Doctor of Philosophy

dissertationPost-transcriptional RNA modifications provide new structural and functional features to modified RNA molecules. Extensive research in the past has resulted in isolation of over 100 distinct nucleotide modifications from different organisms and in different RNA species. These modified nucleotides are distributed within the entire transcriptome comprising the cellular epitranscriptome. The ultimate goal of the research in the field is to address what the specific functions of specific modifications are, and also the impact of each on cellular physiology. However, the first question to be addressed is how these > 100 modified nucleotides are distributed within the transcriptome. RNA modification profiling using conventional techniques has provided a great body of knowledge about the distribution of many modifications in RNAs. However, these findings remained limited mostly to tRNAs and rRNAs, the two most abundant and also highly modified RNA species in different organisms. This is partly because of the lower sensitivity of applied classical technologies. Here in this dissertation, in Chapter 2, we are reporting an optimized new RNA bisulfite protocol suitable for high-throughput RNA cytosine methylation profiling. We present the results of application of this technique for 5-methyl-cytosine (m5C) profiling in mouse embryonic fibroblasts (MEFs) RNAs, isolated from wt and dnmt2-/- mice to explore the target specificity of DNA methyltransferase 2 (DNMT2) enzyme. In Chapter 3, we present a substantially novel technique: Aza-IP, for enrichment and identification of the direct targets of RNA cytosine methyltransferases (m5C-RMTs) as well as iv determination of the exact modified bases in the same experiment. We provide the results of the Aza-IP technique for two human m5C-RMTs; DNMT2 and NSUN2, representing their known and novel RNA targets/modified bases. In Chapter 4 we discuss how similar technologies to both of the RNA bisulfite sequencing and Aza-IP techniques as well as other methodologies can be applied and extended for transcriptome-wide profiling of RNA modifications other than m5C. In Chapter 5 we present the future directions of the work focused on cataloguing the direct targets of all human m5C-RMTs in human cultured cells in mouse and fish model systems, to elucidate the functions of cytosine methylation in RNA molecules

The effects of sildenafil on the hippocampal long-term potentiation in male rats

Introduction: The hippocampal nitric oxide/cGMP signaling pathway plays a crucial role in memory processing. Phosphodiesterase interacts with this signaling pathway. There are controversial reports regarding the effect of sildenafil, a phosphodiesterase inhibitor, on learning and memory. Therefore, the effects of acute administration (intrahippocampal/ intra-dentate gyrus injection) of sildenafil on long-term potentiation (LTP) of rats were investigated. Methods: The rats were anesthetized with urethane and placed in a stereotaxic device for field potential recording. After ensuring a steady-state baseline response, a single intraperitoneal injection of saline or sildenafil (2 and10 µg/kg) was done. The population spike amplitude, the excitatory postsynaptic potentials (EPSPs) slope and paired-pulse stimuli (as an inhibitory interneuron) were compared between groups. Results: The results showed that population spike amplitude and EPSP slope significantly increased after sildenafil administration (10µg/kg) following titanic stimulation compared with the saline group. However, the sildenafil (2µg/kg) and control groups showed no difference regarding population spike amplitude and EPSP slope. Sildenafil had no significant effects on recurrent inhibition. Conclusion: The obtained results indicated that acute administration of sildenafil improved LTP via direct effects on the hippocampus of intact rats. Thus, sildenafil may enhance learning and memory processing by modulating the hippocampal synapse

Introducing a new method of retinoscopy for refraction of infants and young children: The �Mirza� tele lens retinoscopy

Purpose: This study aimed to evaluate the refractive error of the uncooperative infants and children with the new method of retinoscopy called the tele-lens (�Mirza�) retinoscopy. Methods: In the �Mirza� tele-lens retinoscopy, the examiner placed the trial lenses in 1/3 distance between the tested eye person and peephole of the retinoscope (22.2 cm far from the spectacle plane). First, the optical calculations were done to find the correction factors for this new method of retinoscopy. Second, the dry standard and �Mirza� tele-lens retinoscopy were performed in 78 eyes from 39 children aged 7�12 years with good cooperation and next, the procedure was repeated using cyclopentolate drops and then the results of the two methods were compared, and at the end, the dry �Mirza� tele-lens retinoscopy was done in the 60 eyes of 31 uncooperative infants with a mean age of 21.85 ± 8.79 months for evaluating the feasibility of the �Mirza� tele-lens retinoscopy procedure. The intraclass correlation coefficient (ICC) and Bland�Altman plot for assessment of agreement between the findings of two retinoscopic methods in dry and cyclo conditions were used. Results: The comparison between the dry standard and �Mirza� tele-lens retinoscopic results with means of 1.39 ± 1.43 and1.36 ± 1.39, respectively were not statistically significant (p > 0.05). Besides, comparing the mean cycloplegic results of two methods (standard vs. �Mirza� tele-lens), the difference was not statistically significant (2.37 ± 1.44 vs. 2.41 ± 1.37) (p > 0.05). Moreover, Two-way repeated measures ANOVA revealed no significant retinoscopy method � use of drops interaction (P = 0.103) in comparing two methods of the standard and �Mirza� tele-lens retinoscopy. ICC results indicated high agreement between two methods in both dry (ICC = 0.993) and cyclo (ICC = 0.989) conditions. Conclusions: The �Mirza� tele-lens retinoscopy method can be performed with satisfactory results in infants and children who do not cooperate for the standard procedure of measuring the refractive errors. © 2020 Spanish General Council of Optometr

Component Analysis of the Illegal Handmade Pills and Capsules for Self-Medicating Substance Dependence in Tehran, Iran

Background: To self-medicate substance dependence, many substance users consume herbal medicines delivered in herbal medicine shops which are prepared through non-standard methods using a variety of different materials. Hence, the present study was carried out aiming to investigate and analyze the content of such herbal medicines.Methods: Four herbal medicine shops were selected from each of the 22 zones of Tehran City, Iran, and a total of 95 samples were purchased. A package containing 6 types of medication that was advertised by a satellite TV channel, was also purchased. Using high-performance liquid chromatography (HPLC) method, the samples were analyzed in the laboratory to detect different types of materials.Findings: Among the samples, 23 and 72 samples were uncovered compressed pills (Dragon pills) and capsules filled with colored powders (handmade drug-quitting capsules), respectively. The package advertised in the satellite TV was prepared in 6 various forms. The most common substances present in all the samples were as follows: diphenoxylate, tramadol, opioids, acetaminophen, and codeine with values of 90%, 86%, 78%, 69%, and 68%, respectively. On average, 5 of the above mentioned substances were present in each sample; moreover, 63% of the samples contained 5 or more substances. In addition, 42 (41%) of the samples contained all the 5 main substances including opioids, codeine, tramadol, diphenoxylate, and acetaminophen.Conclusion: The findings of this study showed that handmade capsules and pills used for quitting addiction and also medicines advertised in the satellite TV channels contain different amounts of opioids, amphetamine, benzodiazepines, tramadol, codeine, and other substances that cause problems for substance users who are going to abandon substance abuse

Spontaneous spinal subarachnoid hemorrhage associated with subdural hematoma at different spinal levels

We describe the clinical features and MR-imaging findings of spontaneous spinal subarachnoid hemorrhage located in the lumbar spine associated with subdural hematoma at a higher, thoracic level in a 66-year-old man without neurological deficit. The sequential MR-imaging changes of hemorrhage at various stages in its evolution are portrayed. The possible pathogenetic mechanism for these very unusual, combined hemorrhages in both spinal compartments is discussed

Pineal Cavernous Malformations: Report of Two Cases

Pineal hemorrhage only occurs in rare cases, and this known to have several different causes such as germ cell tumors, pineal cysts and vascular malformations, including the cavernous malformations. Pineal cavernous malformations are extremely rare: to date only fifteen cases have been reported worldwide. Although the diagnosis of pineal cavernous malformation is not easy because of the extreme rareness of this condition, the presence of this lesion can be suspected based on its typical radiological findings. Case 1. A 42-year- old man presented with a limitation in his upward gazing. Radiologic examinations showed acute hemorrhage in the pineal region. He underwent ventriculo-peritoneal (VP) shunting but the patient's condition deteriorated after the shunting surgery. We operated and totally removed the tumor and the hemorrhages via an occipital-transtentorial approach. Case 2. A 37-year-old man presented with diplopia. Radiologic examinations showed acute hemorrhage in the third ventricle. He underwent VP shunting, and after this procedure the diplopia was aggravated. We operated and totally removed the tumor and the hemorrhages via an occipital-transtentorial approach. If there is no doubt about the pineal cavernous malformation on MR imaging, we strongly recommend early surgical intervention without performing a risky biopsy. In this study, we describe our experiences for the diagnosis of cavernous malformations in the pineal region with special emphasis on the radiological aspects and the clinical course of this disease