Determining the interaction behavior of calf thymus DNA with berberine hydrochloride in the presence of linker histone: a biophysical study

Abstract

The binding of small molecules with histone-DNA complexes can cause an interference in vital cellular processes such as cell division and the growth of cancerous cells that results in apoptosis. It is significant to study the interaction of small molecules with histone-DNA complex for the purpose of better understanding their mechanism of action, as well as designing novel and more effective drug compounds. The fluorescence quenching of ct-DNA upon interaction with Berberine has determined the binding of Berberine to ct-DNA with K_sv?=?9.46?×?10⁷ M^?1. K_sv value of ct-DNA-Berberine in the presence of H1 has been observed to be 3.10?×?10⁷ M^?1, indicating that the H1 has caused a reduction in the binding affinity of Berberine to ct-DNA. In the competitive emission spectrum, ethidium bromide (EB) and acridine orange (AO) have been examined as intercalators through the addition of Berberine to ct-DNA complexes, which includes ctDNA-EB and ctDNA-AO. Although in the presence of histone H1 , we have observed signs of competition through the induced changes within the emission spectra, yet there has been apparently no competition between the ligands and probes. The viscosity results have confirmed the different behaviors of interaction between ctDNA and Berberine throughout the binary and ternary systems. We have figured out the IC50 and viability percent values at three different time durations of interaction between Berberine and MCF7 cell line. The molecular experiments have been completed by achieving the results of MTT assay, which have been confirmed to be in good agreement with molecular modeling studies.

Communicated by Ramaswamy H. Sarma     

Improving the provision of ecosystem services from urban forest by integrating the species’ potential environmental functions in tree selecting process

Due to the fact that urban environments and population demands are evolving rapidly and species selection is inevitable, it is possible to gain substantial environmental benefit by implementing more effective urban tree planting programs, especially with the aim of increasing the upcoming provision of multiple ecosystem services (ES) through proper species selection. In this paper, we used a new approach to improve the potential of urban trees in optimizing more desirable environmental benefits. This was done by selecting the most appropriate tree species among a vast range of species based on their potential environmental function (both services and disservices) in Tabriz city, Iran. Also, three main planting scenarios (divided to six sub-scenarios) were developed so as to understand the long-term effectiveness of introducing the selected tree species in improving the environmental benefits (both urban forest structure and ES) in comparison with planting the existing tree species. The results indicate that regardless of the quantity of planting, the benefits of introducing the selected trees will be more than planting the existing species. Moreover, as the amount of the annual planting of the recommended species increases, so does the improvement in the projected tree characteristics and ES. This approach creates more opportunities which enable urban forest managers and policymakers to understand the importance of selecting the proper urban tree species when looking for a nature-based solution to promote the wellbeing of the urban population, to create more livable and ecologically sustainable cities and to mitigate urban environmental problems.

     

Interaction Between Oxytocin and Opioidergic System on Food Intake Regulation in Neonatal Layer Type Chicken

The aim of the current study was to determine possible interaction of central oxytocin and opioidergic system on food intake regulation in neonatal layer-type chicken. In experiment 1, FD₃ chicken ICV injected with control solution, oxytocin (10 µg), β-FNA (µ receptor antagonist, 5 µg) and oxytocin (10 µg)?+?β-FNA were injected. Experiments 2–6 were similar to experiments 1, except chicken injected with nor-BNI (κ receptor antagonist, 5 µg), NTI (δ receptor antagonist, 5 µg), DAMGO (µ receptor agonist, 62.25 pmol), U-50488H (κ receptor agonist, 10 nmol), DPDPE (δ receptor agonist, 20 pmol) instead of β-FNA. In experiment 7, control solution, DAMGO (125 pmol), d(CH2)5Tyr(Me)-[Orn8]-vasotocin (oxytocin antagonist, 5 µg) and DAMGO?+?d(CH2)5Tyr(Me)-[Orn8]-vasotocin were ICV injected to FD₃ chicken. Experiments 8 and 9 were similar to experiments 7, except chicken injected with U-50488H (30 nmol) and DPDPE (40 pmol) instead of DAMGO. Then, cumulative food intake was recorded at 30, 60 and 120 min after injection. According to the results, ICV injection of the oxytocin (10 µg) significantly decreased food intake compared to control group (P?<?0.05). Co-injection of the oxytocin?+?β-FNA and oxytocin?+?U-50488H significantly decreased hypophagic effect of the oxytocin (P?<?0.05). While, co-injection of the oxytocin?+?nor-BNI or oxytocin?+?DAMGO significantly amplified hypophagic effect of the oxytocin in chicken (P?<?0.05). In addition, ICV injection of DAMGO (125 pmol) significantly decreased cumulative food intake compared to control group (P?<?0.05). However, co-addministration of the DAMGO?+?(CH2)5Tyr(Me)-[Orn8]-vasotocin significantly decreased hypophagic effect of the DAMGO (P?<?0.05) in chicken. These results suggested there are interconnection between oxytocin and opioidergic system on central food intake regulation, which mediates via µ and κ opioidergic receptors in neonatal layer-type chicken.

     

An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex

V(D)J recombination assembles functional antigen receptor genes during lymphocyte development. Formation of the recombination complex containing the recombination activating proteins, RAG1 and RAG2, is essential for the site-specific DNA cleavage steps in V(D)J recombination. However, little is known concerning how complex formation leads to a catalytically-active complex. Here, we combined limited proteolysis and mass spectrometry methods to identify regions of RAG1 that are sequestered upon association with RAG2. These results show that RAG2 bridges an interdomain boundary in the catalytic region of RAG1. In a second approach, mutation of RAG1 residues within the interdomain boundary were tested for disruption of RAG1:RAG2 complex formation using fluorescence-based pull down assays. The core RAG1 mutants demonstrated varying effects on complex formation with RAG2. Interestingly, two mutants showed opposing results for the ability to interact with core versus full length RAG2, indicating that the non-core region of RAG2 participates in binding to core RAG1. Significantly, all of the RAG1 interdomain mutants demonstrated altered stoichiometries of the RAG complexes, with an increased number of RAG2 per RAG1 subunit compared to the wild type complex. Based on our results, we propose that interaction of RAG2 with RAG1 induces cooperative interactions of multiple binding sites, induced through conformational changes at the RAG1 interdomain boundary, and resulting in formation of the DNA cleavage active site.     

Anthropometric variables accurately predict dual energy x-ray absorptiometric-derived body composition and can be used to screen for diabetes

The current world-wide epidemic of obesity has stimulated interest in developing simple screening methods to identify individuals with undiagnosed diabetes mellitus type 2 (DM2) or metabolic syndrome (MS). Prior work utilizing body composition obtained by sophisticated technology has shown that the ratio of abdominal fat to total fat is a good predictor for DM2 or MS. The goals of this study were to determine how well simple anthropometric variables predict the fat mass distribution as determined by dual energy x-ray absorptometry (DXA), and whether these are useful to screen for DM2 or MS within a population. To accomplish this, the body composition of 341 females spanning a wide range of body mass indices and with a 23% prevalence of DM2 and MS was determined using DXA. Stepwise linear regression models incorporating age, weight, height, waistline, and hipline predicted DXA body composition (i.e., fat mass, trunk fat, fat free mass, and total mass) with good accuracy. Using body composition as independent variables, nominal logistic regression was then performed to estimate the probability of DM2. The results show good discrimination with the receiver operating characteristic (ROC) having an area under the curve (AUC) of 0.78. The anthropometrically-derived body composition equations derived from the full DXA study group were then applied to a group of 1153 female patients selected from a general endocrinology practice. Similar to the smaller study group, the ROC from logistical regression using body composition had an AUC of 0.81 for the detection of DM2. These results are superior to screening based on questionnaires and compare favorably with published data derived from invasive testing, e.g., hemoglobin A1c. This anthropometric approach offers promise for the development of simple, inexpensive, non-invasive screening to identify individuals with metabolic dysfunction within large populations.     

Resveratrol exerts dosage and duration dependent effect on human mesenchymal stem cell development

Studies in the past have illuminated the potential benefit of resveratrol as an anticancer (pro-apoptosis) and life-extending (pro-survival) compound. However, these two different effects were observed at different concentration ranges. Studies of resveratrol in a wide range of concentrations on the same cell type are lacking, which is necessary to comprehend its diverse and sometimes contradictory cellular effects. In this study, we examined the effects of resveratrol on cell self-renewal and differentiation of human mesenchymal stem cells (hMSCs), a type of adult stem cells that reside in a number of tissues, at concentrations ranging from 0.1 to 10 μM after both short- and long-term exposure. Our results reveal that at 0.1 μM, resveratrol promotes cell self-renewal by inhibiting cellular senescence, whereas at 5 μM or above, resveratrol inhibits cell self-renewal by increasing senescence rate, cell doubling time and S-phase cell cycle arrest. At 1 μM, its effect on cell self-renewal is minimal but after long-term exposure it exerts an inhibitory effect, accompanied with increased senescence rate. At all concentrations, resveratrol promotes osteogenic differentiation in a dosage dependent manner, which is offset by its inhibitory effect on cell self-renewal at high concentrations. On the contrary, resveratrol suppresses adipogenic differentiation during short-term exposure but promotes this process after long-term exposure. Our study implicates that resveratrol is the most beneficial to stem cell development at 0.1 μM and caution should be taken in applying resveratrol as an anticancer therapeutic agent or nutraceutical supplement due to its dosage dependent effect on hMSCs.     

Quantification of protein deposits on silicone hydrogel materials using stable-isotopic labeling and multiple reaction monitoring

This study was designed to use multiple reaction monitoring (MRM) for accurate quantification of contact lens protein deposits. Worn lenses used with a multipurpose disinfecting solution were collected after wear. Individual contact lenses were extracted and then digested with trypsin. MRM in conjunction with stable-isotope-labeled peptide standards was used for protein quantification. The results show that lysozyme was the major protein detected from both lens types. The amount of protein extracted from contact lenses was affected by the lens material. Except for keratin-1 (0.83?±?0.61 vs 0.77?±?0.20, p?=?0.81) or proline rich protein-4 (0.11?±?0.04 vs 0.15?±?0.12, p?=?0.97), the amounts of lysozyme, lactoferrin, or lipocalin-1 extracted from balafilcon A lenses (12.9?±?9.01, 0.84?±?0.50 or 2.06?±?1.6, respectively) were significantly higher than that extracted from senofilcon A lenses (0.88?±?0.13, 0.50?±?0.10 or 0.27?±?0.23, respectively) (p?相似文献   

Prevalence of GJB2 (CX26) gene mutations in south Iranian patients with autosomal recessive nonsyndromic sensorineural hearing loss

Hereditary hearing loss is a genetically heterogeneous disorder. Mutations in connexin 26 (CX26), are a major cause in many countries and are largely dependent on ethnic groups. The purpose of our study was to evaluate the prevalence of GJB2 mutations among affected individuals from south of Iran. Fifty patients presenting with autosomal recessive non-syndromic hearing loss from Fars, province in south of Iran, were studied for mutations in GJB2 gene and screened by direct sequencing. Mutations were detected in 15 out of 50 patients (30?%). Eight different mutations were identified; six of them were previously identified (35delG, V27I M34V, V153I, A149T, V198M). The remaining two alleles, L28I and N169T, were novel variants. The most common mutations were 35delG followed by V153I with an allele frequency of 7 and 6?%, respectively. In this study, 30?% of our subjects were found to have the causative variants or polymorphisms in GJB2 and the c.35delG mutation was the most common cause in our patients. However, more study with larger sample size as well as in vitro functional study for these new variants in Xenopus oocytes is required.     

Evaluating soil biochemical/microbial indices as ecological indicators of different land use/cover in northern Iran

The objective of the study was to examine changes in microbial parameters have been used to monitor changes in soil quality under different land uses in north of Iran. The microbial parameters included microbial respiration (MR), substrate induced respiration (SIR), carbon availability index (CAI), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), ratio of MBC/MBN, metabolic quotient (qCO₂) and microbial ratio were determined under different land use/cover, i.e. virgin natural forest (VNF), degraded natural forest (DNF), alder plantation (AP), sequoia plantation (SP), improved fallow (IF) and home garden (HG) areas in northern Iran. Five composed samples per land use/cover were taken from the top 10 cm of the soil. MR and SIR (0.45 and 1.66 mg CO₂-C g^?1 day^?1, respectively) were found to be significantly higher under AP land uses than in the other areas. CAI did not differ for the land uses; MBC (591 and 590 mg kg^?1, respectively) had higher significantly under SP and VNF land uses than in the other areas. MBN (64.25 and 62.33, respectively mg kg^?1) was significantly higher in AP and VNF land uses, ratio of MBC/MBN (17.02) was higher in SP land use than other areas, HG had significantly higher qCO₂ (0.0012 μg CO₂-C mg^?1 MBC day^?1) and finally microbial ratio was significantly higher under IF (599.16) in comparison with HG > AP ≈ DNF > VNF > SP areas. Overall, our results indicate that AP land use (Alnus subcordata C. A. Mey.) increase of soil quality and alder plantation is suitable for rehabilitation of degraded natural forests.     

Vitamin D receptor genotypes and kidney allograft rejection

Objective Transplantation of renal grafts is an established treatment for renal failure in a variety of medical conditions. Polymorphisms in genes, coding for proteins involved in immune response, may influence immunological and non-immunological mechanisms that lead to allograft loss. Vitamin D receptor (VDR) agonist has been shown to reduce short and long term allograft rejection in animal model. There are functional polymorphisms in VDR gene. Materials and methods A total of 75 renal allograft recipients with at least 2 years follow-up were selected and genotyped for two polymorphisms in the VDR genes (FokI and BsmI) and the association of each genotype with renal allograft survival and acute rejection was evaluated. Results We are unable to find statistically significant association between any of the study polymorphisms and clinical outcomes. Conclusion We have found no evidence to suggest that either VDR FokI or BsmI polymorphism determines the incidence of acute rejection or graft survival after renal transplantation. A larger sample size is necessary to confirm these findings.