Enriched Regions Research Articles

Constraints on the water, chlorine, and fluorine content of the Martian mantle

AbstractPrevious estimates of the volatile contents of Martian basalts, and hence their source regions, ranged from nearly volatile‐free through estimates similar to those found in terrestrial subduction zones. Here, we use the bulk chemistry of Martian meteorites, along with Martian apatite and amphibole chemistry, to constrain the volatile contents of the Martian interior. Our estimates show that the volatile content of the source region for the Martian meteorites is similar to the terrestrial Mid‐Ocean‐Ridge Mantle source. Chlorine is enriched compared with the depleted terrestrial mantle but is similar to the terrestrial enriched source region; fluorine is similar to the terrestrial primitive mantle; and water is consistent with the terrestrial mantle. Our results show that Martian magmas were not volatile saturated; had water/chlorine and water/fluorine ratios ~0.4–18; and are most similar, in terms of volatiles, to terrestrial MORBs. Presumably, there are variations in volatile content in the Martian interior as suggested by apatite compositions, but more bulk chemical data, especially for fluorine and water, are required to investigate these variations. Finally, the Noachian Martian interior, as exemplified by surface basalts and NWA 7034, may have had higher volatile contents.

Abstract B16: Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer

Abstract Triple negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. Cancer genome sequencing studies focusing on TNBC failed to identify novel recurrently mutated cancer-driving genes, obviating immediate opportunities for targeted therapeutic development. Here we have identified BET bromodomain inhibitors (BBDIs) as promising novel therapeutic agents in TNBC. Specifically, we have found that TNBC cells are significantly and preferentially growth inhibited by BBDIs (e.g., JQ1) with IC50s in the low nM range compared to luminal breast cancer cells. The growth of established xenografts derived from TNBC cell lines and primary patient samples were also efficiently inhibited by BBDIs treatment. BRD4, a target of BBDIs, is highly expressed in TNBCs compared to luminal cell lines and its downregulation using shRNAs inhibits TNBC cell growth in cell culture and induces tumor regression in vivo. In line with the role of BRD4 in transcription restart after G2/M, BBDI treatment prevented cell cycle re-entry, arrested TNBC cells in early G1, apoptosis, and induced luminal epithelial cell differentiation. Using integrated epigenomic analysis, we have identified the direct transcriptional targets of BBDI in TNBC. BBDI was found to efficiently displace chromatin-bound BRD4 in sensitive TNBC cells. This effect was more pronounced at genomic regions exhibiting elevated Bio-JQ1 binding by Chem-seq, implying strong association between BRD4 and JQ1 genomic binding patterns. By genome-wide study with ChIP-seq and RNA-seq, we have also found that selective disruption of super-enhancers associated genes by JQ1, leading to deregulation of coordinated transcriptional pathways involved in cell proliferation, invasion, and survival. The sensitivity of TNBC and other tumor types to BET inhibition establishes a rationale for clinical investigation and a motivation to understand mechanisms of resistance. After selecting derivatives with acquired resistance to BET inhibition in previously sensitive TNBCs, we identified a unique mechanism of epigenomic resistance to this epigenetic therapy. Resistant cells remained dependent on BRD4. However, TNBC cells adapt to BET bromodomain inhibition by maintaining recruitment of unmutated BRD4 to super-enhancers in a bromodomain-independent manner. Differential super-enhancer analysis found a significant gain in the number of SEs in resistant cells, and a less pronounced loss of fewer SEs. The gain of Bio-JQ1 SEs was associated with gain of BRD4 binding to these genomic loci and also with increased transcription of the associated genes. Among the top gained super-enhancers in resistant cells was an upstream and intragenic region of H3K27ac enrichment at the BCL-xL locus. Notably, BCL-xL was among the few highly up-regulated genes in resistant cells by expression profiling. Proteomic studies of resistant TNBC identify strong association with MED1 and hyper-phosphorylation of BRD4 due to decreased activity of PP2A that we identified as a BRD4 phosphatase. We have defined that hyper-phosphorylation of BRD4 increases the recruitment of BRD4 to MED1 and contributes to BBDI resistance. To explore the translational relevance of our findings, we conducted synergy screens with JQ1 and molecules targeting BCL-XL (ABT737), a gained super-enhancer in resistant cells, and modulators of BRD4 phosphorylation, a CK2 inhibitor CX-4945, and PP2A activator perphenazine (PPZ). We observed significant synergy between JQ1 and ABT737, CX-4945, and also PPZ implying that these drug combinations will likely achieve even higher efficacy in TNBCs than BBDIs alone. Together, these studies provide a rationale for BET inhibition in TNBC and argue for combination strategies to anticipate clinical drug resistance. Citation Format: Shaokun Shu, Charles Lin, Housheng Hansen He, Robert Witwicki, Justin Roberts, Doris Tabassum, Yi Liang, Muhammad Ekram, Ernest Doherty, Jonathan Brown, Hisham Mohammed, Clive D'Santos, Michael McKeown, Christopher Ott, Jun Qi, Min Ni, Prakash Rao, Melissa Duarte, Shwu-Yuan Wu, Cheng-Ming Chiang, Richard Young, Jason Carroll, Henry Long, Myles Brown, Shirley X. Liu, Clifford Meyer, James Bradner, Kornelia Polyak. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B16.

Membrane Induced Peptide Folding and Aggregation

Antimicrobial peptides (AMPs) are short cationic peptides with a significant level of hydrophobicity, which fold onto a secondary structure upon partitioning onto an lipidic interface. AMPs are ideal systems to study how the heterogeneous membrane environment influences peptide folding. The effect of lipid composition on the folding and aggregation of the cationic SVS-1 peptide are explored by a series of coarse-grained (CG) molecular dynamics simulations using a recently developed CG model from our group. By varying the composition of a mixed bilayer of phosphatidylserine(PS)/phosphatidylcholine(PC) we have found different folding and aggregation scenarios. While charge attraction between positively charged side-chains and phosphate groups is found to be the initial driving force for peptide-membrane association, hydrophobicity is observed to play a crucial role in stabilizing peptide-membrane bound conformations. Interestingly, dipole interactions between the serine group of phosphatidylserine with the peptide is the major driving force for folding when the peptide is associated at the lipid-bilayer interface. A localization of SVS-1 peptides is observed in enriched PS regions.

Analysis of Genes Involved in Body Weight Regulation by Targeted Re-Sequencing.

IntroductionGenes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing.MethodsWe enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) ≥ 99th percentile and 176 lean adults (BMI ≤ 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults.Results and ConclusionWe detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (pTDT = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted.

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell.

Metabolic stable isotope incorporation and secondary ion mass spectrometry (SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the (18)O-cholesterol and (15)N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of (18)O-cholesterol and (15)N-sphingolipid enrichment that seem to be separate subcellular compartments. The low levels of nitrogen-containing secondary ions detected at the (18)O-enriched regions suggest that these (18)O-cholesterol-rich structures may be lipid droplets, which have a core consisting of cholesterol esters and triacylglycerides.

Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

Tumor-Priming Smoothened Inhibitor Enhances Deposition and Efficacy of Cytotoxic Nanoparticles in a Pancreatic Cancer Model.

Most pancreatic adenocarcinoma patients present with unresectable disease and benefit little from chemotherapy. Poor tumor perfusion and vascular permeability limit drug deposition. Previous work showed that Smoothened inhibitors of hedgehog signaling (sHHI) promote neovascularization in spontaneous mouse models of pancreatic cancer (PaCA) and enhance tumor permeability to low-molecular weight compounds. Here, we tested the hypothesis that sHHI can enhance tumor deposition and efficacy of drug-containing nanoparticles consisting of 80 to 100 nm sterically-stabilized liposomes (SSL) containing doxorubicin (SSL-DXR). SCID mice bearing low-passage patient-derived PaCA xenografts (PDX) were pretreated p.o. for 10 days with 40 mg/kg/d NVP-LDE225 (erismodegib), followed by i.v. SSL-DXR. Microvessel density, permeability, perfusion, and morphology were compared with untreated controls, as was SSL deposition and therapeutic efficacy. The sHHI alone affected tumor growth minimally, but markedly increased extravasation of nanoparticles into adenocarcinoma cell-enriched regions of the tumor. Immunostaining showed that sHHI treatment decreased pericyte coverage (α-SMA(+)) of CD31(+) vascular endothelium structures, and increased the abundance of endothelium-poor (CD31(-)) basement membrane structures (collagen IV(+)), suggesting increased immature microvessels. SSL-DXR (15 mg/kg) administered after sHHI pretreatment arrested tumor volume progression and decreased tumor perfusion/permeability, suggesting an initial vascular pruning response. Compared with controls, one cycle of 10-day sHHI pretreatment followed by 6 mg/kg SSL-DXR doubled median tumor progression time. Three cycles of treatment with sHHI and SSL-DXR, with a 10-day between-cycle drug holiday, nearly tripled median tumor progression time. Based upon these data, short-term sHHI treatment sequenced with nanoparticulate drug carriers constitutes a potential strategy to enhance efficacy of pancreatic cancer therapy.

Abstract B04: An in vitro model for glioblastoma using microfluidics: Generating pseudopalisades on a chip

Abstract Glioblastoma (GBM), also named grade IV astrocytoma, is the most common and lethal malignant primary brain tumor. GBM is characterized by two main histopathological conditions: necrotic foci typically surrounded by areas of high cellularity and microvascular proliferation. The causes of such densely populated regions, known a “pseudopalisades”, remain poorly understood. Firstly, high cellularity was thought to be due to the rapid proliferation of GBM cells, however recent histological studies have shown that proliferation in pseudopalisading areas is significantly lower than in adjacent regions. Additionally, in pseudopalisades, apoptosis is substantially larger than in neighboring regions. These evidences suggest that pseudopalisades are due to other causes than simply higher proliferation or survival rates. Recent reports have pointed out that, in histological slices from GBM patients, more than 50% of pseudopalisades present clearly a central obstructed blood vessel and in more than 90% microscopic evidences of thrombosis are observed. As a consequence, oxygen and nutrients supply is compromised around the surrounding zones. It has been proposed that one of the driven forces of glioma aggressiveness is these nutrient and oxygen starvation. According to this hypothesis, GBM cell proliferation and secretion of pro-coagulant signals would cause thrombotic events, leading to hypoxia and nutrient depletion in the microenvironment. As a consequence, cells migrate towards nutrients and oxygen enriched regions, creating the characteristic GBM pseudopalisades. Eventually, these migrating cells would reach other blood vessels and eventually cause the collapse of these vessels, restarting the process and creating an expansive wave of tumor cells across the brain. This complex process is hardly reproducible using “in vitro” models because the conventional migration assays are unable to mimic the complex microenvironment described. Recently, microfabrication and microfluidic technologies have arisen as interesting alternatives for creating high-performance cell culture systems. In this paper we describe the design, fabrication and biological validation of a microfluidic device using SU-8 technology for three-dimensional GBM cell cultures under thrombotic conditions. The fabricated microdevice possesses a central microchamber to locate the cells embedded within a hydrogel, mimicking the ECM and allowing migration in three dimensions. On both sides of the microchamber, two lateral microchannels are filled with culture medium, allowing nutrient and oxygen diffusion towards the microchamber, mimicking the brain blood vessels. In this study we have demonstrated the GBM cells (U-251-MG) viability within the microdevice. Moreover, controlling medium flow through lateral microchannels we can mimic the GBM-associated thrombotic pathophysiological conditions. Under these thrombotic circumstances nutrient starvation leads to a chemotactic process and the formation of a migratory front similar to the pseudopalisades observed in vivo and validated with mathematical algorithms. Moreover, our results suggest that the whole process stimulates a more aggressive behavior of GBM cells. In an early stage when nutrients are plenty, GBM cells remain in a non-invasive phenotype. When nutrients are depleted, GBM cells initiate a migration process towards enriched regions, leading to the pseudopalisade formation. When compared with patient´s tumor pathology images, GBM cell invasion behavior follow the same pattern observed in vivo. This novel technique could help us to understand the mechanism of the pseudopalisade formation and to suggest novel therapeutic targets to avoid tumor progression. Besides, these microfluidic devices could represent an extremely useful platform to test new anticancer agents in a preclinical setting that mimics the complex GBM microenvironment. Citation Format: Jose M. Ayuso, Rosa Monge, Alicia Martínez-González, Guillermo A. Llamazares, Javier Berganzo, Aurelio Hernández-Laín, Jorge Santolaria, Manuel Doblaré, Pilar Sánchez-Gómez, Víctor M. Pérez-García, Ignacio Ochoa, Luis J. Fernández. An in vitro model for glioblastoma using microfluidics: Generating pseudopalisades on a chip. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr B04.

Identification of an archaeal mercury regulon by chromatin immunoprecipitation.

Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified, but it is not known whether metal transport is a member of this system. To identify such missing components, a peptide-tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis. Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci, a subset of five was pursued as potential candidates based on their current annotations. Quantitative reverse transcription-PCR analysis of these regions with and without mercury treatment in WT and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute-binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. Inductively coupled plasma-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared with the isogenic WT strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.

Investigation on K and Cl release and migration in micro-spatial distribution during rice straw pyrolysis

This study investigates the release and migration of potassium (K) and chlorine (Cl) in micro-spatial distribution during rice straw pyrolysis in a lab-scale reactor at temperatures from 300°C to 900°C. The K and Cl enrichment region and the morphology of K- and Cl-rich particles in rice straw and char obtained after pyrolysis was clearly revealed for the first time in this field of research. Scanning Electron Microscope/Energy-Dispersive Spectrometry (SEM/EDS) was used to analyze the morphology and distribution of inorganic matters in raw rice straw and water-washed rice straw, as well as the char obtained from raw rice straw pyrolysis, both upon the epidermis (outside surface) and the ground tissue (internal surface). X-ray Diffraction (XRD) was used to analyze the inorganic matters in the obtained char. The particles dispersedly distributed on the cell walls in the ground tissue were proven to be inorganic salt, rich in K and Cl. The ground tissue rather than the epidermis is the main part that decomposes and loses weight during pyrolysis. K and Cl diffuse from the ground tissue to the epidermis and they might be partly restricted to the epidermis during rice straw pyrolysis. The release of K and Cl is determined by both the mobility of K and Cl and the resistance along the diffusion way inside rice straw.

Parametric Study of Dry Sliding Wear Behaviour of Functionally Graded Al LM25/Si3N4 Composite by Response Surface Methodology

Functionally graded aluminium LM25/silicon nitride composite was produced through stir casting followed by centrifugal casting and obtained a hollow cylindrical cast component with dimensions of 150 × 150 × 20 mm. The microstructural examination and the hardness test were carried out on the outer (1 mm) and inner surface (17 mm) as the function of radial distance from the outer periphery. The outer surface was observed with particle enriched region compared to inner surface and exhibited higher hardness. Hence the outer surface of the functionally graded composite was only further subjected to sliding wear test in pin-on-disc tribometer. The Central Composite Design in Response Surface Methodology was used to design the experiments for the selected parameters such as load (15–45 N), velocity (0.5–2.5 m/s) and sliding distance (500–2000 m). Regression test and Analysis of Variance were conducted to check the adequacy of the constructed model. The surface plots for wear rate showed that wear rate increased with increase in load and non-linearly varied with increase in velocity and sliding distance. Scanning Electron Microscopy analysis was conducted on the worn-out surfaces and observed mild to severe wear transition on increase of load.

Peak shape clustering reveals biological insights.

BackgroundChIP-seq experiments are widely used to detect and study DNA-protein interactions, such as transcription factor binding and chromatin modifications. However, downstream analysis of ChIP-seq data is currently restricted to the evaluation of signal intensity and the detection of enriched regions (peaks) in the genome. Other features of peak shape are almost always neglected, despite the remarkable differences shown by ChIP-seq for different proteins, as well as by distinct regions in a single experiment.ResultsWe hypothesize that statistically significant differences in peak shape might have a functional role and a biological meaning. Thus, we design five indices able to summarize peak shapes and we employ multivariate clustering techniques to divide peaks into groups according to both their complexity and the intensity of their coverage function. In addition, our novel analysis pipeline employs a range of statistical and bioinformatics techniques to relate the obtained peak shapes to several independent genomic datasets, including other genome-wide protein-DNA maps and gene expression experiments. To clarify the meaning of peak shape, we apply our methodology to the study of the erythroid transcription factor GATA-1 in K562 cell line and in megakaryocytes.ConclusionsOur study demonstrates that ChIP-seq profiles include information regarding the binding of other proteins beside the one used for precipitation. In particular, peak shape provides new insights into cooperative transcriptional regulation and is correlated to gene expression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0787-6) contains supplementary material, which is available to authorized users.

A Novel Investigation of Initial Solidified Shell Thickness of Continuously Cast Slab Based on Solidification Structure

Considering the big deviation of the measured initial shell thickness obtained by directly measuring the breakout shell in previous works, a new method has been proposed in this study in a microscopic and mesoscopic view. This innovative measuring method is based on the transformation point of the solidification structure of the initial solidified shell before and after the breakout occurs, which avoids the deviation induced by the attachment of the residual liquid steel. Due to the different heat transfer conditions along the casting direction of the mold, causing different segregation behaviors of the solute elements at the different positions, the micromorphology of solidified shell cannot be revealed just through the same etchant. In the present work, the appropriate etchants for the breakout shell at different positions along the casting direction have been explored through dendrite and grain etching experiments, and a black solute enrichment region appearing in the solidified structure after being etched is chosen to determine the shell thickness, therefore, the solidified structure of the initial solidified shell has been investigated in detail based on the experimental results. The result shows that solidification coefficient within the mold obtained by fitting the change curve of the initial shell thickness with the empirical equation is more competitive than the previous works.

Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H.

Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.

Viralign: A tool for uncovering functional viral elements

The availability of broad epigenomic profiles of human tissues provides an opportunity to uncover viral sequences and their corresponding functional regulatory elements in otherwise overlooked datasets. We developed Viralign, a throughput screening method to discover and interpret viral functional information in existing short read archive data. Using a comprehensive reference database, Viralign scans sequence data for known viral sequences and generates an alignment report with read information and genome coverage. Viralign analyzes functional datasets for regulatory elements and provides coordinate and visualization files that can be viewed in a genome browser. Additionally, this method searches for potential integration sites and variants by genome assembly. In a pilot study, we performed H3K27me3 ChIP-seq in monocytes of an HHV6 infected individual and compared this to U2OS cells infected with HHV6A and HHV6B and use Viralign to detect HHV6 insertion loci and H3K27me3 enriched regions. The source code as well as additional data for Viralign will be made publicly available.

Nano-composite microstructure model for the classification of hydrogenated nanocrystalline silicon oxide thin films

Abstract The unique microstructure of nanocrystalline silicon oxide (nc-SiO X :H) thin films results in excellent optoelectronic properties that can be tuned in a wide range to fulfill the requirements of the specific application. For photovoltaic applications, this material is used as doped layers in silicon heterojunction solar cells and intermediate reflectors in multijunction thin-film solar cell. In this paper, we present a microstructure model based on a large number of n- and p-doped nc-SiO X :H films that were deposited under various deposition pressures, plasma powers, plasma frequencies and gas mixtures. This model is meant to provide guidelines for the systematic classification of the complex material system nc-SiO X :H by establishing a link between the structure of the deposited films and the optoelectronic performance of nc-SiO X :H. Based on this model, the deposition of nc-SiO X :H films can be divided into four characteristic regions: (i) fully amorphous region, (ii) onset of nc-Si formation, (iii) oxygen and nc-Si enrichment region, and (iv) deterioration of nc-Si. According to our microstructure model, an optimal phase composition with respect to the optoelectronic performance can be achieved with a high amount of highly conductive nc-Si percolation paths embedded in an oxygen rich a-SiO X :H matrix.

The characteristics of dolomite reservoir in saline lacustrine Basin, Qaidam, China

Qaidam is a plateau saline lacustrine basin in China. The Eocene in western Qaidam mainly consists of lacustrine carbonate, and the sedimentary rocks mainly include micrite, bioclastic limestone, algal limestone, dolomicrite, algal dolomite and so on. Among these rocks, dolomite is the most important petroleum reservoir rock, which mainly includes algal dolomite and dolomicrite. The pores of carbonate are mainly the intercrystalline pores, and there are dissolution pores locally. The analysis based on electronic probe energy spectrum scanning instrument shows that the enrichment region of element Mg in the algal dolomite is highly consistent with the distribution of algal laminas, which means the algal dolomite is a biogenic primary dolomite, because the microbial activities can overcome the kinetic obstacles and create a favorable microenvironment for the formation of dolomite. The analysis based on X-ray diffraction instrument shows that most dolomicrite includes clastic particles and argillaceous components because of the combined sedimentation of clastic materials brought from the peripheral fan delta deposit. The rock composition analysis based on the electronic probe shows that the average content of FeO in the dolomicrite is 0.942 %, and that of MnO is 0.052 %, which are obviously lower than the average contents of Fe and Mn in the hydrothermal dolomite. Meanwhile, due to the high contents of SiO2 and Al2O3, it is considered that the dolomicrite has a penecontemporaneous metasomatic formation mechanism. This type of dolomicrite generated a lot of disseminated intercrystalline pores during the metasomatism. The pore radius is small and the pore number is enormous, which are the main cause of relatively high porosity and relatively low permeability. The type of dolomicrite is a good petroleum reservoir in the study area, so adequate attention shall be given to the dolomicrite during the oil and gas exploration in the carbonate rock reservoir of Eocene in Qaidam Basin.

Abstract 2098: Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line

Abstract Background. The E26-transformation-specific (ETS) transcription factor Spi-B is required for the survival of Activated B Cell-type Diffuse Large B Cell Lymphoma cell lines and is recurrently amplified in B cell lymphoma. The ETS transcription factor PU.1 is highly related to Spi-B. Both PU.1 and Spi-B are expressed in B lymphoma cell lines, and have been demonstrated to redundantly activate transcription of genes required for differentiation and function. We hypothesized that Spi-B and PU.1 occupy similar regions of chromatin within the genome of a B lymphoma cell line. Results. To compare binding regions of Spi-B and PU.1, murine WEHI-279 lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) was performed. Analysis for high-stringency enriched genomic regions demonstrated that PU.1 occupied 4528 regions and Spi-B occupied 3360 regions. 1900 of these regions exhibited at least 100 base pairs of overlap for both factors. Regions bound by Spi-B and PU.1 were frequently located within genes associated with immune response and activation of B cells. Motif-finding revealed that both transcription factors were predominantly located at the ETS core domain (GGAA), however, other unique motifs were identified when examining regions associated with only one of the two factors. Motifs associated with unique PU.1 binding included POU2F2, while unique motifs in the Spi-B regions contained a combined ETS-IRF motif. Conclusions. Our results suggest that complementary biological functions of PU.1 and Spi-B may be explained by their interaction with a similar set of regions in the genome of B lymphoma cells. However, sites uniquely occupied by PU.1 or Spi-B provide insight into their unique functions. Citation Format: Lauren A. Solomon, Stephen K.h. Li, Jan Piskorz, Li S. Xu, Rodney P. DeKoter. Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2098. doi:10.1158/1538-7445.AM2015-2098

Investigation of morphology evolution of the In‐rich inclusions and the corresponding defects in InP single crystals

Submicron, micron and millimeter-scale In-rich inclusions with different polyhedral morphologies are observed, which are directionally embedded in the InP matrix along direction. The arrangement direction and morphological change of the In-rich inclusions at different scales are investigated to reveal their morphology evolution. The relative size of the facets ({100} and {111}P/In) bounding the polyhedral In-rich inclusions is different from the reported results in other crystals, especially when the size of In-rich inclusions is up to millimeter-scale. The growth rate dispersion effect and the initial morphologies of the In-rich droplets have an obvious effect on the final shape of the In-rich inclusions. Dislocation enrichment surrounding the In-rich inclusion is observed, which is contributed to the volume expansion of liquid-solid phase transition and the difference of the thermal expansion coefficient and thermal conductivity between In-rich droplet and InP matrix. The size and shape of the dislocation enriched region are closely related to the size and shape of the originating In-rich droplet and the growth condition.

Rapid determination of coalbed methane exploration target region utilizing hyperspectral remote sensing

This study reveals the common surface mineral characteristics over coalbed methane (CBM) enrichment regions from spaceborne Hyperion images and the possibility of hyperspectral remote sensing for prospecting coalbed methane exploration target region with an inexpensive, large-scale, rapid and convenient way. For this study, a typical scheme including bands removal, atmospheric correction, SNR estimation, Minimum Noise Fraction (MNF), Pixel Purity Index (PPI) and n-dimensional visualization, was applied on Hyperion image in Qinshui Basin, China, to accurately extract mineral endmembers. The endmember spectra of carbonate and clay mineral were identified based on the diagnostic absorption feature, while no endmember of ferrous iron mineral was found. The absorption feature parameters of carbonate (absorption position and especially asymmetric factor) and clay mineral (absorption position, left and right shoulder positions) were quantitatively estimated, which showed the endmember spectra of carbonate and clay mineral from hyperspectral images in this paper were correct. In addition, this study proposed an interesting research direction: measuring the asymmetric absorption factor to facilitate the identification of carbonates. Furthermore, Spectral Angle Mapper (SAM) and Spectral Feature Fitting (SFF) were used to map carbonates and clay minerals. Two assessment methods, visual interpretation based on field spectra and X-ray diffraction (XRD) analysis, were utilized to evaluate the mapping accuracy, which showed total agreements of 84.03% and 72.58%, respectively. The results in this paper suggested that both carbonates and clay minerals were rich while there was hardly any ferrous iron mineral, on the surface of CBM enrichment regions. In addition, another similar experiment was carried out in Ordos Basin and also showed similar surface mineral characteristics on CBM enrichment region.