bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters
Authors: Feng Youjun , Cronan John E. 
Published: January 2011

SummaryTwo transcriptional regulators, the FadR activator and the FabR repressor, control biosynthesis of unsaturated fatty acids in Escherichia coli. FabR represses expression of the two genes, fabA and fabB, required for unsaturated fatty acid synthesis and has been reported to require the presence of an unsaturated thioester (of either acyl carrier protein or CoA) in order to bind the fabA and fabB promoters in vitro. We report in vivo experiments in which unsaturated fatty acid synthesis was blocked in the absence of exogenous unsaturated fatty acids in a ΔfadR strain and found that the rates of transcription of fabA and fabB were unaffected by the lack of unsaturated thioesters. To examine the discrepancy between our in vivo results and the prior in vitro results we obtained active, natively folded forms of the E. coli and Vibrio cholerae FabRs by use of an in vitro transcription–translation system. We report that FabR bound the intact promoter regions of both fabA and fabB in the absence of unsaturated acyl thioesters, but bound the two promoters differently. Native FabR bound the fabA promoter region provided that the canonical FabR binding site is extended by inclusion of flanking sequences that overlap the neighbouring FadR binding site. In contrast, although binding to the fabB operator also required a flanking sequence, a non‐specific sequence could suffice. However, unsaturated thioesters did allow FabR binding to the minimal FabR operator sites of both promoters which otherwise were not bound. Thus unsaturated thioester ligands were not essential for FabR/target DNA interaction, but acted to enhance binding. The gel mobility shift data plus in vivo expression data indicate that despite the remarkably similar arrangements of promoter elements, FadR predominately regulates fabA expression whereas FabR is the dominant regulator of fabB expression. We also report that E. coli fabR expression is not autoregulated. Complementation, qRT‐PCR and fatty acid composition analyses demonstrated that V. cholerae FabR was a functional repressor of unsaturated fatty acid synthesis. However, in contrast to E. coli, gel mobility shift assays indicated that neither E. coli nor V. cholerae FabRs bound the V. cholerae fabB promoter, although both proteins efficiently bound the V. cholerae fabA promoter. This asymmetry was shown to be due to the lack of a FabR binding site within the V. cholerae fabB promoter region.
Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources
Authors: Mulley G. , White J. P. , Karunakaran R. , Prell J. , Bourdes A. , Bunnewell S. , Hill L. , Poole P. S. 
Published: January 2011

SummaryMutation of gltB (encoding glutamate oxoglutarate amidotransferase or GOGAT) in RU2307 increased the intracellular Gln : Glu ratio and inhibited amino acid transport via Aap and Bra. The mechanism probably involves global post‐translational inhibition independent of Ntr. Transport was separately restored by increased gene expression of Aap or heterologous transporters. Likewise, second site suppressor mutations in the RNA chaperone Hfq elevated transport by Aap and Bra by increasing mRNA levels. Microarrays showed Hfq regulates 34 ABC transporter genes, including aap, bra and opp. The genes coding for integral membrane proteins and ABC subunits aapQMP braDEFGC were more strongly elevated in the hfq mutants than solute‐binding proteins (aapJ braC). aapQMP and braDEFG are immediately downstream of stem‐loops, indicating Hfq attenuates downstream translation and stability of mRNA, explaining differential expression of ABC genes. RU2307 nodulated peas and bacteria grew down infection threads, but bacteroid development was arrested and N2 was not fixed. This probably results from an inability to synthesize or transport amino acids. However, GOGAT and GOGAT/AldA double mutants carrying suppressor mutations that increased amino acid uptake fixed N2 on pea plants. Thus de novo ammonium assimilation into amino acids is unnecessary in bacteroids demonstrating sufficient amino acids are supplied by plants.
δ13C of leaf‐respired CO2 reflects intrinsic water‐use efficiency in barley
Authors: BARBOUR MARGARET M. , TCHERKEZ GUILLAUME , BICKFORD CHRISTOPHER P. , MAUVE CAROLINE , LAMOTHE MARLENE , SINTON SARAH , BROWN HAMISH 
Published: January 2011

ABSTRACTLeaf intrinsic water‐use efficiency (WUE), the ratio of photosynthetic rate to stomatal conductance (A/gs), is a key plant trait linking terrestrial carbon and water cycles. A rapid, integrative proxy for A/gs is of benefit to crop breeding programmes aiming to improve WUE, but also for ecologists interested in plant carbon‐water balance in natural systems. We hypothesize that the carbon isotope composition of leaf‐respired CO2 (δ13CRl), two hours after leaves are transferred to the dark, records photosynthetic carbon isotope discrimination and so provides a proxy for A/gs. To test this hypothesis, δ13CRl was measured in four barley cultivars grown in the field at two levels of water availability and compared to leaf‐level gas exchange (the ratio of leaf intercellular to ambient CO2 partial pressure, Ci/Ca, and A/gs). Leaf‐respired CO2 was more 13C‐depleted in plants grown at higher water availability, varied between days as environmental conditions changed, and was significantly different between cultivars. A strong relationship between δ13CRl and δ13C of sucrose was observed. δ13CRl was converted into apparent photosynthetic discrimination (Δ13CRl) revealing strong relationships between Δ13CRl and Ci/Ca and A/gs during the vegetative stage of growth. We therefore conclude that δ13CRl may provide a rapid, integrative proxy for A/gs in barley.
Ultra‐small TiO2 nanoparticles disrupt microtubular networks in Arabidopsis thaliana
Authors: WANG SONGHU , KUREPA JASMINA , SMALLE JAN A. 
Published: January 2011

ABSTRACTIn spite of the mounting concerns, current understanding of the extent and mechanisms of phytotoxicity of manufactured nanomaterials remains limited. Here we show that in Arabidopsis thaliana, ultra‐small anatase TiO2 nanoparticles cause reorganization and elimination of microtubules followed by the accelerated and 26S proteasome‐dependent degradation of tubulin monomers. Similar to other microtubule‐disrupting agents, TiO2 nanoparticles induce isotropic growth of root cells. Because microtubules are essential for the normal function of all eukaryotic cells, these results reveal a potentially important consequence of environmental pollution by this widely used nanomaterial.
Changes to the proteome and targeted metabolites of xylem sap in Brassica oleracea in response to salt stress
Authors: FERNANDEZ‐GARCIA N. , HERNANDEZ M. , CASADO‐VELA J. , BRU R. , ELORTZA F. , HEDDEN P. , OLMOS E. 
Published: January 2011

ABSTRACTRoot‐to‐shoot signalling via xylem sap is an important mechanism by which plants respond to stress. This signalling could be mediated by alteration in the concentrations of inorganic and/or organic molecules.The effect of salt stress on the contents of xylem sap in Brassica olarecea has been analysed by mass spectrometry in order to quantify these changes. Subcellular location of arabinogalactan proteins (AGPs) by immunogold labelling and peroxidase isozymes was also analysed by isoelectrofocusing.The xylem sap metabolome analysis demonstrated the presence of many organic compounds such as sugars, organic acids and amino acids. Of these, amino acid concentrations, particularly that of glutamine, the major amino acid in the sap, were substantially reduced by salt stress. The xylem sap proteome analysis demonstrated the accumulation of enzymes involved in xylem differentiation and lignification, such as cystein proteinases, acid peroxidases, and a putative hydroxycinnamoyl‐CoA:shikimate hydroxycinnamoyl transferase under salt stress. The peroxidase isozyme pattern showed that salt stress induced a high accumulation of an acid isoform.These results suggest that xylem differentiation and lignification is induced by salt stress. The combination of different methods to analyse the xylem sap composition provides new insights into mechanisms in plant development and signalling under salt stress.
Bacterial screening by flow cytometry offers potential for extension of platelet storage: results of 14 months of active surveillance
Authors: Vollmer T. , Engemann J. , Kleesiek K. , Dreier J. 
Published: January 2011

Background: Bacterial contamination is currently the major infectious hazard of platelet transfusion in developed countries. It has been demonstrated that a significant transfusion risk remains, in particular with older platelet concentrates (PCs). In 2009, the shelf life of PCs was therefore reduced in Germany to 4 days after the day of production according to Vote 38. The aim of the present study was the application and implementation of a recently developed flow cytometry‐based rapid screening method (BactiFlow) for bacterial contamination at the end of PC shelf life as a routine in‐process control. Study design and methods: A total of 472 apheresis‐derived PCs were tested using the BactiFlow flow cytometric assay to detect and count bacteria based on esterase activity in viable bacterial cells, while the BacT/Alert automated culture system served as the reference method. The automation potential of the flow cytometric assay was analysed by applying the semi‐automated BactiFlow ALS system. Results: An algorithm was developed for use in routine blood bank operations to extend the storage period of PCs. Two of the 472 apheresis PCs tested were positive in culture and identified as Propionibacterium species. One PC was positive for Staphylococcus aureus by both methods. All remaining specimens were tested negative by both methods. Conclusions: Our study demonstrates that routine bacterial testing of PCs was successfully implemented and the established algorithm proved efficient. The BactiFlow flow cytometric assay is the first rapid screening method which is suitable for a routine application combined with a high sensitivity.
Outcomes of patients with cystic fibrosis undergoing lung transplantation with and without cystic fibrosis‐associated liver cirrhosis*
Authors: Nash E.F. , Volling C. , Gutierrez C.A. , Tullis E. , Coonar A. , McRae K. , Keshavjee S. , Singer L.G. , Durie P.R. , Chaparro C. 
Published: January 2011

Nash EF, Volling C, Gutierrez CA, Tullis E, Coonar A, McRae K, Keshavjee S, Singer LG, Durie PR, Chaparro C. Outcomes of patients with cystic fibrosis undergoing lung transplantation with and without cystic fibrosis‐associated liver cirrhosis.  Clin Transplant 2012: 26: 34–41.  © 2011 John Wiley & Sons A/S.Abstract:  People with severe cystic fibrosis (CF) lung disease with co‐existent CF‐associated liver disease (CFLD) are often excluded from consideration of sole lung transplantation, largely because of the concerns that they will subsequently develop hepatic decompensation. This retrospective cohort study aimed at determining whether patients with severe cirrhosis caused by CFLD have any differences in perioperative and relevant post‐transplant outcomes compared to CF patients without CFLD when undergoing sole lung transplantation. Six patients with CFLD were matched with 18 CF patients without CFLD undergoing sole lung transplant at the same institution. There were no differences in total operative time or intra‐operative requirements for cardiopulmonary bypass or blood products. Over a period of five yr post‐transplant, no differences were observed between the two groups in body mass index, six‐min walk, lung function, and survival. None of the CFLD subjects developed variceal bleeding; however, one developed hepatocellular and renal failure at four yr post‐transplant and is being assessed for liver–kidney transplant. One additional patient with CFLD required repeat lung transplantation for bronchiolitis obliterans syndrome. This study provides evidence that CF patients with liver cirrhosis caused by CFLD can safely be considered for sole lung transplantation provided there is no evidence of significant hepatocellular dysfunction with decompensated cirrhosis or hepatic synthetic failure.
Blood transfusions in kidney transplant candidates are common and associated with adverse outcomes
Authors: Ibrahim Hassan N. , Skeans Melissa A. , Li Qi , Ishani Areef , Snyder Jon J. 
Published: January 2011

Ibrahim HN, Skeans MA, Li Q, Ishani A, Snyder JJ. Blood transfusions in kidney transplant candidates are common and associated with adverse outcomes. Clin Transplant 2011: 25: 653–659. © 2011 John Wiley & Sons A/S.Abstract:  Surprisingly, there are no data regarding transfusion frequency, factors associated with transfusion administration in patients on the kidney transplant waiting list, or transfusion impact on graft and recipient outcomes. We used United States Renal Data System data to identify 43 025 patients added to the waiting list in 1999–2004 and followed through 2006 to assess the relative risk of post‐listing transfusions. In 69 991 patients who underwent transplants during the same time period, we assessed the association between pre‐transplant transfusions and level of panel‐reactive antibody (PRA) at the time of transplant, and associations between PRA and patient outcomes. The three‐yr cumulative incidence of transfusions was 26% for patients added to the waiting list in 1999, rising to 30% in 2004. Post‐listing transfusions were associated with a 28% decreased likelihood of undergoing transplant, and a more than fourfold increased risk of death. There was a graded association between percent PRA at the time of transplant and adjusted risk of death‐censored graft failure, death with function, and the combined event of graft failure and death. These data demonstrate that transfusions remain common and confirm the adverse association between transfusions and PRA, and high PRA and inferior graft and patient outcomes.
Impaired cellular immune response to diphtheria and tetanus vaccines in children after thoracic transplantation
Authors: Urschel Simon , Rieck Birgit D. , Birnbaum Julia , Dalla Pozza Robert , Rieber Nikolaus , Januszewska Katarzyna , Fuchs Alexandra , West Lori J. , Netz Heinrich , Belohradsky Bernd H. 
Published: January 2011

Urschel S, Rieck BD, Birnbaum J, Dalla Pozza R, Rieber N, Januszewska K, Fuchs A, West LJ, Netz H, Belohradsky BH. Impaired cellular immune response to diphtheria and tetanus vaccines in children after thoracic transplantation. Pediatr Transplantation 2011: 15: 272–280. © 2011 John Wiley & Sons A/S.Abstract:  Safety and immunogenicity of diphtheria and tetanus booster vaccination were evaluated in 28 children after thoracic transplantation. Adverse events were documented in a patient diary. Blood was collected prior to and four wk after vaccination. Specific antibody concentrations were measured by ELISA. Lymphocytes were investigated for expression of activation markers (CD25, HLA‐DR) by flow cytometry and proliferation assays with and without stimulation. Post‐vaccination antibody titers were higher than prevaccination (p < 0.001), with more patients having protective antibody levels against diphtheria (p < 0.02) and tetanus (p < 0.001). There was no increased proliferation in non‐stimulated or stimulated cultures after vaccination. The number of T‐lymphocytes activated by the vaccination antigens was similar pre‐ and post‐vaccination, whereas HLA‐DR‐expression on stimulated and non‐stimulated CD4+ T‐cells increased significantly. Increase in antibodies was negatively correlated with tacrolimus dose, and impaired cellular immunity was associated with higher tacrolimus dose and steroid use. Adverse events were similar to the general population; serious adverse events and rejection did not occur. Vaccination with inactivated vaccines can be performed safely in immunosuppressed children after thoracic transplantation and induces protective antibody levels in the majority of patients. Impaired induction of specific cellular immunity is correlated with intensity of immunosuppression and may explain reduced sustainability of antibodies.
Charles Darwin and marine biology
Authors: Rainbow Philip S. 
Published: January 2011

AbstractIn a celebration of the 200th anniversary of his birth in 1809, this short essay explores the influence of marine biology on Charles Darwin, and vice versa. Darwin made his first forays into the world of marine biology as a medical student in Edinburgh from 1825 to 1827. He came under the influence there of the Lamarckian Robert Grant, and developed an understanding of the simple organisation of the early developmental stages of marine invertebrates. Yet Darwin balked at Lamarckian transmutation. The voyage of the Beagle led to Darwin’s perceptive theory of the origin of coral reefs, an origin still mainly accepted today. This theory was steeped in the uniformitarianism of the geologist Lyell, depending on the slow, gradual growth of billions of coral polyps keeping pace with slow sinking of land to produce an atoll. From 1846 to 1854 Darwin revolutionised the understanding of barnacles, producing monographs still relevant today. His barnacle studies gave him the credibility to pronounce on the origin of species; he found great variation in morphology, and a series of related species with remarkable reproductive adaptation culminating in the presence of dwarf males. Barnacles showed him an evolutionary narrative laid out before him, and contributed greatly to his qualification and confidence to write with authority on the origin of species.
Temporal change in UK marine communities: trends or regime shifts?
Authors: Spencer M. , Birchenough S. N. R. , Mieszkowska N. , Robinson L. A. , Simpson S. D. , Burrows M. T. , Capasso E. , Cleall‐Harding P. , Crummy J. , Duck C. , Eloire D. , Frost M. , Hall A. J. , Hawkins S. J. , Johns D. G. , Sims D. W. , Smyth T. J. , Frid C. L. J. 
Published: January 2011

AbstractA regime shift is a large, sudden, and long‐lasting change in the dynamics of an ecosystem, affecting multiple trophic levels. There are a growing number of papers that report regime shifts in marine ecosystems. However, the evidence for regime shifts is equivocal, because the methods used to detect them are not yet well developed. We have collated over 300 biological time series from seven marine regions around the UK, covering the ecosystem from phytoplankton to marine mammals. Each time series consists of annual measures of abundance for a single group of organisms over several decades. We summarised the data for each region using the first principal component, weighting either each time series or each biological component (e.g. plankton, fish, benthos) equally. We then searched for regime shifts using Rodionov’s regime shift detection (RSD) method, which found regime shifts in the first principal component for all seven marine regions. However, there are consistent temporal trends in the data for six of the seven regions. Such trends violate the assumptions of RSD. Thus, the regime shifts detected by RSD in six of the seven regions are likely to be artefacts caused by temporal trends. We are therefore developing more appropriate time series models for both single populations and whole communities that will explicitly model temporal trends and should increase our ability to detect true regime shift events.
Short and mid‐long term effects of cockle‐dredging on non‐target macrobenthic species: a before‐after‐control‐impact experiment on a tidal mudflat in the Oosterschelde (The Netherlands)
Authors: Wijnhoven Sander , Escaravage Vincent , Herman Peter M. J. , Smaal Aad C. , Hummel Herman 
Published: January 2011

AbstractTo study the possible environmental impact of hydraulic cockle‐dredging on macrobenthic communities and the environment, a fishing experiment was executed on a tidal mudflat in the Oosterschelde (SW Netherlands) according to a BACI (before‐after‐control‐impact) design. Following the characterization of the initial situation, a part of the mudflat was commercially fished, after which dredged and undredged areas were compared on the basis of macrofauna descriptors and sediment constitution approximately 2 months (short term) and 1 year (mid‐long term) after fishing. Whereas a clear reduction of the larger Cerastoderma edule cockles (>23 mm) in the fished areas was found, no effect of dredging on total macrofauna densities or median grain size was observed. No negative effect of fishing on total macrofauna biomass was found; in contrast, an increase of the biomass of the non‐target species almost compensated for the loss in weight due to the extraction of the larger cockles. No significant effect of dredging on species diversity, richness or evenness was found in the short or mid‐long term, these descriptors tending to have increased rather than decreased in the dredged plots after 1 year. The selective fishing for larger cockles reduced the average cockle size, but 1 year after fishing the average size had returned to the initial values in the dredged area. However, compared to the control area, the average size might still be reduced, as the size of the cockles in the control area also increased during the year. Local environmental conditions, with their specific macrobenthic communities, seem to be crucial for the type of effects and the impact of dredging. It is therefore of eminent importance to follow a research design with pre‐defined environmental conditions, rather than a comparison of different areas that are open or closed to fisheries. The present study based on a BACI approach indicates that mechanical cockle fisheries had no overall negative impact in our study area.
Effects of Induction of Ovulation with GnRH or hCG on Follicular and Luteal Blood Flow in Holstein–Friesian Heifers
Authors: Aslan S , Arslanbas D , Beindorff N , Bollwein H 
Published: January 2011

ContentsThe objective of this study was to compare the effects of gonadotropin‐releasing hormone (GnRH) and human chorionic gonadotropin (hCG) on follicular blood flow (FBF) during the pre‐ovulatory period and on luteal blood flow (LBF) during dioestrus in Holstein–Friesian heifers. Twelve animals were randomly divided into two groups and treated with either intramuscular injection of 100 μg GnRH or intravenous (IV) injection of 5000 IU hCG on Day 0 (oestrus, 48 h after administration of PGF2α) to induce ovulation. Follicular size (FS), FBF and time of ovulation were recorded with colour Doppler sonography at 0, 1, 3, 6, 12 and 24 h after GnRH and hCG treatment. Luteal size (LS) and LBF were investigated on Day 9 and 12 after ovulation. Plasma samples were taken to determine total oestrogens (Etot) and progesterone (P4) after each examination. Ovulation occurred between 24 and 48 h after treatment in all animals. No difference (p > 0.05) was observed in FS between the two treatment groups. Follicular blood flow was higher in the hCG group than that was in GnRH group at 1 h after treatment (p < 0.01). Total oestrogens were also higher (p < 0.01) in the hCG group than GnRH group; however, this difference was only obvious at 12 h after treatment. No difference (p > 0.05) was observed in LS, LBF or P4 levels on Day 9 and 12 between treatment groups. In conclusion, the results suggest that induction of ovulation with hCG and GnRH has a temporary effect on FBF and oestrogen levels while no effect on the size of corpora lutea, LBF and P4 levels was observed.