NMR evidence for specific intercalation of Δ-rh(phen)_2phi^(3+) in [d(GTCGAC)_2]

The anchoring of metal complexes in the major groove of DNA through intercalation has been increasingly useful in the shape-selective design of novel metal complexes which bind DNA with high sequence-selectivity. Toward that goal, direct structural information regarding this intercalative interaction is essential. Phenanthrenequinone diimine (phi) complexes of Rh(III) bind avidly (K_b 1 ≥ 10^7) to DNA by intercalation in the major groove. Here we report the first ^1H-NMR studies of Δ-rh(phen)_2phi^(3+) bound to an oligonucleotide. These studies provide direct structural evidence for specific intercalation by this octahedral complex in the major groove of DNA

How to make DNA methylome wide association studies more powerful

Genome-wide association studies had a troublesome adolescence, while researchers increased statistical power, in part by increasing subject numbers. Interrogating the interaction of genetic and environmental influences raised new challenges of statistical power, which were not easily bested by the addition of subjects. Screening the DNA methylome offers an attractive alternative as methylation can be thought of as a proxy for the combined influences of genetics and environment. There are statistical challenges unique to DNA methylome data and also multiple features, which can be exploited to increase power. We anticipate the development of DNA methylome association study designs and new analytical methods, together with integration of data from other molecular species and other studies, which will boost statistical power and tackle causality. In this way, the molecular trajectories that underlie disease development will be uncovered

MicroRNA expression profiling of single whole embryonic stem cells

MicroRNAs (miRNAs) are a class of 17–25 nt non-coding RNAs that have been shown to have critical functions in a wide variety of biological processes during development. Recently developed miRNA microarray techniques have helped to accelerate research on miRNAs. However, in some instances there is only a limited amount of material available for analysis, which requires more sensitive techniques that can preferably work on single cells. Here we demonstrate that it is possible to analyse miRNA in single cells by using a real-time PCR-based 220-plex miRNA expression profiling method. Development of this technique will greatly facilitate miRNA-related research on cells, such as the founder population of primordial germ cells where rapid and dynamic changes occur in a few cells, and for analysing heterogeneous population of cells. In these and similar cases, our method of single cell analysis is critical for elucidating the diverse roles of miRNAs

Protein-DNA charge transport: Redox activation of a DNA repair protein by guanine radical

DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair

NMR evidence for specific intercalation of Δ-rh(phen)_2phi^(3+) in [d(GTCGAC)_2]

The anchoring of metal complexes in the major groove of DNA through intercalation has been increasingly useful in the shape-selective design of novel metal complexes which bind DNA with high sequence-selectivity. Toward that goal, direct structural information regarding this intercalative interaction is essential. Phenanthrenequinone diimine (phi) complexes of Rh(III) bind avidly (K_b 1 ≥ 10^7) to DNA by intercalation in the major groove. Here we report the first ^1H-NMR studies of Δ-rh(phen)_2phi^(3+) bound to an oligonucleotide. These studies provide direct structural evidence for specific intercalation by this octahedral complex in the major groove of DNA

Pediatric wound care: Establishing a consensus group to develop clinical practice guidelines

Introduction. Wound care practices for neonatal and pediatric patients have created a lack of standardized evidence-based guidelines for treatments in clinical practices. Unfortunately, published clinical guidelines for the evaluation and management of wounds in pediatric populations is limited. Consensus groups are used to develop clinical guidelines which define key aspects of the quality of health care, particularly appropriate indications for interventions. The aim of this initiative was to conduct the first two steps of the guideline development process, and to report on the findings from the expert consensus group for pediatric wound care. Methods. The goal was to recruit a multidisciplinary team that consisted of board certified Pediatric Plastic and Pediatric General Surgeons, WOCN, and research specialists active in the International Society of Pediatric Wound Care (ISPEW). All recruited individuals were emailed and invited to participate. For this study, an adapted questionnaire was created to assess eligibility criteria, information sources, systematic review database search strategies, study selection criteria including keywords. Data was collected on the clinical consensus group’s experience with clinical guideline development, and other clinically significant domains for which the the evidence should be evaluated. Results. All six invited individuals agreed to participate. 100% of respondents provided the number of years in their current role within their respective institutions and their length of experience with pediatric wound care management. 17% of respondents had 7 to 10 years in their current role, while 66% had more than 10 years practice in pediatric wound care. Domains identified as important to consider included: Cost of Product/Treatment Duration of Treatment, Ease of Applying Product/Performing Treatment, Accessibility of Product, Storage of Product, Length of Time to Apply Product/Perform Treatment. Discussion. The agreed-upon domains from our study align with previously published consensus group studies. We identified several domains to inform a future systematic review. At this time, no systematic review has been published that has been guided by consensus group domains and search terms for pediatric wound care. Conclusion. Through the use of this consensus group and conducted surveys, we identified the primary domains necessary to complete a practice-informed systematic review, as well as other key domains that are important in clinical pediatric wound care management

Forming Young Bulges within Existing Disks: Statistical Evidence for External Drivers

Contrary to traditional models of galaxy formation, recent observations suggest that some bulges form within preexisting disk galaxies. Such late-epoch bulge formation within disks seems to be linked to disk gas inflow and central star formation, caused by either internal secular processes or galaxy mergers and interactions. We identify a population of galaxies likely to be experiencing active bulge growth within disks, using the criterion that the color within the half-light radius is bluer than the outer disk color. Such blue-centered galaxies make up >10% of star-forming disk galaxies within the Nearby Field Galaxy Survey, a broad survey designed to represent the natural diversity of the low-z galaxy population over a wide range of luminosities and environments. Blue-centered galaxies correlate at 99% confidence with morphological peculiarities suggestive of minor mergers and interactions. From this and other evidence, we argue that external drivers rather than internal secular processes probably account for the majority of blue-centered galaxies. We go on to discuss quantitative plausibility arguments indicating that blue-centered evolutionary phases may represent an important mode of bulge growth for most disk galaxies, leading to significant changes in bulge-to-disk ratio without destroying disks. If this view is correct, bulge growth within disks may be a natural consequence of the repeated galaxy mergers and interactions inherent in hierarchical galaxy formation.Comment: 18 pages including 12 figures, AJ, accepte

Cdkn1c (p57Kip2) is the major regulator of embryonic growth within its imprinted domain on mouse distal chromosome 7

Background: Cdkn1c encodes an embryonic cyclin-dependant kinase inhibitor that acts to negatively regulate cell proliferation and, in some tissues, to actively direct differentiation. This gene, which is an imprinted gene expressed only from the maternal allele, lies within a complex region on mouse distal chromosome 7, called the IC2 domain, which contains several other imprinted genes. Studies on mouse embryos suggest a key role for genomic imprinting in regulating embryonic growth and this has led to the proposal that imprinting evolved as a consequence of the mismatched contribution of parental resources in mammals. Results: In this study, we characterised the phenotype of mice carrying different copy number integrations of a bacterial artificial chromosome spanning Cdkn1c. Excess Cdkn1c resulted in embryonic growth retardation that was dosage-dependent and also responsive to the genetic background. Two-fold expression of Cdkn1c in a subset of tissues caused a 10–30% reduction in embryonic weight, embryonic lethality and was associated with a reduction in the expression of the potent, non-imprinted embryonic growth factor, Igf1. Conversely, loss of expression of Cdkn1c resulted in embryos that were 11% heavier with a two-fold increase in Igf1. Conclusion: We have shown that embryonic growth in mice is exquisitely sensitive to the precise dosage of Cdkn1c. Cdkn1c is a maternally expressed gene and our findings support the prediction of the parental conflict hypothesis that that the paternal genome silences genes that have an inhibitory role in embryonic growth. Within the IC2 imprinted domain, Cdkn1c encodes the major regulator of embryonic growth and we propose that Cdkn1c was the focal point of the selective pressure for imprinting of this domain