The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

Abstract

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.

Communicated by Ramaswamy H. Sarma     

Spectroscopic and DFT investigation of interactions between cyclophosphamide and aspirin with lysozyme as binary and ternary systems

Multi-spectroscopic and density functional theory (DFT) calculations was used to study the interaction between cyclophosphamide (CYP) and aspirin (ASA) with lysozyme (LYS). The experimental results showed that fluorescence quenching of LYS by drug was a result of the formation of drug–LYS complex; static quenching was confirmed to result in fluorescence quenching. Modified Stern–Volmer plots of interaction between CYP and ASA with protein in the binary and ternary systems were used to determine the binding parameters. Molecular distances between the donor (LYS) and acceptor (CYP and ASA) for all systems were estimated according to Forster’s theory. The quantitative analysis obtained by CD spectra suggested that the presence of ASA and CYP decreased the α-helical content of LYS and induced the destabilizing of it. Theoretical studies on the interaction between LYS with ASA and CYP have been carried out using DFT at the B3LYP/6-31G level in the solvent phase. Binding energy of the mentioned complexes was calculated. It showed that tryptophan (Trp) 62 had the most affinity toward ASA and CYP. Analyzing the calculated results revealed that the five member ring of Trp has a key role in interaction of LYS with ASA and CYP.     

Internal ethnicity in the ethnic economy

Internal ethnicity refers to ethnic subgroups within an immigrant group. An ‘ethnic economy’ includes the self‐employed and their co‐ethnic workers. Although most research treats the boundaries of ‘ethnic economy’ and its variant, the ‘ethnic enclave economy’, as though they were coterminous with those of national‐origin immigrant groups, this assumption is unreliable. Ethnic boundaries need not coincide with those of nationality origin when internal ethnicity exists. To test this hypothesis, we utilize survey data collected from a sample of Iranians in Los Angeles. Because this national‐origin immigrant group contains four ethno‐religious subgroups (Armenians, Bahais, Jews and Muslims), the Iranians in Los Angeles operated four distinctive ethnic economies, not one. Each ethno‐religious subgroup had its own ethnic economy, and these separate economies were only weakly tied to an encompassing Iranian ethnic economy.     

Panethnicity revisited: contested group boundaries in the post-9/11 era

Existing theories of panethnicity in the USA concentrate on Asian Americans and Latinos, two umbrella groups that originally coalesced during the 1960s civil rights era. Although the role played by the state is recognized as central to panethnic development, we argue that the influence of this pivotal variable is contingent on historical context. Through a case study of emerging minority groups (Middle Eastern and South Asian Americans in the post-9/11 era), we re-examine the existing conceptualization of panethnicity at a time when the state plays a more punitive than compensatory role. Using a methodology that draws on a range of novel sources, we document the way that pre-existing ethnic, religious and national-origin labels have been reinforced instead of panethnic labels for the populations under study. Accordingly, we develop an updated conceptualization of group formation that incorporates historical context and the role of the state in the post-9/11 era.     

Primary colonospheres maintain stem cell-like key features after cryopreservation

The development of efficient and repeatable protocols for biobanking and prolonged storage of cancer stem cells (CSCs), with minimum alterations in biological function, is valuable and desired, particularly for retrospective analysis and clinical applications. In particular, data regarding the effect of cryopreservation on CSCs's functional features is scarce. In this regard, few studies have been shown that 3D spheroid structures, which enriched for CSCs, can keep their biological phenotype and genetic profiles. Here, for the first time, we present data on cryopreservation of CT-26 colonospheres, with the focus on essential stem cell-like properties after thawing. Tumor biopsy-derived colonospheres were frozen in standard freezing media (90% fetal bovine serum + 10% dimethyl sulfoxide) and stored in liquid nitrogen for 10 months. Then, cryopreservation effect on preservation of CSCs-related features was verified using real-time polymerase chain reaction for evaluation of stemness genes and flow cytometry for the putative colorectal CSC surface biomarkers. The self-renewal capacity of thawed spheres was also compared with their fresh counterparts using serial formation assay. Finally, tumorigenic capacity of both groups was evaluated in immunocompetence mouse model. Our data indicated that postthawed colonospheres had high viability without drastic alteration in biological and structural features and maintained self-renewal potential after sequential passages. Real-time analysis showed that both fresh and frozen colonospheres displayed similar expression pattern for key stemness genes: SOX2 and OCT4. Cryopreserved spheroids expressed CD133, CD166, and DCLK1 CSCs surface biomarkers at elevated levels when compared with parental as non-cryopreserved counterparts. Our electron scanning microscopy micrographs clearly demonstrated that postthawed colonospheres retain their integrity and cell surface morphology and characteristics. We also found that both fresh and frozen spheroids were equally tumorigenic. This study represented an effective strategy for reliable storage of intact CT-26 colonospheres; this can provide researchers with a functionally reliable repository of murine colorectal CSCs for their future CSCs projects.     

Assessment of Treg/Th17 axis role in immunopathogenesis of chronic injuries of mustard lung disease

Purpose: Sulfur mustard (SM) lung is a heterogeneous disease associated with abnormal inflammatory immune responses. The Th17/Treg axis imbalance is associated with the pathogenesis of chronic inflammatory pulmonary disease. We aimed to determine the distribution of different Th17 and Treg cells in patients with SM lung and chronic obstructive pulmonary disease (COPD) and evaluate the clinical implications in this homeostasis. Methods: In this analytical cross-sectional study, CD4?⁺?Foxp3^+?Treg and CD4⁺?IL-17^+?Th17 cells were measured in peripheral blood mononuclear cells (PBMCs) and transbronchial biopsy (TBB) samples of 15 SM-exposed patients, 12 COPD and 13 healthy controls (HCs). The potential correlation between the ratio of Th17/Tregs and lung function was evaluated with multivariate logistic regression (MLR) analysis. Results: The frequency of CD4?⁺?FoxP3⁺?Tregs and CD4?⁺?IL-17⁺?Th17 was increased ～1.7-fold (8.71/4.95) and ～2.7-fold (1.028/0.371) respectively, in the PBMC of SM patients compared with the health controls (p?<?0.001). The results indicated that there were increases in the frequency of Th17 and Tregs cells in the patients with COPD versus the HC, that is, ～2.6-fold (0.987/0.371) and ～1.4-fold (7.12/4.95), respectively; but they did not reach to SM level (p?≥?0.05). Moreover, in the TBB samples, the CD4?⁺?IL-17^+?Th17 and CD4⁺?FoxP3^+?Tregs numbers were significantly higher in SM and COPD patients than HC (p?<?0.05). The Th17 and Treg cells were inversely correlated with forced expiratory volume in 1s (FEV1%) (r?=??0.351, p =?0.001; r?=??0.344, p?=?0.021) and FEV1/FVC (r?=??0.44, p?=?0.001; r?=??0.302, p?=?0.011), respectively. Instead, positive correlations were found between Treg/Th17 ratios and forced FEV1%pred (r?=?0.156, p?=?0.007), as well as FEV1/FVC ratio (r?=?0.334, p?=?0.006). Conclusions: The imbalance of Th17/Treg has a key role in immunopathogenesis of chronic phase of mustard lung disease.     

Dendritic cells loaded with exosomes derived from cancer stem cell-enriched spheroids as a potential immunotherapeutic option

Cancer stem cells (CSCs) are responsible for therapeutic resistance and recurrence in colorectal cancer. Despite advances in immunotherapy, the inability to specifically eradicate CSCs has led to treatment failure. Hence, identification of appropriate antigen sources is a major challenge in designing dendritic cell (DC)-based therapeutic strategies against CSCs. Here, in an in vitro model using the HT-29 colon cancer cell line, we explored the efficacy of DCs loaded with exosomes derived from CSC-enriched colonospheres (CSC_enr-EXOs) as an antigen source in activating CSC-specific T-cell responses. HT-29 lysate, HT-29-EXOs and CSC_enr lysate were independently assessed as separate antigen sources. Having confirmed CSCs enrichment in spheroids, CSC_enr-EXOs were purified and characterized, and their impact on DC maturation was investigated. Finally, the impact of the antigen-pulsed DCs on the proliferation rate and also spheroid destructive capacity of autologous T cells was assessed. CSC_enr-EXOs similar to other antigen groups had no suppressive/negative impacts on phenotypic maturation of DCs as judged by the expression level of costimulatory molecules. Notably, similar to CSC_enr lysate, CSC_enr-EXOs significantly increased the IL-12/IL-10 ratio in supernatants of mature DCs. CSC_enr-EXO-loaded DCs effectively promoted T-cell proliferation. Importantly, T cells stimulated with CSC_enr-EXOs disrupted spheroids' structure. Thus, CSC_enr-EXOs present a novel and promising antigen source that in combination with conventional tumour bulk-derived antigens should be further explored in pre-clinical immunotherapeutic settings for the efficacy in hampering recurrence and metastatic spread.