacin has increased in the strains of this bacteria.