NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP

The structures of RNA-aptamer-ligand complexes solved in the last two decades were instrumental in realizing the amazing potential of RNA for forming complex tertiary structures and for molecular recognition of small molecules. For GTP as ligand the sequences and secondary structures for multiple families of aptamers were reported which differ widely in their structural complexity, ligand affinity and ligand functional groups involved in RNA-binding. However, for only one of these families the structure of the GTP-RNA complex was solved. In order to gain further insights into the variability of ligand recognition modes we are currently determining the structure of another GTP-aptamer—the so-called class II aptamer—bound to GTP using NMR-spectroscopy in solution. As a prerequisite for a full structure determination, we report here ¹H, ¹³C, ¹⁵N and partial ³¹P-NMR resonance assignments for the class II GTP-aptamer bound to GTP.     

Proteomic and Post‐Translational Modification Profiling of Exosome‐Mimetic Nanovesicles Compared to Exosomes

Issues associated with upscaling exosome production for therapeutic use may be overcome through utilizing artificial exosomes. Cell‐derived mimetic nanovesicles (M‐NVs) are a potentially promising alternative to exosomes for clinical applicability, demonstrating higher yield without incumbent production and isolation issues. Although several studies have shown that M‐NVs have similar morphology, size and therapeutic potential compared to exosomes, comprehensive characterization and to what extent M‐NVs components mimic exosomes remain elusive. M‐NVs were generated through the extrusion of cells and proteomic profiling demonstrated an enrichment of proteins associated with membrane and cytosolic components. The proteomic data herein reveal a subset of proteins that are highly abundant in M‐NVs in comparison to exosomes. M‐NVs contain proteins that largely represent the parental cell proteome, whereas the profile of exosomal proteins highlight their endosomally derived origin. This advantage of M‐NVs alleviates the necessity of endosomal sorting of endogenous therapeutic proteins or RNA into exosomes. This study also highlights differences in protein post‐translational modifications among M‐NVs, as distinct from exosomes. Overall this study provides key insights into defining the proteome composition of M‐NVs as a distinct from exosomes, and the potential advantage of M‐NVs as an alternative nanocarrier when spontaneous endosomal sorting of therapeutics are limited.     

Genetic Diversity of Selected Iranian Quinces Using SSRs from Apples and Pears

An Iranian National Quince collection containing 40 quince genotypes, originating from six distinct geographic areas, was screened using 15 SSR markers developed originally for apple and pear genomes. Overall, 13 markers exhibited polymorphism, with an average of 5.36 putative alleles per locus and a mean PIC value of 0.76. An UPGMA analysis divided the quince genotypes into five major clusters. The same results were obtained when the principal coordinates were plotted. The assignment test successfully allocated 83% of individuals into their place of origin. These results agree somewhat with the geographic origin of the quince accessions, and we conclude that geographic isolation leads to considerable genetic differentiation among Iranian quince collections. A significant ratio of transferability with a mean of 87.86% was measured, and we deduced that STMS markers derived from pear and apple have enough potential to detect polymorphism and differentiation in quince.     

Comparison of human-induced pluripotent stem cells and mesenchymal stem cell differentiation potential to insulin producing cells in 2D and 3D culture systems in vitro

Diabetes is one of the most common diseases in the world that is chronic, progressive, and costly, and causes many complications. Common drug therapies are not able to cure it, and pancreas transplantation is not responsive to the high number of patients. The production of the insulin producing cells (IPCs) from the stem cells in the laboratory and their transplantation to the patient's body is one of the most promising new approaches. In this study, the differentiation potential of the induced pluripotent stem cells (iPSCs) and mesenchymal stem cells (MSCs) into IPCs was compared to each other while cultured on poly(lactic-co-glycolic) acid (PLGA)/polyethylene glycol (PEG) nanofibrous scaffold as a 3D substrate and tissue culture polystyrene (TCPS) as a 2D substrate. Although the expression level of the insulin, Glut2 and pdx-1 genes in stem cells cultured on 3D substrate was significantly higher than the stem cells cultured on 2D substrate, the highest expression level of these genes was detected in the iPSCs cultured on PLGA-PEG. Insulin and C-peptide secretions from differentiated cells were also investigated and the results showed that secretions in cultured iPSCs on the PLGA-PEG were significantly higher than cultured iPSCs on the TCPS and cultured MSCs on both PLGA-PEG and TCPS. In addition, insulin protein was also expressed in the cultured iPSCs on the PLGA-PEG significantly higher than cultured MSCs on the PLGA-PEG. It can be concluded that differentiation potential of iPSCs into IPCs is significantly higher than human MSCs at both 2D and 3D culture systems.     

Reactivation of electron flow in chloroplasts of in vitro shootlets of apple through elimination of carbon source and evaluation of its activity by inhibitors of electron transport chain and chlorophyll fluorescence quenching

Electron transport chains (ETC) are drastically inactivated in chloroplasts of in vitro shootlets due to presence of carbon source in the growth media. This inactivation consequently creates limitations for in vitro studies on the role of chloroplasts in biotic and abiotic stresses. This research was carried out to evaluate reactivation of electron flow in chloroplasts ETC by elimination of carbon source and subsequent comparison of the effects of ETC inhibitors in the presence and absence of carbon source (i.e., sucrose) on the in vitro shootlets of apple rootstock, MM-111. All the tested ETC inhibitors, including uracil; glutaraldehyde, methyl viologen (MV) and DCMU triggered necrosis appearance on the in vitro apple shootlets exclusively on the carbon source-free media. Moreover, exposure of the in vitro shootlets to the various concentrations of ETC inhibitors demonstrated different severity of ETC inhibition by these inhibitors and their concentration-dependent effects on chloroplasts ETC. Uracil, the inhibitor of photosystem II, triggered the weakest shootlets necrosis, while DCMU exhibited no necrogenic effects at 50 mg/L and lower concentrations. MV, contrary to glutaraldehyde, did not have necrogenesis effects at 1 mg/L, but both of them caused sharp necrosis trigger on the shootlets as soon as 48–96 h after exposure to their effective concentrations. Evaluation of the shootlets H⁺-ATPase activity revealed that proton extrusion and pH decline in the growth media were mainly associated with the sucrose uptake by the shootlets, while no considerable pH decline observed in the presence of carbon source in the media. Finally, chloroplasts ETC activity of the shootlets was confirmed by higher percentage of O₂ and less CO₂ quantity in the atmospheres of the jars containing sucrose-free media, as well as by higher initial fluorescence (Fo) and maximum fluorescence (Fm) quenching parameters in the shootlets, in comparison with the sucrose-enriched condition.     

Tracing the tail of ubiquinone in mitochondrial complex I

Mitochondrial complex I (proton pumping NADH:ubiquinone oxidoreductase) is the largest and most complicated component of the respiratory electron transfer chain. Despite its central role in biological energy conversion the structure and function of this membrane integral multiprotein complex is still poorly understood. Recent insights into the structure of complex I by X-ray crystallography have shown that iron–sulfur cluster N2, the immediate electron donor for ubiquinone, resides about 30 Å above the membrane domain and mutagenesis studies suggested that the active site for the hydrophobic substrate is located next to this redox-center. To trace the path for the hydrophobic tail of ubiquinone when it enters the peripheral arm of complex I, we performed an extensive structure/function analysis of complex I from Yarrowia lipolytica monitoring the interaction of site-directed mutants with five ubiquinone derivatives carrying different tails. The catalytic activity of a subset of mutants was strictly dependent on the presence of intact isoprenoid moieties in the tail. Overall a consistent picture emerged suggesting that the tail of ubiquinone enters through a narrow path at the interface between the 49-kDa and PSST subunits. Most notably we identified a set of methionines that seems to form a hydrophobic gate to the active site reminiscent to the M-domains involved in the interaction with hydrophobic targeting sequences with the signal recognition particle of the endoplasmic reticulum. Interestingly, two of the amino acids critical for the interaction with the ubiquinone tail are different in bovine complex I and we could show that one of these exchanges is responsible for the lower sensitivity of Y. lipolytica complex I towards the inhibitor rotenone. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).     

Kit ligand and glial‐derived neurotrophic factor as alternative supplements for activation and development of ovine preantral follicles in vitro

In vitro growth of preantral follicles has the potential to produce considerable numbers of competent oocytes for use in medicine, agriculture, and even wildlife conservation. The critical regulatory role of growth factors and hormones in the development of preantral follicles has been established. This study investigated the effect of glial‐derived neurotropic factor (GDNF) and kit ligand (KL) on the in vitro development of ovine preantral follicles. Results indicated that both GDNF and KL significantly improved activation of primordial follicles, similar to co‐addition of epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF), which are commonly used for in vitro follicular development. Importantly, GDNF had a more profound effect on follicle health, development, and differentiation compared with KL alone. Furthermore, the combination of GDNF and KL in the presence of EGF and bFGF had a positive, synergic effect on health, development, and differentiation of preantral follicles, as determined by histological and hormonal assessments. The results of this study may provide a foundation for further studies that will unravel the molecular mechanisms of follicular development to further improve the current status of in vitro preantral follicle culture. Mol. Reprod. Dev. 80: 35–47, 2013. © 2012 Wiley Periodicals, Inc.     

An evolutionary relationship between Stearoyl-CoA Desaturase (SCD) protein sequences involved in fatty acid metabolism

Background:

Stearoyl-CoA desaturase (SCD) is a key enzyme that converts saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs) in fat biosynthesis. Despite being crucial for interpreting SCDs’ roles across species, the evolutionary relationship of SCD proteins across species has yet to be elucidated. This study aims to present this evolutionary relationship based on amino acid sequences.

Methods:

Using Multiple Sequence Alignment (MSA) and phylogenetic construction methods, a hypothetical evolutionary relationship was generated between the stearoyl-CoA desaturase (SCD) protein sequences between 18 different species.

Results:

SCD protein sequences from Homo sapiens, Pan troglodytes (chimpanzee), and Pongo abelii (orangutan) have the lowest genetic distances of 0.006 of the 18 species studied. Capra hircus (goat) and Ovis aries (Sheep) had the next lowest genetic distance of 0.023. These farm animals are 99.987% identical at the amino acid level.

Conclusions:

The SCD proteins are conserved in these 18 species, and their evolutionary relationships are similar. Key Words: Phylogenetic analysis, Stearoyl-CoA desaturase (SCD) proteins, Multiple sequence alignment