bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions
Authors: Gierga Gregor , Voss Björn , Hess Wolfgang R 
Published: January 2012

Abstract
Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs.
AnnTools: a comprehensive and versatile annotation toolkit for genomic variants
Authors: Makarov Vladimir , O'Grady Tina , Cai Guiqing , Lihm Jayon , Buxbaum Joseph D. , Yoon Seungtai 
Published: January 2012

Abstract
Summary: AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps with regulatory elements, disease/trait associated loci, known segmental duplications and artifact prone regions, thereby offering an integrated and comprehensive analysis of genomic data. The tool conveniently accepts user-provided tracks for custom annotation and offers flexibility in input data formats. The output is generated in the universal Variant Call Format. High annotation speed makes AnnTools suitable for high-throughput sequencing facilities, while a low-memory footprint and modest CPU requirements allow it to operate on a personal computer. The application is freely available for public use; the package includes installation scripts and a set of helper tools.
Availability: http://anntools.sourceforge.net/
Contact: vladimir.makarov@mssm.edu; chris.yoon@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Routes to the Tonoplast: The Sorting of Tonoplast Transporters in Arabidopsis Mesophyll Protoplasts
Authors: Wolfenstetter Susanne , Wirsching Petra , Dotzauer Dorina , Schneider Sabine , Sauer Norbert 
Published: January 2012

Abstract
Vacuoles perform a multitude of functions in plant cells, including the storage of amino acids and sugars. Tonoplast-localized transporters catalyze the import and release of these molecules. The mechanisms determining the targeting of these transporters to the tonoplast are largely unknown. Using the paralogous Arabidopsis thaliana inositol transporters INT1 (tonoplast) and INT4 (plasma membrane), we performed domain swapping and mutational analyses and identified a C-terminal di-leucine motif responsible for the sorting of higher plant INT1-type transporters to the tonoplast in Arabidopsis mesophyll protoplasts. We demonstrate that this motif can reroute other proteins, such as INT4, SUCROSE TRANSPORTER2 (SUC2), or SWEET1, to the tonoplast and that the position of the motif relative to the transmembrane helix is critical. Rerouted INT4 is functionally active in the tonoplast and complements the growth phenotype of an int1 mutant. In Arabidopsis plants defective in the β-subunit of the AP-3 adaptor complex, INT1 is correctly localized to the tonoplast, while sorting of the vacuolar sucrose transporter SUC4 is blocked in cis-Golgi stacks. Moreover, we demonstrate that both INT1 and SUC4 trafficking to the tonoplast is sensitive to brefeldin A. Our data show that plants possess at least two different Golgi-dependent targeting mechanisms for newly synthesized transporters to the tonoplast.
Does alcohol consumption really affect asymmetry perception? A three‐armed placebo‐controlled experimental study
Authors: Halsey Lewis G. , Huber Joerg W. , Hardwick Jennifer C. 
Published: January 2012

ABSTRACTAims  A possible explanation for increased levels of attractiveness of faces when under the influence of alcohol is the reduced ability to perceive bilateral asymmetry. This study tested the degree of preference by alcohol‐dosed and non‐alcohol‐dosed participants for symmetrical faces and their ability to detect facial symmetry, while controlling for other explanations.Design  Volunteers were recruited to a random allocation experiment with three conditions: alcoholic drink (alcohol dosed), non‐alcoholic drink (placebo) and diluted orange cordial (control). Data on concentration, personality and demographics were collected. Dependent variables were symmetry preference and detection.Setting  Laboratory, University of Roehampton.Participants  A total of 101 participants, mainly students (41 alcohol‐dosed, 40 placebo, 20 control).Measurements  Participants provided verbal responses to images of faces which were presented on a computer screen for 5 seconds each; the first task required a preference judgement and the second task consisted of a forced‐choice response of whether or not a face was symmetrical. Levels of concentration, weight and level of alcohol dose were measured, and demographics plus additional psychological and health information were collected using a computer‐based questionnaire.Findings  In contrast to a previous investigation, there was no difference in symmetry preference between conditions (P = 0.846). In agreement with previous findings, participants who had not drunk alcohol were better at detecting whether a face was symmetrical or asymmetrical (P = 0.043). Measures of concentration did not differ between conditions (P = 0.214–0.438). Gender did not affect ability to detect symmetry in placebo or alcohol‐dosed participants (P = 0.984, 0.499); however, alcohol‐dosed females were shown to demonstrate greater symmetry preference than alcohol‐dosed males (P = 0.004).Conclusions  People who are alcohol‐dosed are subtly less able to perceive vertical, bilateral asymmetry in faces, with gender being a possible moderating factor.
The clinical impact of single inhaler therapy in asthma
Authors: Czarnecka K. , Chapman K. R. 
Published: January 2012

SummaryBackgroundLow‐dose budesonide/formoterol combination used in the SMART fashion with symptom‐reactive supplemental dosing has been reported to reduce asthma exacerbations as compared to the use of budesonide alone or to lower doses of budesonide/formoterol without supplemental dosing.ObjectiveWe undertook to review the non‐exacerbation outcomes of SMART therapy and to assess the patient education implications of this treatment strategy.Materials & MethodsSystematic review.ResultsPatients treated with this strategy appear to be under‐treated in that the majority fail to achieve guideline‐defined control standards. The SMART strategy has not been tested against equivalent or higher doses of budesonide/formoterol given in symptom‐prevention fashion. Existing educational strategies that focus on recognition of poor disease control may not be applicable with SMART therapy and the use of action plans has not been clarified with this symptom‐reactive strategy. There is some evidence from that the current clinical use of SMART therapy may be contaminated frequently by the concurrent prescription of short‐acting bronchodilators. There is no information on long‐term outcomes with a symptom‐reactive ICS/LABA strategy but the use of the strategy for one year has been associated with rising sputum and airway biopsy eosinophil counts.ConclusionDespite fewer severe exacerbations with SMART therapy as compared to ICS monotherapy or lower dose ICS/LABA therapy, the strategy produces poor day‐to‐day control of symptoms and is associated with increasing inflammation.Clinical RelevanceThe symptom‐reactive strategy described as SMART therapy is associated with poor symptom control of asthma.
Severe asthma: from characteristics to phenotypes to endotypes
Authors: Wenzel S. 
Published: January 2012

AbstractAsthma, and severe asthma, in particular, is increasingly recognized as a heterogeneous disease. While traditional views of asthma have centered around a childhood onset disease with an allergic component, several large scale network studies are now confirming that severe asthma can present in multiple different ways, only 30–50% of which meet traditional childhood onset allergic criteria. To understand the different groups better, initial studies have attempted to define phenotypes of severe asthma. A phenotype is defined as the integration of different characteristics that are the product of the interaction of the patient's genes with the environment. Both clinical and statistical approaches have identified at least 3–5 phenotypes of severe asthma. However, these phenotypes, in isolation, do not identify the immunopathology that makes these clinical phenotypes distinct or identifies a target population for a specific approach to therapy. As biological characteristics are identified, phenotypes should continue to evolve towards asthma endotypes. The identification of these endotypes, either by matching biology, genetics and therapeutic responses to therapy with clinically or statistically defined phenotypes or through unbiased genetic and genomic approaches, remains limited. Moving forward, this integration of genetics, biology and clinical characteristics should substantially enhance our ability to effectively treat complex heterogeneous diseases, such as severe asthma.
Increased serum activin‐A differentiates alcoholic from cirrhosis of other aetiologies
Authors: Voumvouraki Argyro , Notas George , Koulentaki Mairi , Georgiadou Maria , Klironomos Stefanos , Kouroumalis Elias 
Published: January 2012

Eur J Clin Invest 2012AbstractBackground  Activin‐A is a molecule of the TGF superfamily, implicated in liver fibrosis, regeneration and stem cell differentiation. However, data on activins in liver diseases are few. We therefore studied serum levels of activin‐A in chronic liver diseases. To identify the origin of activin‐A, levels in the hepatic vein were also estimated.Materials and methods  Nineteen controls and 162 patients participated in the study: 39 with hepatocellular carcinoma (HCC: 19 viral associated and 20 alcohol associated), 18 with chronic hepatitis C (CHC), 47 with primary biliary cirrhosis (26 PBC stage I–II and 21 stage IV), 22 with alcoholic cirrhosis (AC, hepatic vein blood available in 16), 20 with HCV cirrhosis (hepatic vein blood available in 18) and 16 patients with alcoholic fatty liver with mild to moderate fibrosis but no cirrhosis.Results  Activin‐A levels were significantly increased (P < 0·001) in serum of patients with AC (median 673 pg/mL, range 449–3279), compared with either controls (149 pg/mL, 91–193) or patients with viral cirrhosis (189 pg/mL, 81–480), CHC (142 pg/mL, 65–559) PBC stage I–II (100 pg/mL, 59–597) and PBC stage IV (104 pg/mL, 81–579). Only patients with AC‐associated HCC had significantly increased levels of activin‐A (2403 pg/mL, 1561–7220 pg/mL). Activin‐A serum levels could accurately discriminate AC from cirrhosis of other aetiologies and noncirrhotic alcoholic fatty liver with fibrosis.Conclusions  Increased serum levels of activin‐A only in patients with alcohol‐related cirrhosis or HCC suggest a possible role of this molecule in the pathophysiology of AC. Further research is warranted to elucidate its role during the profibrotic process and its possible clinical applications.
Contrasting introduction scenarios among continents in the worldwide invasion of the banana fungal pathogen Mycosphaerella fijiensis
Authors: ROBERT S. , RAVIGNE V. , ZAPATER M‐F. , ABADIE C. , CARLIER J. 
Published: January 2012

AbstractReconstructing and characterizing introduction routes is a key step towards understanding the ecological and evolutionary factors underlying successful invasions and disease emergence. Here, we aimed to decipher scenarios of introduction and stochastic demographic events associated with the global spread of an emerging disease of bananas caused by the destructive fungal pathogen Mycosphaerella fijiensis. We analysed the worldwide population structure of this fungus using 21 microsatellites and 8 sequence‐based markers on 735 individuals from 37 countries. Our analyses designated South‐East Asia as the source of the global invasion and supported the location of the centre of origin of M. fijiensis within this area. We confirmed the occurrence of bottlenecks upon introduction into other continents followed by widespread founder events within continents. Furthermore, this study suggested contrasting introduction scenarios of the pathogen between the African and American continents. While potential signatures of admixture resulting from multiple introductions were detected in America, all the African samples examined seem to descend from a single successful founder event. In combination with historical information, our study reveals an original and unprecedented global scenario of invasion for this recently emerging disease caused by a wind‐dispersed pathogen.
Small regulatory RNAs control the multi‐cellular adhesive lifestyle of Escherichia coli
Authors: Jørgensen Mikkel Girke , Nielsen Jesper S. , Boysen Anders , Franch Thomas , Møller‐Jensen Jakob , Valentin‐Hansen Poul 
Published: January 2012

SummarySmall regulatory RNA molecules have recently been recognized as important regulatory elements of developmental processes in both eukaryotes and bacteria. We here describe a striking example in Escherichia coli that can switch between a single‐cell motile lifestyle and a multi‐cellular, sessile and adhesive state that enables biofilm formation on surfaces. For this, the bacterium needs to reprogramme its gene expression, and in many E. coli and Salmonella strains the lifestyle shift relies on control cascades that inhibit flagellar expression and activate the synthesis of curli, extracellular adhesive fibres important for co‐aggregation of cells and adhesion to biotic and abiotic surfaces. By combining bioinformatics, genetic and biochemical analysis we identified three small RNAs that act by an antisense mechanism to downregulate translation of CsgD, the master regulator of curli synthesis. Our demonstration that basal expression of each of the three RNA species is sufficient to downregulate CsgD synthesis and prevent curli formation indicates that all play a prominent role in the curli regulatory network. Our findings provide the first clue as to how the Rcs signalling pathway negatively regulates curli synthesis and increase the number of small regulatory RNAs that act directly on the csgD mRNA to five.
Implications of nasopharynx‐associated lymphoid tissue (NALT) in the development of allergic responses in an allergic rhinitis mouse model
Authors: Kim D.‐Y. , Fukuyama S. , Nagatake T. , Takamura K. , Kong I. G. , Yokota Y. , Lee C. H. , Kiyono H. 
Published: January 2012

AbstractBackgroundNasopharynx‐associated lymphoid tissue (NALT) serves as an important inductive site for mucosal immunity in the upper respiratory tract. Despite its importance in the mucosal immune system, little is known regarding the role of NALT in airway allergic immune responses. We aimed to elucidate the role of NALT in the induction of upper airway allergic responses in a mouse model.MethodsInhibitor of DNA binding/differentiation 2 (Id2)−/− and Id2+/− mice was exposed to the ovalbumin (OVA)‐induced allergic rhinitis model, because the former resulted in the NALT deficiency. The allergic parameters, such as allergic symptoms, serum OVA‐specific immunoglobulin E (IgE) levels, eosinophil infiltration, and cytokine profiles in the nasal mucosa, were compared between Id2−/− and Id2+/− groups.ResultsNALT‐null, Id2−/− mice displayed significantly lower allergic responses compared with Id2+/− mice, as demonstrated by lower levels of allergic symptoms, serum OVA‐specific IgE, eosinophilic infiltration, and local Th2 cytokine transcriptions. To determine which of two factors, that is, the absence of NALT or the alteration of immunocompetent cell populations caused by the Id2 deficiency, has a larger effect on the attenuated allergic immune responses in Id2−/− mice, lethally irradiated Id2−/− mice were engrafted with C57BL/6 wild‐type bone marrow cells and showed still significantly lower allergic immune responses compared with equally treated Id2+/− mice. In addition, IgE class switch recombination‐associated molecules, such as ε immunoglobulin heavy‐chain germline gene transcript, ε mRNA, and activation‐induced cytidine deaminase mRNA, were detected in NALT from OVA‐sensitized wild‐type mice.ConclusionThese results show the critical role of NALT for the induction of allergic responses in the upper airway at least in part by means of class switching to IgE in situ.
Venous flow dynamics during spinal block in normotensive and hypertensive elderly patients: a duplex ultrasonographic study
Authors: KIL H. K. , SUK E. H. , LEE M. H. , BANG E. C. , HONG J‐Y. 
Published: January 2012

BackgroundSpinal block induces hyperkinetic change in lower extremity blood flow. We compared the venous flow dynamic responses to spinal block in normotensive and hypertensive elderly patients.MethodsFollowing spinal block using 10 mg 0.5% (w/v) bupivacaine, we measured changes in blood pressure, heart rate, and venous flow dynamics of the popliteal vein by duplex ultrasonography in 20 normotensive (NBP group) and 18 hypertensive (HIBP group) patients.ResultsSpinal block caused significant decreases in blood pressure in both groups; similar rates of hypotension were observed. At baseline, peak velocity, time‐averaged maximum velocity, and time‐averaged mean velocity were higher in the HIBP than in the NBP group. During spinal block, peak velocity increased in both groups, and the between‐group differences were no longer significant. At baseline, volume flow in the two groups was similar and increased by 141.5% in the NBP and 131.7% in the HIBP group during spinal block.ConclusionsBlood pressure and flow dynamics in the popliteal vein showed similar changes during spinal anaesthesia in elderly patients taking antihypertensive medication and normotensive patients, despite differences in baseline values.
Central venous oxygen saturation is a good indicator of altered oxygen balance in isovolemic anemia
Authors: KOCSI S. , DEMETER G. , FOGAS J. , ÉRCES D. , KASZAKI J. , MOLNÁR Z. 
Published: January 2012

BackgroundRed blood cell transfusion is done primarily as a means to improve oxygen delivery (DO2). Current transfusion guidelines are based solely on hemoglobin levels, regardless of actual DO2 need. As central venous oxygen saturation (ScvO2) may reflect imbalances in DO2 and consumption (VO2) the aim of this study was to investigate the value of ScvO2 as an indicator of oxygen balance in isovolemic anemia.MethodsAfter splenectomy, anesthetized Vietnamese mini pigs (n = 13, weight range: 18–30 kg) underwent controlled bleeding in five stages (T0–T5). During each stage approximately 10% of the estimated starting total blood volume was removed and immediately replaced with an equal volume of colloid. Hemodynamic measurements and blood gas analysis were then performed.ResultsEach stage of bleeding resulted in a significant fall in hemoglobin, T0: 125 (113–134) to T5: 49 (43–55) g/l [T0: 7.7 (6.9–8.2) to T5: 3.0 (2.6–3.4) mmol/l]. The O2‐extraction (VO2/DO2) increased significantly only from T3: 35 (21–40) %, P < 0.05. The change of ScvO2 showed a similar pattern and dropped below the physiological threshold of 70% at T4: 68 (61–76) %. At this point, hemoglobin was below the recommended transfusion trigger value, 59 (53–67) g/l [3.6 (3.3–4.1) mmol/l]. There was a strong significant association between ScvO2 (< 70%) and VO2/DO2 (> 30%): r = −0.71, r2 = 0.50, P < 0.001.ConclusionThe results of this study show that ScvO2 reflects changes of VO2/DO2 in isovolemic anemia better than Hb alone, therefore it may be used as an additional indicator of blood transfusion in clinical practice.
Xenon is not superior to isoflurane on cardiovascular function during experimental acute pulmonary hypertension
Authors: ROEHL A. B. , STEENDIJK P. , ROSSAINT R. , BLEILEVENS C. , GOETZENICH A. , HEIN M. 
Published: January 2012

BackgroundAcute right ventricular afterload increase is a known perioperative challenge for the anaesthetic regime especially for patients with a compromised right ventricle. The accused negative inotropic action of volatile anaesthetics, with the exception of xenon, might be crucial for the adaptation of the right ventricle.MethodsReversible pulmonary hypertension (mean pressure 40 mmHg) was induced by an infusion of the stable thromboxane A2 analog U46619 in a porcine model (n = 35). The effects of 70 vol% xenon and 0.9 vol% isoflurane on biventricular function were studied by conductance catheter technique. Inflammation and myocardial injury was quantified using serum probes [tumour necrosis factor α (TNFα), interleukin 6 (IL‐6), troponin] and myocardial tissue [B natriuretic peptide (BNP), TNFα, activated caspase 3] by enzyme‐linked immunosorbance assays and reverse‐transcription polymerase chain reaction.ResultsAfter wash in of xenon global haemodynamic parameters remained stable whereas isoflurane caused a systemic vasodilation. This led to a significant decrease in mean arterial pressure in the isoflurane group whereas cardiac output remained stable. Both substances did not alter the biventricular contractility nor did they induce changes in preload for both ventricles. Xenon led to an additional increase in right ventricular afterload, whereas isoflurane reduced pulmonary vascular resistance. No effects on systemic inflammatory response and myocardial injury were found, whereas higher apoptosis rate and expression of BNP and IL‐6 was determined in the right ventricle.ConclusionsThese results do not support the idea that xenon is more beneficial than isoflurane in right ventricular failure during pulmonary hypertension. Isoflurane did not compromise systolic ventricular function during acute PHT it only led to vasodilation in contrast to xenon.