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MOTIVATION - High-throughput genomic data often contain unexpected information that can be mined for alternative applications. Despite the rise of high-throughput sequencing, Illumina genotyping arrays remain a driving force in large scale genetic and epidemiology studies. By processing and analyzing genotyping data of over 100,000 samples genotyped on Illumina genotyping arrays, we discovered evidence that indicates that mitochondrial heteroplasmy can be estimated from the fluorescence intensity data of the array. To verify our hypothesis, we conducted a sequencing validation study.
RESULT - Mitochondrial DNA targeted sequencing was performed on three samples that had been genotyped using the Illumina exome genotyping array. In each sample chosen, one heteroplasmy target was identified from the genotyping array, and sequencing data verified all three putative heteroplasmic sites. The estimated heteroplasmy level difference between that estimated from the genotyping fluorescence intensity and that directly measured from sequencing was 3.2% on average. Our analysis showed that an Illumina genotyping array can accurately and reliably estimate high-level heteroplasmy (>40%); however, intensity data from a genotyping array is not suitable for estimating low level heteroplasmy (<25%).
Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.
We report herein a method to track the migration of dendritic cells (DCs) using optical imaging. With the assistance of the delivery module, fluorescein isothiocyanate (FITC) could internalize inside DCs within 15 minutes of incubation. The fluorescent signal was mostly cytoplasmic and could be detected using in vivo imaging. Furthermore, we observed that the probe did not interfere with the DCs maturation as we assessed the expression of several surface markers. The labeled DCs secreted interleukin-12 (IL-12) and tumor necrosis factor-alpha (TNF-alpha) and stimulated the proliferation of CD4+ T lymphocytes responding to lipopolysaccharide (LPS) stimulation. We have systematically compared the probe uptake between mature and immature DCs. The study showed that the latter phagocytosed the probe slightly better than the former. Intravital imaging of treated mice showed the migration of DCs to lymph nodes (LNs), which is confirmed by immunohistochemistry. Taken together, we demonstrated the potential use of optical imaging for tracking the migration of DCs and homing in vivo. The delivery molecules could also be used on other imaging modalities or for delivery of antigens.
The serotonin 5-HT(1A) receptor couples to heterotrimeric G proteins and intracellular second messengers, yet no studies have investigated the possible role of additional receptor-interacting proteins in 5-HT(1A) receptor signaling. We have found that the ubiquitous Ca(2+)-sensor calmodulin (CaM) co-immunoprecipitates with the 5-HT(1A) receptor in Chinese hamster ovary fibroblasts. The human 5-HT(1A) receptor contains two putative CaM binding motifs, located in the N- and C-terminal juxtamembrane regions of the third intracellular loop of the receptor. Peptides encompassing both the N-terminal (i3N) and C-terminal (i3C) CaM-binding domains were tested for CaM binding. Using in vitro binding assays in combination with gel shift analysis, we demonstrated Ca(2+)-dependent formation of complexes between CaM and both peptides. We determined kinetic data using a combination of BIAcore surface plasmon resonance (SPR) and dansyl-CaM fluorescence. SPR analysis gave an apparent K(D) of approximately 110 nm for the i3N peptide and approximately 700 nm for the i3C peptide. Both peptides also caused characteristic shifts in the fluorescence emission spectrum of dansyl-CaM, with apparent affinities of 87 +/- 23 nm and 1.70 +/- 0.16 microm. We used bioluminescence resonance energy transfer to show that CaM interacts with the 5-HT(1A) receptor in living cells, representing the first in vivo evidence of a G protein-coupled receptor interacting with CaM. Finally, we showed that CaM binding and phosphorylation of the 5-HT(1A) receptor i3 loop peptides by protein kinase C are antagonistic in vitro, suggesting a possible role for CaM in the regulation of 5-HT(1A) receptor phosphorylation and desensitization. These data suggest that the 5-HT(1A) receptor contains high and moderate affinity CaM binding regions that may play important roles in receptor signaling and function.
The sodium/proton exchanger type 1 (NHE-1) plays an important role in the proliferation of vascular smooth muscle cells (VSMC). We have examined the regulation of NHE-1 by two potent mitogens, serotonin (5-HT, 5-hydroxytryptamine) and angiotensin II (Ang II), in cultured VSMC derived from rat aorta. 5-HT and Ang II rapidly activated NHE-1 via their G protein-coupled receptors (5-HT(2A) and AT(1)) as assessed by proton microphysiometry of quiescent cells and by measurements of intracellular pH on a FLIPR (fluorometric imaging plate reader). Activation of NHE-1 was blocked by inhibitors of phospholipase C, CaM, and Jak2 but not by pertussis toxin or inhibitors of protein kinase C. Immunoprecipitation/immunoblot studies showed that 5-HT and Ang II induce phosphorylation of Jak2 and induce the formation of signal transduction complexes that included Jak2, CaM, and NHE-1. The cell-permeable Ca(2+) chelator BAPTA-AM blocked activation of Jak2, complex formation between Jak2 and CaM, and tyrosine phosphorylation of CaM, demonstrating that elevated intracellular Ca(2+) is essential for those events. Thus, mitogen-induced activation of NHE-1 in VSMC is dependent upon elevated intracellular Ca(2+) and is mediated by the Jak2-dependent tyrosine phosphorylation of CaM and subsequent increased binding of CaM to NHE-1, similar to the pathway previously described for the bradykinin B(2) receptor in inner medullary collecting duct cells of the kidney [Mukhin, Y. V., et al. (2001) J. Biol. Chem. 276, 17339-17346]. We propose that this pathway represents a fundamental mechanism for the rapid regulation of NHE-1 by G(q/11) protein-coupled receptors in multiple cell types.
Chinese hamster ovary (CHO) cells were treated with the thiol oxidant diamide for 1 hr at 37 degrees, incubated in diamide-free medium for 4 hr at 37 degrees, and then exposed to hyperthermic treatment (43 degrees) or assayed for the presence of 110, 90 and 66 kilodalton (kD) stress (heat shock) proteins. Cellular inactivation produced by the hyperthermic treatment was measured using colony formation as the end point. Low concentrations of diamide, which did not result in depletion of intracellular GSH, induced a moderate degree of protection against thermal toxicity but did not affect the pattern of protein synthesis. Exposure to 0.4 mM diamide, which reduced intracellular GSH concentrations by 50-60%, significantly reduced the rate of hyperthermic cellular inactivation. This occurred coincidentally with the synthesis of stress proteins of approximate molecular weights of 110, 90 and 66 kD. Furthermore, this concentration of diamide protected cells from thermal inhibition of protein synthesis. These results indicate that thiol oxidation by diamide can induce both the development of thermal resistance to cellular inactivation and the synthesis of stress proteins.