Blood-Based Protein Biomarker Panel for the Detection of Colorectal Cancer

Background

The majority of colorectal cancer (CRC) cases are preventable by early detection and removal of precancerous polyps. Even though CRC is the second most common internal cancer in Australia, only 30 per cent of the population considered to have risk factors participate in stool-based test screening programs. Evidence indicates a robust, blood-based, diagnostic assay would increase screening compliance. A number of potential diagnostic blood-based protein biomarkers for CRC have been reported, but all lack sensitivity or specificity for use as a stand-alone diagnostic. The aim of this study was to identify and validate a panel of protein-based biomarkers in independent cohorts that could be translated to a reliable, non-invasive blood-based screening test.

Principal Findings

In two independent cohorts (n = 145 and n = 197), we evaluated seven single biomarkers in serum of CRC patients and age/gender matched controls that showed a significant difference between controls and CRC, but individually lack the sensitivity for diagnostic application. Using logistic regression strategies, we identified a panel of three biomarkers that discriminated between controls and CRC with 73% sensitivity at 95% specificity, when applied to either of the two cohorts. This panel comprised of Insulin like growth factor binding protein 2 (IGFBP2), Dickkopf-3 (DKK3), and Pyruvate kinase M2(PKM2).

Conclusions

Due to the heterogeneous nature of CRC, a single biomarker is unlikely to have sufficient sensitivity or specificity for use as a stand-alone diagnostic screening test and a panel of markers may be more effective. We have identified a 3 biomarker panel that has higher sensitivity and specificity for early stage (Stage I and -II) disease than the faecal occult blood test, raising the possibility for its use as a non-invasive blood diagnostic or screening test.     

The Ry-fsto gene from Solanum stoloniferum for extreme resistant to Potato virus Y maps to potato chromosome XII and is diagnosed by PCR marker GP122718 in PVY resistant potato cultivars

A novel locus for extreme resistance to Potato virus Y (PVY), Ry-f_sto, was identified on potato chromosome XII. The gene Ry-f_sto has been introgressed from the wild potato species Solanum stoloniferum. Inheritance of Ry-f_sto in the tetraploid potato population Rysto was consistent with the model of a single, dominant gene. Bulked segregant analysis identified an ISSR (inter-simple sequence repeat) marker UBC 857₉₈₀ linked to Ry-f_sto. This marker mapped to linkage group XII of a reference potato RFLP (restriction fragment length polymorphism) map. Chromosome XII specific RFLP markers were converted into PCR-based STS and CAPS markers and tested for linkage with Ry-f_sto in the population Rysto. CAPS marker GP122₇₁₈ was tightly linked to the resistance gene and was successfully used to identify Polish and German cultivars expressing extreme resistance to PVY. This indicates that the source of Ry-f_sto has been widely utilized in various potato breeding programs and can be monitored by a diagnostic marker in marker-assisted selection.     

Railway Embankments as New Habitat for Pollinators in an Agricultural Landscape

Pollinating insect populations, essential for maintaining wild plant diversity and agricultural productivity, rely on (semi)natural habitats. An increasing human population is encroaching upon and deteriorating pollinator habitats. Thus the population persistence of pollinating insects and their associated ecosystem services may depend upon on man-made novel habitats; however, their importance for ecosystem services is barely understood. We tested if man-made infrastructure (railway embankments) in an agricultural landscape establishes novel habitats that support large populations of pollinators (bees, butterflies, hoverflies) when compared to typical habitats for these insects, i.e., semi-natural grasslands. We also identified key environmental factors affecting the species richness and abundance of pollinators on embankments. Species richness and abundance of bees and butterflies were higher for railway embankments than for grasslands. The occurrence of bare (non-vegetated) ground on embankments positively affected bee species richness and abundance, but negatively affected butterfly populations. Species richness and abundance of butterflies positively depended on species richness of native plants on embankments, whereas bee species richness was positively affected by species richness of non-native flowering plants. The density of shrubs on embankments negatively affected the number of bee species and their abundance. Bee and hoverfly species richness were positively related to wood cover in a landscape surrounding embankments. This is the first study showing that railway embankments constitute valuable habitat for the conservation of pollinators in farmland. Specific conservation strategies involving embankments should focus on preventing habitat deterioration due to encroachment of dense shrubs and maintaining grassland vegetation with patches of bare ground.     

The role of Ca2+ ions in modulating changes induced in bean plants by an excess of Cu2+ ions. Chlorophyll fluorescence measurements

Ca²⁺-dependent influence of excess Cu²⁺ on the photosynthetic akpparatus monitored through chlorophyll fluorescence measurements was investigated in runner bean plants (Phaseolus coccineus L. cv. Pie kny Ja?) at three different growth stages. It was observed that the toxic effect of excess Cu²⁺ on plants depends both on their growth stages and the Ca²⁺ content in the medium. Increased Ca²⁺ content limits Cu²⁺ action on plants at their initial growth stage (I) through: stabilization of the PSII complex (increase of the ratio of variable to minimal fluorescence [F_v/F₀]), improved electron flow and reoxidative processes of the quinone primary electron acceptor of PSII (Q_A) (increase of quantum yield of PSII electron transport [φ_e] and photochemical quenching of fluorescence [q_P] values) and elimination of nonphotochemical energy dissipation (decrease of nonphotochemical fluorescence quenching from the Stern-Volmer equation [NPQ] and fraction of the absorbed light energy not used for photochemistry [LNU] values). At this growth stage excess Cu²⁺ decreases the rates of Q_A reduction as a result of decreased PSII activity at its donor side only at lower Ca²⁺ level. At the intermediate growth stage (II) the plants were less sensitive to Cu²⁺ treatment and also to changed Ca²⁺ content. A weakening of some photochemical processes by excess Cu²⁺ could be observed only at a higher Ca²⁺ dose. At the final growth stage of plants (III) Ca²⁺ ions exerted a decisively different effect on the mechanism of excess Cu²⁺ action on bean plants, visualized by decreased PSII stabilization and utilization of absorbed light energy at increased Ca²⁺ content in the medium.     

High Performance Liquid Chromatography of Molecular Species from Free Sterols and Sterylglycosides Isolated from Oat Leaves and Seeds

Free sterols and sterylglycosides (SG) from oat leaves and seedswere isolated by conventional thin layer chromatography (TLC)and subjected to high performance liquid chromatography (HPLC)for resolution of molecular species. Acylsterylglycosides, isolatedby TLC, were converted to SG by mild alkaline hydrolysis anddetermined as SG. Sterols and SG were injected onto the columnwithout any chemical treatment and the separated species weredetected at 200 nm. The separation of SG-species follows exactlythe separation of free sterols. Though gas liquid chromatography still is the method of choice,advantages of HPLC is to analyse directly the SG-species withouthydrolysis and derivatization as compared to GLC. After TLCthe sterol- and the SG-fraction are injected directly onto thecolumn. This is extremely important for labile sterylglycosidesor sterols, as demonstrated for the avenasterols. ¹ Preliminary reports have been presented on the "4. Arbeitstagung,Pflanzliche Lipide", October 7–8, 1983 in M?nster (FRG)and on the "6th International Symposium on the Structure, Functionand Metabolism of Plant Lipids", Neuchatel, Switzerland, July16–20, 1984. (Received November 12, 1984; Accepted January 14, 1985)     

Fast Approximate Quadratic Programming for Graph Matching

Quadratic assignment problems arise in a wide variety of domains, spanning operations research, graph theory, computer vision, and neuroscience, to name a few. The graph matching problem is a special case of the quadratic assignment problem, and graph matching is increasingly important as graph-valued data is becoming more prominent. With the aim of efficiently and accurately matching the large graphs common in big data, we present our graph matching algorithm, the Fast Approximate Quadratic assignment algorithm. We empirically demonstrate that our algorithm is faster and achieves a lower objective value on over 80% of the QAPLIB benchmark library, compared with the previous state-of-the-art. Applying our algorithm to our motivating example, matching C. elegans connectomes (brain-graphs), we find that it efficiently achieves performance.     

IL-17 is a critical component of vaccine-induced protection against lung infection by lipopolysaccharide-heterologous strains of Pseudomonas aeruginosa

In a murine model of acute fatal pneumonia, we previously showed that nasal immunization with a live-attenuated aroA deletant of Pseudomonas aeruginosa strain PAO1 elicited LPS serogroup-specific protection, indicating that opsonic Ab to the LPS O Ag was the most important immune effector. Because P. aeruginosa strain PA14 possesses additional virulence factors, we hypothesized that a live-attenuated vaccine based on PA14 might elicit a broader array of immune effectors. Thus, an aroA deletant of PA14, denoted PA14DeltaaroA, was constructed. PA14DeltaaroA-immunized mice were protected against lethal pneumonia caused not only by the parental strain but also by cytotoxic variants of the O Ag-heterologous P. aeruginosa strains PAO1 and PAO6a,d. Remarkably, serum from PA14DeltaaroA-immunized mice had very low levels of opsonic activity against strain PAO1 and could not passively transfer protection, suggesting that an antibody-independent mechanism was needed for the observed cross-serogroup protection. Compared with control mice, PA14DeltaaroA-immunized mice had more rapid recruitment of neutrophils to the airways early after challenge. T cells isolated from P. aeruginosa DeltaaroA-immunized mice proliferated and produced IL-17 in high quantities after coculture with gentamicin-killed P. aeruginosa. Six hours following challenge, PA14DeltaaroA-immunized mice had significantly higher levels of IL-17 in bronchoalveolar lavage fluid compared with unimmunized, Escherichia coli-immunized, or PAO1DeltaaroA-immunized mice. Antibody-mediated depletion of IL-17 before challenge or absence of the IL-17 receptor abrogated the PA14DeltaaroA vaccine's protection against lethal pneumonia. These data show that IL-17 plays a critical role in antibody-independent vaccine-induced protection against LPS-heterologous strains of P. aeruginosa in the lung.     

Non-water miscible ionic liquid improves biocatalytic production of geranyl glucoside with <Emphasis Type="Italic">Escherichia coli</Emphasis> overexpressing a glucosyltransferase

Whole cells of Escherichia coli overexpressing a glucosyltransferase from Vitis vinifera were used for the glucosylation of geraniol to geranyl glucoside. A high cell density cultivation process for the production of whole-cell biocatalysts was developed, gaining a dry cell mass concentration of up to 67.6 ± 1.2 g L^?1 and a glucosyltransferase concentration of up to 2.7 ± 0.1 g protein L^?1 within a process time of 48 h. Whole-cell batch biotransformations in milliliter-scale stirred-tank bioreactors showed highest conversion of geraniol at pH 7.0 although the pH optimum of the purified glucosyltransferase was at pH 8.5. The biocatalytic batch process performance was improved significantly by the addition of a water-immiscible ionic liquid (N-hexylpyridinium bis(trifluoromethylsulfonyl)imid) for in situ substrate supply. The so far highest final geranyl glucoside concentration (291 ± 9 mg L^?1) and conversion (71 ± 2 %) reported for whole-cell biotransformations of geraniol were achieved with 5 % (v/v) of the ionic liquid.     

Reinstitutionalisation in mental health care: comparison of data on service provision from six European countries

Objective To establish whether reinstitutionalisation is occurring in mental health care and, if so, with what variations between western European countries.Design Comparison of data on changes in service provision.Setting Six European countries with different traditions of mental health care that have all experienced deinstitutionalisation since the 1970s—England, Germany, Italy, the Netherlands, Spain, and Sweden.Outcome measures Changes in the number of forensic hospital beds, involuntary hospital admissions, places in supported housing, general psychiatric hospital beds, and general prison population between 1990-1 and 2002-3.Results Forensic beds and places in supported housing have increased in all countries, whereas changes in involuntary hospital admissions have been inconsistent. The number of psychiatric hospital beds has been reduced in five countries, but only in two countries does this reduction outweigh the number of additional places in forensic institutions and supported housing. The general prison population has substantially increased in all countries.Conclusions Reinstitutionalisation is taking place in European countries with different traditions of health care, although with significant variation between the six countries studied. The precise reasons for the phenomenon remain unclear. General attitudes to risk containment in a society, as indicated by the size of the prison population, may be more important than changing morbidity and new methods of mental healthcare delivery.