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!).

Abstract 6111: Design of a small molecule screening assay to detect DNA trapping of PARP1/2

Poly(ADP-ribose) polymerase (PARP) inhibitors are currently used in the clinic for the treatment of tumors with a defective DNA damage response (DDR). When PARP1 or PARP2 binds damaged DNA, it adds poly(ADP-ribose) chains to its own backbone and to other DDR proteins, which recruits and activates them. PARylated PARP1/2 next detaches from the DNA so that the other PARylated proteins can initiate the repair process. It has been observed that some PARP inhibitors prevent PARP1/2 from dissociating the DNA. The continuous presence of PARP at the site of damage prevents repair and blocks replication, leading to cell death. Therefore, drugs that trap PARP1/2 to the DNA tend to be significantly more cytotoxic than other PARP inhibitors, which is highly desirable. This study describes the design and optimization of novel PARPtrap assays to specifically assess the ability of a drug to trap PARP onto DNA. The assay is based on principles of fluorescence polarization and uses fluorescently labeled DNA probes that are excited by polarized light and emit light with a degree of polarization that is proportional to the rate of molecular rotation. The free DNA probes that rotate fast have low fluorescence polarization (FP), but high FP when are bound to PARP1 or PARP2. When NAD+ is added, the PARylated enzymes detach from the probe, reducing FP levels. If a PARP inhibitor is added, the inhibitor’s trapping ability increases FP in a dose-dependent manner. Proof-of-principle titration of known PARP-trapping inhibitors (Talazoparib, AZD305, Olaparib and Veliparib) was performed to validate the assay. We observed that: i)The known relative trapping efficacies of Talazoparib, Olaparib and Veliparib were similar to known relative efficacies. ii)Talazoparib, Olaparib and Veliparib had similar trapping efficacy against PARP1 and PARP2, as measured by their EC50, whereas AZD305 was 1,000 times more efficient at trapping PARP1 than it was PARP2, demonstrating selectivity between PARP1 and PARP2. iii)AZD305 displayed as efficient DNA trapping activity toward PARP1 as best-in-class Talazoparib. In summary, we have designed an innovative PARPtrap assay designed for the high throughput screening of small molecule libraries to specifically identify or compare inhibitors that are capable of trapping PARP1 and/or PARP2 onto DNA.

Citation Format: Kasia Zientara-Rytter, Veronique T. Baron, Junguk Park, Pavel Shashkin, Henry Zhu. Design of a small molecule screening assay to detect DNA trapping of PARP1/2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6111.

Abstract 2548: Substrate binding, not phosphorylation, activates CBL poly-ubiquitination activity

Casitas B-lineage lymphoma (CBL) is a family of RING-type E3 ligases that target proteins for degradation via the proteasomal pathway. CBL-b specifically functions as a negative effector of T cell activation by down regulating the T cell receptor, whereas c-CBL interacts with various receptor tyrosine kinases involved in cell signaling and activation, targeting them for degradation. Therefore, the CBL family regulates the biology of immune cells and targeting CBL-b or c-CBL is a potential therapeutic strategy for the treatment of cancer, infection, or autoimmune diseases. In this study, we used TR-FRET (Time-Resolved Fluorescence Resonance Energy Transfer) to uncover new mechanistic aspects of CBL activation. Our assays were designed and optimized using purified components (E1/E2/c-CBL or CBL-b E3 ligase and kinase substrate Tyro3 or Axl) to recreate the polyubiquitination cascade in vitro. The assays use a Europium cryptate-labeled Ubiquitin (donor) and a Cy5-labeled Ubiquitin (acceptor) to complete the TR-FRET pairing. Since both the TR-FRET donor and acceptor are incorporated into poly-ubiquitin chains formed on the E3 ligase, the technique measures only poly-ubiquitination and not mono-ubiquitination. This FRET-based assay is homogeneous, making it especially suitable for screening applications and real-time kinetics. Validation of the assay indicated that the presence of a kinase substrate (Tyro3 or Axl) activates CBL-b and c-CBL, which are known to display a similar mechanism of activation. Importantly, our assay design allowed us to show that known CBL-B inhibitor CBL-B-IN-1 is not strictly selective toward CBL-B but also affects c-CBL E3 ligase activity to similar extend since the IC50 of the compound for c-CBL and CBL-B differ by only 2-fold. Finally, it has been proposed that CBL-b phosphorylation at Y106, Y133, and Y363 by Tyro3 kinase is required for its activation. Indeed, in our assay, we observed that CBL-b mutation at Y363F decreases TYRO3 ubiquitination drastically. Surprisingly, phospho-mimetic mutation Y363E did not restore CBL-b-mediated ubiquitination of Tyro3, indicating that substrate binding close to Y363 is the predominant requirement for CBL activation. The weak E3 ligase activity of CBL-b Y363E mutant was insensitive to CBL-B-IN-1 treatment.In conclusion, our data indicates that no significant difference in the parameters of substrate ubiquitination exists between CBL-B and c-CBL, and that ubiquitination of receptor tyrosine kinase Tyro3 by either c-CBL or CBL-B depends on the kinase binding to CBL but not on the phosphorylation of CBL.

Citation Format: Kasia Zientara-Rytter, Veronique Baron, Pavel Shashkin, Henry Zhu. Substrate binding, not phosphorylation, activates CBL poly-ubiquitination activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2548.

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.

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-α) 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.

North Atlantic contourite sand channels

Two sand-rich channelized depositional systems, formed by strong contour currents, were studied west of the Faeroe Bank Channel and in the Gulf of Cadiz. Both are areas beyond the exit of constrictions where water overflows from the Norwegian Sea and the Mediterranean Sea, respectively. West of the Faeroe Bank, newly mapped channels are developed mainly under the influence of a geostrophic current and are characterized by significant lateral migration, which determines the marked cross-sectional asymmetry and the architecture of the deposits. The pathways of the Mediterranean Undercurrent in the Gulf of Cadiz are complex, with the greater proportion flowing under geostrophic conditions along a terrace but with some of the denser water becoming ageostrophic and descending downslope owing to gravity. A series of ‘peel-off’ channels is formed, with the largest one, Gil Eanes, being about 40 km long. Most of the channel fills consist of medium-coarse sand. Levees are mainly silts with a higher sand content in the vicinity of the channel. Both depositional systems have a variety of contourite sand channels, which in most respects are remarkably similar. In both cases there are stretches where the flow is ageostrophic, with water descending downslope for as much as 400 m before resuming geostrophic flow at deeper levels. In each case the main pathway of the densest water is the shallowest and several branches turn off to the left of this main pathway before bending to the right under the influence of Coriolis forces. In both cases there are channel fills of medium-coarse sand, probably cross-bedded, and up to 200 ms thick. Sheets of sand with a thickness of a few metres to a few tens of metres are common. Similarities to turbidite channels are the aggradational nature of some channel floors and the flanking muddy or silty sediment waves. Contourite channel depositional complexes are distinguished from turbiditic ones by their coarsening-up rather than fining-up sand units, the asymmetry in channel architecture, the presence of regional unconformities, and the distribution pattern with well-marked boundaries of current-derived deposits.

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.

A new glycogen synthase activity ratio in skeletal muscle: effects of exercise and insulin

It was recently reported that MnSO4 stimulates glycogen synthase-dependent glucose transfer from UDPglucose into trichloroacetic acid precipitable endogenous glycoproteins (GSMn(T)) in human muscle extracts. To determine the physiologic significance of this reaction, we compared a new GS activity ratio, GSMn(T)/GSH(E) (where GSH(E) represents the usual glucose transfer to ethanol precipitable exogenous glycogen by GS at 7.2 mM glucose 6-phosphate), with the generally used GSL(E)/GSH(E) ratio (where GSL(E) represents glucose transfer at 0.17 mM glucose 6-P concentration). Biopsies were obtained from the quadriceps femoris muscle of healthy subjects at rest, after 40 min of bicycle exercise at approximately 65% of maximal oxygen uptake and after isometric contraction at 2/3 maximal force to fatigue (approximately 1 min). GSMn(T)/GSH(E) increased from 0.012+/-0.002 at rest to 0.054+/-0.008 (P<0.01) after 40 min of bicycle exercise and the increase in GSMn(T) activity was strongly related to the decrease in endogenous glycogen (i.e.. increase in short-chain endogenous glycoproteins) (r=0.90; P<0.05). On the other hand, GSL(E)/GSH(E) did not change significantly after bicycle exercise (rest = 0.49+/-0.04; exercise = 0.58+/-0.08, P>0.05). GSMn(T)/GSH(E) increased from 0.010+/-0.001 at rest to 0.016+/-0.002 (P<0.05) after isometric exercise, whereas GSL(E)/GSH(E) decreased from 0.27+/-0.04 to 0.20+/-0.02 (P<0.05) under corresponding conditions. Last, insulin, which stimulates glycogen synthesis, also increased GSMn(T)/GSH(E) (1.8-fold, P<0.05), as well as GSL(E)/GSH(E) (1.4-fold, P<0.05), in isolated rat soleus muscle. These data indicate that GSMn(T)/GSH(E) is influenced by endogenous substrate availability and covalent modification. Therefore, GSMn(T)/GSH(E) ratio may prove to be a useful alternative to other GS activity ratios that only reflect changes in the phosphorylation state of GS.

Altered glycogen synthase and phosphorylase activities in skeletal muscle of tetraplegic patients

Despite marked differences in both the extent of physical activity and in muscle metabolism and structure between tetraplegic and control subjects, the glycogen content in the skeletal muscle of both groups is similar. We determined whether this similarity could be explained by the activities of key enzymes of glycogen metabolism. Muscle biopsies were analysed for glycogen synthase (GS) and glycogen phosphorylase (GP) activities, as well as for metabolites. Glycogen content did not differ significantly between the two groups. Total glycogen synthase activity was reduced by almost 60 % in tetraplegics (P < 0.01), whereas total phosphorylase activity did not differ between groups. GS fractional activity did not differ between groups, whereas phosphorylase fractional activity (-/+ AMP) was significantly higher in the tetraplegics (0.08 +/- 0.01, control; 0.25 +/- 0.02, tetraplegics; P < 0.001). Neither uridine diphosphate (UDP)-glucose nor glucose 6-phosphate (G-6-P) content in muscle differed significantly between groups. These data demonstrate that, in tetraplegics, muscle glycogen content is preserved despite decreases in GS activity and increases in phosphorylase fractional activity. Muscle paralysis has differential effects on the activities of GS and GP. Experimental Physiology (2001) 86.2, 205-209.

Manganese sulfate-dependent glycosylation of endogenous glycoproteins in human skeletal muscle is catalyzed by a nonglucose 6-P-dependent glycogen synthase and not glycogenin

Glycogenin, a Mn2+-dependent, self-glucosylating protein, is considered to catalyze the initial glucosyl transfer steps in glycogen biogenesis. To study the physiologic significance of this enzyme, measurements of glycogenin mediated glucose transfer to endogenous trichloroacetic acid precipitable material (protein-bound glycogen, i.e., glycoproteins) in human skeletal muscle were attempted. Although glycogenin protein was detected in muscle extracts, activity was not, even after exercise that resulted in marked glycogen depletion. Instead, a MnSO4-dependent glucose transfer to glycoproteins, inhibited by glycogen and UDP-pyridoxal (which do not affect glycogenin), and unaffected by CDP (a potent inhibitor of glycogenin), was consistently detected. MnSO4-dependent activity increased in concert with glycogen synthase fractional activity after prolonged exercise, and the MnSO4-dependent enzyme stimulated glucosylation of glycoproteins with molecular masses lower than those glucosylated by glucose 6-P-dependent glycogen synthase. Addition of purified glucose 6-P-dependent glycogen synthase to the muscle extract did not affect MnSO4-dependent glucose transfer, whereas glycogen synthase antibody completely abolished MnSO4-dependent activity. It is concluded that: (1) MnSO4-dependent glucose transfer to glycoproteins is catalyzed by a nonglucose 6-P-dependent form of glycogen synthase; (2) MnSO4-dependent glycogen synthase has a greater affinity for low molecular mass glycoproteins and may thus play a more important role than glucose 6-P-dependent glycogen synthase in the initial stages of glycogen biogenesis; and (3) glycogenin is generally inactive in human muscle in vivo.

Effects of CGS 9343B (a putative calmodulin antagonist) on isolated skeletal muscle. Dissociation of signaling pathways for insulin-mediated activation of glycogen synthase and hexose transport

The role of calmoudulin in control of carbohydrate metabolism in the absence and presence of insulin in isolated mouse soleus muscle was investigated. The calmodulin antagonist CGS 9343B had no effect on basal glycogen synthase activity, the contents of high energy phosphates, glucose-6-P, or glycogen synthesis. However, CGS 9343B inhibited the basal rates of 2-deoxyglucose uptake and 3-O-methylglucose transport by 30% (p < 0.05) and 40% (p < 0.001), respectively. Insulin activated glycogen synthase by almost 40% (p < 0.01) and this increase was not altered in the presence of CGS 9343B. Insulin increased the muscle content of glucose-6-P (approximately equal to 2-fold), as well as glycogen synthesis (approximately equal to 8-fold), 2-deoxyglucose uptake (approximately equal to 3-fold), and 3-O-methylglucose transport (approximately equal to 2-fold), and these increases were inhibited by CGS 9343B. In additional experiments on isolated rat epitrochlearis muscle, it was found that the hypoxia-mediated activation of 3-O-methylglucose transport was also inhibited by CGS 9343B. These data demonstrate that: 1) hexose transport, both in the absence and presence of external stimuli (insulin and hypoxia), requires functional calmodulin; and 2) insulin-mediated activation of glycogen synthase does not require functional calmodulin, nor can it be accounted for by increases in glucose transport or glucose-6-P.