The Effect of the Method of Downhole Deployment on Distributed Acoustic Sensor Measurements: Field Experiments and Numerical Simulations.

Distributed acoustic sensing (DAS) is a promising technology for seismic data acquisition, particularly in downhole applications. However, downhole DAS measurements can be affected by the deployment method of the fibre-optic cable. These effects were explored in a field trial in two wells (one vertical and one deviated) drilled at the Otway International Test Centre. The trial in the vertical well shows that (1) fibre-optic cables cemented behind the casing provide data of the highest quality due to the best coupling to the formation, and (2) tubing-conveyed cable shows only slightly weaker coupling, but the data quality can be severely degraded by source-generated noise. A cable loosely suspended in the deviated well provided data quality comparable to that of the cemented DAS cable. To better understand the nature of the observed effects, the field experiments were supplemented by numerical modelling with a 1.5D full wave reflectivity algorithm (3D wave propagation in a 1D model), where cement, casing and wellbore were represented by infinite vertical layers. The results show that (1) a cement layer has only a slight effect (<5%) on the DAS amplitude; (2) the vertical strain in a liquid-filled borehole is comparable to that in the formation; and (3) the strain amplitude in the cable is of the same order of magnitude both in the formation and in the fluid. The strain in the cable is zero both when the cable's Poisson's ratio is zero and when the borehole fluid is air. The results confirm the feasibility of borehole DAS measurements with fibre-optic cables suspended in a borehole liquid (but not gas!).

Effect of Source Mispositioning on the Repeatability of 4D Vertical Seismic Profiling Acquired with Distributed Acoustic Sensors.

Vertical seismic profiling (VSP) with distributed acoustic sensing (DAS) is an increasingly popular evolving technique for reservoir monitoring. DAS technology enables permanent fibre installations in wells and simultaneous seismic data recording along an entire borehole. Deploying the receivers closer to the reservoir allows for better detectability of smaller signals. A high level of repeatability is essential for the robust time-lapse monitoring of geological reservoirs. One of the prominent factors of repeatability degradation is a shift between source/receiver locations (mispositioning) during baseline and monitor surveys. While the mispositioning effect has been extensively studied for surface 4D seismic, the number of such studies for VSP is quite limited. To study the effects of source mispositioning on time-lapse data repeatability, we performed two VSP experiments at two on-shore sites with vibroseis. The first study was carried out at the Otway International Test Centre during Stage 3 of the Otway project and showed that the effect of source mispositioning on repeatability is negligible in comparison with the effect of temporal variations of the near-surface conditions. To avoid these limitations, we conducted a same-day controlled experiment at the Curtin University site. This second experiment showed that the effect of source mispositioning on repeatability is controlled by the degree of lateral variations of the near-surface conditions. Unlike in marine seismic measurements, lateral variations of near-surface properties can be strong and rapid and can degrade the repeatability for shifts of the source of a few meters. The greater the mispositioning, the higher the chance of such significant variations. When the near-surface conditions are laterally homogeneous, the effect of typical source mispositioning is small, and in all practical monitoring applications its contribution to non-repeatability is negligible.

Monitoring Injected CO2 Using Earthquake Waves Measured by Downhole Fibre-Optic Sensors: CO2CRC Otway Stage 3 Case Study.

Monitoring changes of formation properties along the well bore associated with the presence of carbon dioxide can be important for both tracking the plume inside of the primary containment and detecting leakage into the zone located above the reservoir. This can be achieved with time lapse wireline logging, but this approach requires well intervention and is not always possible. If the well is permanently instrumented with an optical fibre, it can be used as a distributed seismic receiver array to detect gas behind the casing by monitoring changes in amplitude of the seismic waves generated by active or passive seismic sources. Previous research showed the efficacy of this technique using continuous seismic sources. The Stage 3 Otway Project presented an opportunity to test this technique using passive seismic recording, as downhole fibre-optic arrays recorded numerous regional earthquakes over the period of nearly 2 years before, during, and after CO2 injection. Analysis of P-wave amplitudes extracted from these downhole gathers shows a consistent amplitude anomaly at the injection level, visible in all events that occurred after the start of injection. This indicates that the anomaly is caused by changes in elastic properties in the reservoir caused by CO2 saturation. However, extracted amplitudes show significant variability between earthquakes even without subsurface changes; thus, multiple events are required to distinguish the time-lapse anomaly from time-lapse noise. Ubiquity of these events even in a tectonically quiet region (such as Australia) makes this technique a viable and cost-effective option for downhole monitoring.

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin.

Follicular lymphoma (FL) and the GCB subtype of diffuse large B-cell lymphoma (DLBCL) derive from germinal center B cells. Targeted resequencing studies have revealed mutations in various genes encoding proteins in the NF-kappaB pathway that contribute to the activated B-cell (ABC) DLBCL subtype, but thus far few GCB-specific mutations have been identified. Here we report recurrent somatic mutations affecting the polycomb-group oncogene EZH2, which encodes a histone methyltransferase responsible for trimethylating Lys27 of histone H3 (H3K27). After the recent discovery of mutations in KDM6A (UTX), which encodes the histone H3K27me3 demethylase UTX, in several cancer types, EZH2 is the second histone methyltransferase gene found to be mutated in cancer. These mutations, which result in the replacement of a single tyrosine in the SET domain of the EZH2 protein (Tyr641), occur in 21.7% of GCB DLBCLs and 7.2% of FLs and are absent from ABC DLBCLs. Our data are consistent with the notion that EZH2 proteins with mutant Tyr641 have reduced enzymatic activity in vitro.

Lipopolysaccharide is a direct agonist for platelet RNA splicing.

Platelets express TLR4 receptors, but its ligand LPS does not directly activate thrombotic functions nor, obviously, transcription by these anucleate cells. Platelets, however, store information that changes their phenotype over a few hours in the form of unprocessed RNA transcripts. We show even low concentrations of LPS in the presence of soluble CD14 initiated splicing of unprocessed IL-1beta RNA, with translation and accumulation of IL-1beta protein. LPS was a more robust agonist for this response than thrombin. Platelets also contained cyclooxygenase-2 pre-mRNA, which also was spliced and translated after LPS stimulation. Flow cytometry and immunocytochemistry of platelets extensively purified by negative immunodepletion showed platelets contained IL-1beta, and quantitative assessment of white blood cell contamination by CD14 real time PCR confirms that leukocytes were not the IL-1beta source, nor were they required for platelet stimulation. LPS did not initiate rapid platelet responses, but over time did prime platelet aggregation to soluble agonists, induced actin rearrangement, and initiated granule secretion with P-selectin expression that resulted the coating of quiescent leukocytes with activated platelets. LPS is a direct agonist for platelets that allows these cells to directly participate in the innate immune response to bacteria.

Induction of dendritic cell-like phenotype in macrophages during foam cell formation.

Foam cell formation from monocyte-derived macrophages is a hallmark of atherosclerotic lesions. Aspects of this process can be recapitulated in vitro by exposing M-CSF-induced or platelet factor 4 (CXCL4)-induced macrophages to oxidized (ox) or minimally modified (mm) low density lipoprotein (LDL). We measured gene expression in peripheral blood mononuclear cells, monocytes, and macrophages treated with CXCL1 (GRO-alpha) or CCL2 (MCP-1), as well as foam cells induced by native LDL, mmLDL, or oxLDL using 22 Affymetrix gene chips. Using an advanced Bayesian error-pooling approach and a heterogeneous error model with a false discovery rate <0.05, we found 5,303 of 22,215 probe sets to be significantly regulated in at least one of the conditions. Among a subset of 917 candidate genes that were preselected for their known biological functions in macrophage foam-cell differentiation, we found that 290 genes met the above statistical criteria for significant differential expression patterns. While many expected genes were found to be upregulated by LDL and oxLDL, very few were induced by mmLDL. We also found induction of unexpected genes, most strikingly MHC-II and other dendritic cell markers such as CD11c. The gene expression patterns in response to oxLDL were similar in M-CSF-induced and CXCL4-induced macrophages. Our findings suggest that LDL and oxLDL, but not mmLDL, induce a dendritic cell-like phenotype in macrophages, suggesting that these cells may be able to present antigens and support an immune response.

Insulin and glucose play a role in foam cell formation and function.

BACKGROUND: Foam cell formation in diabetic patients often occurs in the presence of high insulin and glucose levels. To test whether hyperinsulinemic hyperglycemic conditions affect foam cell differentiation, we examined gene expression, cytokine production, and Akt phosphorylation in human monocyte-derived macrophages incubated with two types of oxidized low density lipoprotein (LDL), minimally modified LDL (mmLDL) and extensively oxidized LDL (OxLDL). METHODS AND RESULTS: Using Affymetrix GeneChip arrays, we found that several genes directly related to insulin signaling were changed. The insulin receptor and glucose-6-phosphate dehydrogenase were upregulated by mmLDL and OxLDL, whereas insulin-induced gene 1 was significantly down-regulated. In hyperinsulinemic hyperglycemic conditions, modified LDL upregulated Akt phosphorylation and expression of the insulin-regulated aminopeptidase. The level of proinflammatory cytokines, IL-lbeta, IL-12, and IL-6, and of a 5-lipoxygenase eicosanoid, 5-hydroxyeicosatetraenoic acid (5-HETE), was also increased. CONCLUSION: These results suggest that the exposure of macrophages to modified low density lipoproteins in hyperglycemic hyperinsulinemic conditions affects insulin signaling and promotes the release of proinflammatory stimuli, such as cytokines and eicosanoids. These in turn may contribute to the development of insulin resistance.

Macrophage differentiation to foam cells.

Foam cell formation from macrophages with subsequent fatty streak formation plays a key role in early atherogenesis. Foam cell formation is thought to be induced by Low Density Lipoproteins (LDL), including oxidized LDL (OxLDL) or minimally modified LDL (mmLDL). Understanding the molecular mechanisms involved in OxLDL- and mmLDL-induced foam cell formation is of fundamental importance for atherosclerosis and cardiovascular disease. The expression of many genes is likely modulated during macrophage transformation into a foam cell. In this mini-review we describe functional consequences of modulation of three groups of genes: Scavenger Receptors (SR-A, CLA-1/SR-BI, CD36, CD68, LOX-1, and SR-PSOX), the PPAR family of nuclear receptors, and a number of genes involved in eicosanoid biosynthesis, including lipoxygenases and leukotriene receptors. Scavenger receptors appear to play a key role in uptake of OxLDL, while mmLDL appears to interact with CD14/TLR4. The regulation of scavenger receptors is, in part, mediated by the PPAR family of nuclear receptors. PPARalpha and PPARgamma agonists, such as thiazolidinediones and fibrates, and PPARdelta agonists were tested as atheroprotective drugs and showed some beneficial effects. Eicosanoids are naturally occuring agonists for PPARs. Recent observations indicate a role of the components of the eicosanoid cascade, such as 5-lipoxygenase, 15-lipoxygenase and the leukotriene receptors in foam cell formation. Selective inhibitors of lipoxygenases and leukotriene receptors could be useful in the treatment of atherosclerosis by preventing or reducing foam cell formation.

Critical role of macrophage 12/15-lipoxygenase for atherosclerosis in apolipoprotein E-deficient mice.

BACKGROUND: Mice lacking leukocyte type 12/15-lipoxygenase (12/15-LO) show reduced atherosclerosis in several models. 12/15-LO is expressed in a variety of cells, including vascular cells, adipocytes, macrophages, and cardiomyocytes. The purpose of this study was to determine which cellular source of 12/15-LO is important for atherosclerosis. METHODS AND RESULTS: Bone marrow from 12/15-LO-/-/apoE-/- mice was transplanted into apoE-/- mice and vice versa. Deficiency of 12/15-LO in bone marrow cells protected apoE-/- mice fed a Western diet from atherosclerosis to the same extent as complete absence of 12/15-LO, although plasma 8,12-iso-iPF2alpha-IV, a measure of lipid peroxidation, remained elevated. 12/15-LO-/-/apoE-/- mice regained the severity of atherosclerotic lesion typical of apoE-/- mice after replacement of their bone marrow cells with bone marrow from apoE-/- mice. Peritoneal macrophages obtained from wild-type but not 12/15-LO-/- mice caused endothelial activation in the presence of native LDL. Absence of 12/15-LO decreased the ability of macrophages to form foam cells when exposed to LDL. CONCLUSIONS: We conclude that macrophage 12/15-LO plays a dominant role in the development of atherosclerosis by promoting endothelial inflammation and foam cell formation.

Fasting decreases the content of D-chiroinositol in human skeletal muscle.

Two classes of inositol phosphoglycans have been implicated as second messengers of insulin, one that activates pyruvate dehydrogenase and contains D-chiroinositol, and one that inhibits cyclic AMP-dependent protein kinase and contains myoinositol. We examined the effects of a 3-day fast on muscle contents of inositols in healthy humans. An oral glucose tolerance test was performed and a biopsy was obtained from the quadriceps femoris muscle after an overnight fast and after a 72-hour fast. The 72-hour fast significantly increased plasma glucose (1.5- to 2-fold) and insulin (2- to 4-fold) after glucose ingestion versus the values after the overnight fast, indicating the manifestation of peripheral insulin resistance. The 72-hour fast resulted in an approximately 20% decrease in the muscle content of D-chiroinositol (P < 0.02), but no change in the myoinositol content. These data demonstrate that fasting specifically decreases the muscle content of D-chiroinositol in human muscle and this may contribute to the finding that insulin-mediated activation of pyruvate dehydrogenase is attenuated after short-term starvation.