Changes in Dry State Hemoglobin over Time Do Not Increase the Potential for Oxidative DNA Damage in Dried Blood

BACKGROUND: Hemoglobin (Hb) is the iron-containing oxygen transport protein present in the red blood cells of vertebrates. Ancient DNA and forensic scientists are particularly interested in Hb reactions in the dry state because both regularly encounter aged, dried bloodstains. The DNA in such stains may be oxidatively damaged and, in theory, may be deteriorated by the presence of Hb. To understand the nature of the oxidative systems potentially available to degrade DNA in the presence of dried Hb, we need to determine what molecular species Hb forms over time. These species will determine what type of iron (i.e. Fe(2+)/Fe(3+)/Fe(4+)) is available to participate in further chemical reactions. The availability of "free" iron will affect the ability of the system to undergo Fenton-type reactions which generate the highly reactive hydroxyl radical (OH*). The OH* can directly damage DNA. METHODOLOGY/PRINCIPAL FINDINGS: Oxygenated Hb (oxyHb) converts over time to oxidized Hb (metHb), but this happens more quickly in the dry state than in the hydrated state, as shown by monitoring stabilized oxyHb. In addition, dry state oxyHb converts into at least one other unknown species other than metHb. Although "free" iron was detectable as both Fe(2+) and Fe(3+) in dry and hydrated oxyHb and metHb, the amount of ions detected did not increase over time. There was no evidence that Hb becomes more prone to generating OH* as it ages in either the hydrated or dry states. CONCLUSIONS: The Hb molecule in the dried state undergoes oxidative changes and releases reactive Fe(II) cations. These changes, however, do not appear to increase the ability of Hb to act as a more aggressive Fenton reagent over time. Nevertheless, the presence of Hb in the vicinity of DNA in dried bloodstains creates the opportunity for OH*-induced oxidative damage to the deoxyribose sugar and the DNA nucleobases

Benchmarking network propagation methods for disease gene identification

In-silico identification of potential target genes for disease is an essential aspect of drug target discovery. Recent studies suggest that successful targets can be found through by leveraging genetic, genomic and protein interaction information. Here, we systematically tested the ability of 12 varied algorithms, based on network propagation, to identify genes that have been targeted by any drug, on gene-disease data from 22 common non-cancerous diseases in OpenTargets. We considered two biological networks, six performance metrics and compared two types of input gene-disease association scores. The impact of the design factors in performance was quantified through additive explanatory models. Standard cross-validation led to over-optimistic performance estimates due to the presence of protein complexes. In order to obtain realistic estimates, we introduced two novel protein complex-aware cross-validation schemes. When seeding biological networks with known drug targets, machine learning and diffusion-based methods found around 2-4 true targets within the top 20 suggestions. Seeding the networks with genes associated to disease by genetics decreased performance below 1 true hit on average. The use of a larger network, although noisier, improved overall performance. We conclude that diffusion-based prioritisers and machine learning applied to diffusion-based features are suited for drug discovery in practice and improve over simpler neighbour-voting methods. We also demonstrate the large impact of choosing an adequate validation strategy and the definition of seed disease genesPeer ReviewedPostprint (published version

eBank UK: linking research data, scholarly communication and learning

This paper includes an overview of the changing landscape of scholarly communication and describes outcomes from the innovative eBank UK project, which seeks to build links from e-research through to e-learning. As introduction, the scholarly knowledge cycle is described and the role of digital repositories and aggregator services in linking data-sets from Grid-enabled projects to e-prints through to peer-reviewed articles as resources in portals and Learning Management Systems, are assessed. The development outcomes from the eBank UK project are presented including the distributed information architecture, requirements for common ontologies, data models, metadata schema, open linking technologies, provenance and workflows. Some emerging challenges for the future are presented in conclusion

Sedimentary context and palaeoecology of Gigantoproductus shell beds in the Mississippian Eyam Limestone Formation, Derbyshire carbonate platform, central England

A sedimentological study was conducted at two localities exposing the Mississippian Eyam Limestone Formation of the Derbyshire carbonate platform, UK. Ricklow Quarry comprises seven facies with diverse skeletal assemblages, representing deposition on the inner to middle ramp within open marine waters. Once-a-Week Quarry comprises four facies, dominated by crinoidal debris representing deposition on the inner ramp. Both localities expose Gigantoproductus shell beds. Palaeoecological analysis of a single shell bed from each locality enabled investigation of the rapid colonization and success of this taxon on the platform. At Ricklow Quarry, on the eastern side of a localized mud mound, both life (>72% of thin and thick-shelled brachiopods in life position) and neighbourhood assemblages are present. A low-moderate diversity community (<1.37 and <0.8 Shannon diversity index) rapidly established over relict Brigantian mud mounds. Shell beds are preluded by intervals of decreased energy that allowed larvae to settle. Once established, the dominance of thick-shelled individuals enabled baffling, potentially providing localized shelter for larvae and nearby individuals. At Once-a-Week Quarry, where no mud mound is present, only thick-shelled Gigantoproductus species and a low diversity community (<1.07 Shannon diversity index) exclusively comprising neighbourhood assemblages (37% in life position) is present. The presence of inactive mud mounds at Ricklow Quarry appears to have been the key to the success of Gigantoproductus species enabling the onset of stable communities in the shelter provided by the relict mound. Once the first palaeocommunities were established, larvae dispersed and colonized higher energy settings, such as at Once-a-Week Quarry

Tests of amounts and times of application of nitrogen and of sequential sprays of aphicide and fungicides on winter wheat, following either beans or wheat, and the effects of take-all (Gaeumannomyces graminis var. tritici ), on two varieties at Saxmundham, Suffolk 1980-3

RESP-9258 and RESP-924

Directing Differentiation of Pluripotent Stem Cells Toward Retinal Pigment Epithelium Lineage

Development of efficient and reproducible conditions for directed differentiation of pluripotent stem cells into specific cell types is important not only to understand early human development but also to enable more practical applications, such as in vitro disease modeling, drug discovery, and cell therapies. The differentiation of stem cells to retinal pigment epithelium (RPE) in particular holds promise as a source of cells for therapeutic replacement in age-related macular degeneration. Here we show development of an efficient method for deriving homogeneous RPE populations in a period of 45 days using an adherent, monolayer system and defined xeno-free media and matrices. The method utilizes sequential inhibition and activation of the Activin and bone morphogenetic protein signaling pathways and can be applied to both human embryonic stem cells and induced pluripotent stem cells as the starting population. In addition, we use whole genome transcript analysis to characterize cells at different stages of differentiation that provides further understanding of the developmental dynamics and fate specification of RPE. We show that with the described method, RPE develop through stages consistent with their formation during embryonic development. This characterization- together with the absence of steps involving embryoid bodies, three-dimensional culture, or manual dissections, which are common features of other protocols-makes this process very attractive for use in research as well as for clinical applications. SIGNIFICANCE: This report describes a novel method of directed differentiation to generate retinal pigment epithelium (RPE) cells from pluripotent stem cells. The employed method is based on adherent monolayer culture using xeno-free conditions and manipulation of the Activin and bone morphogenetic protein signaling pathway using small molecules and recombinant proteins. Whole genome microarray analysis was performed to characterize the differentiation process and understand the developmental path of RPE generation in vitro. This method can be applied for generation of RPE for research as well as for clinical applications