bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y
Authors: Lehnik‐Habrink Martin , Schaffer Marc , Mäder Ulrike , Diethmaier Christine , Herzberg Christina , Stülke Jörg 
Published: August 2011

SummaryRNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram‐positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in RNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the global impact of RNase Y, we compared the transcriptomes in response to the expression level of RNase Y. Our results demonstrate that processing by RNase Y results in accumulation of about 550 mRNAs. Some of these targets were substantially stabilized by RNase Y depletion, resulting in half‐lives in the range of an hour. Moreover, about 350 mRNAs were less abundant when RNase Y was depleted among them the mRNAs of the operons required for biofilm formation. Interestingly, overexpression of RNase Y was sufficient to induce biofilm formation. The results presented in this work emphasize the importance of RNase Y as the global acting endoribonuclease for B. subtilis.
Different routes to the same ending: comparing the N‐glycosylation processes of Haloferax volcanii and Haloarcula marismortui, two halophilic archaea from the Dead Sea
Authors: Calo Doron , Guan Ziqiang , Naparstek Shai , Eichler Jerry 
Published: August 2011

SummaryRecent insight into the N‐glycosylation pathway of the haloarchaeon, Haloferax volcanii, is helping to bridge the gap between our limited understanding of the archaeal version of this universal post‐translational modification and the better‐described eukaryal and bacterial processes. To delineate as yet undefined steps of the Hfx. volcanii N‐glycosylation pathway, a comparative approach was taken with the initial characterization of N‐glycosylation in Haloarcula marismortui, a second haloarchaeon also originating from the Dead Sea. While both species decorate the reporter glycoprotein, the S‐layer glycoprotein, with the same N‐linked pentasaccharide and employ dolichol phosphate as lipid glycan carrier, species‐specific differences in the two N‐glycosylation pathways exist. Specifically, Har. marismortui first assembles the complete pentasaccharide on dolichol phosphate and only then transfers the glycan to the target protein, as in the bacterial N‐glycosylation pathway. In contrast, Hfx. volcanii initially transfers the first four pentasaccharide subunits from a common dolichol phosphate carrier to the target protein and only then delivers the final pentasaccharide subunit from a distinct dolichol phosphate to the N‐linked tetrasaccharide, reminiscent of what occurs in eukaryal N‐glycosylation. This study further indicates the extraordinary diversity of N‐glycosylation pathways in Archaea, as compared with the relatively conserved parallel processes in Eukarya and Bacteria.
Changes in leaf optical properties associated with light‐dependent chloroplast movements
Authors: DAVIS PHILLIP A. , CAYLOR STEVEN , WHIPPO CRAIG W. , HANGARTER ROGER P. 
Published: August 2011

ABSTRACTWe surveyed 24 plant species to examine how leaf anatomy influenced chloroplast movement and how the optical properties of leaves change with chloroplast position. All species examined exhibited light‐dependent chloroplast movements but the associated changes in leaf absorptance varied considerably in magnitude. Chloroplast movement‐dependent changes in leaf absorptance were greatest in shade species, in which absorptance changes of >10% were observed between high‐ and low‐light treatments. Using the Kubelka–Munk theory, we found that changes in the absorption (k) and chlorophyll a absorption efficiency (k*) associated with chloroplast movement correlated with cell diameter, such that the narrower, more columnar cells found in sun leaves restricted the ability of chloroplasts to move. The broader, more spherical cells of shade leaves allowed greater chloroplast rearrangements and in low‐light conditions allowed efficient light capture. Across the species tested, light‐dependent chloroplast movements modulated leaf optical properties and light absorption efficiency by manipulating the package (sieve or flattening) effect but not the detour (path lengthening) effect.
Physiological characterization of cadmium‐exposed Chlamydomonas reinhardtii
Authors: BRÄUTIGAM ANJA , SCHAUMLÖFFEL DIRK , PREUD'HOMME HUGUES , THONDORF IRIS , WESENBERG DIRK 
Published: August 2011

ABSTRACTChlamydomonas reinhardtii is a common model organism for investigation of metal stress. This green alga produces phytochelatins in the presence of metal ions. The influence of cadmium is of main interest, because it is a strong activator of phytochelatin synthase. Cell wall bound and intracellular cadmium content was determined after exposition to 70 µm CdCl2, showing the main portion of the metal outside the cell. Nevertheless, imported cadmium was sufficient to cause significant changes in thiolpeptide metabolism and its transcriptional regulation. Modern analytical approaches enable new insights into phytochelatin (PC) distribution. A new rapid and precise UPLC‐MS method allowed high‐throughput PC quantification in algal samples after 1, 4, 24 and 48 h cadmium stress. Initially, canonic PCs were synthesized in C. reinhardtii during cadmium exposition, but afterwards CysPCs became the major thiolpeptides. Thus, after 48 h the concentration of the PC‐isoforms CysPC2‐3 and CysGSH attained between 105 and 199 nmol g−1 fresh weight (FW), whereas the PC2‐3 concentrations were only 15 nmol g−1 FW. The relative quantification of γ‐glutamyl transpeptidase (γ‐GT) mRNA suggests the generation of CysPCs by glutamate cleavage from canonic PCs by γ‐GT. Furthermore, a homology model of C. reinhardtii phytochelatin synthase was constructed to verify the use of crystal structures from Anabaena sp. phytochelatin synthase (PCS) for docking studies with canonical PCs and CysPCs. From the difference in energy scores, we hypothesize that CysPC may prevent the synthesis of canonical PCs by blocking the binding pocket. Finally, possible physiological reasons for the high abundance of CysPC compared with their canonic precursors are discussed.
Leaf gas films of Spartina anglica enhance rhizome and root oxygen during tidal submergence
Authors: WINKEL ANDERS , COLMER TIMOTHY DAVID , PEDERSEN OLE 
Published: August 2011

ABSTRACTGas films on hydrophobic surfaces of leaves of some wetland plants can improve O2 and CO2 exchange when completely submerged during floods. Here we investigated the in situ aeration of rhizomes of cordgrass (Spartina anglica) during natural tidal submergence, with focus on the role of leaf gas films on underwater gas exchange. Underwater net photosynthesis was also studied in controlled laboratory experiments. In field experiments, O2 microelectrodes were inserted into rhizomes and pO2 measured throughout two tidal submergence events; one during daylight and one during night‐time. Plants had leaf gas films intact or removed. Rhizome pO2 dropped significantly during complete submergence and most severely during night. Leaf gas films: (1) enhanced underwater photosynthesis and pO2 in rhizomes remained above 10 kPa during submergence in light; and (2) facilitated O2 entry from the water into leaves so that rhizome pO2 was about 5 kPa during darkness. This study is the first in situ demonstration of the beneficial effects of leaf gas films on internal aeration in a submerged wetland plant. Leaf gas films likely contribute to submergence tolerance of S. anglica and this feature is expected to also benefit other wetland plant species when submerged.
Potassium channel‐oxidative phosphorylation relationship in durum wheat mitochondria from control and hyperosmotic‐stressed seedlings
Authors: TRONO DANIELA , SOCCIO MARIO , LAUS MAURA N. , PASTORE DONATO 
Published: August 2011

ABSTRACTDurum wheat mitochondria (DWM) possess an ATP‐inhibited K+ channel, the plant mitoKATP (PmitoKATP), which is activated under environmental stress to control mitochondrial ROS production. To do this, PmitoKATP collapses membrane potential (ΔΨ), thus suggesting mitochondrial uncoupling. We tested this point by studying oxidative phosphorylation (OXPHOS) in DWM purified from control seedlings and from seedlings subjected both to severe mannitol and NaCl stress. In severely‐stressed DWM, the ATP synthesis via OXPHOS, continuously monitored by a spectrophotometric assay, was about 90% inhibited when the PmitoKATP was activated by KCl. Contrarily, in control DWM, although PmitoKATP collapsed ΔΨ, ATP synthesis, as well as coupling [respiratory control (RC) ratio and ratio between phosphorylated ADP and reduced oxygen (ADP/O)] checked by oxygen uptake experiments, were unaffected. We suggest that PmitoKATP may play an important defensive role at the onset of the environmental/oxidative stress by preserving energy in a crucial moment for cell and mitochondrial bioenergetics. Consistently, under moderate mannitol stress, miming an early stress condition, the channel may efficiently control reactive oxygen species (ROS) generation (about 35‐fold from fully open to closed state) without impairing ATP synthesis. Anyway, if the stress significantly proceeds, the PmitoKATP becomes fully activated by decrease of ATP concentration (25–40%) and increase of activators [free fatty acids (FFAs) and superoxide anion], thus impairing ATP synthesis.
Gene–vitamin D interactions on food sensitization: a prospective birth cohort study
Authors: Liu X. , Wang G. , Hong X. , Wang D. , Tsai H.‐J. , Zhang S. , Arguelles L. , Kumar R. , Wang H. , Liu R. , Zhou Y. , Pearson C. , Ortiz K. , Schleimer R. , Holt P. G. , Pongracic J. , Price H. E. , Langman C. , Wang X. 
Published: August 2011

To cite this article: Liu X, Wang G, Hong X, Wang D, Tsai H‐J, Zhang S, Arguelles L, Kumar R, Wang H, Liu R, Zhou Y, Pearson C, Ortiz K, Schleimer R, Holt P, Pongracic J, Price HE, Langman C, Wang X. Gene–vitamin D interactions on food sensitization: a prospective birth cohort study. Allergy 2011; 66: 1442–1448.AbstractBackground:  It has been hypothesized that vitamin D deficiency (VDD) contributes to the development of food sensitization (FS) and then food allergy. However, the epidemiological evidence is conflicting. We aim to examine whether cord blood VDD is associated with FS and whether such association can be modified by genetic variants in a prospective birth cohort.Methods:  This study included 649 children who were enrolled at birth and followed from birth onward at the Boston Medical Center. We defined VDD as cord blood 25(OH)D < 11 ng/ml, and FS as specific IgE ≥ 0.35 kUA/l to any of eight common food allergens in early childhood. We genotyped potentially functional single‐nucleotide polymorphisms (SNPs) in 11 genes known to be involved in regulating IgE and 25(OH)D concentrations. Logistic regressions were used to test the effects of VDD on FS individually and jointly with SNPs.Results:  Among the 649 children, 44% had VDD and 37% had FS. When examined alone, VDD was not associated with FS. When examined jointly with SNPs, a significant interaction between IL4 gene polymorphism (rs2243250) and VDD (pinteraction = 0.003, pFDR = 0.10) was found: VDD increased the risk of FS among children carrying CC/CT genotypes (OR = 1.79, 95%CI: 1.15–2.77). Similar but weaker interactions were observed for SNPs in MS4A2 (rs512555), FCER1G (rs2070901), and CYP24A1 (rs2762934). When all four SNPs were simultaneously considered, a strong gene–VDD interaction was evident (pinteraction = 9 × 10−6).Conclusions:  Our data demonstrate that VDD may increase the risk of FS among individuals with certain genotypes, providing evidence of gene–vitamin D interaction on FS.
Phytophthora ramorum in England and Wales: which environmental variables predict county disease incidence?
Authors: Chadfield V. , Pautasso M. 
Published: August 2011

SummaryPhytophthora ramorum is the oomycete pathogen responsible for Sudden Oak Death on the West Coast of the USA and Sudden Larch Death in the British Isles. It also causes twig dieback and leaf blight on a series of ornamental hosts (e.g. Rhododendron, Viburnum, Pieris and Camellia) commonly grown in plant nurseries, traded by garden centres and cultivated in public and private gardens. The role of the plant trade in the dispersal of P. ramorum has been well documented, but there is a need for regional analyses of which environmental variables can predict disease expression in the trade and in the wild, so as to be able to better predict the further development of this worldwide plant health issue. In this study, we analyse data on the incidence of P. ramorum (2002–2009, thus before the reports in Japanese larch plantations) in counties in England and Wales as a function of environmental variables such as temperature and rainfall, controlling for confounding factors such as county area, human population and spatial autocorrelation. While P. ramorum county incidence in nurseries and retail centres was positively related to county area and human population density, county incidence in gardens and the wild did not show such correlations, declined significantly towards the East and was positively correlated with disease incidence in the trade. The latter finding, although not conclusively proving causation, suggests a role of the trade in the dispersal of this pathogen across English and Welsh landscapes. Combined together, P. ramorum county incidence in the trade and in the semi‐natural environment increased with increasing precipitation and with declining latitude. This study shows the importance of environmental variables in shaping regional plant epidemics, but also yields results that are suggestive of a role of people in spreading plant diseases across entire countries.
Evidence that whales (Balaenoptera borealis) visit drifting fish aggregating devices: do their presence affect the processes underlying fish aggregation?
Authors: Brehmer Patrice , Josse Erwan , Nøttestad Leif 
Published: August 2011

AbstractEvidence of the presence of a group of sei whales (Balaenoptera borealis) detected around drifting fish aggregating devices (FADs) was provided by omnidirectional multi‐beam sonar during a survey off the Seychelles (Indian Ocean). The short visit by the sei whales produced a significant change in the behaviour of the fish assemblage associated with the FAD. There was first a significant increase in fish density when the whales approached the FAD, then a marked decrease after the whales had moved away from the FAD. Furthermore, the fish density was still low, 3 h after the whales had left the FAD. We assume that the presence and behaviour of the sei whales led some of the fish initially associated with the FAD to move away from it. There has been a considerable increase in the use of drifting artificial FADs in the Indian Ocean in recent decades. The frequency of cetacean visits to drifting FADs in the Indian Ocean is unknown, but they may have a major impact on assemblages of pelagic fish species around FADs. The effect of marine mammals on FAD‐associated fish could be relevant to the ecological trap theory (FAD acting as a trap for their associated fish) because of their impact on the dynamics of fish aggregation processes, through commensalism and/or predator–prey interactions.
What can we learn from genomics approaches in marine ecology? From sequences to eco‐systems biology!
Authors: Mock Thomas , Kirkham Amy 
Published: August 2011

AbstractThe application of genomic approaches to marine biota has profoundly altered our understanding of life in the oceans, especially regarding concepts of adaptation, speciation and evolution. The avalanche of genomic data has provided an unbiased view of marine biology that has never been seen before. In particular, comparative and metagenomic approaches with microbes from different biogeochemical marine provinces provided the first insights into how they acquire and discard genes as needed, even across kingdom boundaries, in response to their environment. These data clearly reveal that marine microbes have remarkable abilities to change their genomes according to both environmental stresses and biotic interactions. Thus, it is most likely that the flux of energy and matter in the marine system is reflected by the presence or absence of genes and proteins in marine organisms, which could provide novel tools to understand biogeochemical processes of global significance. However, the challenge is to put the reductionistic knowledge gained by genomics and metagenomics into the larger contexts of cellular systems and ecosystems to identify emergent properties that could not have been predicted by breaking down the whole into its individual parts.
Cryptococcus gattii serotype‐C strains isolated in Bangalore, Karnataka, India
Authors: Cogliati Massimo , Chandrashekar Nagarathna , Esposto Maria Carmela , Chandramuki Akepati , Petrini Björn , Viviani Maria Anna 
Published: August 2011

SummaryDuring a retrospective study on cryptococcosis carried out in Bangalore, Karnataka, India, four Cryptococcus gattii strains were isolated from one HIV‐positive and three HIV‐negative patients, two of which had unknown predisposing conditions. Serotyping and genotyping showed that the isolates were C. gattii serotype C, mating‐type α and genotype VGIV. All the isolates were identical by multilocus sequence typing, but presented a low similarity compared with a set of 17 C. gattii global control strains. The comparison with a larger number of previously reported C. gattii strains, including African isolates, revealed a close relationship between Indian and African serotype‐C isolates.
Decompressive surgery in combination with preoperative transcatheter arterial embolization: Successful improvement of ambulatory function in renal cell carcinoma patients with metastatic extradural spinal cord compression
Authors: Suzuki Hiroko , Kondo Tsunenori , Kuwatsuru Ryohei , Wada Keiji , Kubota Motoya , Kobayashi Hirohito , Iizuka Junpei , Ikezawa Eri , Takagi Toshio , Tanabe Kazunari 
Published: August 2011

AbstractWe analyzed the results of direct decompressive surgery plus stabilization of the vertebrae involved (DDSS) in six non‐ambulatory patients with metastatic extradural spinal cord compression (MESCC) due to renal cell carcinoma (RCC). Transcatheter arterial embolization (TAE) was performed prior to surgery to reduce intraoperative blood loss. Radiotherapy and systemic therapy, including cytokine or targeted therapy and zoledronic acid, were added to the surgery. The DDSS procedure was performed successfully in all patients, with an estimated mean blood loss of 1726 mL. After surgery, all patients regained ambulatory function within 2 months. Patients were ambulatory with the use of assisting apparatus for 4–29 months (median 10.5 months). Median overall survival time after surgery was 15 months (range 4–38 months). In conclusion, DDSS with preoperative TAE can be performed safely and significantly improves the ambulatory function of non‐ambulatory RCC patients with MESCC.
Long‐term results of surgery plus fibrin sealant for anal fistula
Authors: de Oca J. , Millán M. , Jiménez A. , Golda T. , Biondo S. 
Published: August 2011

AbstractAim  The long‐term recurrence rate of fibrin glue treatment was analysed in patients with trans‐sphincteric cryptoglandular fistula operated by a two‐phase procedure: (i) fistulectomy with seton placement; (ii) fibrin sealant (Tissucol Duo®, Baxter) insertion in the track.Method  Clinical data were collected prospectively for all patients operated between 2004 and 2010. The statistical association of clinical variables and recurrence was analysed and a disease‐free curve was constructed using the Kaplan–Meier method.Results  Twenty‐eight consecutive patients (mean age 48.3 ± 13.3 years; 22 men) were enrolled in the study. Middle and high trans‐sphincteric fistulae were diagnosed in 20 (71.4%) and eight (28.6%) patients. Seven (25%) had secondary track formation. The mean interval between the first operation and the fibrin sealant treatment was 12.5 ± 7.6 months. There were no complications related to the procedure. Nine (32.1%, 95% CI 17.9–50.7%) patients developed recurrence between 3 and 27 months after fibrin sealant treatment. Disease‐free curves showed that the highest probability of recurrence occurred in the first 2 years. No incontinence was found at a mean follow‐up of 20.6 (3–60) months among the 67.8% patients with no evidence of recurrence.Conclusion  Fibrin sealant is safe and simple. The healing rate is satisfactory without the risk of incontinence.
The historical equity risk premium in Australia: post‐GFC and 128 years of data
Authors: Brailsford Tim , Handley John C. , Maheswaran Krishnan 
Published: August 2011

AbstractWe present an updated set of estimates of the historical equity risk premium in Australia covering the 128 calendar years from January 1883 to December 2010. Relative to bonds (bills), the observed equity premium has averaged 6.1 per cent (6.5 per cent) p.a. over this period, and we report a similar number for later periods of relatively good quality data. We also provide estimates that incorporate an adjustment for distributed imputation credits and include the annual time series of data relating to each of the underlying components – stock, bill and bond returns and inflation.
DOES PERCEPTION OUTSTRIP OUR CONCEPTS IN FINENESS OF GRAIN?
Authors: Connolly Kevin 
Published: August 2011

AbstractWe seem perfectly able to perceive fine‐grained shades of colour even without possessing precise concepts for them. The same might be said of shapes. I argue that this is in fact not the case. A subject can perceive a colour or shape only if she possesses a concept of that type of colour or shape. I provide new justification for this thesis, and do not rely on demonstrative concepts such as THIS SHADE or THAT SHAPE, a move first suggested by John McDowell, but rejected by Christopher Peacocke and Richard Heck among others.
IMAGINATION AND THE EXPRESSION OF EMOTION
Authors: Lennon Kathleen 
Published: August 2011

AbstractMany writers offer accounts of our grasp of the expressive gestures of others, or of the expressive content of works of art, in terms of our imagining the experiences of another, or ourselves having certain experiences, or, in the case of works of art, a persona to have experiences. This invocation of what Kant would term, the reproductive imagination, in the perception of expressive content, is contested in this paper. In its place it is suggested that the detection of expressive content is a form of direct, but reason constituting perception. In such perception it is the Kantian productive, rather than the reproductive, imagination which plays a central role.