bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corals shed bacteria as a potential mechanism of resilience to organic matter enrichment
Authors: Garren Melissa , Azam Farooq 
Published: December 2011

Abstract
Understanding the mechanisms of resilience of coral reefs to anthropogenic stressors is a critical step toward mitigating their current global decline. Coral–bacteria associations are fundamental to reef health and disease, but direct observations of these interactions remain largely unexplored. Here, we use novel technology, high-speed laser scanning confocal microscopy on live coral (Pocillopora damicornis), to test the hypothesis that corals exert control over the abundance of their associated bacterial communities by releasing (‘shedding’) bacteria from their surface, and that this mechanism can counteract bacterial growth stimulated by organic inputs. We also test the hypothesis that the coral pathogen Vibrio coralliilyticus can evade such a defense mechanism. This first report of direct observation with high-speed confocal microscopy of living coral and its associated bacterial community revealed a layer (3.3–146.8 μm thick) on the coral surface where bacteria were concentrated. The results of two independent experiments showed that the bacterial abundance in this layer was not sensitive to enrichment (5 mg l−1 peptone), and that coral fragments exposed to enrichment released significantly more bacteria from their surfaces than control corals (P&lt;0.01; 35.9±1.4 × 105 cells cm−2 coral versus 1.3±0.5 × 105 cells cm−2 coral). Our results provide direct support to the hypothesis that shedding bacteria may be an important mechanism by which coral-associated bacterial abundances are regulated under organic matter stress. Additionally, the novel ability to watch this ecological behavior in real-time at the microscale opens an unexplored avenue for mechanistic studies of coral–microbe interactions.
Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice
Authors: Knief Claudia , Delmotte Nathanaël , Chaffron Samuel , Stark Manuel , Innerebner Gerd , Wassmann Reiner , von Mering Christian , Vorholt Julia A 
Published: December 2011

Abstract
The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.
Coral-associated marine fungi form novel lineages and heterogeneous assemblages
Authors: Amend Anthony S , Barshis Daniel J , Oliver Thomas A 
Published: December 2011

Abstract
Coral stress tolerance is intricately tied to the animal's association with microbial symbionts. The most well-known of these symbioses is that between corals and their dinoflagellate photobionts (Symbiodinium spp.), whose genotype indirectly affects whether a coral can survive cyclical and anthropogenic warming events. Fungi comprise a lesser-known coral symbiotic community whose taxonomy, stability and function is largely un-examined. To assess how fungal communities inside a coral host correlate with water temperature and the genotype of co-occurring Symbiodinium, we sampled Acropora hyacinthus coral colonies from adjacent natural pools with different water temperatures and Symbiodinium identities. Phylogenetic analysis of coral-associated fungal ribosomal DNA amplicons showed a high diversity of Basidiomycetes and Ascomycetes, including several clades separated from known fungal taxa by long and well-supported branches. Community similarity did not correlate with any measured variables, and total fungal community composition was highly variable among A. hyacinthus coral colonies. Colonies in the warmer pool contained more phylogenetically diverse fungal communities than the colder pool and contained statistically significant ‘indicator’ species. Four taxa were present in all coral colonies sampled, and may represent obligate associates. Messenger RNA sequenced from a subset of these same colonies contained an abundance of transcripts involved in metabolism of complex biological molecules. Coincidence between the taxonomic diversity found in the DNA and RNA analysis indicates a metabolically active and diverse resident marine fungal community.
Characterization and adaptive optical correction of aberrations during in vivo imaging in the mouse cortex
Authors: Ji Na , Sato Takashi R. , Betzig Eric 
Published: December 2011

The signal and resolution during in vivo imaging of the mouse brain is limited by sample-induced optical aberrations. We find that, although the optical aberrations can vary across the sample and increase in magnitude with depth, they remain stable for hours. As a result, two-photon adaptive optics can recover diffraction-limited performance to depths of 450 μm and improve imaging quality over fields of view of hundreds of microns. Adaptive optical correction yielded fivefold signal enhancement for small neuronal structures and a threefold increase in axial resolution. The corrections allowed us to detect smaller neuronal structures at greater contrast and also improve the signal-to-noise ratio during functional Ca2+imaging in single neurons.
Aortic arch enlargement and coarctation repair through a left thoracotomy: significance of ductal perfusion
Authors: Dave Hitendu , Rosser Barbara , Reineke Kim , Nguyen-Minh Sylvie , Knirsch Walter , Prêtre René 
Published: December 2011

Abstract

OBJECTIVE
To analyse the technique of neonatal aortic arch enlargement without cardiopulmonary bypass through a left posterior thoracotomy, as an adjunct to extended resection for Coarctation and severe arch hypoplasia.

METHODS
Ten neonates with coarctation, severe arch hypoplasia and a persistent ductus arteriosus (PDA) were subjected to arch repair through a left posterior thoracotomy. Nine of these patients had associated significant intracardiac anomalies; three of them received pulmonary artery (PA) banding. After exclusion from circulation, the roof of the intervening arch between left carotid and left subclavian was enlarged using a patch. After adequate reperfusion, a classic resection and extended end-to-end anastomosis was performed. Median age and weight were 5.5 (1–10) days and 3.3 (2.2–4.1) kg respectively. The median preoperative arch diameter was 1.07 (0.75–1.32) mm/kg body weight.

RESULTS
All patients could be successfully operated with this approach. The non-ischaemic and ischaemic aortic clamp times were 40 (15–68) and 23 (18–32) min, respectively. The median postoperative arch diameter achieved was 1.43 (1.06–1.46) mm/kg body weight. None of the patients had significant gradient early postoperatively. Two patients with recurrent stenosis were successfully treated with balloon dilatation (1) or surgery with cardiopulmonary bypass (CPB) (1). One patient has a corrected gradient of 16 mmHg in the proximal arch which is being observed. The remaining patients are free from stenosis at a median follow-up of 30.1 (13.2–57.8) months.

CONCLUSIONS
Use of PDA for lower body perfusion allows complex reconstruction of the arch without incurring lower body ischaemia. The extended resection could then be performed without excessive stretch. This modification saves these patients from undergoing a complex arch reconstruction with CPB in the early neonatal period.
CCA1 and ELF3 Interact in the Control of Hypocotyl Length and Flowering Time in Arabidopsis
Authors: Lu Sheen X. , Webb Candace J. , Knowles Stephen M. , Kim Sally H.J. , Wang Zhiyong , Tobin Elaine M. 
Published: December 2011

Abstract
The circadian clock is an endogenous oscillator with a period of approximately 24 h that allows organisms to anticipate, and respond to, changes in the environment. In Arabidopsis (Arabidopsis thaliana), the circadian clock regulates a wide variety of physiological processes, including hypocotyl elongation and flowering time. CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is a central clock component, and CCA1 overexpression causes circadian dysfunction, elongated hypocotyls, and late flowering. EARLY FLOWERING3 (ELF3) modulates light input to the clock and is also postulated to be part of the clock mechanism. elf3 mutations cause light-dependent arrhythmicity, elongated hypocotyls, and early flowering. Although both genes affect similar processes, their relationship is not clear. Here, we show that CCA1 represses ELF3 by associating with its promoter, completing a CCA1-ELF3 negative feedback loop that places ELF3 within the oscillator. We also show that ELF3 acts downstream of CCA1, mediating the repression of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5 in the control of hypocotyl elongation. In the regulation of flowering, our findings show that ELF3 and CCA1 either cooperate or act in parallel through the CONSTANS/FLOWERING LOCUS T pathway. In addition, we show that CCA1 represses GIGANTEA and SUPPRESSOR OF CONSTANS1 by direct interaction with their promoters, revealing additional connections between the circadian clock and the flowering pathways.
Seasonal Abscisic Acid Signal and a Basic Leucine Zipper Transcription Factor, DkbZIP5, Regulate Proanthocyanidin Biosynthesis in Persimmon Fruit
Authors: Akagi Takashi , Katayama-Ikegami Ayako , Kobayashi Shozo , Sato Akihiko , Kono Atsushi , Yonemori Keizo 
Published: December 2011

AbstractProanthocyanidins (PAs) are secondary metabolites that contribute to plant protection and crop quality. Persimmon (Diospyros kaki) has a unique characteristic of accumulating large amounts of PAs, particularly in its fruit. Normal astringent-type and mutant nonastringent-type fruits show different PA accumulation patterns depending on the seasonal expression patterns of DkMyb4, which is a Myb transcription factor (TF) regulating many PA pathway genes in persimmon. In this study, attempts were made to identify the factors involved in DkMyb4 expression and the resultant PA accumulation in persimmon fruit. Treatment with abscisic acid (ABA) and an ABA biosynthesis inhibitor resulted in differential changes in the expression patterns of DkMyb4 and PA biosynthesis in astringent-type and nonastringent-type fruits depending on the development stage. To obtain an ABA-signaling TF, we isolated a full-length basic leucine zipper (bZIP) TF, DkbZIP5, which is highly expressed in persimmon fruit. We also showed that ectopic DkbZIP5 overexpression in persimmon calluses induced the up-regulation of DkMyb4 and the resultant PA biosynthesis. In addition, a detailed molecular characterization using the electrophoretic mobility shift assay and transient reporter assay indicated that DkbZIP5 recognized ABA-responsive elements in the promoter region of DkMyb4 and acted as a direct regulator of DkMyb4 in an ABA-dependent manner. These results suggest that ABA signals may be involved in PA biosynthesis in persimmon fruit via DkMyb4 activation by DkbZIP5.
Is epitope recognition of shrimp allergens useful to predict clinical reactivity?
Authors: Ayuso R. , Sánchez‐Garcia S. , Pascal M. , Lin J. , Grishina G. , Fu Z. , Ibáñez M. D. , Sastre J. , Sampson H. A. 
Published: December 2011

SummaryBackgroundShrimp is a frequent cause of severe allergic reactions world‐wide. Due to issues such as cross‐reactivity, diagnosis of shrimp allergy is still inaccurate, requiring the need for double‐blind, placebo‐controlled food challenges (DBPCFC). A better understanding of the relationship between laboratory findings and clinical reactivity is needed.ObjectiveTo determine whether sensitization to certain shrimp allergens or recognition of particular IgE epitopes of those allergens are good biomarkers of clinical reactivity to shrimp.MethodsThirty‐seven consecutive patients were selected with clinical histories of shrimp allergy. Skin prick test, specific IgE determinations, DBPCFC and immunoblot assays to shrimp extract were performed. IgE binding to synthetic overlapping peptides representing the sequence of the four allergens from the Pacific white shrimp (Litopenaeus vannamei) identified to date (Lit v1, Lit v2, Lit v3 and Lit v4) was analysed.ResultsOf 37 (46%) patients, 17 had a positive challenge to shrimp (11 children and 6 adults). By microarray, patients with positive challenges showed more intense binding to shrimp peptides than those with negative challenges. Statistically significant differences in terms of the frequency and intensity of IgE binding to some epitopes were observed between the two groups. Diagnostic efficiency was higher for individual epitopes than for proteins. Particularly, efficiency was highest for certain Lit v 1 and Lit v 2 epitopes, followed by Lit v 3 and Lit v 4 epitopes.Conclusion and Clinical RelevancePatients with positive shrimp challenges present in general more intense and diverse epitope recognition to all four shrimp allergens. IgE antibodies to these shrimp epitopes could be used as biomarkers for prediction of clinical reactivity in subjects with sensitization to shrimp. Patients with positive shrimp challenges show more intense sensitization and more diverse epitope recognition. Several IgE‐binding shrimp epitopes could be used as biomarkers for predicting clinical reactivity in subjects with sensitization to shrimp.
T‐cell receptor affinity in thymic development
Authors: Moran Amy E. , Hogquist Kristin A. 
Published: December 2011

SummaryUnderstanding the thymic processes that support the generation of functionally competent and self‐tolerant lymphocytes requires dissection of the T‐cell receptor (TCR) response to ligands of different affinities. In spatially segregated regions of the thymus, with unique expression of proteases and cytokines, TCR affinity guides a number of cell fate decisions. Yet affinity alone does not explain the selection paradox. Increasing evidence suggests that the ‘altered peptide’ model of the 1980s together with the affinity model might best explain how the thymus supports conventional and regulatory T‐cell development. Development of new tools to study the strength of TCR signals perceived by T cells, novel regulatory T‐cell transgenic mice, and tetramer enrichment strategies have provided an insight into the nature of TCR signals perceived during thymocyte development. These topics are discussed and support for the prevailing hypotheses is presented.
BiodentineTM induces TGF‐β1 release from human pulp cells and early dental pulp mineralization
Authors: Laurent P. , Camps J. , About I. 
Published: December 2011

Laurent P, Camps J, About I. Biodentine™ induces TGF‐β1 release from human pulp cells and early dental pulp mineralization. International Endodontic Journal, 45, 439–448, 2012.AbstractAim  To assess the ability of a recently developed tricalcium silicate‐based cement (Biodentine™) to induce reparative dentine synthesis and to investigate its capacity to modulate pulp cells TGF‐β1 secretion.Methodology  Biodentine™ was directly applied onto the dental pulp in an entire human tooth culture model. After various culture periods, the interaction of the material with dental pulp tissue was analysed on tissue sections. The effect of increasing surface area of this material on TGF‐β1 secretion was investigated on pulp cell cultures and compared with that of MTA, calcium hydroxide and Xeno®III adhesive resin. After performing artificial injuries on pulp cell cultures, the materials eluates were added for 24 h and then TGF‐β1 secretion was quantified by ELISA. Controls were performed by incubating intact cells with the culture medium, while injured cells TGF‐β1 level was used as the baseline value.Results  Biodentine™ induced mineralized foci formation early after its application. The mineralization appeared under the form of osteodentine and expressed markers of odontoblasts. Biodentine™ significantly increased TGF‐β1 secretion from pulp cells (P < 0.03) independently of the contact surface increase. This increase was also observed with calcium hydroxide and MTA, but not with the resinous Xeno®III. The statistical analysis showed statistically significant differences between capping materials and the resinous Xeno®III (P < 0.001).Conclusions  When Biodentine™ was applied directly onto the pulp, it induced an early form of reparative dentine synthesis, probably due to a modulation of pulp cell TGF‐β1 secretion.
Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents
Authors: Kissling W. D. , Dormann Carsten F. , Groeneveld Jürgen , Hickler Thomas , Kühn Ingolf , McInerny Greg J. , Montoya José M. , Römermann Christine , Schiffers Katja , Schurr Frank M. , Singer Alexander , Svenning Jens‐Christian , Zimmermann Niklaus E. , O’Hara Robert B. 
Published: December 2011

AbstractAim  Biotic interactions – within guilds or across trophic levels – have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of ‘species interaction distribution models’ (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices.Location  Local to global.Methods  We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions.Results  Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co‐occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non‐stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio‐temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species’ effect and response traits.Main conclusions  There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co‐occurrence datasets across large‐scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio‐temporal data on biotic interactions in multispecies communities.
A new timeframe for the diversification of Japan’s mammals
Authors: McKay Bailey D. 
Published: December 2011

AbstractAim The main Japanese islands are land‐bridge islands divided by the biogeographic division Blakiston’s Line and represent two natural laboratories for studying land‐bridge diversification. Colonization of the current mammal fauna has been dated to the middle to late Pleistocene using fossil evidence. The purpose of this paper is to apply a molecular clock to the genetic divergences between Japanese mammalian taxa and their sister mainland taxa to test the late Pleistocene land‐bridge colonization hypothesis.Location The main Japanese islands (Kyushu, Shikoku, Honshu and Hokkaido).Methods I used mitochondrial DNA (cytochromeb) and a species tree approach to estimate the divergence times of 24 Japanese non‐volant terrestrial mammal taxa and their mainland sister taxa using the program *beast. I then tested for evidence of non‐simultaneous divergence among these taxon‐pairs by controlling for expected coalescent stochasticity using the program MsBayes.Results Divergence events between taxa on Japan and their mainland sister taxa were significantly older than expected under the current paradigm, which is based on fossil data. Consistent with the land‐bridge colonization hypothesis, there was evidence of multiple divergence events.Main conclusions These results implicate a colonization timeframe that is older than posited by the current paradigm based on fossil evidence. However, these results are still consistent with the land‐bridge colonization hypothesis. Multiple periods of land‐bridge connectivity may account for the current mammalian fauna in Japan. In addition, half of the divergence time estimates in the Honshu–Shikoku–Kyushu region were clumped around 2.4 Ma, which might suggest a dramatic interchange period, concordant with a period of significant global cooling, when the first land bridge may have connected Japan to the mainland.
Spore formation in Myxococcus xanthus is tied to cytoskeleton functions and polysaccharide spore coat deposition
Authors: Müller Frank D. , Schink Christian W. , Hoiczyk Egbert , Cserti Emöke , Higgs Penelope I. 
Published: December 2011

SummaryMyxococcus xanthus is a Gram‐negative bacterium that differentiates into environmentally resistant spores. Spore differentiation involves septation‐independent remodelling of the rod‐shaped vegetative cell into a spherical spore and deposition of a thick and compact spore coat outside of the outer membrane. Our analyses suggest that spore coat polysaccharides are exported to the cell surface by the Exo outer membrane polysaccharide export/polysaccharide co‐polymerase 2a (OPX/PCP‐2a) machinery. Conversion of the capsule‐like polysaccharide layer into a compact spore coat layer requires the Nfs proteins which likely form a complex in the cell envelope. Mutants in either nfs, exo or two other genetic loci encoding homologues of polysaccharide synthesis enzymes fail to complete morphogenesis from rods to spherical spores and instead produce a transient state of deformed cell morphology before reversion into typical rods. We additionally provide evidence that the cell cytoskeletal protein, MreB, plays an important role in rod to spore morphogenesis and for spore outgrowth. These studies provide evidence that this novel Gram‐negative differentiation process is tied to cytoskeleton functions and polysaccharide spore coat deposition.