bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ca2+ Signaling, TRP Channels, and Endothelial Permeability
Authors: TIRUPPATHI CHINNASWAMY , AHMMED GIAS U. , VOGEL STEPHEN M. , MALIK ASRAR B. 
Published: November 2006

ABSTRACTIncreased endothelial permeability is the hallmark of inflammatory vascular edema. Inflammatory mediators that bind to heptahelical G protein‐coupled receptors trigger increased endothelial permeability by increasing the intracellular Ca2+ concentration ([Ca2+]i). The rise in [Ca2+]i activates key signaling pathways that mediate cytoskeletal reorganization (through myosin‐light‐chain‐dependent contraction) and the disassembly of VE‐cadherin at the adherens junctions. The Ca2+‐dependent protein kinase C (PKC) isoform PKCα plays a crucial role in initiating endothelial cell contraction and disassembly of VE‐cadherin junctions. The increase in [Ca2+]i induced by inflammatory agonists such as thrombin and histamine is achieved by the generation of inositol 1,4,5‐trisphosphate (IP3), activation of IP3‐receptors, release of stored intracellular Ca2+, and Ca2+ entry through plasma membrane channels. IP3‐sensitive Ca2+‐store depletion activates plasma membrane cation channels (i.e., store‐operated cation channels [SOCs] or Ca2+ release‐activated channels [CRACs]) to cause Ca2+ influx into endothelial cells. Recent studies have identified members of Drosophila transient receptor potential (TRP) gene family of channels that encode functional SOCs in endothelial cells. These studies also suggest that the canonical TRPC homologue TRPC1 is the predominant isoform expressed in human vascular endothelial cells, and is the essential component of the SOC in this cell type. Further, evidence suggests that the inflammatory cytokine tumor necrosis factor‐α can induce the expression of TRPC1 in human vascular endothelial cells signaling via the nuclear factor‐κB pathway. Increased expression of TRPC1 augments Ca2+ influx via SOCs and potentiates the thrombin‐induced increase in permeability in human vascular endothelial cells. Deletion of the canonical TRPC homologue in mouse, TRPC4, caused impairment in store‐operated Ca2+ current and Ca2+‐store release‐activated Ca2+ influx in aortic and lung endothelial cells. In TRPC4 knockout (TRPC4−/−) mice, acetylcholine‐induced endothelium‐dependent smooth muscle relaxation was drastically reduced. In addition, TRPC4−/− mouse‐lung endothelial cells exhibited lack of actin‐stress fiber formation and cell retraction in response to thrombin activation of protease‐activated receptor‐1 (PAR‐1) in endothelial cells. The increase in lung microvascular permeability in response to PAR‐1 activation was inhibited in TRPC4−/− mice. These results indicate that endothelial TRP channels such as TRPC1 and TRPC4 play an important role in signaling agonist‐induced increases in endothelial permeability.
Ca2+ Channels and Pulmonary Endothelial Permeability: Insights from Study of Intact Lung and Chronic Pulmonary Hypertension
Authors: TOWNSLEY MARY I. , KING JUDY A. , ALVAREZ DIEGO F. 
Published: November 2006

ABSTRACTPhenotypic heterogeneity in pulmonary vascular endothelial cells extends to regulation of endothelial permeability, a process which often depends upon Ca2 + entry from the extracellular space. Scanning electron microscopy of vascular corrosion casts has documented distinct patterns of barrier disruption. Store depletion and activation of Ca2 + entry via canonical transient potential channels (TRPC1 and TRPC4) disrupts the barrier in extraalveolar vessels. In contrast, numerous other models of acute lung injury, including high vascular pressure‐ or epoxyeicosatrienoic acid‐induced injury, specifically disrupt the alveolar septal barrier. This review discusses Ca2 + permeant channels which potentially could be involved in regulation of barrier integrity in the alveolar septal compartment: transient receptor potential channels, cyclic nucleotide gated channels, purinergic (P2X) channels, and T‐type voltage gated channels. The evidence for the vanilloid transient receptor potential channel TRPV4 in regulating septal barrier function is discussed. Adaptations in barrier function in chronic pulmonary hypertension are reviewed, notably the loss of a store depletion‐dependent permeability response in the intact lung. Finally, the authors propose that since specific disruption of the alveolar septal barrier will have deleterious functional consequences, such as alveolar flooding and impairment of gas exchange, identification of specific molecular targets for Ca2 + entry‐dependent regulation of barrier function in this compartment is needed.
Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA and Multiprotein-DNA Complexes
Authors: Naryshkin Nikolai , Revyakin Andrey , Ebright Richard H. 
Published: November 2006

INTRODUCTIONSite-specific protein-DNA photo-cross-linking is able to define positions of proteins relative to DNA within large multiprotein-DNA complexes. Chemical and enzymatic reactions are used to prepare a DNA fragment containing a phenyl-azide photoactivatible cross-linking agent and an adjacent radiolabel incorporated at a single, defined DNA phosphate. The multiprotein-DNA complex of interest is formed using the site-specifically derivatized DNA fragment. The complex is then UV-irradiated, initiating covalent cross-linking with proteins in direct physical proximity to the cross-linking agent. Extensive nuclease digestion is performed to eliminate uncross-linked DNA and convert cross-linked DNA to a cross-linked, radiolabeled nucleotide “tag.” The “tagged” proteins are identified, usually by denaturing polyacrylamide gel electrophoresis followed by autoradiography. The procedure is performed in a systematic fashion: At least 10 derivatized DNA fragments, each having the cross-linking agent incorporated at a defined DNA phosphate within the region of interest, are analyzed. The results of the procedure define the translational positions of proteins relative to the DNA sequence. Plotted on a three-dimensional representation of a DNA helix, the results also define the rotational orientations of proteins relative to the DNA helix axis and the groove orientations of proteins relative to the DNA major and minor grooves. Here, we present a detailed protocol for the cross-linking of protein-DNA complexes immobilized on streptavidin-coated paramagnetic beads (“on-bead” cross-linking).
Split Luciferase Complementation Assay for Studying Interaction of Proteins X and Y in Living Mice
Authors: Paulmurugan Ramasam , Ray Pritha , De Abhijit , Chan Carmel T. , Gambhir Sanjir Sam 
Published: November 2006

INTRODUCTIONThis protocol describes a split luciferase complementation assay that can be used to repetitively and noninvasively study the interaction of proteins in small living animals. After the expression of the appropriate vectors has been checked in cell culture in vivo, studies can be performed either by implanting transiently transfected cells for short-term analysis (maximum of 7 days), as described below, or with tumor models grown from tumor cells stably expressing the complete reporter system. For optical imaging, the number of cells implanted can be relatively low (~1-5 × 106), and imaging can begin even before the tumors are palpable. When using a regulated reporter gene, it may be necessary to perform a dose-dependent pilot experiment with the inducer or repressor before performing the primary experiments. Animal models other than mice can be used, including rats and, in theory, transgenic animals in which the reporter constructs have been stably integrated into the genome. Animals larger than the rat would be difficult to image due to poor penetration of light. For these larger-animal models, the use of other imaging technologies such as microPET should be considered.
Split Luciferase Complementation Assay for Studying Interaction of Proteins X and Y in Cells
Authors: Paulmurugan Ramasam , Ray Pritha , De Abhijit , Chan Carmel T. , Gambhir Sanjir Sam 
Published: November 2006

INTRODUCTIONThis protocol describes a split luciferase complementation assay used to study the interaction of proteins in cells. In the “split protein” strategy, a single reporter protein/enzyme (in this case, firefly luciferase [Fluc]) is cleaved into amino-terminal and carboxy-terminal halves; each half is fused to one of two interacting proteins, X and Y. Physical interactions between the two proteins, X and Y, reconstitute the functional reporter protein, leading to enzymatic activities that can be measured by in vitro or in vivo assays. It is important to perform the assay initially in cell culture before proceeding with animal imaging, not only to conserve animals, but also to establish the sensitivity of the assay.
Identification of Positive GATEWAY Expression Clones When Both the pENTRY and pDEST Vectors Contain the Same Marker for Bacterial Selection
Authors: Basherudin Norlia , Curtis Mark D. 
Published: November 2006

INTRODUCTIONGATEWAY cloning technology (Invitrogen) takes advantage of bacteriophage λ site-specific recombination. The life cycle of λ alternates between the lytic and lysogenic stages. DNA can be inserted or excised from the Escherichia coli host genome by recombination between specific sites, AttB (bacterial) and AttP (phage). This process is mediated by the λ proteins int (integrase) and xis (excisionase), and a host protein IHF (integration host factor). GATEWAY cloning technology uses this process to insert fragments of DNA directionally into specially adapted vectors. These vectors contain a negative selectable marker, the ccdB gene, to select against nonrecombinant clones. Promoter or gene fragments are made GATEWAY compatible with adapter primers and amplified by PCR. These fragments are used in a BP clonase reaction to create ENTRY clones. Usually the pDONR vector used to generate such ENTRY clones is chosen so that the antibiotic selection marker is different from that of the pDEST vector, which finally generates an expression clone. This favors the selection of the expression clone and selects against the pENTRY clone. Now that many pENTRY and pDEST vectors have been generated and made available in stock centers, the antibiotic resistance genes are predetermined and may not always be compatible with each other. This problem is frequently experienced by plant researchers, since many full-length cDNA libraries have been generated using the pDONR-TOPO, pDONR221, or pENTR1A vectors, which are all kanamycin resistant in bacteria, and many pDEST vectors have been adapted from conventional plant transformation vectors, which are also frequently kanamycin resistant in bacteria. The following protocol describes ways in which such difficult vector combinations can be used effectively to obtain the appropriate expression clone without having to convert the pENTRY clone or pDEST clone to vectors with compatible antibiotic resistances.
Hedgehog signal pathway is activated in ovarian carcinomas, correlating with cell proliferation: It's inhibition leads to growth suppression and apoptosis
Authors: Chen Xiaojun , Horiuchi Akiko , Kikuchi Norihiko , Osada Ryosuke , Yoshida Junko , Shiozawa Tanri , Konishi Ikuo 
Published: November 2006

The hedgehog (Hh) signal pathway has recently been shown to be activated in human malignancies. However, little is known about its role in the development or patient prognosis of epithelial ovarian carcinoma. In the present study, we examined in vivo and in vitro the expression and functional role of Hh signal molecules in epithelial ovarian tumors and normal ovarian surface epithelial (OSE) cells. The expression of Shh, Dhh, Ptch, Smo and Gli1 proteins was not observed in normal OSE, but was increased stepwise in benign, borderline and malignant neoplasms. In addition, immunoreactivity for Shh, Dhh, Ptch, Smo and Gli1 was highly correlated with cell proliferation assessed by Ki‐67. Blocking the Hh signal using either the Hh pathway inhibitor cyclopamine or Gli1 siRNA led to remarkably decreased cell proliferation in ovarian carcinoma cells. Treatment with cyclopamine induced not only G1 arrest but also apoptosis along with the downregulation of cyclin A and cyclin D1, and the upregulation of p21 and p27. Among the Hh signal molecules, Dhh expression was correlated with poor prognosis of ovarian carcinoma patients. These findings suggest that the Hh signal pathway plays an important role in ovarian tumorigenesis as well as in the activation of cell proliferation in ovarian carcinomas. Thus, the Hh signal pathway is a possible molecular target of new treatment strategies for ovarian carcinoma. (Cancer Sci 2007; 98: 68–76)
A role for tissue transglutaminase in α-gliadin peptide cytotoxicity
Authors: Sakly W , Thomas V , Quash G , El Alaoui S 
Published: November 2006

Summary
In coeliac disease, gliadin peptides p56–88, p57–68 and p31–49 have been demonstrated to be involved in the pathogenic damage of the small intestine via their immunogenicity or toxicity to epithelial cells. To try to understand the mechanism of their toxicity, we investigated the effect of synthetic peptides (p31–49, p56–88, p57–68, p69–82) and of their deamidated analogues on Caco2 and FHs 74 Int cell toxicity and tissue tranglutaminase activity. Apoptosis, necrosis and cell viability were assessed by flow cytometry, and peptide deamidation was determined indirectly by measuring its capacity to inhibit tTG activity. The results showed that p56–88 and p57–68 reduced cell growth and concomitantly inhibited tTG activity in both cell types. This effect was abolished when Caco2 cells were treated with antibodies to tTG. Deamidated peptide p57–68 (E65) lost practically all of its inhibitory effect on cell growth and on tTG activity. Cellular toxicity was also observed with p31–49, which was not a substrate for tTG. p69–82 was not cytotoxic but became so when glutamine 72 was substituted by glutamic acid. These findings provide evidence for the existence of three types of toxicity among gliadin peptides: (i) peptides that are intrinsically toxic and are not substrates of tTG; (ii) peptides that are non-toxic but become so when they act as substrates of tTG; and (iii) peptides that are non-toxic and are not substrates of tTG but become so when deamidated. A mechanism other than that involving tTG could be responsible for the deamidation of glutamine residues of gliadin in the intestinal tract.
CRS‐stack‐based residual static correction
Authors: Koglin I. , Mann J. , Heilmann Z. 
Published: November 2006

ABSTRACTIn the case of onshore data sets, the acquired reflection events can be strongly impaired due to rough top‐surface topography and inhomogeneities in the uppermost low‐velocity layer, the so‐called weathering layer. Without accounting for these influences, the poor data quality will make data processing very difficult.Usually, the correction for the top‐surface topography is not perfect. The residuals from this correction and the influence of the weathering layers lead to small distortions along the reflection events. We integrated a residual static correction method into our data‐driven common‐reflection‐surface‐stack‐based imaging workflow to further eliminate such distortions. The moveout‐corrected traces and the stacked pilot trace are cross‐correlated to determine a final estimate of the surface‐consistent residual statics in an iterative manner.As the handling of top‐surface topography within the common‐reflection‐surface stack is discussed in a separate paper in this special issue, the corresponding residual static correction will be explained in more detail. For this purpose, the results obtained with a data set from the Arabian Peninsula will be presented.
CRS‐stack‐based seismic imaging considering top‐surface topography
Authors: Heilmann Z. , Mann J. , Koglin I. 
Published: November 2006

ABSTRACTIn this case study we consider the seismic processing of a challenging land data set from the Arabian Peninsula. It suffers from rough top‐surface topography, a strongly varying weathering layer, and complex near‐surface geology. We aim at establishing a new seismic imaging workflow, well‐suited to these specific problems of land data processing. This workflow is based on the common‐reflection‐surface stack for topography, a generalized high‐density velocity analysis and stacking process. It is applied in a non‐interactive manner and provides an entire set of physically interpretable stacking parameters that include and complement the conventional stacking velocity.The implementation introduced combines two different approaches to topography handling to minimize the computational effort: after initial values of the stacking parameters are determined for a smoothly curved floating datum using conventional elevation statics, the final stack and also the related residual static correction are applied to the original prestack data, considering the true source and receiver elevations without the assumption of nearly vertical rays. Finally, we extrapolate all results to a chosen planar reference level using the stacking parameters. This redatuming procedure removes the influence of the rough measurement surface and provides standardized input for interpretation, tomographic velocity model determination, and post‐stack depth migration. The methodology of the residual static correction employed and the details of its application to this data example are discussed in a separate paper in this issue.In view of the complex near‐surface conditions, the imaging workflow that is conducted, i.e. stack – residual static correction – redatuming – tomographic inversion – prestack and post‐stack depth migration, leads to a significant improvement in resolution, signal‐to‐noise ratio and reflector continuity.
Tomographic joint inversion of first arrivals in a real case fromSaudi Arabia
Authors: Böhm Gualtiero , Accaino Flavio , Rossi Giuliana , Tinivella Umberta 
Published: November 2006

ABSTRACTA joint inversion of both first and refracted arrivals is applied on a seismic line, acquired onshore, in order to obtain a well‐resolved velocity field for the computation of static corrections. The use of different arrivals in the inversion involves exploiting the information derived from the different raypaths associated with each wave type, thus enhancing the reliability of the inversion. The data was gathered by Saudi Aramco in an area of the Arabian Peninsula characterized by strong lateral variations, both in topography and shallow velocity, and where therefore a well‐defined near‐surface velocity field is important. In addition to velocity, the depth distribution of the quality factor Q is computed from the tomographic inversion of the seismic‐signal frequency shift. Thus, the Q‐factor field is used to perform an inverse Q‐data filtering and improve the resolution of the final stacked section.
Comparing state‐of the art near‐surface models of a seismic test line from Saudi Arabia
Authors: Bridle Ralph , Barsoukov Nikolai , Al‐Homaili Mohammad , Ley Robert , Al‐Mustafa Ameerah 
Published: November 2006

ABSTRACTWe present a seismic Test Line, provided by Saudi Aramco for various research teams, to highlight a few major challenges in land data processing due to near‐surface anomalies. We discuss state‐of‐the‐art methods used to compensate for shallow distortions, including single‐layer, multilayer, plus/minus, refraction and tomostatics methods. They are a starting point for the new technologies presented in other papers, all dealing with the same challenging data described here.The difficulties on the Test Line are mostly due to the assumption of vertical raypaths, inherent in classical applications of near‐surface correction statics. Even the most detailed velocity/depth model presents difficulties, due to the compleX‐raypath. There is a need for methods which are based on more complex models andtheories.
Geostatistical integration of near‐surface geophysical data
Authors: Vesnaver A. , Bridle R. , Henry B. , Ley R. , Rowe R. , Wyllie A. 
Published: November 2006

ABSTRACTAccurate statics calculation and near‐surface related noise removal require a detailed knowledge of the near‐surface velocity field. Conventional seismic surveys currently are not designed to provide this information, and 3D high‐resolution reflection/refraction acquisition is not feasible for large survey areas. Satellite images and vibrator plate attributes are dense low‐cost data, which can be used in spatially extrapolating velocities from sparse uphole data by geostatistics. We tested this approach in two different areas of Saudi Arabia and found that the optimal recipe depends on the local geology.
An integrated method for resolving the seismic complex near‐surface problem
Authors: Al‐Ali M.N. , Verschuur D.J. 
Published: November 2006

ABSTRACTWe describe an integrated method for solving the complex near‐surface problem in land seismic imaging. This solution is based on an imaging approach and is obtained without deriving a complex near‐surface velocity model. We start by obtaining from the data the kinematics of the one‐way focusing operators (i.e. time‐reversed Green's functions) that describe propagation between the acquisition surface and a chosen datum reflector using the common‐focus‐point technology. The conventional statics solutions obtained from prior information about the near surface are integrated in the initial estimates of the focusing operators. The focusing operators are updated iteratively until the imaging principle of equal traveltime is fulfilled for each subsurface gridpoint of the datum reflector. Therefore, the seismic data is left intact without any application of time shifts, which makes this method an uncommitted statics solution. The focusing operators can be used directly for wave‐equation redatuming to the respective reflector or for prestack imaging if determined for multiple reflecting boundaries. The underlying velocity model is determined by tomographic inversion of the focusing operators while also integrating any hard prior information (e.g. well information). This velocity model can be used to perform prestack depth imaging or to calculate the depth of the new datum level. We demonstrate this approach on 2D seismic data acquired in Saudi Arabia in an area characterized by rugged topography and complex near‐surface geology.
The impact of field‐survey characteristics on surface‐relatedmultiple attenuation
Authors: Dragoset B. , Moore I. , Kostov C. 
Published: November 2006

ABSTRACTField‐survey characteristics can have an important impact on the quality of multiples predicted by surface‐related multiple elimination (SRME) algorithms. This paperexamines the effects of three particular characteristics: in‐line spatial sampling, source stability, and cable feathering. Inadequate spatial sampling causes aliasing artefacts. These can be reduced by f–k filtering at the expense of limiting the bandwidth in the predicted multiples. Source‐signature variations create artefacts in predicted multiples due to spatial discontinuities. Variations from a well‐behaved airgun array produced artefacts having an rms amplitude about 26 dB below the rms amplitude of multiples predicted with no variations. Cable feathering has a large impact on the timingerrors in multiples predicted by 2D SRME when it is applied in areas having cross dip. All these problems can be reduced by a combination of better survey design, use of advanced data‐acquisition technologies, and additional data‐processing steps.