Deciphering Normal Blood Gene Expression Variation—The NOWAC Postgenome Study

There is growing evidence that gene expression profiling of peripheral blood cells is a valuable tool for assessing gene signatures related to exposure, drug-response, or disease. However, the true promise of this approach can not be estimated until the scientific community has robust baseline data describing variation in gene expression patterns in normal individuals. Using a large representative sample set of postmenopausal women (N = 286) in the Norwegian Women and Cancer (NOWAC) postgenome study, we investigated variability of whole blood gene expression in the general population. In particular, we examined changes in blood gene expression caused by technical variability, normal inter-individual differences, and exposure variables at proportions and levels relevant to real-life situations. We observe that the overall changes in gene expression are subtle, implying the need for careful analytic approaches of the data. In particular, technical variability may not be ignored and subsequent adjustments must be considered in any analysis. Many new candidate genes were identified that are differentially expressed according to inter-individual (i.e. fasting, BMI) and exposure (i.e. smoking) factors, thus establishing that these effects are mirrored in blood. By focusing on the biological implications instead of directly comparing gene lists from several related studies in the literature, our analytic approach was able to identify significant similarities and effects consistent across these reports. This establishes the feasibility of blood gene expression profiling, if they are predicated upon careful experimental design and analysis in order to minimize confounding signals, artifacts of sample preparation and processing, and inter-individual differences

Transport of Pb and Zn by carboxylate complexes in basinal ore fluids and related petroleum-field brines at 100°C: the influence of pH and oxygen fugacity

It is well established through field observations, experiments, and chemical models that oxidation (redox) state and pH exert a strong influence on the speciation of dissolved components and the solubility of minerals in hydrothermal fluids. log [Image: see text] –pH diagrams were used to depict the influence of oxygen fugacity and pH on monocarboxylate- and dicarboxylate-transport of Pb and Zn in low-temperature (100°C) hydrothermal ore fluids that are related to diagenetic processes in deep sedimentary basins, and allow a first-order comparison of Pb and Zn transport among proposed model fluids for Mississippi Valley-type (MVT) and red-bed related base metal (RBRBM) deposits in terms of their approximate pH and [Image: see text] conditions. To construct these diagrams, total Pb and Zn concentrations and Pb and Zn speciation were calculated as a function of log [Image: see text] and pH for a composite ore-brine with concentrations of major elements, total sulfur, and total carbonate that approximate the composition of MVT and RBRBM model ore fluids and modern basinal brines. In addition to acetate and malonate complexation, complexes involving the ligands Cl(-), HS(-), H(2)S, and OH(- )were included in the model of calculated total metal concentration and metal speciation. Also, in the model, Zn and Pb are competing with the common-rock forming metals Ca, Mg, Na, Fe, and Al for the same ligands. Calculated total Pb concentration and calculated total Zn concentration are constrained by galena and sphalerite solubility, respectively. Isopleths, in log [Image: see text] –pH space, of the concentration of Pb and concentration of Zn in carboxylate (acetate + malonate) complexes illustrate that the oxidized model fluids of T. H. Giordano (in Organic Acids in Geological Processes, ed. E. D. Pittman and M. D. Lewan, Springer-Verlag, New York, 1994, pp. 319–354) and G. M. Anderson (Econ. Geol., 1975, 70, 937–942) are capable of transporting sufficient amounts of Pb (up to 10 ppm) and Zn (up to 100 ppm) in the form of carboxylate complexes to form economic deposits of these metals. On the other hand, the reduced ore fluid models of D. A. Sverjensky (Econ. Geol., 1984, 79, 23–37) and T. H. Giordano and H. L. Barnes (Econ. Geol., 1981, 76, 2200–2211) can at best transport amounts of Pb and Zn, as carboxylate complexes, that are many orders of magnitude below the 1 to 10 ppm minimum required to form economic deposits. Lead and zinc speciation (mol% of total Pb or Zn) in the model ore fluid was calculated at specific log [Image: see text] –pH conditions along the 100, 0.01, and 0.001 ppm total Pb and total Zn isopleths. Along the 100 ppm isopleth conditions are oxidized (∑SO(4 )>> ∑H(2)S) with Pb and Zn predominantly in the form of chloride complexes under acid to mildly alkaline conditions (pH from 3 to approximately 7.5), while hydroxide complexes dominate Pb and Zn speciation under more alkaline conditions. Sulfide complexes are insignificant under these oxidized conditions. For more reduced conditions along the 0.01 and 0.001 ppm isopleths chloride complexes dominate Pb and Zn speciation in the SO(4)(2- )field and near the SO(4)(2-)-reduced sulfur boundary from pH = 4 to approximately 7.5, while hydroxide complexes dominate Pb and Zn speciation under alkaline conditions above pH = 7.5 in the SO(4)(2- )field. In the most reduced fluids (∑H(2)S >> ∑SO(4)) along the 0.01 and 0.001 isopleths, sulfide complexes account for almost 100% of the Pb and Zn in the model fluid. Acetate (monocarboxylate) complexation is significant only under conditions of chloride and hydroxide complex dominance and its effect is maximized in the pH range 5 to 7, where it complexes 2 to 2.6% of the total Pb and 1 to 1.25% of the total Zn. Malonate (dicarboxylate) complexes are insignificant along all isopleths. The speciation results from this study show that deep formation waters characterized by temperatures near 100°C, high oxidation states and ∑H(2)S < 0.03 mg L(-1 )([Image: see text] < 10(-6)), high chlorinities (~ 100000 mg L(-1)), and high but reasonable concentrations of carboxylate anions can mobilize up to 3% of the total Pb and up to 1.3% of the total Zn as carboxylate complexes. Furthermore, these percentages, under the most favorable conditions, correspond to approximately 1 to 100 ppm of these metals in solution; concentrations that are adequate to form economic deposits of these metals. However, the field evidence suggests that all of these optimum conditions for carboxylate complexation are rarely met at the same time. A comparison of the composite ore fluid compositions from this study and modern brine data shows that the ore brines, corresponding to log [Image: see text] –pH conditions based on the Anderson (1975) and Giordano (1994) model fluids, are similar in many respects to modern, high trace-metal petroleum-field brines. The principal differences between modern high trace-metal brines and the composite ore fluids of Anderson (1975) and Giordano (1994) relate to their carboxylate anion content. The reported concentrations of monocarboxylate anions (∑monocbx) and dicarboxylate anions (Edicbx) in high trace-metal petroleum-field brines (< 1 to 300 mg L(-1 )and < 1 mg L(-1), respectively) are significantly lower than the concentrations assumed in the modelled brines of this study (∑monocbx = 7 700 mg L(-1 )and ∑dicbx = 300 mg L(-1)). There are also major differences in the corresponding total chloride to carboxylate ratio (∑m(Cl)/∑m(cbx)) and monocarboxylate to dicarboxylate ratio (∑m(monocbx)/∑m(dicbx)). Modern high trace-metal brines have much higher ∑m(Cl)/∑m(cbx )values and, therefore, the contribution of carboxylate complexes to the total Pb and Zn content in these modern brines is likely to be significantly less than the 1 to 3 percent for the composite ore fluids of Anderson (1975) and Giordano (1994). The composite ore-brine based on the Giordano and Barnes (1981) MVT ore fluid is comparable to the high salinity (> 170 000 mg L(-1 )TDS) subset of modern brines characterized by low trace-metal content and high total reduced sulfur (∑H(2)S). A comparison of the Sverjensky (1984) composite ore-brine with modern petroleum-field brines in terms of ∑H(2)S and Zn content, reveals that this ore fluid corresponds to a "border-type" brine, between modern high trace-metal brines and those with low trace-metal content and high ∑H(2)S. A brine of this type is characterized by values of ∑H(2)S, ∑Zn, and/or ∑Pb within or near the 1 to 10 mg L(-1 )range. Based on brine-composition data from numerous references cited in this paper, border-type brines do exist but are rare. The model results and field evidence presented in this study are consistent with other chemical simulation studies of carboxylate complexation in modern petroleum-field brines. Thus, it appears that carboxylate complexation plays a minor, if not insignificant, role as a transport mechanism for Pb and Zn in high salinity Na–Cl and Na–Ca–Cl basinal brines and related ore fluids

The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review

Background: The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types. Methods: The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded. Results: The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods). Conclusion: We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection

Reactive oxygen species in phagocytic leukocytes

Phagocytic leukocytes consume oxygen and generate reactive oxygen species in response to appropriate stimuli. The phagocyte NADPH oxidase, a multiprotein complex, existing in the dissociated state in resting cells becomes assembled into the functional oxidase complex upon stimulation and then generates superoxide anions. Biochemical aspects of the NADPH oxidase are briefly discussed in this review; however, the major focus relates to the contributions of various modes of microscopy to our understanding of the NADPH oxidase and the cell biology of phagocytic leukocytes

Fish Intelligence, Sentience and Ethics

Fish are one of the most highly utilised vertebrate taxa by humans; they are harvested from wild stocks as part of global fishing industries, grown under intensive aquaculture conditions, are the most common pet and are widely used for scientific research. But fish are seldom afforded the same level of compassion or welfare as warm-blooded vertebrates. Part of the problem is the large gap between people’s perception of fish intelligence and the scientific reality. This is an important issue because public perception guides government policy. The perception of an animal’s intelligence often drives our decision whether or not to include them in our moral circle. From a welfare perspective, most researchers would suggest that if an animal is sentient, then it can most likely suffer and should therefore be offered some form of formal protection. There has been a debate about fish welfare for decades which centres on the question of whether they are sentient or conscious. The implications for affording the same level of protection to fish as other vertebrates are great, not least because of fishing-related industries. Here, I review the current state of knowledge of fish cognition starting with their sensory perception and moving on to cognition. The review reveals that fish perception and cognitive abilities often match or exceed other vertebrates. A review of the evidence for pain perception strongly suggests that fish experience pain in a manner similar to the rest of the vertebrates. Although scientists cannot provide a definitive answer on the level of consciousness for any nonhuman vertebrate, the extensive evidence of fish behavioural and cognitive sophistication and pain perception suggests that best practice would be to lend fish the same level of protection as any other vertebrate

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

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Exploring the views of being a proxy from the perspective of unpaid carers and paid carers: developing a proxy version of the Adult Social Care Outcomes Toolkit (ASCOT)

Background: Outcomes-based policy and administration of public services present a compelling argument for the value of outcomes data. However, there are a number of challenges inherent in collecting these data from people who are unable to complete a paper-based survey or interview due to cognitive or communication impairments. In this paper, we explore the views of being a proxy from the perspective of unpaid carers and paid carers who may be asked to act as a proxy on behalf of the person(s) they care for. We consider the key issues that need to be addressed when adapting an instrument designed to measure social care outcomes, the Adult Social Care Outcomes Tool (ASCOT), into a proxy-report tool. Methods: Participants took part in either a focus group (35 paid carers in eight focus groups), or a one-to-one interview (eight unpaid carers). All participants were recruited via carer organisations and care providers. Transcripts, field notes and audio data collected during focus groups and interviews were analysed using a thematic framework approach. Results: Participants agreed that any person acting as a proxy would need to be very familiar with the care recipient, as well as their needs and care provision. A number of provisions for proxy respondents were proposed to improve face validity and acceptability of completing a questionnaire by proxy, and to ensure that any potential bias is reduced in the design of the questionnaire. These included: providing two sets of response options for each proxy perspective (the proxy themselves and the proxy view of how they think the care recipient would respond); a comments box to help people explain why they have selected a given response option (especially where these indicate unmet need); and providing clear guidance for the proxy respondent on how they should complete the questionnaire. Conclusions: This study has shown some of the challenges involved in assessing outcomes by proxy and explored some potential ways these can be mitigated. The findings highlight the benefits of developing and testing proxy measures in a robust way to widen participation in social care research

Characterization of the Golgi c10orf76-PI4KB complex, and its necessity for Golgi PI4P levels and enterovirus replication

The lipid kinase PI4KB, which generates phosphatidylinositol 4-phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB-associated protein that increases PI4P levels at the Golgi and is essential for the viral replication of specific enteroviruses. We used hydrogen-deuterium exchange mass spectrometry to characterize the c10orf76-PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA-dependent phosphorylation. Complex-disrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76-PI4KB complex is required for the replication of c10orf76-dependent enteroviruses. Intriguingly, c10orf76 also contributed to proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76-dependent increase in PI4P levels at the Golgi