bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Although 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

Time‐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

The 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

Flavin‐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

The 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

Light 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

Polyextremophiles 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

BlsA 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

Light 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

In 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

Background

Photodynamic therapy (PDT) has been reported as an effective alternative treatment for patients with acne.

Purpose

To 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.

Methods

Patients 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.

Results

Twenty‐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.

Conclusion

DL‐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

Background

Patient 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.

Aim

To explore differences in how persons with diabetes experience diabetes‐related patient education programmes.

Methods

Qualitative 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.

Results

Although 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.

Conclusion

Patient 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

This 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

Objective

To determine the biomechanical properties of 5 suture constructs in the equine cricoid under cyclic loading and load to failure testing.

Study design

Ex vivo study.

Samples

Seventy‐five equine cadaver larynges.

Methods

Each 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.

Results

LRQ 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.

Conclusion

Loss 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.
A Piecewise Nonpolynomial Collocation Method for Fractional Differential Equations
Authors: Esmaeili Shahrokh
Published: May 2017

Since the solutions of the fractional differential equations (FDEs) have unbounded derivatives at zero, their numerical solutions by piecewise polynomial collocation method on uniform meshes will lead to poor convergence rates. This paper presents a piecewise nonpolynomial collocation method for solving such equations reflecting the singularity of the exact solution. The entire domain is divided into several small subdomains, and the nonpolynomial pieces are constructed using a block-by-block scheme on each subdomain. The method is applied to solve linear and nonlinear fractional differential equations. Numerical examples are given and discussed to illustrate the effectiveness of the proposed approach.
Electroplating lithium transition metal oxides
Authors: Zhang Huigang , Ning Hailong , Busbee John , Shen Zihan , Kiggins Chadd , Hua Yuyan , Eaves Janna , Davis Jerome , Shi Tan , Shao Yu-Tsun , Zuo Jian-Min , Hong Xuhao , Chan Yanbin , Wang Shuangbao , Wang Peng , Sun Pengcheng , Xu Sheng , Liu Jinyun , Braun Paul V.
Published: May 2017

Electrodeposition of lithium-ion battery cathodes enables ultraflexible, ultrathick, and high-power rechargeable batteries.
Three-dimensional system enabling the maintenance and directed differentiation of pluripotent stem cells under defined conditions
Authors: Zujur Denise , Kanke Kosuke , Lichtler Alexander C. , Hojo Hironori , Chung Ung-il , Ohba Shinsuke
Published: May 2017

A three-dimensional culture system enables maintenance of pluripotent stem cells (PSCs) and formation of PSC-derived organoids.
Fast iodide-SAD phasing for high-throughput membrane protein structure determination
Authors: Melnikov Igor , Polovinkin Vitaly , Kovalev Kirill , Gushchin Ivan , Shevtsov Mikhail , Shevchenko Vitaly , Mishin Alexey , Alekseev Alexey , Rodriguez-Valera Francisco , Borshchevskiy Valentin , Cherezov Vadim , Leonard Gordon A. , Gordeliy Valentin , Popov Alexander
Published: May 2017

A potentially universal method for the de novo solution of the crystal structures of membrane proteins is described.
Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy
Authors: Kawai Shigeki , Nishiuchi Tomohiko , Kodama Takuya , Spijker Peter , Pawlak Rémy , Meier Tobias , Tracey John , Kubo Takashi , Meyer Ernst , Foster Adam S.
Published: May 2017

Atomic force microscopy can image the hydrogen atoms of single molecules via very weak hydrogen bonding.
A subcellular map of the human proteome
Authors: Thul Peter J. , Åkesson Lovisa , Wiking Mikaela , Mahdessian Diana , Geladaki Aikaterini , Ait Blal Hammou , Alm Tove , Asplund Anna , Björk Lars , Breckels Lisa M. , Bäckström Anna , Danielsson Frida , Fagerberg Linn , Fall Jenny , Gatto Laurent , Gnann Christian , Hober Sophia , Hjelmare Martin , Johansson Fredric , Lee Sunjae , Lindskog Cecilia , Mulder Jan , Mulvey Claire M. , Nilsson Peter , Oksvold Per , Rockberg Johan , Schutten Rutger , Schwenk Jochen M. , Sivertsson Åsa , Sjöstedt Evelina , Skogs Marie , Stadler Charlotte , Sullivan Devin P. , Tegel Hanna , Winsnes Casper , Zhang Cheng , Zwahlen Martin , Mardinoglu Adil , Pontén Fredrik , von Feilitzen Kalle , Lilley Kathryn S. , Uhlén Mathias , Lundberg Emma
Published: May 2017

Mapping the proteome

Proteins function in the context of their environment, so an understanding of cellular processes requires a knowledge of protein localization. Thul
et al.
used immunofluorescence microscopy to map 12,003 human proteins at a single-cell level into 30 cellular compartments and substructures (see the Perspective by Horwitz and Johnson). They validated their results by mass spectroscopy and used them to model and refine protein-protein interaction networks. The cellular proteome is highly spatiotemporally regulated. Many proteins localize to multiple compartments, and many show cell-to-cell variation in their expression patterns. Presented as an interactive database called the Cell Atlas, this work provides an important resource for ongoing efforts to understand human biology.

Science
, this issue p.
eaal3321
; see also p.
806
Virion incorporation of integrin α4β7 facilitates HIV-1 infection and intestinal homing
Authors: Guzzo Christina , Ichikawa David , Park Chung , Phillips Damilola , Liu Qingbo , Zhang Peng , Kwon Alice , Miao Huiyi , Lu Jacky , Rehm Catherine , Arthos James , Cicala Claudia , Cohen Myron S. , Fauci Anthony S. , Kehrl John H. , Lusso Paolo
Published: May 2017

Anti–integrin α4β7 therapy might directly interfere with the ability of HIV to home to intestinal reserviors.
Carboxyl Analogue of Mutacin 1140, a Scaffold for Lead Antibacterial Discovery
Authors: Escano Jerome , Ravichandran Akshaya , Salamat Bita , Smith Leif
Published: May 2017

Mutacin 1140 belongs to the epidermin group of lantibiotics. Epidermin class lantibiotics are ribosomally synthesized and posttranslationally modified antibiotics with potent activity against Gram-positive bacteria. In particular, this class is effective at targeting drug-resistant
Streptococcus pneumoniae
, methicillin-resistant
Staphylococcus aureus
(MRSA),
Mycobacterium tuberculosis
, and
Clostridium difficile
. A C-terminal
S
-[(Z)-2-aminovinyl]-
d
-cysteine (AviCys) residue is derived from a decarboxylation of a terminal cysteine that is involved in lanthionine ring formation. Studies on mutacin 1140 have revealed new insight into the structural importance of the C-terminal AviCys residue. A C-terminal carboxyl analogue of mutacin 1140 was engineered. Capping the C-terminal carboxyl group with a primary amine restores bioactivity and affords a novel opportunity to synthesize new analogues. A C-terminal fluorescein-labeled mutacin 1140 analogue traps lipid II into a large lipid II lantibiotic complex, similar to that observed
in vivo
for the lantibiotic nisin. A C-terminal carboxyl analogue of mutacin 1140 competitively inhibits the activity of native mutacin 1140 and nisin. The presence of a C-terminal carboxyl group prevents the formation of the large lipid II lantibiotic complexes but does not prevent the binding of the lantibiotic to lipid II.

IMPORTANCE
This study addressed the importance of the C-terminal
S
-[(Z)-2-aminovinyl]-
d
-cysteine (AviCys) residue for antibacterial activity. We have learned that the posttranslational modification for making the AviCys residue is presumably important for the lateral assembly mechanism of activity that traps lipid II into a large complex. The C-terminal carboxyl analogue of this class of lantibiotics is agreeable to the addition of a wide variety of substrates. The addition of fluorescein enabled
in vivo
visualization of the epidermin class of lantibiotics in action. These results are significant because, as we demonstrate, the presence of the AviCys residue is not essential for bioactivity, but, more importantly, the removal of the carboxyl group is essential. The ability to make a C-terminal carboxyl analogue that is modifiable will facilitate the synthesis of novel analogues of the epidermin class of lantibiotics that can be developed for new applications.
RpoN (σ
54
) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain
Authors: Yu Dianzhen , Xia Ming , Zhang Liping , Song Yulong , Duan You , Yuan Tong , Yao Minjie , Wu Liyou , Tian Chunyuan , Wu Zhenbin , Li Xiangzhen , Zhou Jizhong , Qiu Dongru
Published: May 2017

Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium,
Aquincola
tertiaricarbonis
RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. A large gene cluster for exopolysaccharide biosynthesis and a gene encoding the alternative sigma factor RpoN1, one of the four paralogues, have been identified in floc formation-deficient mutants generated by transposon mutagenesis, and the gene functions have been further confirmed by genetic complementation analyses. Interestingly, the biosynthesis of exopolysaccharides remained in the
rpoN1
-disrupted flocculation-defective mutants, but most of the exopolysaccharides were secreted and released rather than bound to the cells. Furthermore, the expression of exopolysaccharide biosynthesis genes seemed not to be regulated by RpoN1. Taken together, our results indicate that RpoN1 may play a role in regulating the expression of a certain gene(s) involved in the self-flocculation of bacterial cells but not in the biosynthesis and secretion of exopolysaccharides required for floc formation.

IMPORTANCE
Floc formation confers bacterial resistance to predation of protozoa and plays a central role in the widely used activated sludge process. In this study, we not only identified a large gene cluster for biosynthesis of extracellular polysaccharides but also identified four
rpoN
paralogues, one of which (
rpoN1
) is required for floc formation in
A. tertiaricarbonis
RN12. In addition, this RpoN sigma factor regulates the transcription of genes involved in biofilm formation and swarming motility, as previously shown in other bacteria. However, this RpoN paralogue is not required for the biosynthesis of exopolysaccharides, which are released and dissolved into culture broth by the
rpoN1
mutant rather than remaining tightly bound to cells, as observed during the flocculation of the wild-type strain. These results indicate that floc formation is a regulated complex process, and other yet-to-be identified RpoN1-dependent factors are involved in self-flocculation of bacterial cells via exopolysaccharides and/or other biopolymers.
Sodium Lactate Negatively Regulates Shewanella putrefaciens CN32 Biofilm Formation via a Three-Component Regulatory System (LrbS-LrbA-LrbR)
Authors: Liu Cong , Yang Jinshui , Liu Liang , Li Baozhen , Yuan Hongli , Liu Weijie
Published: May 2017

The capability of biofilm formation has a major impact on the industrial and biotechnological applications of
Shewanella putrefaciens
CN32. However, the detailed regulatory mechanisms underlying biofilm formation in this strain remain largely unknown. In the present report, we describe a three-component regulatory system which negatively regulates the biofilm formation of
S. putrefaciens
CN32. This system consists of a histidine kinase LrbS (Sputcn32_0303) and two cognate response regulators, including a transcription factor, LrbA (Sputcn32_0304), and a phosphodiesterase, LrbR (Sputcn32_0305). LrbS responds to the signal of the carbon source sodium lactate and subsequently activates LrbA. The activated LrbA then promotes the expression of
lrbR
, the gene for the other response regulator. The bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) phosphodiesterase LrbR, containing an EAL domain, decreases the concentration of intracellular c-di-GMP, thereby negatively regulating biofilm formation. In summary, the carbon source sodium lactate acts as a signal molecule that regulates biofilm formation via a three-component regulatory system (LrbS-LrbA-LrbR) in
S. putrefaciens
CN32.

IMPORTANCE
Biofilm formation is a significant capability used by some bacteria to survive in adverse environments. Numerous environmental factors can affect biofilm formation through different signal transduction pathways. Carbon sources are critical nutrients for bacterial growth, and their concentrations and types significantly influence the biomass and structure of biofilms. However, knowledge about the underlying mechanism of biofilm formation regulation by carbon source is still limited. This work elucidates a modulation pattern of biofilm formation negatively regulated by sodium lactate as a carbon source via a three-component regulatory system in
S. putrefaciens
CN32, which may serve as a good example for studying how the carbon sources impact biofilm development in other bacteria.
Urothelial papilloma: a rare cause of gross haematuria in childhood
Authors: Ribeiro Andreia , Pereira Maria , Reis Armando , Ferreira Graça
Published: May 2017

Bladder urothelial papilloma is extremely rare in the paediatric population. It usually presents as painless gross haematuria and its diagnosis implies a high index of suspicion as other causes of haematuria predominate in this age range. We describe a 9-year-old boy with two episodes of gross haematuria occurring 1 year apart with spontaneous resolution after 2 days. Bladder ultrasound revealed an endovesical papillary lesion of 24×24 mm suggestive of bladder tumour. The diagnosis was confirmed by histopathological examination of the specimen obtained by cystoscopy with transurethral resection. After 3 years of follow-up with ultrasound and cystoscopy, there are no signs of recurrence. Due to the low prevalence of urothelial papilloma, paediatric guidelines for appropriate management and follow-up are unavailable, making this a challenging entity.
Conjunctival lymphangiectasia associated with classic Fabry disease
Authors: Sivley Melanie D , Wallace Eric L , Warnock David G , Benjamin William J
Published: May 2017

Background

Fabry disease (FD) is a treatable multisystem disease caused by a defect in the alpha-galactosidase gene. Ocular signs of FD, including corneal verticillata, are among the earliest diagnostic findings. Conjunctival lymphangiectasia (CL) has not previously been associated with FD.

Methods

We examined the eyes of a cohort of 13 adult patients, eight men and five women, with documented classic FD, all treated with enzyme replacement therapy (ERT) at the University of Alabama at Birmingham between February 2014 and April 2015. The average age was 48 years with a range of 35–55 years for men and 21–71 years for women. The mean duration of ERT was 8.4 years (men 8.9 years, women 7.6 years) with a range of 4–14 years. Classical Fabry mutations included Q283X, R227X, W236X and W277X. A high resolution Haag-Streit BQ-900 slit lamp with EyeCap imaging system was used to record conjunctival images.

Results

CL was observed in 11 of the 13 patients (85%) despite long-term ERT. Clinical presentations included single cysts, beaded dilatations and areas of conjunctival oedema. Lesions were located within 6 mm of the corneal limbus. Ten of the 13 subjects (77%) had Fabry-related cataracts and all 13 demonstrated bilateral corneal verticillata. Twelve of the 13 patients had evidence of dry eye, 9 of whom were symptomatic, and 10 had peripheral lymphoedema.

Conclusion

CL represents a common but under-recognised ocular manifestation of FD, which persists despite ERT, and is often accompanied by peripheral lymphoedema and dry eye syndrome.
Comparison of two accelerometers for measuring physical activity and sedentary behaviour
Authors: Pfister Ted , Matthews Charles E , Wang Qinggang , Kopciuk Karen A , Courneya Kerry , Friedenreich Christine
Published: May 2017

Purpose

A central aspect of physical activity and sedentary behaviour research is accurate exposure assessment in the context of disease outcomes. The primary objectives of this study were to evaluate the convergent validity and test–retest reliability of the ActiGraph GT3X+ and activPAL3 accelerometers.

Methods

Participants from the Breast Cancer and Exercise Trial in Alberta (n=266) wore both devices concurrently during waking hours for 7 days. Summary measures of time (hours/day) for physical activity and sedentary behaviour were compared between devices using Student’s t-tests. Bland-Altman plots were used to assess or evaluate the mean differences and limits of agreement between monitors, and intraclass correlation coefficients (ICCs) were used to assess the test–retest reliability of two 7-day activity monitor administrations separated by 2 weeks (n=29).

Results

When comparing the ActiGraph Vector Magnitude (VM), which incorporates all three axes of movement (x, y, z), and the Vertical Axis (VT), which detects movement on the vertical or y-axis only, with the activPAL3, all measures of physical activity were statistically significantly different. The difference in measured time in sedentary behaviour was not statistically significant different when comparing the activPAL3 and ActiGraph (VT) estimates (p=0.47) but was statistically significant different for activPAL3 compared with ActiGraph (VM) (p<0.001). ICCs were high and consistent for each method across all behaviours, ranging from 0.87 to 0.93, with the exception of moderate activity and moderate-to-vigorous activity by the ActiGraph (VT) at 0.66 and 0.67, respectively.

Conclusion

Despite small mean differences and comparable recordings by both devices at the group level, the precision of estimates between methods was low with wide limits of agreement, suggesting these devices may not be used interchangeably for measuring physical activity and sedentary behaviour using common data reduction methods.
An exploration of patients’ experiences of participation in a randomised controlled trial of the Manchester Acute Coronary Syndromes (MACS) decision rule
Authors: van den Berg Patricia , Kendal Sarah , Alderson Helen V , Body Richard
Published: May 2017

Background

As an important part of a pilot study to determine the feasibility of a large randomised controlled trial (RCT) comparing use of the Manchester Acute Coronary Syndromes (MACS) decision rule with standard care, we aimed to explore patient attitudes and potential barriers to participation in a trial of this nature.

Methods

We conducted a qualitative study nested within a pilot RCT comparing use of the MACS rule (which could enable some patients with chest pain to be discharged earlier) with standard care. Semi-structured interviews with consenting participants were conducted with reference to a bespoke topic guide. Interviews were audio recorded, transcribed verbatim and analysed using the Framework method with an inductive approach.

Results

The 10 interviewees expressed that participation in the trial was generally acceptable. All but one recommended participation to others. Participants who were in pain or anxious at the time of arrival reported that the initial invitation to participate in the trial was sometimes made too early. The approach was welcome, providing they had been given time to settle. Interviewees welcomed the opportunity that trial participation offered for them to play a more active role in their healthcare and to reduce unnecessary waiting time. Participants appeared to like the fact that participation in the trial might mean they could return home sooner and welcomed the provision of follow-up. Although several participants described being generally sceptical of medical research, they were amenable to participation in this trial. This appears to be because they agreed with the need for research in this field and perceived the intervention as non-invasive.

Conclusions

Patients were positive about their participation in this RCT comparing the MACS rule with standard care. A number of areas for improving trial design were identified and should be considered in the planning of future large trials.

Trial registration

ISRCTN 86818215

Research ethics committee reference

13/NW/0081

UKCRN registration ID

14334
Evaluating the pictorial warnings on tobacco products in Arabian Gulf countries against other international pictorial warnings
Authors: BinDhim Nasser F , McGeechan Kevin , Alanazi Anwar K T , Alanazi Hossam M S , Alanazi Sasoun A J , Al-Hadlaq Solaiman M , Aljadhey Hisham , Alhawassi Tariq M , Alghamdi Nadia A , Shaman Ahmed M , Alquwayzani Meshari S , Basyouni Mada H
Published: May 2017

Background

Few assessments of pictorial warnings (PWs) on cigarette packs implemented in Gulf Cooperation Council (GCC) countries have been done.

Methods

This article includes two cross-sectional studies. In Study 1, convenience samples of adults from the Kingdom of Saudi Arabia (n=111) and USA (n=115) participated in a consumer survey to rate a total of nine PWs from the GCC, Australia and the UK. Outcome measures were affective responses to PWs and concerns about smoking. In Study 2, tobacco control experts (n=14) from multiple countries rated the same PWs on a potential efficacy scale and completed one open-ended question about each. The PWs were altered to mask their country of origin. Analyses compared ranking on multiple outcomes and examined ratings by country of origin and by smoking status.

Results

In the consumer survey, participants from both countries rated the PWs from GCC lower than PWs from other countries on the two measures. The mixed-model analysis showed significant differences between the PWs from Australia and those from the GCC and between the PWs from the UK and those from the GCC (p<0.001) in the consumer and expert samples. The experts’ comments about the PWs implemented in the GCC were negative overall and confirmed previously identified themes about effective PWs.

Conclusion

This study shows PWs originating from the GCC had significantly lower ratings than those implemented in Australia and the UK. The GCC countries may need to re-evaluate the currently implemented PWs and update them periodically.
Suspected adverse events, 2015
Authors: Cooles S. , Diesel G. , Blenkinsop J.
Published: May 2017

The following article has been produced by the pharmacovigilance unit at the Veterinary Medicines Directorate (VMD) to provide a summary of some of the results from its surveillance work carried out in 2015

Decrease in number of reports for food‐producing species

Increase in number of pet animal reports

Reports of dogs affected by medicines intended for large animals
Making an impact through research
Authors: Fitzpatrick Julie
Published: May 2017

Julie Fitzpatrick grew up in rural Ayrshire, surrounded by dogs, cats, ponies and other animals, with aspirations of working in mixed practice. She now heads the Moredun Group in Edinburgh
Lifetimes, oscillator strengths, and transition probabilities for Ce IV
Authors: Karaçoban Usta Betül , Alparslan Büşra
Published: May 2017

The lifetimes for the levels of 5p6nf (n = 5–30), 5p6np (n = 6–30), 5p6nd (n = 5–30), 5p6ng (n = 5–30), and 5p6ns (n = 7–30) configurations and the transition parameters for the electric dipole transitions between these levels have been calculated using the relativistic Hartree–Fock (HFR) method for triply ionized cerium (Ce IV, Z = 58). We have compared the results with the previously reported available calculations and experiments in the literature. Moreover, some new transition probabilities, oscillator strengths, and lifetime values for highly excited levels in Ce IV, not appearing in databases, have been obtained using this method.
Evaluation of the role of oxygen vacancies in La3GaGe5O16:Tb3+ persistent phosphor
Authors: Duan He , Lin Ze Jia , Dong You Zhong , Huang Yan
Published: May 2017

The persistent luminescence performance of a novel color-tunable Tb[Formula: see text]-doped La[Formula: see text]GaGe[Formula: see text]O[Formula: see text] phosphor has been modified by oxygen-deficiency control with an aim to explore the strategy to improve the persistent luminescence property. First-principles calculations were combined with thermoluminescence (TL) measurements to evaluate the role of oxygen vacancies in persistent luminescence of La[Formula: see text]GaGe[Formula: see text]O[Formula: see text]:Tb[Formula: see text] persistent phosphor. Our results show that the oxygen vacancies that act as an electron trap center have a limited contribution to the persistent luminescence. The formation of the ring structure of La[Formula: see text]GaGe[Formula: see text]O[Formula: see text] crystal and the resulting localized trap levels are very different from that of other outstanding persistent phosphors, like Sr[Formula: see text]MgSi[Formula: see text]O[Formula: see text], etc. Such differences are closely related to the inferior performance of La[Formula: see text]GaGe[Formula: see text]O[Formula: see text]:Tb[Formula: see text] persistent phosphor.
Admissible boundary conditions for Hamiltonian field theories
Authors: Asorey Manuel , Ibort Alberto , Spivak Amelia
Published: May 2017

In the setting of a multisymplectic formalism for Hamiltonian theories on manifolds with boundary a class of admissible boundary conditions based on the principle of preservation of the gauge symmetries of the theory is presented. Such admissible conditions are characterized as those boundary conditions determined by Lagrangian submanifolds on the space of fields at the boundary lying in the zero level set of the moment map of the group of gauge transformations at the boundary. The examples of gauge covariant fields and pure Yang–Mills theories are analyzed.
A Closer Look at Variance Implementations In Modern Database Systems
Authors: Kamat Niranjan , Nandi Arnab
Published: May 2017

Variance is a popular and often necessary component of aggregation queries. It is typically used as a secondary measure to ascertain statistical properties of the result such as its error. Yet, it is more expensive to compute than primary measures such as SUM, MEAN, and COUNT.

There exist numerous techniques to compute variance. While the definition of variance implies two passes overthe data, other mathematical formulations lead to a singlepass computation. Some single-pass formulations, however, can suffer from severe precision loss, especially for large datasets.

In this paper, we study variance implementations in various real-world systems and find that major database systems such as PostgreSQL and most likely System X, a major commercial closed-source database, use a representation that is efficient, but suffers from floating point precision loss resulting from catastrophic cancellation. We review literature over the past five decades on variance calculation in both the statistics and database communities, and summarize recommendations on implementing variance functions in various settings, such as approximate query processing and large-scale distributed aggregation. Interestingly, we recommend using the mathematical formula for computing variance if two passes over the data are acceptable due to its precision, parallelizability, and surprisingly computation speed.
Delaying decisions in variable concern hierarchies
Authors: Kienzle Jörg , Mussbacher Gunter , Collet Philippe , Alam Omar
Published: May 2017

Concern-Oriented Reuse (CORE) proposes a new way of structuring model-driven software development, where models of the system are modularized by domains of abstraction within units of reuse called concerns. Within a CORE concern, models are further decomposed and modularized by features. This paper extends CORE with a technique that enables developers of high-level concerns to reuse lower-level concerns without unnecessarily committing to a specific feature selection. The developer can select the functionality that is minimally needed to continue development, and reexpose relevant alternative lower-level features of the reused concern in the reusing concern's interface. This effectively delays decision making about alternative functionality until the higher-level reuse context, where more detailed requirements are known and further decisions can be made. The paper describes the algorithms for composing the variation (i.e., feature and impact models), customization, and usage interfaces of a concern, as well as the concern's realization models and finally an entire concern hierarchy, as is necessary to support delayed decision making in CORE.