Design of crRNA to Regulate MicroRNAs Related to Metastasis in Colorectal Cancer Using CRISPR-C2c2 (Cas13a) Technique

Colorectal cancer (CRC) is the third most prevalent cancer with the second-highest mortality rate worldwide. microRNAs(miRNAs) of cancer-derived exosomes have shown promising diagnosis potential. Recent studies have shown themetastatic potential of a specific group of microRNAs called metastasis. Therefore, down-regulation of miRNAs at thetranscriptional level can reduce metastasis probability. The aim of this bioinformatics research is targeting of miRNAsprecursors using CRISPR-C2c2 (Cas13a) technique. The C2c2 (Cas13a) enzyme structure was downloaded fromthe RCSB database, the sequence miRNAs and their precursors were collected from miRbase. The crRNAs weredesigned and evaluated for their specificity by using CRISPR-RT server. The modeling 3D structure of the designedcrRNA was performed by RNAComposer server. Finally, HDOCK server was used to perform molecular docking toevaluate docked molecules' energy level and position. The crRNAs designed for miR-1280, miR-206, miR-195, miR-371a, miR-34a, miR-27a, miR-224, miR-99b, miR-877, miR-495 and miR-384 that showed high structural similaritywith the situation observed in normal and appropriate orientation was obtained. Despite high specificity, the correctorientation was not established in the case of crRNAs that designed to target miR-145, miR-378a, miR-199a, miR-320a and miR-543. The predicted interactions between crRNAs and Cas13a enzyme showed that crRNAs have astrong potential to inhibit metastasis. Therefore, crRNAs may be considered as an effective anticancer agent for furtherresearch in drug development

Evaluation of hematopoietic stem cell expansion in the presence of garcinol

Objective: The application of human cord blood (hCB) is limited to children by using relatively small volume of cord blood that does not contain enough hematopoietic stem cells (HSCs). So, efforts for applying cord blood stem cells in transplantation have led to establishment of some approaches for ex vivo expansion of HSCs such as garcinol. Materials and Methods: CD133+ HSCs were separated by a magnetic-activated cell sorting (MACS) system. Isolated cells were cultured with different doses of garcinol, SCF, TPO and FLT-3L. The optimal dose of garcinol for ex vivo expansion of HSCs was determined by direct counting. Flow cytometry was used to evaluate the expression of CD133 marker to check the ability of garcinol in maintenance of HSCs. Colony forming cell (CFC) assay was performed to evaluate clonogenic capability of treated cells. The level of expression of CXCR4 gene was evaluated by RT-PCR. Data were analyzed using Student’s t test. Results: Our results showed that CD133+ HSCs in the presence of garcinol (5-10 µM) had high expansion activity and cell counting showed that the number of cells in treated group was higher than control group (1.9 –fold) and CFC assay showed that the number of colonies following treatment with garcinol had 1.3-fold increase. Treatment of HSCs with garcinol resulted in 9.6-fold increase in terms of CXCR4 expression in comparison to control group. Conclusion: The present study showed that garcinol can improve ex vivo expansion of HSCs and enhance their potential for homing to bone marrow

Prospective Acid Reflux Study of Iran (PARSI): Methodology and study design

<p>Abstract</p> <p>Background</p> <p>Gastroesophageal reflux disease is a common and chronic disorder but long term, prospective studies of the fate of patients seeking medical advice are scarce. This is especially prominent when looking at non-erosive reflux disease (NERD) patients.</p> <p>Methods</p> <p>We designed a prospective cohort to assess the long term outcome of GERD patients referring to gastroenterologists. Consecutive consenting patients, 15 years of age and older, presenting with symptoms suggestive of GERD referring to our outpatient clinics undergo a 30 minute interview. Upper gastrointestinal endoscopy is performed for them with protocol biopsies and blood samples are drawn. Patients are then treated according to a set protocol and followed regularly either in person or by telephone for at least 10 years.</p> <p>Discussion</p> <p>Our data show that such a study is feasible and follow-ups, which are the main concern, can be done in a fairly reliable way to collect data. The results of this study will help to clarify the course of various subgroups of GERD patients after coming to medical attention and their response to treatment considering different variables. In addition, the basic symptoms and biological database will fuel further molecular epidemiologic studies.</p

Integrated health, safety, environment and ergonomics management system (HSEE-MS): An efficient substitution for conventional HSE-MS

403-411This study presents a framework for development of integrated intelligent human engineering environment in complex critical systems. Health, safety, environment and ergonomics (HSEE) is developed by integration of conventional health, safety and environment (HSE) with job systems by re-engineering organizational structures and teamwork through electronic data interchange. HSEE has been found superior over conventional HSE through identification of major problems with ergonomic factors in power plant

Preventive Effects of NSAIDs on Lung Tissue Oxidative Damage in an Animal Sepsis Model

Background/aim: Sepsis is a very heterogeneous syndrome that is caused by a dysregulated host response to infection. Inflammatory cascades have an important role in sepsis and can potentially be suppressed by anti-inflammatory compounds. So, this study was focused on the antiseptic effects of non-steroidal anti-inflammatory drugs (NSAIDs) on lung injuries based on cecal ligation and puncture (CLP) surgery. Materials and methods: Male wistar rats divided into 6 groups (n=50) as follows: Control, Laparotomy (LAP), CLP and three treatment groups. The rats were killed after 48 h and the lung tissue was subjected to antioxidant enzymes (LP (lipid peroxidation), MPO (myeloperoxidase), and GSH (Glutathione)) and inflammatory genes expression (cyclooxygenase-2 (COX-2), CD177 and MPO). Results: The results indicated that CLP caused lung injury by changes in antioxidant enzymes and genes expression (P&lt;0.05). Treatments with indomethacin, celecoxib and aspirin as anti-inflammatory compounds significantly improved antioxidant enzymes by reducing LP and MPO level as well as genes expression and increasing level of GSH (P&lt;0.05). Conclusion: Our results indicated that sepsis caused oxidative damage in the lung tissue, and the uses of NSAIDs were effective in preventing and improving these injuries

Integrated high-throughput bioinformatics (microarray, RNA-seq, and RNA interaction) and qRT-PCR investigation of BMPR1B axis as a potential diagnostic biomarker of Isfahan breast cancer

Background: According to the bioinformatics analyses and previous studies, bone morphogenetic protein receptor type 1B (BMPR1B) dysregulation could remarkably affect breast cancer (BC) status as a potential biomarker and tumor suppressor. Therefore, the analysis of the expression level of BMPR1B and other relevant biological factors such as microRNAs, long non-coding RNAs, downstream proteins in the relevant signaling pathways, and finding the accurate biological mechanism of BMPR1B could be helpful for a better understanding of BC pathogenicity and discovering the new treatment methods and drugs. Materials and Methods: R Studio software (4.0.2) was used for microarray data analyses. GSE31448 dataset was downloaded by GEOquery package and analyzed by limma package. STRING and miRWalk online databases and Cytoscape software were used for interaction analyses. Quantitative measurement of BMPR1B expression level was performed by qRT-PCR experiment. Result: Microarray and real-time PCR analysis revealed that BMPR1B has a significant downregulation in the transforming growth factor (TGF)-beta and bone morphogenic protein (BMP) signaling pathways in BC samples. BMPR1B is a potential diagnostic biomarker, regulated by hsa-miR-181a-5p. Also, BMPR1B regulates the function of BMP2, BMP6, SMAD4, SMAD5, and SMAD6 proteins. Discussion: BMPR1B have a significant role in the development of BC by regulating the potential proteins' function, playing the diagnostic biomarker role, and regulation of TGF-beta and BMP signaling pathways. The high amount of BMPR1B protein helps in increasing the survival rate of the patients

Benefit of Analog, Programmable and Digital Hearing Aids

Background and Aims: As the hearing aid technology progressively promotes toward replacing analog hearing aids with digital and programmable ones, comparison of the patient satisfaction of those kinds of hearing aids by means of a valuable tool seems so necessary. So, the aim of this study was to compare self-reported benefit of analog, digitally controlled programmable and digital hearing aids for reducing disability caused by hearing impairment in mild to severe sensorineural hearing impaired persons. Materials and Methods: This cross-sectional study was performed on 90 persons with mild to severe sensorineural hearing loss dividing into three groups: 43 subjects were fitted with digital, 15 with programmable, 32 with analog hearing aids. After pure tone audiometry, Abbreviated profile of hearing aid benefit (APHAB) was completed before and one month after using hearing aids to determine the benefit of them. Results: Global APHAB mean scores for digital, programmable and analog hearing aids were 49.05, 33.19 and 39.53, respectively. Ease of Communication subscale mean scores were 53.46 for digitals, 37.66 for programmables and 39.09 for analogs. Background noise subscale mean scores for digital programmable and analog hearing aids were 46.36, 25.53 and 35.31, respectively. Global and also both subscale mean scores showed significant difference between digital hearing aids and programmable and analog ones. There was no significant difference between reverberation subscale mean scores of three groups. Conclusion: It seems digital hearing aids may be more beneficial to reduce disability caused by hearing loss than analog and programmable hearing aids are

The SNP rs3746444 within mir-499a is associated with breast cancer risk in Iranian population

Objective Our study aimed to evaluate the possible association between hsa-mir-499a (rs3746444 A>G) polymorphism and susceptibility to breast cancer in an Isfahanian population. Materials &amp; methods In this case–control study we enrolled 91 healthy subjects and patients with breast cancer. Allele-specific primer PCR was applied for genotyping the SNP. Results Our study showed that the hsa-mir-499a rs3746444 G allele increased the risk of breast cancer regarding to allele frequency differences (OR: 1.922; 95% CI: 1.064–3.470; p = 0.02952) and Armitage's trend test (OR: 1.722; p = 0.04732) in comparison with the A allele. In addition, an in silico attempt to find functional consequences of A>G substation suggested that the G allele may decrease hsa-mir-499a stability based on calculated free energy differences between A and G alleles. Conclusion Our findings illustrated that the mir-499a rs3746444 G polymorphism is associated with higher risk of developing breast cancer in Isfahanian population

Tumor-promoting function of single nucleotide polymorphism rs1836724 (C3388T) alters multiple potential legitimate microRNA binding sites at the 3'-untranslated region of ErbB4 in breast cancer

Free to read on publisher website ErbB4 can act as either a tumor-suppressor gene or an oncogene in breast cancer. Multiple genetic factors including single nucleotide polymorphisms (SNPs) affect gene expression patterns. Multiple 3'-untranslated region (3'-UTR) SNPs reside within the target binding site of microRNAs, which can strengthen or weaken binding to target genes. The present study aimed to predict potential 3'‑UTR variants of ErbB4 that alter the target binding site of microRNAs (miRNAs) and to clarify the association of the potential variant with the risk of developing breast cancer. In silico prediction was performed to identify potential functional SNPs within miRNA target binding sites in the 3'‑UTR of ErbB4. Thus, 146 patients and controls were genotyped using restriction fragment length polymorphism-polymerase chain reaction. In addition to the Cochran-Armitage test for trend, allele and genotype frequency differences were determined to investigate the association between rs1836724 and the susceptibility to breast cancer. Bioinformatics analysis identified rs1836724 to be a polymorphism in the seed region of four miRNA binding sites (hsa-miR335-5p, hsa-miR-28-5p, has‑miR‑708‑5p and has‑miR‑665), which may participate in the development of breast cancer. Logistic regression data indicated that the T allele of the polymorphism [OR (95% CI)=1.72 (1.056‑2.808), P=0.029] is associated with the risk of breast cancer. Using bioinformatics tools, a correlation was indicated between the presence of the T allele and a reduction in ErbB4 RNA silencing based on miRNA interaction. Furthermore, case subgroup data analysis revealed an association between the C/T genotype and an ER positive phenotype [OR (95% CI)=6.00 (1.082‑33.274), P=0.028] compared with the T/T genotype. ErbB4 and estrogen receptor 1 (ESR1) are regulated by identical miRNAs thus there may be a competition for binding sites. Due to this pattern, if the interaction between miRNAs with one gene is reduced, it may be consistent with the increase in interaction with another one. Therefore, more interaction with rs1836724 C variant within ErbB4 may be associated with higher expression of ESR1 (ER‑positive phenotype). miRNAs interact with ErbB4 mRNA more frequently when it carries C allele at the rs1836724 position compared with the T carriers. Therefore, the identical miRNA interacts with ESR1 less frequently when ErbB4 mRNA has a C allele. Therefore, ESR1 expression may be higher when ErbB4 mRNA has a C allele