bluuebunny/crossref_metadata_2025 huggingface dataset:
Anaerovirgula multivorans gen. nov., sp. nov., a novel spore-forming, alkaliphilic anaerobe isolated from Owens Lake, California, USA
Authors: Pikuta Elena V. , Itoh Takashi , Krader Paul , Tang Jane , Whitman William B. , Hoover Richard B.
Published: November 2006

A novel, alkaliphilic, obligately anaerobic bacterium, strain SCAT, was isolated from mud sediments of a soda lake in California, USA. The rod-shaped cells were motile, Gram-positive, formed spores and were 0.4–0.5×2.5–5.0 μm in size. Growth occurred within the pH range 6.7–10.0 and was optimal at pH 8.5. The temperature range for growth was 10–45 °C, with optimal growth at 35 °C. NaCl was required for growth. Growth occurred at 0.5–9.0 % (w/v) NaCl and was optimal at 1–2 % (w/v). The novel isolate was a catalase-negative chemo-organoheterotroph that fermented sugars, proteolysis products, some organic and amino acids, glycerol,d-cellobiose and cellulose. It was also capable of growth by the Stickland reaction. Strain SCATwas sensitive to tetracycline, chloramphenicol, rifampicin and gentamicin, but it was resistant to ampicillin and kanamycin. The G+C content of the genomic DNA was 34.2 mol%. Major fatty acid components were C14 : 0, iso-C15 : 0, C16 : 1ω9cand C16 : 0. 16S rRNA gene sequence analysis of strain SCATshowed a similarity of approximately 97 % with the type strains ofClostridium formicaceticumandClostridium aceticumin clostridial cluster XI and a similarity of less than 94.2 % to any other recognizedClostridiumspecies and those of related genera in this cluster. Strain SCATwas clearly differentiated fromC. formicaceticumandC. aceticumbased on comparison of their phenotypic properties and fatty acid profiles, as well as low levels of DNA–DNA relatedness between strain SCATand the type strains of these two species. Therefore, strain SCATis considered to represent a novel species of a new genus,Anaerovirgula multivoransgen. nov., sp. nov., in clostridial cluster XI. The type strain is SCAT(=ATCC BAA-1084T=JCM 12857T=DSM 17722T=CIP 107910T).
Devosia soli sp. nov., isolated from greenhouse soil in Korea
Authors: Yoo Seung-Hee , Weon Hang-Yeon , Kim Byung-Yong , Hong Seung-Beom , Kwon Soon-Wo , Cho Yang-Hee , Go Seung-Joo , Stackebrandt Erko
Published: November 2006

A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5 %) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0 %. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18 : 1
ω7c and C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA–DNA hybridization experiments (47 % relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).
Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater
Authors: Tiago Igor , Pires Carlos , Mendes Vítor , Morais Paula V. , da Costa Milton S. , Veríssimo António
Published: November 2006

A low-G+C-content Gram-positive bacterium, designated CV53T, phylogenetically related to species of the genus Bacillus, was isolated from a highly alkaline non-saline groundwater environment (pH 11.4). This organism comprised rod-shaped cells, was aerobic, did not display spore formation, was catalase- and oxidase-negative, had an optimum growth temperature of 40 °C and had an optimum pH of approximately 7.0–8.5. Optimal growth was observed in the absence of NaCl, but growth did occur at NaCl concentrations up to 3.0 %. The strain possessed an A1γ-type peptidoglycan cell wall and the major respiratory quinone was MK-7. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the DNA was 43.1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that the novel isolate is closely related to the type strain of Bacillus jeotgali, forming a coherent cluster supported by bootstrap analysis at a confidence level of 90 %. The pairwise similarity of the 16S rRNA gene sequences of the two strains is 97.7 %. On the basis of the phylogenetic analyses and the distinct phenotypic characteristics, strain CV53T represents a novel species within the genus Bacillus, for which we propose the name Bacillus foraminis sp. nov. The type strain is CV53T (=LMG 23174T=CIP 108889T).
Exophiala crusticola anam. nov. (affinity Herpotrichiellaceae), a novel black yeast from biological soil crusts in the Western United States
Authors: Bates Scott T. , Reddy Gundlapally S. N. , Garcia-Pichel Ferran
Published: November 2006

A novel black yeast-like fungus,Exophiala crusticola, is described based on two closely related isolates from biological soil crust (BSC) samples collected on the Colorado Plateau (Utah) and in the Great Basin desert (Oregon), USA. Their morphology places them in the anamorphic genusExophiala, having affinities to the familyHerpotrichiellaceae(Ascomycota). Phylogenetic analysis of their D1/D2 large subunit nuclear ribosomal RNA (LSU nrRNA) gene sequences suggests that they represent a distinct species. The closest known putative relative toExophiala crusticolaisCapronia coronataSamuels, isolated from decorticated wood in Westland County, New Zealand. The holotype forExophiala crusticolaanam. nov. is UAMH 10686 and the type strain is CP141bT(=ATCC MYA-3639T=CBS 119970T=DSM 16793T). Dark-pigmented fungi appear to constitute an important heterotrophic component of soil crusts andExophiala crusticolarepresents the first description of a dematiaceous fungus isolated from BSCs.
Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave
Authors: Jurado Valme , Gonzalez Juan M. , Laiz Leonila , Saiz-Jimenez Cesareo
Published: November 2006

A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram-negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family ‘Aurantimonadaceae’ (showing 96 % sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16 : 0 and C18 : 1
ω7c. The G+C content of the DNA from strain S21BT was 71.8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T).
Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae
Authors: Greenberg David E. , Porcella Stephen F. , Stock Frida , Wong Alexandra , Conville Patricia S. , Murray Patrick R. , Holland Steven M. , Zelazny Adrian M.
Published: November 2006

A Gram-negative, aerobic, coccobacillus to rod-shaped bacterium was isolated from three patients with chronic granulomatous disease. The organism was subjected to a polyphasic taxonomic study. A multilocus phylogenetic analysis based on the 16S rRNA gene, the internal transcribed spacer (ITS) region and the RecA protein demonstrated that the organism belongs to a new sublineage within the acetic acid bacteria in the familyAcetobacteraceae. Phenotypic features are summarized as follows: the organism grew at an optimum temperature of 35–37 °C and optimum pH of 5.0–6.5. It produced a yellow pigment, oxidized lactate and acetate, the latter weakly, produced little acetic acid from ethanol and could use methanol as a sole carbon source. The two major fatty acids were a straight-chain unsaturated acid (C18 : 1ω7c) and C16 : 0. The DNA base composition was 59.1 mol% G+C. The very weak production of acetic acid from ethanol, the ability to use methanol, the yellow pigmentation and high optimum temperature for growth distinguished this organism from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the bacterium should be classified within a separate genus, for which the nameGranulibacter bethesdensisgen. nov., sp. nov. is proposed. The type strain is CGDNIH1T(=ATCC BAA-1260T=DSM 17861T).
Cryptococcus anemochoreius sp. nov., a novel anamorphic basidiomycetous yeast isolated from the atmosphere in central South Africa
Authors: Pohl Carolina H. , Kock Johan L. F. , van Wyk Pieter W. J. , Albertyn Jacobus
Published: November 2006

A novel yeast strain, CBS 10258T, was isolated from the atmosphere in central South Africa. Sequence analysis of the D1/D2 domain and internal transcribed spacer region of the novel strain indicates that it represents a novel species within theCryptococcus laurentiicomplex. Phylogenetic analyses based on the D1/D2 domain revealed that the novel strain occupies a relatively isolated position within this complex withPapiliotrema bandonii,Cryptococcus perniciosus,Cryptococcus nemorosusandCryptococcussp. CBS 8363 being the closest relatives. However, the novel strain could be distinguished from related species by standard physiological tests including the inability to assimilate rhamnose, methylα-d-glucoside, salicin, lactose, erythritol, ribitol, xylitol, citrate and ethanol. In addition, no extracellular starch production was observed and the isolate was able to grow in the absence of additional vitamins. On the basis of these results, we suggest that the new strain represents a novel species for which the nameCryptococcus anemochoreiussp. nov. is proposed [type strain CBS 10258T(=NRRL Y-27920T)].
Paracoccus sulfuroxidans sp. nov., a sulfur oxidizer from activated sludge
Authors: Liu Xing-Yu , Wang Bao-Jun , Jiang Cheng-Ying , Liu Shuang-Jiang
Published: November 2006

Bacterial strain LW36Twas isolated from activated sludge of a wastewater-treatment bioreactor. Cells of strain LW36Twere Gram-negative coccoids to short rods, 1.0–1.2×0.5 μm in size. Colonies were cream-coloured, smooth and circular. Strain LW36Twas hetero-organotrophic and chemolithotrophic and was able to use reduced sulfur as an energy resource. Growth was observed at 25–36 °C and pH 5–10. The most abundant cellular fatty acid of strain LW36Twas C18 : 1ω7c(64.2 %). The sole respiratory quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.3 mol% (Tm). 16S rRNA gene sequence analysis indicated that strain LW36Twas phylogenetically related to members of the genusParacoccus, with similarities ranging from 92.4 to 94.9 %. Based on these results, it is concluded that strain LW36Trepresents a novel species of the genusParacoccus, for which the nameParacoccus sulfuroxidansis proposed. The type strain is strain LW36T(=CGMCC 1.5364T=JCM 14013T).
Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice
Authors: Tindall Brian J. , Kämpfer Peter , Euzéby Jean P. , Oren Aharon
Published: November 2006

It is now 30 years since the concept of valid publication was introduced into prokaryote systematics in such a way that a system of registration/indexing was integrated. Despite the success of this system and the introduction of the Approved Lists of Bacterial Names, accompanied by a new starting date in prokaryote nomenclature, there is a need to review both the historical aspects and current practices so that the current generation of prokaryote systematists have an up-to-date overview of some of the key elements.
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

INTRODUCTION

Site-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

INTRODUCTION

This 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

INTRODUCTION

This 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.
Bradford Assay
Authors: Harlow Ed , Lane David
Published: November 2006

INTRODUCTION

This assay is used for protein quantitation. It is relatively accurate for most proteins, except for small basic polypeptides such as ribonuclease or lysozyme. It is also hampered by detergent concentrations over ~0.2%.
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

INTRODUCTION

GATEWAY 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.
It's just ducky to be clean: the water repellency and water penetration resistance of swimming mallard Anas platyrhynchos ducklings
Authors: Bakken George S. , Banta Marilyn R. , Higginbotham Clay M. , Lynott Aaron J.
Published: November 2006

Ducklings reared by a hen swim with dry plumage a day or two after hatching, while incubator‐hatched ducklings of the same age may sink and even drown when placed in water. The common interpretation is that wild‐reared chicks receive preen oil from the parent, and this oil makes them more waterproof. Using mallard ducklings Anas platyrhynchos we tested the effect of preen and other oils, as well as hydrophilic or surfactant contaminants, on the water resistance of down. We found that the true cause for the difference between incubator and hen‐reared ducklings is the presence of hydrophilic hatching fluid residues in the down of incubator‐hatched ducklings. Once well rinsed and dried, incubator‐hatched ducklings can swim for over an hour with essentially dry down. Other tests showed that clean down is quite water resistant, and that water resistance was not improved by preen or other oils. Small amounts of preen or other oils had no effect on water repellency or wetting during surface swimming. However, oil decreased the hydraulic pressure needed to penetrate down. Down lacks the stabilizing interlocking structure of adult contour feathers, and small amounts of oil apparently cause barbules to stick together and reduce the effective number of down fibers. Detergent decreases water repellency and increases water retention, and has a more severe effect on oiled down or when applied in combination with oil. The penetration pressure of a clean down coat, 866±154 Pa, could allow static immersion to ca. 8cm before water would saturate the down and increase thermal conductance. Thus, clean ducklings have a 2×–3× safety margin for surface swimming. Saturation increases the thermal conductance of the down coat from 14.3±1.38 W/m2‐°C to 193±25 W/m2‐°C. Thus, water pollution or down contamination causing wetting can significantly increase energy use and the frequency of hypothermia.
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

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

In 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

In 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

A 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

We 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

Accurate 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

We 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

Field‐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.
OBC signal fidelity
Authors: Norris Michael W. , Johnson Marvin L. , Walsh Mat
Published: November 2006

A suite of three tests was performed to characterize the signal fidelity of OBC 4C acquisition systems. The test methodology was to evaluate individual sensor stations by acquiring source lines that were parallel to the in‐line and cross‐line horizontal sensors and source lines that were at 45° to the in‐line and cross‐line sensors. This technique provides constant azimuth gathers with a uniform offset range and removes issues associated with source array directivity.

Characterization of the test data identified the frequency content of the geophone signals and the correlation between the vertical and cross‐line geophones as the most sensitive indicators of signal infidelity. In the former case, stations with questionable signal fidelity exhibited a very reverberatory signal. This signal was most evident on the cross‐line sensor. In the latter case, when normalized cross‐correlation coefficients are computed in a moving window, the cross‐line sensor and the vertical sensor are highly correlated, beginning several hundred milliseconds after the first arrivals.

These characteristics can be exploited to allow stations with questionable signal fidelity to be programmatically identified. One means of identifying questionable stations is to compute the histogram of the instantaneous frequency. The frequency distributions from questionable stations are unambiguously distinguishable from stations that exhibit better signal fidelity. It was noted that signal fidelity appeared as a range, between acceptable and poor. To characterize the signal fidelity of an acquisition system adequately, the number of test samples must be statistically significant.
High levels of variation despite genetic fragmentation in populations of the endangered mountain pygmy‐possum,Burramys parvus, in alpine Australia
Authors: MITROVSKI P. , HEINZE D. A. , BROOME L. , HOFFMANN A. A. , WEEKS A. R.
Published: November 2006

In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy‐possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found thatB. parvuspopulations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation.FSTvalues between populations from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individualB. parvuscan move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas whereB. parvusare found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in otherB. parvuspopulations.
MvfR, a key Pseudomonas aeruginosa pathogenicity LTTR‐class regulatory protein, has dual ligands
Authors: Xiao Gaoping , Déziel Eric , He Jianxin , Lépine François , Lesic Biliana , Castonguay Marie‐Hélène , Milot Sylvain , Tampakaki Anastasia P. , Stachel Scott E. , Rahme Laurence G.
Published: November 2006

MvfR (PqsR), a Pseudomonas aeruginosa LysR‐type transcriptional regulator, plays a critical role in the virulence of this pathogen. MvfR modulates the expression of multiple quorum sensing (QS)‐regulated virulence factors; and the expression of the phnAB and pqsA‐E genes that encode functions mediating 4‐hydroxy‐2‐alkylquinolines (HAQs) signalling compounds biosynthesis, including 3,4‐dihydroxy‐2‐heptylquinoline (PQS) and its precursor 4‐hydroxy‐2‐heptylquinoline (HHQ). PQS enhances the in vitro DNA‐binding affinity of MvfR to the pqsA‐E promoter, to suggest it might function as the in vivo MvfR ligand. Here we identify a novel MvfR ligand, as we show that HHQ binds to the MvfR ligand‐binding‐domain and potentiates MvfR binding to the pqsA‐E promoter leading to transcriptional activation of pqsA‐E genes. We show that HHQ is highly produced in vivo, where it is not fully converted into PQS, and demonstrate that it is required for MvfR‐dependent gene expression and pathogenicity; PQS is fully dispensable, as pqsH– mutant cells, which produce HHQ but completely lack PQS, display normal MvfR‐dependent gene expression and virulence. Conversely, PQS is required for full production of pyocyanin. These results uncover a novel biological role for HHQ; and provide novel insights on MvfR activation that may aid in the development of therapies that prevent or treat P. aeruginosa infections in humans.
Identification of an essential gene responsible for d‐Asp incorporation in the Lactococcus lactis peptidoglycan crossbridge
Authors: Veiga Patrick , Piquet Sandra , Maisons Aurélie , Furlan Sylviane , Courtin Pascal , Chapot‐Chartier Marie‐Pierre , Kulakauskas Saulius
Published: November 2006

Bacteria such as Lactococcus lactis have d‐aspartate (d‐Asp) or its amidated derivative d‐asparagine (d‐Asn), in their peptidoglycan (PG) interpeptide crossbridge. We performed a subtractive genome analysis to identify L. lactis gene yxbA, orthologues of which being present only in bacteria containing d‐amino acids in their PG crossbridge, but absent from those that instead insert l‐amino acids or glycine. Inactivation of yxbA required a complementing Streptococcus pneumoniae murMN genes, which express enzymes that incorporate l‐Ser‐l‐Ala or l‐Ala‐l‐Ala in the PG crossbridge. Our results show that (i) yxbA encodes d‐Asp ligase responsible for incorporation of d‐Asp in the PG crossbridge, and we therefore renamed it as aslA, (ii) it is an essential gene, which makes its product a potential target for specific antimicrobials, (iii) the absence of d‐Asp may be complemented by l‐Ser‐l‐Ala or l‐Ala‐l‐Ala in the L. lactis PG, indicating that the PG synthesis machinery is not selective for the side‐chain residues, and (iv) lactococcal strains having l‐amino acids in their PG crossbridge display defects in cell wall integrity, but are able to efficiently anchor cell wall proteins, indicating relative flexibility of lactococcal transpeptidation reactions with respect to changes in PG side‐chain composition.
Anisohydric but isohydrodynamic: seasonally constant plant water potential gradient explained by a stomatal control mechanism incorporating variable plant hydraulic conductance
Authors: FRANKS PETER J. , DRAKE PAUL L. , FROEND RAY H.
Published: November 2006

Isohydric and anisohydric regulations of plant water status have been observed over several decades of field, glasshouse and laboratory studies, yet the functional significance and mechanism of both remain obscure. We studied the seasonal trends in plant water status and hydraulic properties in a natural stand of Eucalyptus gomphocephala through cycles of varying environmental moisture (rainfall, groundwater depth, evaporative demand) in order to test for isohydry and to provide physiological information for the mechanistic interpretation of seasonal trends in plant water status. Over a 16 month period of monitoring, spanning two summers, midday leaf water potential (Ψleaf) correlated with predawn Ψleaf, which was correlated with water table depth below ground level, which in turn was correlated with total monthly rainfall. Eucalyptus gomphocephala was therefore not seasonally isohydric. Despite strong stomatal down‐regulation of transpiration rate in response to increasing evaporative demand, this was insufficient to prevent midday Ψleaf from falling to levels below −2 MPa in the driest month, well into the region likely to induce xylem air embolisms, based on xylem vulnerability curves obtained in the study. However, even though midday Ψleaf varied by over 1.2 MPa across seasons, the hydrodynamic (transpiration‐induced) water potential gradient from roots to shoots (ΔΨplant), measured as the difference between predawn and midday Ψleaf, was relatively constant across seasons, averaging 0.67 MPa. This unusual pattern of hydraulic regulation, referred to here as isohydrodynamic, is explained by a hydromechanical stomatal control model where plant hydraulic conductance is dependent on transpiration rate.
Decreased Expression of VEGF‐A in Rat Experimental Autoimmune Encephalomyelitis and in Cerebrospinal Fluid Mononuclear Cells from Patients with Multiple Sclerosis
Authors: Tham E. , Gielen A. W. , Khademi M. , Martin C. , Piehl F.
Published: November 2006

Vascular endothelial growth factor A (VEGF‐A) stimulates angiogenesis, but is also pro‐inflammatory and plays an important role in the development of neurological disease, where it can have both attenuating and exacerbating effects. VEGF‐B, a related molecule, is highly expressed in the central nervous system and seems to be important in neurological injury. A few studies have indicated that VEGF‐A may play a role in the pathogenesis of multiple sclerosis (MS), but the role of VEGF‐B has not been studied. We have studied the expression of VEGF‐A, ‐B and their receptors by mRNA in situ hybridization, immunohistochemistry and real‐time PCR in spinal cord from LEW rats with experimental autoimmune encephalomyelitis (EAE) and in cerebrospinal fluid (CSF) and blood samples from MS patients. Whereas VEGF‐A is downregulated in glia in EAE, the infiltrating inflammatory cells are positive for VEGF‐A. Expression of VEGF‐B and the VEGF receptors is unaltered. In addition, the levels of VEGF‐A mRNA in monocytes in CSF are lower in MS patients compared with controls. These results demonstrate a complex regulation of VEGF‐A during neuroinflammation and suggest that VEGF‐B is not involved in the pathogenesis of MS.
Impact of thrombocytosis and C‐reactive protein elevation on the prognosis for patients with renal cell carcinoma
Authors: ITO KEIICHI , ASANO TOMOHIKO , YOSHII HIDEHIKO , SATOH AKINORI , SUMITOMO MAKOTO , HAYAKAWA MASAMICHI
Published: November 2006

Aim: C‐reactive protein (CRP) elevation is reportedly a prognostic factor in patients with renal cell carcinoma (RCC). Thrombocytosis has recently been reported also to be a prognostic factor in RCC and, like CRP, to be related to inflammatory cytokines such as interleukin‐6. The aim of this study was to evaluate the importance of both thrombocytosis and CRP elevation in tumor recurrence and prognosis for patients with RCC.

Methods: The clinical records of 178 patients who underwent radical nephrectomy were reviewed. Thrombocytosis was defined as a platelet count ≥350 000/mm3, and CRP elevation was defined as a CRP level ≥1.0 mg/dL. Disease‐free survival and cause‐specific survival rates were calculated. Independent predictors for recurrence and prognosis were determined.

Results: Patients with thrombocytosis and patients with elevated CRP levels had significantly higher pathological T stage, clinical stage, tumor size, histological grade, and percentage of microvascular invasion than did patients without THC and patients with CRP levels <1.0 mg/dL, respectively. There was a significant correlation between platelet counts and CRP levels. Multivariate analysis showed that distant metastasis, tumor size, grade 3 components, and CRP elevation were independent predictors for prognosis but thrombocytosis was not. In N0M0 RCC patients, tumor size, microvascular invasion, and CRP elevation were independent predictors for recurrence. CRP elevation and tumor size were independent predictors for prognosis.

Conclusions: Platelet count and CRP level are strongly correlated in patients with RCC, but only CRP elevation is an independent predictor for recurrence and prognosis.
Gastrointestinal stromal tumor in ileal neobladder
Authors: JOUNG JAE YOUNG , KANG DONG GOO , CHOI HYUCK‐JAE , PARK WEON SEO , SEO HO KYUNG , CHUNG JIN SOO , LEE KANG HYUN
Published: November 2006

Abstract  Gastrointestinal stromal tumor (GIST) is a recently described mesenchymal tumor that can develop in any portion of the gastrointestinal tract. The occurrence of a GIST in the urinary tract is rare, but GIST can present as tumor of the urinary tract or invade the urinary tract. This is the first reported case of GIST in the ileal neobladder, which presented as a submucosal tumor. The patient underwent an open exploration and partial resection of the neobladder pouch.
Development of multiple calculi in the duplex system ureterocele
Authors: NAKANE AKIHIRO , HAYASHI YUTARO , KOJIMA YOSHIYUKI , MIZUNO KENTARO , KUROKAWA SATOSHI , KOHRI KENJIRO
Published: November 2006

Abstract  A 61‐year‐old man presented complaining of pollakisuria and nocturia. A plain radiograph of his kidney, ureter and bladder and intravenous urography revealed numerous calculi in the upper kidney of his left renal pelvis and ureterocele. A transurethral incision of ureterocele (TUI‐ureterocele) and extracorporeal shock wave lithotripsy were performed. On TUI‐ureterocele, the many calculi were found to be almost the same size and spherical in form. The postoperative clinical course was uneventful.
Laparoscopic versus open orchiopexy in the management of abdominal testis: A descriptive study
Authors: ABOLYOSR AHMAD
Published: November 2006

Aims: Treatment of patients with abdominal non‐palpable testis (NPT) is still controversial among pediatric urologists. This is a prospective randomized comparative study between open and laparoscopic orchiopexy for management of abdominal testis. The aim of this study was to evaluate the success rate and morbidity of both approaches.

Methods: Eighty‐two patients with a mean age of 5.3 years were evaluated by laparoscopy for 87 NPT. Patients with viable abdominal testes were randomly treated with either open or laparoscopic orchiopexy procedures.

Results: On laparoscopy, 75 viable abdominal testes were found. According to location: 41 (47.1%) testes were high abdominal, 27 (31%) testes were low abdominal and 7 (8%) testes were peeping from the internal ring. Laparoscopic first stage Fowler–Stephens orchiopexy was done initially for those with high abdominal testes. For further management, all patients were divided randomly into open (36 cases) and laparoscopic (39 cases) groups where primary (with spermatic vessel preservation) or second stage Fowler‐Stephens orchiopexy was done. Statistical analysis was done using Student’s t‐test. Laparoscopic procedures showed significant less morbidity than the open counterparts. Follow up ranged from 9 to 31 months and included evaluation of testicular site and size. All testes were located satisfactorily inside the scrotum. Five cases of testicular atrophy were encountered (three and two testes with open and laparoscopic second stage Fowler‐Stephens orchiopexy respectively) after 1 year follow up.

Conclusion: Results of open versus laparoscopic orchiopexy procedures (primary or staged) are fairly comparable. However, laparoscopy provides significantly less morbidity.