Sharif Digital Repository

Introduction: B lymphocyte-induced maturation protein 1 (BLIMP1) encoded by the positive regulatory domain 1 gene (PRDM1), is a key regulator in T cell differentiation in mouse models. BLIMP1-deficiency results in a lower effector phenotype and a higher memory phenotype. Methods: In this study, we aimed to determine the role of transcription factor BLIMP1 in human T cell differentiation. Specifically, we investigated the role of BLIMP1 in memory differentiation and exhaustion of human T cells. We used CRISPR interference (CRISPRi) to knock-down BLIMP1 and investigated the differential expressions of T cell memory and exhaustion markers in BLIMP1-deficient T cells in comparison with... 

The present work focuses on the development of an interpretable quantitative structure-activity relationship (QSAR) model for predicting the anti-HIV activities of 67 thiazolylthiourea derivatives. This set of molecules has been proposed as potent HIV-1 reverse transcriptase inhibitors (RT-INs). The molecules were encoded to a diverse set of molecular descriptors, spanning different physical and chemical properties. Monte Carlo (MC) sampling and multivariate adaptive regression spline (MARS) techniques were used to select the most important descriptors and to predict the activity of the molecules. The most important descriptor was found to be the aspherisity index. The analysis of variance... 

A new dibenzothiophene (DBT) desulfurizing bacterium was isolated from oil-contaminated soils in Iran. HPLC analysis and PCR-based detection of the presence of the DBT desulfurization genes (dszA, dszB and dszC) indicate that this strain converts DBT to 2-hydroxybiphenyl (2-HBP) via the 4S pathway. The strain, identified as Rhodococcus erythropolis SHT87, can utilize DBT, dibenzothiophene sulfone, thiophene, 2-methylthiophene and dimethylsulfoxide as a sole sulfur source for growth at 30 °C. The maximum specific desulfurization activity of strain SHT87 resting cells in aqueous and biphasic organic-aqueous systems at 30 °C was determined to be 0.36 and 0.47 μmol 2-HBP min-1 (g dry cell)-1,... 

Human parvovirus B19 (B19) is a small, non-enveloped virus and belongs to Parvoviridae family. B19 persists in many tissues such as thyroid tissue and even thyroid cancer. The main aim of this study was to determine the presence of B19, its association with increased inflammation in thyroid tissue, and thus its possible role in thyroid cancer progression. Studies have shown that virus replication in non-permissive tissue leads to overexpression of non-structural protein and results in upregulation of proinflammatory cytokines such as interleukin 6 and tumor necrosis factor alpha. A total of 36 paraffin-embedded thyroid specimens and serum were collected from patients and 12 samples were used... 

In this paper, a bottom-up hydrothermal route is reported for the synthesis of oxygen and nitrogen co-decorated carbon quantum dots (CQDs) using ammonium hydrogen citrate (AHC) as a single precursor. DLS data approved the formation of 4.0 nm (average size) CQDs. XRD pattern shows the interlayer spacing (002) of 3.5 Å for CQDs, which is exactly the same as that of crystalline graphite. XPS and FTIR spectra verified the formation of oxygen and nitrogen functional groups on the CQDs surface. Co-decorated carboxyl, hydroxyl and amine groups on the CQDs surfaces make them as promising polyelectrolyte for gene delivery. Toxicity assay showed a survival rate of 70% under different incubation times... 

Human infertility is a multifactorial disease that affects 8%–12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive... 

Background: Ataxia-telangiectasia (A-T) is a rare autosomal recessive disorder caused by mutations in the ataxia telangiectasia mutated (ATM) gene. A-T patients manifest considerable variability in clinical and immunological features, suggesting the presence of genetic modifying factors. A striking heterogeneity has been observed in class switching recombination (CSR) in A-T patients which cannot be explained by the severity of ATM mutations. Methods: To investigate the cause of variable CSR in A-T patients, we applied whole-exome sequencing (WES) in 20 A-T patients consisting of 10 cases with CSR defect (CSR-D) and 10 controls with normal CSR (CSR-N). Comparative analyses on modifier... 

Metabonomics and other "omic" fields are essential science in analytical chemistry. Modern analytical instruments such as proton nuclear magnetic resonance (1H-NMR) can provide the great quantity of analytical information. In order to assign unknown samples, chemometric methods recognition build classification model based on experimental data. Firstly, some current strategies regarding disease diagnosis are exhibited in metabonomic studies. Some diseases such as crohn's disease can be difficult to diagnose since its signs and symptoms may be similar to other medical problems or often mimic other symptoms. Applications of NMR and supervised pattern recognition in the field of metabonomics are... 

Single-layer reduced graphene oxide nanoribbons (rGONRs) were obtained through an oxidative unzipping of multi-walled carbon nanotubes and a subsequent deoxygenation by hydrazine and bovine serum albumin. Human mesenchymal stem cells (hMSCs) were isolated from umbilical cord blood and used for checking the concentration- and time-dependent cyto- and geno-toxic effects of the rGONRs and reduced graphene oxide sheets (rGOSs). The cell viability assay indicated significant cytotoxic effects of 10 μg/mL rGONRs after 1 h exposure time, while the rGOSs exhibited the same cytotoxicity at concentration of 100 μg/mL after 96 h. The oxidative stress was found as the main mechanism involved in the... 

The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use... 

Reduced graphene oxide nanoribbons functionalized by amphiphilic polyethylene glycol (rGONR-PEG) were applied to attach arginine-glycine-aspartic acid (RGD)-based peptide and cyanine dye 3 (cy3) for targeting ανβ3 integrin receptors on human glioblastoma cell line U87MG and its selective fluorescence imaging, respectively. The rGONR-PEG suspension with a concentration of 100 μg mL -1 showed ∼14 and 2.4-fold higher near infrared (NIR) absorption at 808 nm than GONR (with dimensions of ∼80 nm × 1 μm) and rGO-PEG sheets (with lateral dimensions of ∼2 μm), respectively. The rGONR-PEG-cy3-RGD exhibited highly efficient NIR photothermal therapy performance (concentrations ≥1.0 μg mL-1 resulted in... 

Introduction: It is 23 years since carbon allotrope known as carbon nanotubes (CNT) was discovered by Iijima, who described them as "rolled graphite sheets inserted into each other". Since then, CNTs have been studied in nanoelectronic devices. However, CNTs also possess the versatility to act as drug- and gene-delivery vehicles.Areas covered: This review covers the synthesis, purification and functionalization of CNTs. Arc discharge, laser ablation and chemical vapor deposition are the principle synthesis methods. Non-covalent functionalization relies on attachment of biomolecules by coating the CNT with surfactants, synthetic polymers and biopolymers. Covalent functionalization often...