bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth
Authors: Lu Qiang , Shao Fenjuan , Macmillan Colleen , Wilson Iain W. , van der Merwe Karen , Hussey Steven G. , Myburg Alexander A. , Dong Xiaomei , Qiu Deyou 
Published: May 2017

SummaryLateral Organ Boundaries Domain (LBD) proteins are plant‐specific transcription factors playing crucial roles in growth and development. However, the function of LBD proteins in Eucalyptus grandis remains largely unexplored. In this study, LBD genes in E. grandis were identified and characterized using bioinformatics approaches. Gene expression patterns in various tissues and the transcriptional responses of EgLBDs to exogenous hormones were determined by qRT‐PCR. Functions of the selected EgLBDs were studied by ectopically overexpressing in a hybrid poplar (Populus alba × Populus glandulosa). Expression levels of genes in the transgenic plants were investigated by RNA‐seq. Our results showed that there were forty‐six EgLBD members in the E. grandis genome and three EgLBDs displayed xylem‐ (EgLBD29) or phloem‐preferential expression (EgLBD22 and EgLBD37). Confocal microscopy indicated that EgLBD22, EgLBD29 and EgLBD37 were localized to the nucleus. Furthermore, we found that EgLBD22, EgLBD29 and EgLBD37 were responsive to the treatments of indol‐3‐acetic acid and gibberellic acid. More importantly, we demonstrated EgLBDs exerted different influences on secondary growth. Namely, 35S::EgLBD37 led to significantly increased secondary xylem, 35S::EgLBD29 led to greatly increased phloem fibre production, and 35S::EgLBD22 showed no obvious effects. We revealed that key genes related to gibberellin, ethylene and auxin signalling pathway as well as cell expansion were significantly up‐ or down‐regulated in transgenic plants. Our new findings suggest that LBD genes in E. grandis play important roles in secondary growth. This provides new mechanisms to increase wood or fibre production.
A comprehensive investigation of starch degradation process and identification of a transcriptional activator MabHLH6 during banana fruit ripening
Authors: Xiao Yun‐yi , Kuang Jian‐fei , Qi Xin‐na , Ye Yu‐jie , Wu Zhen‐Xian , Chen Jian‐ye , Lu Wang‐jin 
Published: May 2017

SummaryAlthough starch degradation has been well studied in model systems such as Arabidopsis leaves and cereal seeds, this process in starchy fruits during ripening, especially in bananas, is largely unknown. In this study, 38 genes encoding starch degradation‐related proteins were identified and characterized from banana fruit. Expression analysis revealed that 27 candidate genes were significantly induced during banana fruit ripening, with concomitant conversion of starch‐to‐sugars. Furthermore, iTRAQ‐based proteomics experiments identified 18 starch degradation‐associated enzymes bound to the surface of starch granules, of which 10 were markedly up‐regulated during ripening. More importantly, a novel bHLH transcription factor, MabHLH6, was identified based on a yeast one‐hybrid screening using MaGWD1 promoter as a bait. Transcript and protein levels of MabHLH6 were also increased during fruit ripening. Electrophoretic mobility shift assays, chromatin immunoprecipitation and transient expression experiments confirmed that MabHLH6 activates the promoters of 11 starch degradation‐related genes, including MaGWD1, MaLSF2, MaBAM1, MaBAM2, MaBAM8, MaBAM10, MaAMY3, MaAMY3C, MaISA2, MaISA3 and MapGlcT2‐2 by recognizing their E‐box (CANNTG) motifs present in the promoters. Collectively, these findings suggest that starch degradation during banana fruit ripening may be attributed to the complex actions of numerous enzymes related to starch breakdown at transcriptional and translational levels, and that MabHLH6 may act as a positive regulator of this process via direct activation of a series of starch degradation‐related genes.
Time‐Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome‐Related Photoreceptors
Authors: Losi Aba , Bonomi Hernán R. , Michael Norbert , Tang Kun , Zhao Kai‐Hong 
Published: May 2017

AbstractTime‐resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light‐induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20 ns and 5 μs. Here, we report PA measurements on diverse photochromic bilin‐binding photoreceptors of prokaryotic origin: (1) the chromophore‐binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full‐length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub‐ns scale, reflecting the low photoisomerization quantum yield (<0.2). This “prompt” step is accompanied by a positive ΔV1 = 5–12.5 mL mol−1. Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3‐G for which ΔV1 = +4.5 mL mol−1 is followed by a time‐resolved, energy‐conserving contraction ΔV2 = −11.4 mL mol−1, τ2 = 180 ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3‐G.
RPE65 and the Accumulation of Retinyl Esters in Mouse Retinal Pigment Epithelium
Authors: Sheridan Colleen , Boyer Nicholas P. , Crouch Rosalie K. , Koutalos Yiannis 
Published: May 2017

AbstractThe RPE65 protein of the retinal pigment epithelium (RPE) enables the conversion of retinyl esters to the visual pigment chromophore 11‐cis retinal. Fresh 11‐cis retinal is generated from retinyl esters following photoisomerization of the visual pigment chromophore to all‐trans during light detection. Large amounts of esters accumulate in Rpe65−/− mice, indicating their continuous formation when 11‐cis retinal generation is blocked. We hypothesized that absence of light, by limiting the conversion of esters to 11‐cis retinal, would also result in the build‐up of retinyl esters in the RPE of wild‐type mice. We used HPLC to quantify ester levels in organic extracts of the RPE from wild‐type and Rpe65−/− mice. Retinyl ester levels in Sv/129 wild‐type mice that were dark adapted for various intervals over a 4‐week period were similar to those in mice raised in cyclic light. In C57BL/6 mice however, which contain less Rpe65 protein, dark adaptation was accompanied by an increase in ester levels compared to cyclic light controls. Retinyl ester levels were much higher in Rpe65−/− mice compared to wild type and kept increasing with age. The results suggest that the RPE65 role in retinyl ester homeostasis extends beyond enabling the formation of 11‐cis retinal.
Novel Thermostable Flavin‐binding Fluorescent Proteins from Thermophilic Organisms
Authors: Wingen Marcus , Jaeger Karl‐Erich , Gensch Thomas , Drepper Thomas 
Published: May 2017

AbstractFlavin‐binding fluorescent proteins (FbFPs) are small, oxygen‐independent in vivo reporters, derived from Light Oxygen Voltage (LOV) domains of photoreceptors. Here, we investigated the thermostability of existing, as well as novel FbFPs, whose genes were identified in genome sequences of various thermophilic bacteria as well as metagenomic libraries from hot springs in the Yellowstone National Park. Detailed in vitro analyses revealed that two of those fluorescent reporter proteins were highly thermostable, exhibiting melting temperatures above 75°C.
Proteorhodopsin Photocycle Kinetics Between pH 5 and pH 9
Authors: Köhler Thomas , Weber Ingrid , Glaubitz Clemens , Wachtveitl Josef 
Published: May 2017

AbstractThe retinal protein proteorhodopsin is a homolog of the well‐characterized light‐driven proton pump bacteriorhodopsin. Basic mechanisms of proton transport seem to be conserved, but there are noticeable differences in the pH ranges of proton transport. Proton transport and protonation state of a carboxylic acid side chain, the primary proton acceptor, are correlated. In case of proteorhodopsin, the pKa of the primary proton acceptor Asp‐97 (pKa ≈ 7.5) is unexpectedly close to environmental pH (pH ≈ 8). A significant fraction of proteorhodopsin is possibly inactive at natural pH, in contrast to bacteriorhodopsin. We investigated photoinduced kinetics of proteorhodopsin between pH 5 and pH 9 by time resolved UV/vis absorption spectroscopy. Kinetics is inhomogeneous within that pH region and can be considered as a superposition of two fractions. These fractions are correlated with the Asp‐97 titration curve. Beside Asp‐97, protonation equilibria of other groups influence kinetics, but the observations do not point toward major differences of primary proton acceptor function in proteorhodopsin and bacteriorhodopsin. The pKa of proteorhodopsin and some of its variants is suspected to be an example of molecular adaptation to the physiology of the original organisms.
Bacterial Photosensory Proteins and Their Role in Plant–pathogen Interactions
Authors: Kraiselburd Ivana , Moyano Laura , Carrau Analía , Tano Josefina , Orellano Elena G. 
Published: May 2017

AbstractLight is an important environmental signal for almost all living organisms. The light perception is achieved by photoreceptor proteins. As can be observed from the great number of bacterial genomes sequenced, plant pathogenic bacteria encode for a large number of photoreceptor proteins. The physiological implications of these photoreceptors are still poorly characterized. However, recent studies revealed the participation of these photosensory proteins in the pathogenic process. Here, we summarize what is known about these proteins and their role during the virulence process, concluding that the light environment modulates the plant–pathogen interaction.
UV‐Resistant Actinobacteria from High‐Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities
Authors: Rasuk María Cecilia , Ferrer Gabriela Mónica , Kurth Daniel , Portero Luciano Raúl , Farías María Eugenia , Albarracín Virginia Helena 
Published: May 2017

AbstractPolyextremophiles are present in a wide variety of extreme environments in which they must overcome various hostile conditions simultaneously such as high UVB radiation, extreme pHs and temperatures, elevated salt and heavy‐metal concentration, low‐oxygen pressure and scarce nutrients. High‐altitude Andean lakes (HAALs; between 2000 and 4000 m) are one example of these kinds of ecosystems suffering from the highest total solar and UVB radiation on Earth where an abundant and diverse polyextremophilic microbiota was reported. In this work, we performed the first extensive isolation of UV‐resistant actinobacteria from soils, water, sediments and modern stromatolites at HAALs. Based on the 16S rRNA sequence, the strains were identified as members of the genera Streptomyces, Micrococcus, Nesterenkonia, Rhodococcus, Microbacterium, Kocuria, Arthrobacter, Micromonospora, Blastococcus, Citrococcus and Brevibacterium. Most isolates displayed resistance to multiple environmental stress factors confirming their polyextremophilic nature and were able to produce effective antimicrobial compounds. HAALs constitute a largely unexplored repository of UV‐resistant actinobacteria, with high potential for the biodiscovery of novel natural products.
Integration of Temperature and Blue‐Light Sensing in Acinetobacter baumannii Through the BlsA Sensor
Authors: Abatedaga Inés , Valle Lorena , Golic Adrián E. , Müller Gabriela L. , Cabruja Matías , Morán Vieyra Faustino E. , Jaime Paula C. , Mussi María Alejandra , Borsarelli Claudio D. 
Published: May 2017

AbstractBlsA is a BLUF photoreceptor present in Acinetobacter baumannii, responsible for modulation of motility, biofilm formation and virulence by light. In this work, we have combined physiological and biophysical evidences to begin to understand the basis of the differential photoregulation observed as a function of temperature. Indeed, we show that blsA expression is reduced at 37°C, which correlates with negligible photoreceptor levels in the cells, likely accounting for absence of photoregulation at this temperature. Another point of control occurs on the functionality of the BlsA photocycle itself at different temperatures, which occurs with an average quantum yield of photoactivation of the signaling state of 0.20 ± 0.03 at 15°C < T < 25°C, but is practically inoperative at T > 30°C, as a result of conformational changes produced in the nanocavity of FAD. This effect would be important when the photoreceptor is already present in the cell to avoid almost instantaneously further signaling process when it is no longer necessary, for example under circumstances of temperature changes possibly faced by the bacteria. This complex interplay between light and temperature would provide the bacteria clues of environmental location and dictate/modulate light photosensing in A. baumannii.
Casting Away the Shadows: Elucidating the Role of Light‐mediated Posttranscriptional Control in Plants
Authors: Hernando Carlos E. , Garcia Carolina , Mateos Julieta L. 
Published: May 2017

AbstractLight signals trigger precise changes in gene expression networks that activate distinctive developmental programs in plants. The transcriptome is shaped at different stages, both by the regulation of gene expression and also by posttranscriptional mechanisms that alter the sequence or abundance of the transcripts generated. Posttranscriptional mechanisms have attracted much interest in recent years with the advent of high‐throughput technologies and bioinformatics tools. One such posttranscriptional process, alternative splicing, increases proteome diversity without increasing gene number by changing the function of individual proteins, while another, miRNA‐mediated gene silencing, fine‐tunes the amount of mRNA produced. The manner in which plants make use of these two crucial posttranscriptional mechanisms to respond to light and adapt to their environment is the focus of active research. In this review, we summarize the current knowledge of light‐mediated posttranscriptional control in Arabidopsis thaliana and focus on the biological impact of the various posttranscriptional processes. We also discuss a potential cross talk between the alternative splicing and miRNA pathways, highlighting the complexity of light responsiveness.
Excitation Energies of Canonical Nucleobases Computed by Multiconfigurational Perturbation Theories
Authors: Wiebeler Christian , Borin Veniamin , Sanchez de Araújo Adalberto Vasconcelos , Schapiro Igor , Borin Antonio Carlos 
Published: May 2017

AbstractIn this computational work, we assessed the performance of ab initio multireference (MR) methods for the calculation of vertical excitation energies of five nucleobases: adenine, guanine, cytosine, thymine and uracil. In total, we have studied 38 singlet and 30 triplet excited states. Where possible we used the multireference configuration interaction (MRCI) method as a reference for various flavors of multireference perturbation theory to second order. In particular, we have benchmarked CASPT2, NEVPT2 and XMCQDPT2. For CASPT2, we have analyzed the single‐state, multistate (MS) and extended MS variants. In addition, we have assessed the effect of the ionization potential electron affinity (IPEA) shift. For NEVPT2, we have used the partially and the strongly contracted variants. Further, we have tested the commonly used RI‐CC2, RI‐ADC2 and EOM‐CCSD methods. Generally, we observe the following trends for singlet excited states: NEVPT2 is the closest MR method to MRCISD+Q, closely followed by CASPT2 with the default IPEA shift. The same trend is observed for triplet states, although NEVPT2 and CASPT2‐IPEA are getting closer. Interestingly, the n, π* singlet excited states were described more accurately than π, π* excited states, while for triplet states the trend is inverted except for NEVPT2. This work is an important benchmark for future photochemical investigations.
Nonablative fractional laser‐assisted daylight photodynamic therapy with topical methyl aminolevulinate for moderate to severe facial acne vulgaris: Results of a randomized and comparative study
Authors: Kim Tae In , Ahn Hye‐Jin , Kang In Hye , Jeong Ki‐Heon , Kim Nack In , Shin Min Kyung 
Published: May 2017

SummaryBackgroundPhotodynamic therapy (PDT) has been reported as an effective alternative treatment for patients with acne.PurposeTo evaluate the efficacy and safety of DL‐PDT in moderate to severe acne and to compare outcomes with those of laser‐assisted daylight photodynamic therapy.MethodsPatients were randomly assigned to either a DL‐PDT group (D group) or a fractional laser‐assisted DL‐PDT group (F group). The outcomes were assessed by measuring acne lesion counts and severity grade at 4, 8, 12, and 16 weeks after therapy commenced.ResultsTwenty‐eight subjects completed the study. Compared with baseline, the mean inflammatory lesion counts significantly decreased by 36.0% in the D group and 51.8% in the F group at 8 weeks (P<.001). The mean acne severity grades in both groups significantly decreased starting at 4 weeks (P=.012), and the beneficial effects lasted 16 weeks.ConclusionDL‐PDT with MAL shows clinically good responses to inflammatory lesions and is well tolerated in patients with moderate to severe acne.
Patients’ perception of disease and experience with type 2 diabetes patient education in Denmark
Authors: Laursen Ditte Hjorth , Frølich Anne , Christensen Ulla 
Published: May 2017

BackgroundPatient education programmes for a range of chronic conditions are widely implemented, but studies have shown that not all participants benefit equally from the patient education programmes.AimTo explore differences in how persons with diabetes experience diabetes‐related patient education programmes.MethodsQualitative in‐depth interviews were conducted with eleven participants 6 months after participation in patient education. Using thematic analysis, we identified three themes: programme elements, interactions between participants and the role of facilitators. We used Alonzo's theory of Everyday Illness Behaviour and reported restrictions in daily activities to categorise seven participants as ‘healthy’ and four as ‘ill’ and compare their experiences of patient education.ResultsAlthough all participants identified information on diet and exercise as the most beneficial programme element, healthy participants found this information easy to understand and apply to make healthy changes in their daily lives. Ill participants found the information difficult to understand and were much less likely to implement related changes. Healthy participants valued social interactions occurring during interactive programme components such as weigh‐in sessions, physical exercise and cooking classes. In contrast, ill participants did not value these social interactions. Healthy participants also tended to view programme facilitators more positively. Regardless of disease status, participants found it motivating to compare their health status to that of participants they perceived as more ill than themselves.ConclusionPatient education experiences differ according to self‐perceived disease status. Programme facilitators should be sensitive to the possibility that participants who are more ill may be less likely to perceive patient education as beneficial and implement new behaviours. Knowledge about factors leading to differences in patient experiences of chronic disease self‐management education programmes is essential for the development of programmes that benefit all patients. Future research should explore the value of programmes differentiated for participants with different levels of health.
Phaeohyphomycosis due to Exophiala infections in solid organ transplant recipients: Case report and literature review
Authors: Oberlin Kate E. , Nichols Anna J. , Rosa Rossana , Dejman Adriana , Mattiazzi Adela , Guerra Giselle , Elgart George W. , Abbo Lilian M. 
Published: May 2017

AbstractThis case report and literature review underscores the cutaneous presentations of phaeohyphomycosis in the solid organ transplant population. Increased cognizance with prompt identification is critical. The therapy and clinical outcomes of phaeohyphomycosis, caused by the Exophiala genus, in the solid organ transplant population, is analyzed to examine optimal care. This review highlights the inherent difficulties in providing the appropriate duration of antifungal therapy to avoid relapsing infections in immunosuppressed patients.
Ex vivo biomechanical stability of 5 cricoid‐suture constructs for equine laryngoplasty
Authors: Brandenberger Olivier , Rossignol Fabrice , Perkins Justin D. , Lechartier Antoine , Mespoulhès‐Rivière Céline , Vitte Amelie , Rossignol Anthony , Ducharme Norm , Boening Karl Joseph 
Published: May 2017

AbstractObjectiveTo determine the biomechanical properties of 5 suture constructs in the equine cricoid under cyclic loading and load to failure testing.Study designEx vivo study.SamplesSeventy‐five equine cadaver larynges.MethodsEach larynx was implanted with 1 of 5 cricoid‐suture constructs. The standard laryngoplasty, where a suture is passed once through the cricoid, including its caudal edge, was used in 2 constructs: 1 with 5 USP Ethibond (ES) and 1 with 2 mm Fibertape (FS). In the third construct, the 2 mm Fibertape was passed twice through the cricoid including its caudal edge (Double Loop—DL). Constructs 4 and 5 used 2 mm Fibertape in a U‐shaped loop passed through the cricoid but excluding its caudal edge. One construct was supported with a metallic button (MB) on the caudo‐ventral aspect of the cricoid while the other included only the U‐shaped loop (U). Constructs were subjected to cyclic loading and to single cycle to failure. Reduction of the left‐to‐right arytenoid angle quotient (LRQ), suture migration, and load at failure were compared.ResultsLRQ reduction after cyclic loading was lower in MB and U than ES constructs. During cyclic loading, suture migration was reduced in MB, U, and DL compared to ES constructs. Mean load at failure was lower in FS and U than in ES constructs.ConclusionLoss of abduction after equine laryngoplasty may be reduced and pullout forces increased by applying a MB construct in the cricoid cartilage. In vivo testing is required to verify these results.