Distinctive growth requirements and gene expression patterns distinguish progenitor B cells from pre-B cells.

Long-term bone marrow cultures have been useful in determining gene expression patterns in pre-B cells and in the identification of cytokines such as interleukin 7 (IL-7). We have developed a culture system to selectively grow populations of B lineage restricted progenitors (pro-B cells) from murine bone marrow. Pro-B cells do not grow in response to IL-7, Steel locus factor (SLF), or a combination of the two. c-kit, the SLF receptor, and the IL-7 receptor are both expressed by pro-B cells, indicating that the lack of response is not simply due to the absence of receptors. Furthermore, SLF is not necessary for the growth of pro-B cells since they could be expanded on a stromal line derived from Steel mice that produces no SLF. IL-7 responsiveness in pre-B cells is associated with an increase in n-myc expression and is correlated with immunoglobulin (Ig) gene rearrangements. Although members of the ets family of transcription factors and the Pim-1 kinase are expressed by pro-B cells, n-myc is not expressed. Pro-B cells maintain Ig genes in the germline configuration, which is correlated with a low level of recombination activating genes 1 and 2 (Rag-1 and 2) mRNA expression, but high expression of sterile mu and terminal deoxynucleotidyl transferase. Pro-B cells are unable to grow separated from the stromal layer by a porous membrane, indicating that stromal contact is required for growth. These results suggest that pro-B cells are dependent on alternative growth signals derived from bone marrow stroma and can be distinguished from pre-B cells by specific patterns of gene expression

Well-to-Well Log Correlation Using Knowledge-Based Systems and Dynamic Depth Warping

We present a novel system for well-to-well log correlation using knowledge-based systems and dynamic depth warping techniques. This approach overcomes a major drawback inherent in previous methods, namely the difficulty in correlating missing or discontinuous rock units. The system has three components: (1) A Dynamic Programming algorithm to correlate the logs and to find the minimum-cost or "best" match; (2) A set of "rules" to guide the correlation; (3) A data base that contains the logs and other relevant geologic and seismic information. The Dynamic Programming algorithm calculates the cost of correlating each point in the first well with each of the points in the second well. The resulting matrix of dissimilarity contains cost information about every possible operation which matches the well logs. The cost of matching the two wells is measured by the difference in the log values. The dynamic programming approach allows correlation across geologic structures, thinning beds, and missing or discontinuous units. A path finding algorithm then traces through the matrix to define a function which maps the first well onto the second. The minimum cost path is the optimal correlation between the wells. The system's database contains the well logs themselves and other relevant data including information about the geologic setting, seismic ties, interpreted lithologies, and dipmeter information. Rules operating on the data affect the dynamic programming and path finding algorithms in several ways: (1) Seismic ties or marker beds define a point in the warping path, thereby removing calculations over large portions of the search space; (2) Dipmeter results and knowledge of geologic structure further constrain the path to certain global areas and save calculation time; (3) The system assigns weights to different logs based on log quality and sensitivity; (4) Knowledge of the paleoenvironment allows the program to choose a set of rules (model) which accounts for changes in sediment type or thickness within a field. For example, when the program is operating in a deltaic environment, it will correlate the shales before attempting to correlate the sands. We demonstrate the method with synthetic examples in which the program successfully correlates across geologic structures and pinch-outs. We also applied the program to field examples from two widely separated oil provinces. In both cases, the automated correlation agreed very well with correlations provided by geologic experts

Seismoelectric measurements on artifical porous media and Berea sandstone

Seismic to electromagnetic wave conversion has been proposed as a possible exploration method. We present laboratory measurements of the conversion of an acoustic wave into electric potential, which occurs at a fluid/porous-medium interface. The conversion is measured for artificial porous media and Berea sandstone. Recorded electric potentials are smaller for large grain samples. We also show variability of the conversion over a time span of 120 hours.Shell Refining Compan

Energy Partitioning and Attenuation of Guided Waves in a Radially Layered Borehole

Recently published results (Tubman et al., 1984; Baker,. 1984) indicate that synthetic full waveform acoustic logs generated in cased or damaged boreholes differ significantly from those generated in an open hole with the same formation parameters. In particular, the guided waves appear to be the most affected by such radial layering. In order to gain some understanding of these effects, the amplitude response and energy distribution of the pseudo-Rayleigh and Stoneley waves are studied for the cased and invaded borehole models. The expressions derived by Cheng et al. (1 982) are used to calculate partition coefficients (partial derivatives of phase velocity with respect to body wave velocities) for the guided wave modes. The attenuation of the guided wave can then be represented by the sum of the layer attenuation values weighted by their respective partition coefficients. The results indicate that the attenuation of the Stoneley wave is dominated by the fluid attenuation at all frequencies in fast formations, both in the open hole geometry and in the presence of casing or invaded zones. In a slow formation, the Stoneley wave attenuation becomes more sensitive to the shear wave attenuation of the formation at higher frequencies in both the open and cased hole situations. For the pseudo-Rayleigh wave, the introduction of casing reduces the effect of the fluid attenuation, while the presence of an invaded zone reduces the effect of the formation shear attenuation. Plots of the partition coefficients indicate that the casing and invasion layers are most important over a limited frequency range which is related to the thickness of the layer. Radial displacement curves illustrate the depth of penetration of the various frequency components of the pseudo-Rayleigh wave.Massachusetts Institute of Technology. Full Waveform Acoustic Logging Consortiu

Seismology on Mars

A three-axis short period seismometer has been operating on the surface of Mars in the Utopia Planitia region since September 4, 1976. During the first five months of operation approx. 640 hours of high quality data, uncontaminated by Lander or wind noise, have been obtained. The detection threshold is estimated to be magnitude 3 to about 200 km and about 6.5 for the planet as a whole. No large events have been seen during this period indicating that Mars is less seismically active than Earth

Mid-ocean microseisms

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 6 (2005): Q04009, doi:10.1029/2004GC000768.The Hawaii-2 Observatory (H2O) is an excellent site for studying the source regions and propagation of microseisms since it is located far from shorelines and shallow water. During Leg 200 of the Ocean Drilling Program, the officers of the JOIDES Resolution took wind and wave measurements for comparison with double-frequency (DF) microseism data collected at nearby H2O. The DF microseism band can be divided into short period and long period bands, SPDF and LPDF, respectively. Comparison of the ship’s weather log with the seismic data in the SPDF band from about 0.20 to 0.45 Hz shows a strong correlation of seismic amplitude with wind speed and direction, implying that the energy reaching the ocean floor is generated locally by ocean gravity waves. Near-shore land seismic stations see similar SPDF spectra, also generated locally by wind seas. At H2O, SPDF microseism amplitudes lag sustained changes in wind speed and direction by several hours, with the lag increasing with wave period. This lag may be associated with the time necessary for the development of opposing seas for DF microseism generation. Correlation of swell height above H2O with the LPDF band from 0.085 to 0.20 Hz is often poor, implying that a significant portion of this energy originates at distant locations. Correlation of the H2O seismic data with NOAA buoy data, with hindcast wave height data from the North Pacific, and with seismic data from mainland and island stations, defines likely source areas of the LPDF signals. Most of the LPDF energy at H2O appears to be generated by high amplitude storm waves impacting long stretches of coastline nearly simultaneously, and the Hawaiian Islands appear to be a significant source of LPDF energy in the North Pacific when waves arrive from particular directions. The highest DF levels observed at mid-ocean site H2O occur in the SPDF band when two coincident nearby storm systems develop. Mid-ocean generated DF microseisms are not observed at interior continental sites, indicating high attenuation of these signals. At near-coastal seismic stations, both SPDF and LPDF microseism levels are generally dominated by local generation at nearby shorelines.This work was supported by the U.S. Science Support Program (User Reference: 418920-BA372; Task Order F001602) associated with the Ocean Drilling Program and is sponsored by the National Science Foundation and the Joint Oceanographic Institutions, Inc. Additional support was provided by the California Energy Commission and the California Department of Boating and Waterways as part of their program to improve boating facilities, access, safety, and education. Support for Ralph Stephen was also provided by the National Science Foundation under Grant #OCE-0424633

Quantification of Epstein-Barr virus DNA load, interleukin-6, interleukin-10, transforming growth factor-β1 and stem cell factor in plasma of patients with nasopharyngeal carcinoma

BACKGROUND: Nasopharyngeal carcinoma (NPC) is a common epithelial neoplasm among the Chinese populations in Southern China and South East Asia. Epstein-Barr virus (EBV) is known to be an important etiologic agent of NPC and the viral gene products are frequently detected in NPC tissues along with elevated antibody titres to the viral proteins (VCA and EA) in a majority of patients. Elevated plasma EBV DNA load is regarded as an important marker for the presence of the disease and for the monitoring of disease progression. However, other serum/plasma parameters such as the levels of certain interleukins and growth factors have also been implicated in NPC. The objectives of the present study are, 1) to investigate the correlations between plasma EBV DNA load and the levels of interleukin (IL)-6, IL-10, TGF-β1 and SCF (steel factor) and 2) to relate these parameters to the stages of NPC and the effect of treatment. METHODS: A total of 78 untreated NPC patients were enrolled in this study. Of these, 51 were followed-up after treatment. The remaining patients had irregular or were lost to follow-up. Plasma EBV DNA was quantified using real-time quantitative PCR. The levels of plasma interleukins and growth factors were quantified using ELISA. RESULTS: A significant decrease in EBV DNA load was detected in plasma of untreated NPC patients (1669 ± 637 copies/mL; n = 51) following treatment (57 ± 37 copies/mL, p < 0.05); n = 51). Plasma EBV DNA load was shown to be a good prognosticator for disease progression and clinical outcome in five of the follow-up patients. A significant difference in IL-6 levels was noted between the untreated patients (164 ± 37 pg/mL; n = 51) and following treatment (58 ± 16 pg/mL, p < 0.05; n = 51). Positive correlations between EBV DNA load and IL-10 (r(49) = 0.535, p < 0.01), between IL6 and IL-10 (r(49) = 0.474, p < 0.01) and between TGF and SCF (r(49) = 0.464, p < 0.01) were observed in patients following treatment. None of the parameters tested including IgA-VCA were associated with tumour stages. CONCLUSION: We conclude that among the parameters investigated, EBV DNA load and IL-6 levels were promising markers for the presence of NPC and for the assessment of treatment outcome

Co expression of SCF and KIT in gastrointestinal stromal tumours (GISTs) suggests an autocrine/paracrine mechanism

KIT is a tyrosine kinase receptor expressed by several tumours, which has for specific ligand the stem cell factor (SCF). KIT is the main oncogene in gastrointestinal stromal tumours (GISTs), and gain-of-function KIT mutations are present in 70% of these tumours. The aim of the study was to measure and investigate the mechanisms of KIT activation in 80 KIT-positive GIST patients. KIT activation was quantified by detecting phosphotyrosine residues in Western blotting. SCF production was determined by reverse transcriptase–PCR, ELISA and/or immunohistochemistry. Primary cultures established from three GISTs were also analysed. The results show that KIT activation was detected in all cases, even in absence of KIT mutations. The fraction of activated KIT was not correlated with the mutational status of GISTs. Membrane and soluble isoforms of SCF mRNA were present in all GISTs analysed. Additionally, SCF was also detected in up to 93% of GISTs, and seen to be present within GIST cells. Likewise, the two SCF mRNA isoforms were found to be expressed in GIST-derived primary cultures. Thus, KIT activation in GISTs may in part result from the presence of SCF within the tumours

The Hemopoietic Stem Cell Niche Versus the Microenvironment of the Multiple Myeloma-Tumor Initiating Cell

Multiple myeloma cells are reminiscent of hemopoietic stem cells in their strict dependence upon the bone marrow microenvironment. However, from all other points of view, multiple myeloma cells differ markedly from stem cells. The cells possess a mature phenotype and secrete antibodies, and have thus made the whole journey to maturity, while maintaining a tumor phenotype. Not much credence was given to the possibility that the bulk of plasma-like multiple myeloma tumor cells is generated from tumor-initiating cells. Although interleukin-6 is a major contributor to the formation of the tumor’s microenvironment in multiple myeloma, it is not a major factor within hemopoietic stem cell niches. The bone marrow niche for myeloma cells includes the activity of inflammatory cytokines released through osteoclastogenesis. These permit maintenance of myeloma cells within the bone marrow. In contrast, osteoclastogenesis constitutes a signal that drives hemopoietic stem cells away from their bone marrow niches. The properties of the bone marrow microenvironment, which supports myeloma cell maintenance and proliferation, is therefore markedly different from the characteristics of the hemopoietic stem cell niche. Thus, multiple myeloma presents an example of a hemopoietic tumor microenvironment that does not resemble the corresponding stem cell renewal niche