bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of an Uptake Hydrogenase Required for Hydrogen-Dependent Reduction of Fe(III) and Other Electron Acceptors by
Geobacter sulfurreducens
Authors: Coppi Maddalena V. , O'Neil Regina A. , Lovley Derek R. 
Published: May 2004

ABSTRACT

Geobacter sulfurreducens
, a representative of the family
Geobacteraceae
that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the
G. sulfurreducens
genome revealed two operons,
hya
and
hyb
, which appeared to encode periplasmically oriented respiratory uptake hydrogenases. In order to assess the roles of these two enzymes in hydrogen-dependent growth, Hya- and Hyb-deficient mutants were generated by gene replacement. Hyb was found to be required for hydrogen-dependent reduction of Fe(III), anthraquinone-2,6-disulfonate, and fumarate by resting cell suspensions and to be essential for growth with hydrogen and these three electron acceptors. Hya, in contrast, was not. These findings suggest that Hyb is an essential respiratory hydrogenase in
G. sulfurreducens
.
Regulation of Photosynthesis Genes in
Rubrivivax gelatinosus
: Transcription Factor PpsR Is Involved in both Negative and Positive Control
Authors: Steunou Anne-Soisig , Astier Chantal , Ouchane Soufian 
Published: May 2004

ABSTRACT

Induction of biosynthesis of the photosystem in anoxygenic photosynthetic bacteria occurs when the oxygen concentration drops. Control of this induction takes place primarily at the transcriptional level, with photosynthesis genes expressed preferentially under anaerobic conditions. Here, we report analysis of the transcriptional control of two photosynthesis promoters,
pucBA
and
crtI
, by the PpsR factor in
Rubrivivax gelatinosus
. This was accomplished by analyzing the photosystem production in the wild type and in the PPSRK (
ppsR
::Km) mutant grown under anaerobic and semiaerobic conditions and by assessing the β-galactosidase activity of
lacZ
transcriptionally fused to promoters possessing the putative PpsR-binding consensus sequences. It was found that under semiaerobic conditions, inactivation of the
ppsR
gene resulted in overproduction of carotenoid and bacteriochlorophyll pigments, while the production of LH2 was drastically reduced. The β-galactosidase activity showed that, in contrast to what has been found previously for
Rhodobacter
species, PpsR acts in
R. gelatinosus
as an aerobic repressor of the
crtI
gene while it acts as an activator for the expression of
pucBA
. Inspection of the putative PpsR-binding consensus sequences revealed significant differences that may explain the different levels of expression of the two genes studied.
Involvement of the C-Terminal Extension of the α Polypeptide and of the PucC Protein in LH2 Complex Biosynthesis inRubrivivax gelatinosus
Authors: Steunou Anne-Soisig , Ouchane Soufian , Reiss-Husson Françoise , Astier Chantal 
Published: May 2004

ABSTRACTThe facultative phototrophic nonsulfur bacteriumRubrivivax gelatinosusexhibits several differences from other species of purple bacteria in the organization of its photosynthetic genes. In particular, thepucoperon contains only thepucBandpucAgenes encoding the β and α polypeptides of the light-harvesting 2 (LH2) complex. Downstream of thepucBAoperon is thepucCgene in the opposite transcriptional orientation. The transcription ofpucBAandpucChas been studied. NopucCtranscript was detected either by Northern blotting or by reverse transcription-PCR analysis. The initiation site ofpucBAtranscription was determined by primer extension, and Northern blot analysis revealed the presence of two transcripts of 0.8 and 0.65 kb. The half-lives of both transcripts are longer in cells grown semiaerobically than in photosynthetically grown cells, and the small transcript is the less stable. It was reported that the α polypeptide, encoded by thepucAgene, presents a C-terminal extension which is not essential for LH2 function in vitro. The biological role of this alanine- and proline-rich C-terminal extension in vivo has been investigated. Two mutants with C-terminal deletions of 13 and 18 residues have been constructed. Both present the twopucBAtranscripts, while their phenotypes are, respectively, LH2+and LH2−, suggesting that a minimal length of the C-terminal extension is required for LH2 biogenesis. Another important factor involved in the LH2 biogenesis is the PucC protein. To gain insight into the function of this protein inR. gelatinosus, we constructed and characterized a PucC mutant. The mutant is devoid of LH2 complex under semiaerobiosis but still produces a small amount of these antennae under photosynthetic growth conditions. This conditional phenotype suggests the involvement of another factor in LH2 biogenesis.
Genome-Wide Analysis of Lipoprotein Expression in
Escherichia coli
MG1655
Authors: Brokx Stephen J. , Ellison Michael , Locke Troy , Bottorff Drell , Frost Laura , Weiner Joel H. 
Published: May 2004

ABSTRACT

To
gain insight into the cell envelope of
Escherichia coli
grown
under aerobic and anaerobic conditions, lipoproteins were examined by
using functional genomics. The mRNA expression levels of each of these
genes under three growth conditions—aerobic, anaerobic, and
anaerobic with nitrate—were examined by using both Affymetrix
GeneChip
E. coli
antisense genome arrays and
real-time PCR (RT-PCR). Many genes showed significant changes in
expression level. The RT-PCR results were in very good
agreement with the microarray data. The results of this study represent
the first insights into the possible roles of unknown lipoprotein genes
and broaden our understanding of the composition of the cell envelope
under different environmental conditions. Additionally, these data
serve as a test set for the refinement of high-throughput bioinformatic
and global gene expression
methods.
Unique Morphology and Focal Adhesion Development of Valvular Endothelial Cells in Static and Fluid Flow Environments
Authors: Butcher Jonathan T. , Penrod Andrea M. , García Andrés J. , Nerem Robert M. 
Published: May 2004

Background—The influence of mechanical forces on cell function has been well documented for many different cell types. Endothelial cells native to the aortic valve may play an important role in mediating tissue responses to the complex fluid environment, and may therefore respond to fluid flow in a different manner than more characterized vascular endothelial cells.Methods and Results—Porcine endothelial cells of aortic and aortic valvular origin were subjected to 20 dynes/cm2steady laminar shear stress for up to 48 hours, with static cultures serving as controls. The aortic valve endothelial cells were observed to align perpendicular to flow, in direct contrast to the aortic endothelial cells, which aligned parallel to flow. Focal adhesion complexes reorganized prominently at the ends of the long axis of aligned cells. Valvular endothelial cell alignment was dependent on Rho-kinase signaling, whereas vascular endothelial cell alignment was dependent on both Rho-kinase and phosphatidylinositol 3-kinase signal pathways.Conclusions—These differences in response to mechanical forces suggest a unique phenotype of valvular endothelial cells not mimicked by vascular endothelial cells, and could have implications for cardiovascular cell biology and cell-source considerations for tissue-engineered valvular substitutes.
Analysis of Apolipoprotein A5, C3, and Plasma Triglyceride Concentrations in Genetically Engineered Mice
Authors: Baroukh Nadine , Bauge Eric , Akiyama Jennifer , Chang Jessie , Afzal Veena , Fruchart Jean-Charles , Rubin Edward M. , Fruchart-Najib Jamila , Pennacchio Len A. 
Published: May 2004

Objective—Both the apolipoprotein A5 and C3 genes have repeatedly been shown to play an important role in determining plasma triglyceride concentrations in humans and mice. In mice, transgenic and knockout experiments indicate that plasma triglyceride levels are strongly altered by changes in the expression of either of these 2 genes. In humans, common polymorphisms in both genes have also been associated with plasma triglyceride concentrations. These similar findings raised the issue of the relationship between these 2 genes and altered triglycerides.Methods and Results—To address this issue, we generated independent lines of mice that either overexpressed (“double transgenic”) or completely lacked (“double knockout”) both apolipoprotein genes. We report that both “double transgenic” and “double knockout” mice display normal triglyceride concentrations compared with overexpression or deletion of either gene alone. Furthermore, we find that human ApoAV plasma protein levels in the “double transgenic” mice are ≈500-fold lower than human ApoCIII levels, supporting ApoAV as a potent triglyceride modulator despite its low concentration.Conclusions—Together, these data support thatAPOA5andAPOC3independently influence plasma triglyceride concentrations but in an opposing manner.
Results of the MRC pilot study show autografting for younger patients with chronic lymphocytic leukemia is safe and achieves a high percentage of molecular responses
Authors: Milligan Donald W. , Fernandes Savio , Dasgupta Ranjit , Davies Faith E. , Matutes Estella , Fegan Christopher D. , McConkey Christopher , Child J. Anthony , Cunningham David , Morgan Gareth J. , Catovsky Daniel ,   for the National Cancer Research Institute (NCRI) Haematological Studies Group
Published: May 2004

Abstract
We have assessed autologous stem cell transplantation after treatment with fludarabine in previously untreated patients with chronic lymphocytic leukemia (CLL). This study is the first to enroll previously untreated patients and follow them prospectively. The initial response rate to fludarabine was 82% (94 of 115 patients). Stem cell mobilization was attempted in 88 patients and was successful in 59 (67%). Overall 65 of 115 patients (56%) entered into the study proceeded to autologous transplantation. The early transplant-related mortality rate was 1.5% (1 of 65 patients). The number of patients in complete remission after transplantation increased from 37% (24 of 65) to 74% (48 of 65), and 26 of 41 patients (63%) who were not in complete remission at the time of their transplantation achieved a complete remission after transplantation. The 5-year overall and disease-free survival rates from transplantation were 77.5% (CI, 57.2%-97.8%) and 51.5% (CI, 33.2%-69.8%), respectively. None of the variables examined at study entry were found to be predictors of either overall or disease-free survival. Sixteen of 20 evaluable patients achieved a molecular remission on a polymerase chain reaction (PCR) for immunoglobulin heavy-chain gene rearrangements in the first 6 months following transplantation. Detectable molecular disease by PCR was highly predictive of disease recurrence. It is of concern that 5 of 65 (8%) patients developed posttransplant acute myeloid leukemia/myelodysplastic syndrome. (Blood. 2005;105:397-404)
Comparing morbidity and mortality of HLA-matched unrelated donor hematopoietic cell transplantation after nonmyeloablative and myeloablative conditioning: influence of pretransplantation comorbidities
Authors: Sorror Mohamed L. , Maris Michael B. , Storer Barry , Sandmaier Brenda M. , Diaconescu Razvan , Flowers Christopher , Maloney David G. , Storb Rainer 
Published: May 2004

AbstractWe have carried out HLA-matched unrelated donor hematopoietic cell transplantation (HCT) after nonmyeloablative conditioning in patients with hematologic malignancies who were ineligible for conventional transplantations because of age, comorbidities, or both. The nonmyeloablative regimen consisted of 90 mg/m2 fludarabine and 2 Gy total body irradiation given before and mycophenolate mofetil and cyclosporine given after HCT. This report compares, retrospectively, morbidity and mortality among 60 consecutive patients given nonmyeloablative conditioning (nonablative patients) to those among 74 concurrent and consecutive patients given myeloablative conditioning (ablative patients) before unrelated HCT. The Charlson Comorbidity Index was used to assess pretransplantation comorbidities. Even though nonablative patients had significantly higher pretransplantation comorbidity scores, were older, and had more often failed preceding ablative transplantations and cytotoxic therapies, they experienced fewer grades III to IV toxicities than ablative patients. Further, the incidence of grades III to IV acute graft-versus-host disease (GVHD) was significantly lower in nonablative patients. Both patient groups had comparable 1-year probabilities of chronic GVHD. The 1-year nonrelapse mortality rate was 20% in nonablative patients compared to 32% in ablative patients (hazard ratio = 1.4). After adjustment for pretransplantation differences between the 2 patient groups, the hazard ratio was 3.0 (P = .04). Multivariate analyses showed higher pretransplantation comorbidity scores to result in increased toxicity and mortality.
P-selectin glycoprotein ligand-1 is required for the development of cutaneous vasculitis induced by immune complex deposition
Authors: Yanaba Koichi , Komura Kazuhiro , Horikawa Mayuka , Matsushita Yukiyo , Takehara Kazuhiko , Sato Shinichi 
Published: May 2004

AbstractImmune complex (IC)-induced tissue injury is mediated by inflammatory cell infiltration that is highly regulated by various adhesion molecules. To assess the contribution of P-selectin glycoprotein ligand-1 (PSGL-1) and selectins in the pathogenetic process, the cutaneous reverse-passive Arthus reaction was examined in mice treated with monoclonal antibodies (mAb) to PSGL-1 or P- and/or E-selectin. Edema and hemorrhage were significantly reduced in mice treated with anti-P-selectin mAb compared with control mice while they were not inhibited in mice treated with anti-E-selectin mAb. It is remarkable that blocking PSGL-1 by mAb resulted in significant, further reduction in edema and hemorrhage compared with blocking anti-P- or anti-E-selectin. However, blockade of E- and P-selectins exhibited more significant reduction relative to PSGL-1 blockade. The inhibited edema and hemorrhage paralleled reduced infiltration of neutrophils and mast cells. Reduced infiltration of neutrophils and mast cells was observed in the peritoneal Arthus reaction and was associated with the decreased production of tumor necrosis factor α and interleukin-6. The results of this study indicate that PSGL-1 contributes to the Arthus reaction mainly as a ligand of P-selectin and partly as a ligand of E- and/or L-selectin by regulating neutrophil and mast-cell recruitment and that PSGL-1 would be a therapeutic target for human IC-mediated diseases.
The cerebroprotective effects of pentoxifylline and aprotinin during cardiopulmonary bypass in dogs
Authors: Durgut Kadir , Hosgor Kemalettin , Gormus Niyazi , Ozergin Ufuk , Solak Hasan 
Published: May 2004

Objective: The purpose of this study was to investigate the cerebroprotective effects of pentoxifylline (PNX) and aprotinin in dogs using cardiopulmonary bypass (CPB). Materials and methods: Eighteen clinically healthy dogs were divided into three groups: Group 1 (control, n = 6), Group 2 (PNX, n = 6), and Group 3 (aprotinin, n = 6). PNX was administered at a dose of 300 mg/day in Group 2 three days before the operation and during the operation. Half a million IU aprotinin were added to the prime solution and 500 000 IU were transfused via a central venous jugular catheter preoperatively in Group 3. Blood samples were taken from the central jugular vein before and after CPB and interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and S100β protein were measured. Gliosis was investigated histopathologically in cerebral cortex biopsy samples under light microscopy. Results: The preoperative results of IL-6, TNF-α, and S100β protein values were found to be significantly higher ( p < 0.001) when compared with postoperative values. This significant difference was observed in the same parameters between Groups 1 and 2, and 1 and 3 ( p < 0.001). There was no significant difference between Groups 2 and 3. Comparison between pre- and postoperative levels of IL-6 and TNF-α for Group 2 and Group 3 revealed statistically significant differences ( p < 0.001), whereas S100β protein levels did not. Histopathological examinations showed significant differences between the control group and PNX and aprotinin, and between aprotinin and PNX groups ( p < 0.001). Conclusion: PNX and aprotinin might be useful in order to reduce postoperative cerebral damage in patients undergoing cardiac surgery with CPB.
In vitro assessment of the vacuum-assisted venous drainage (VAVD) system: risks and benefits
Authors: Fiorucci Angelo , Gerometta Pier Silvio , DeVecchi Massimo , Guzman Cesare , Costantino Maria Laura , Arena Vincenzo 
Published: May 2004

The vacuum-assisted venous drainage (VAVD) technique has been introduced with the utilization of small-bore venous cannulae to facilitate minimally invasive cardiac surgery and it has found widespread use for traditional surgical approaches. Although this technique was devised to increase venous return, it may cause a reduction of blood flow through a negative pressure effect on the raceway tubing. In this study, the potential of this system to increase the venous drainage was evaluated in vitro together with the measurements of delivered blood flow. The VAVD has been tested in association with normal gravitational drainage or as a substitute for gravitational drainage. The flow was calculated by multiplying the pump rate by the stroke volume and it was simultaneously measured by a magnetic flowmeter. A steady state maximal flow was defined as the flow that could maintain a constant level of fluid in the graduated canister used to act as the patient. Based on our results, the VAVD can increase venous drainage by as much as 50% above baseline levels. However, delivered blood flow may be overestimated, particularly when negative pressure values >60 mmHg are employed. A 100 mmHg negative pressure may produce an overestimate of blood flow as great as 54% of the measured flow.
Differential Roles for Cholecystokinin A Receptors in Energy Balance in Rats and Mice
Authors: Bi Sheng , Scott Karen A. , Kopin Alan S. , Moran Timothy H. 
Published: May 2004

AbstractAlthough cholecystokinin A (CCK-A) receptors (CCK-AR) mediate the feeding inhibitory actions of CCK in both rats and mice, the absence of CCK-AR results in species-specific phenotypes. The lack of CCK-AR in Otsuka Long-Evans Tokushima fatty (OLETF) rats results in hyperphagia and obesity. We have suggested that demonstrated increases in meal size and elevated levels of dorsomedial hypothalamic (DMH) neuropeptide Y (NPY) gene expression may contribute to this phenotype. In contrast to OLETF rats, CCK-AR−/− mice have normal total daily food intake and do not develop obesity. To assess the basis underlying the different phenotypes in rats and mice lacking CCK-AR, we characterized meal patterns in CCK-AR−/− mice and determined whether CCK-AR−/− mice exhibited an alteration in DMH NPY gene expression. We demonstrate that although CCK-AR−/− mice show a similar dysregulation in meal size as OLETF rats, they do not have an elevation in DMH NPY mRNA expression levels. In fact, intact mice have no CCK-AR in the DMH. Furthermore, in intact rats, NPY and CCK-AR are colocalized in DMH neurons, and parenchymal injection of CCK into the DMH reduces food intake and down-regulates DMH NPY mRNA expression. These results suggest that although CCK-AR plays a role in the mediation of CCK actions in the control of meal size in both rats and mice, CCK-AR seems to contribute to modulating DMH NPY levels only in rats. The deficit in CCK’s action in the control of DMH NPY gene expression may play a major role in the obese phenotype in OLETF rats.
Singular vectors for moisture‐measuring norms
Authors: Errico Ronald M. , Raeder Kevin , Ehrendorfer Martin 
Published: May 2004

AbstractSingular vectors (SVs) are determined for 12‐hour forecasts using a regional mesoscale model. Norms used as constraints at the initial time include the usual total‐energy norm, a related moisture‐measuring norm, and norms using weights equal to the inverse of estimated variances of initial‐condition uncertainty. Norms used to measure perturbations at the end of the forecast include either the total energy or mean‐squared perturbed rate of precipitation. Four synoptic cases are examined. The locations of the four leading SVs for each pair of norms considered differ widely for some cases but are collocated for others. The initial vertical structures of the SVs are also sensitive to norms and cases. Most importantly, both final‐time norms are sensitive to initial perturbations of both moisture and dynamic fields. For some cases, similar structures are optimal for maximizing both perturbation energy and precipitation. When the initial moisture SVs are introduced in the nonlinear forecast model with perturbation magnitudes of the size of initial‐condition uncertainties, many of the results remarkably match corresponding tangent‐linear estimates. In other nonlinear experiments, however, the matches are poor in terms of either correlation or magnitude measures, or both, indicating that the tangent‐linear results are sometimes informative but at other times can be misleading. For the present study the key reported tangent‐linear model results were, therefore, all confirmed in the nonlinear context. An implication of the results is that as much attention must be paid to moisture analysis as to analysis of other fields, and that ensemble forecast techniques should consider initial moisture uncertainty. Copyright © 2004 Royal Meteorological Society.
Organization of near‐inertial energy by an eddy field
Authors: Klein Patrice , Smith Stefan Llewellyn , Lapeyre Guillaume 
Published: May 2004

AbstractWe propose an analytical solution for the evolution of the spatial variability of wind‐forced inertial energy in the presence of an oceanic mesoscale eddy field. The solution requires knowledge of only the stream function of the eddy field and the Rossby radii of the normal modes associated with the near‐inertial oscillations. It also shows that, when the vorticity spectrum slope is shallower than k−4, inertial energy is trapped inside structures in which the Laplacian of the vorticity field is positive and whose size matches a critical length‐scale that increases with time. Numerical simulations using different models, including a fully nonlinear shallow‐water model, confirm the analytical results. Copyright © 2004 Royal Meteorological Society.
Application of SSM/I satellite data to a hurricane simulation
Authors: Chen Shu‐hua , Vandenberghe Francois , Petty Grant W. , Bresch James F. 
Published: May 2004

AbstractThe impact of Special Sensor Microwave/Imager (SSM/I) data on simulations of hurricane Danny is assessed. The assimilation of SSM/I data is found to increase the atmospheric moisture content over the Gulf of Mexico, strengthen the low‐level cyclonic circulation, shorten the model spin‐up time, and significantly improve the simulation of the storm's intensity. Two different approaches for assimilating SSM/I data, namely assimilating retrieved products and assimilating raw measurements, are further compared. The data‐assimilation analyses from these two approaches give different moisture distributions in both the horizontal and vertical directions in the storm's vicinity, which may potentially affect the simulated storm's development; however, the simulated storm intensities are considered comparable for the Danny case. From sensitivity tests performed in this study, it is also found that the choice of the observational error variances could be potentially important to the model simulations. Copyright © 2004 Royal Meteorological Society.