Nano-scavengers for blood biomarker discovery in ovarian carcinoma

The development and implementation of biomarker-based screening tools for ovarian cancer require novel analytical platforms to enable the discovery of biomarker panels that will overcome the limitations associated with the clinically used CA-125.The systematic discovery of protein biomarkers directly from human plasma using proteomics remains extremely challenging, due to the wide concentration range of plasma proteins. Here, we describe the use of lipid-based nanoparticles (NPs) as an 'omics' enrichment tool to amplify cancer signals in the blood and to uncover disease specific signatures. We aimed to exploit the spontaneous interaction of clinically-used liposomes (Caelyx®) with plasma proteins, also known as' protein corona' formation, in order to facilitate the discovery of previously unreported differentially abundant molecules. Caelyx® liposomes were incubated with plasma samples obtained from advanced ovarian carcinoma patients and healthy donors and corona-coated liposomes were subsequently recovered. Comprehensive comparison between 'healthy' and 'diseased' corona samples by label-free proteomics resulted in the identification of multiple differentially abundant proteins. Moreover, immunoassay-based validation of selected proteins demonstrated the potential of nanoparticle-platform proposed to discover novel molecules with great diagnostic potential. This study proposes a nanoparticle-enabled workflow for plasma proteomic analysis in healthy and diseased states and paves the way for further work needed to discover and validate panels of novel biomarkers for disease diagnosis and monitoring

The Application of a Hypothesis-driven Strategy to the Sensitive Detection and Location of Acetylated Lysine Residues

The application of a hypothesis-driven method for the sensitive determination of lysine acetylation sites on enzymatically digested proteins is described. Comparative sensitivity tests were carried out using serial dilution of an acetylated bovine serum albumin (AcBSA) digest to assess the performance of a multiple reaction monitoring (MRM)–based approach as compared to a more conventional precursor scanning (PS) method. Both methods were capable of selectively detecting an acetylated peptide at the low femtomole level when spiked into a background of 500 fmol six-protein tryptic digest. The MRM approach was roughly tenfold more sensitive than precursor scanning with one acetylated peptide detected and sequenced at the level of 2 fmol on-column. The technique was subsequently applied to a gel-derived sample of cytokeratin-8 (CK8) shown to contain acetylated lysine residues by Western blot analysis. The strategy applied herein, termed MRM-initiated detection and sequencing (MIDAS), resulted in the facile identification of novel sites of acetylation on this protein

Pan-cerebral sodium elevations in vascular dementia: Evidence for disturbed brain-sodium homeostasis

Vascular dementia (VaD) is the second most common cause of cognitive impairment amongst the elderly. However, there are no known disease-modifying therapies for VaD, probably due to incomplete understanding of the molecular basis of the disease. Despite the complex etiology of neurodegenerative conditions, a growing body of research now suggests the potential involvement of metal dyshomeostasis in the pathogenesis of several of the age-related dementias. However, by comparison, there remains little research investigating brain metal levels in VaD. In order to shed light on the possible involvement of metal dyshomeostasis in VaD, we employed inductively coupled plasma-mass spectrometry to quantify the levels of essential metals in post-mortem VaD brain tissue (n = 10) and age-/sex-matched controls (n = 10) from seven brain regions. We found novel evidence for elevated wet-weight cerebral sodium levels in VaD brain tissue in six out of the seven regions analyzed. Decreased cerebral-potassium levels as well as increased Na/K ratios (consistent with high tissue sodium and low potassium levels) were also observed in several brain regions. These data suggest that reduced Na+/K+-exchanging ATPase (EC 7.2.2.13) activity could contribute to the contrasting changes in sodium and potassium measured here

Identification and Prioritization of Analysis Cases for Marine and Hydrokinetic Energy Risk Screening

In this report we describe the development of the Environmental Risk Evaluation System (ERES), a risk-informed analytical process for estimating the environmental risks associated with the construction and operation of marine and hydrokinetic energy generation projects. The development process consists of two main phases of analysis. In the first phase, preliminary risk analyses will take the form of screening studies in which key environmental impacts and the uncertainties that create risk are identified, leading to a better-focused characterization of the relevant environmental effects. Existence of critical data gaps will suggest areas in which specific modeling and/or data collection activities should take place. In the second phase, more detailed quantitative risk analyses will be conducted, with residual uncertainties providing the basis for recommending risk mitigation and monitoring activities. We also describe the process used for selecting three cases for fiscal year 2010 risk screening analysis using the ERES. A case is defined as a specific technology deployed in a particular location involving certain environmental receptors specific to that location. The three cases selected satisfy a number of desirable criteria: 1) they correspond to real projects whose deployment is likely to take place in the foreseeable future; 2) the technology developers are willing to share technology and project-related data; 3) the projects represent a diversity of technology-site-receptor characteristics; 4) the projects are of national interest, and 5) environmental effects data may be available for the projects

Risk-Informed Monitoring, Verification and Accounting (RI-MVA). An NRAP White Paper Documenting Methods and a Demonstration Model for Risk-Informed MVA System Design and Operations in Geologic Carbon Sequestration

This white paper accompanies a demonstration model that implements methods for the risk-informed design of monitoring, verification and accounting (RI-MVA) systems in geologic carbon sequestration projects. The intent is that this model will ultimately be integrated with, or interfaced with, the National Risk Assessment Partnership (NRAP) integrated assessment model (IAM). The RI-MVA methods described here apply optimization techniques in the analytical environment of NRAP risk profiles to allow systematic identification and comparison of the risk and cost attributes of MVA design options

Characterizing Uncertainty for Regional Climate Change Mitigation and Adaptation Decisions

This white paper describes the results of new research to develop an uncertainty characterization process to help address the challenges of regional climate change mitigation and adaptation decisions

Conceptual Model of Offshore Wind Environmental Risk Evaluation System

In this report we describe the development of the Environmental Risk Evaluation System (ERES), a risk-informed analytical process for estimating the environmental risks associated with the construction and operation of offshore wind energy generation projects. The development of ERES for offshore wind is closely allied to a concurrent process undertaken to examine environmental effects of marine and hydrokinetic (MHK) energy generation, although specific risk-relevant attributes will differ between the MHK and offshore wind domains. During FY10, a conceptual design of ERES for offshore wind will be developed. The offshore wind ERES mockup described in this report will provide a preview of the functionality of a fully developed risk evaluation system that will use risk assessment techniques to determine priority stressors on aquatic organisms and environments from specific technology aspects, identify key uncertainties underlying high-risk issues, compile a wide-range of data types in an innovative and flexible data organizing scheme, and inform planning and decision processes with a transparent and technically robust decision-support tool. A fully functional version of ERES for offshore wind will be developed in a subsequent phase of the project