bluuebunny/crossref_metadata_2025 huggingface dataset:
The structured core domain of αB-crystallin can prevent amyloid fibrillation and associated toxicity
Authors: Hochberg Georg K. A. , Ecroyd Heath , Liu Cong , Cox Dezerae , Cascio Duilio , Sawaya Michael R. , Collier Miranda P. , Stroud James , Carver John A. , Baldwin Andrew J. , Robinson Carol V. , Eisenberg David S. , Benesch Justin L. P. , Laganowsky Arthur
Published: April 2014

Significance

We find that the core domain of the human molecular chaperone αB-crystallin can function effectively in preventing protein aggregation and amyloid toxicity. The core domain represents only half the total sequence of the protein, but it is one of the most potent known inhibitors of the aggregation of amyloid-β, a process implicated in Alzheimer’s disease. We have determined high-resolution structures of this core domain and investigated its biophysical properties in solution. We find that the excised domain efficiently prevents amyloid aggregation and thereby reduces the toxicity of the resulting aggregates to cells. The structures of these domains that we present should represent useful scaffolds for the design of novel amyloid inhibitors.
Natural auditory scene statistics shapes human spatial hearing
Authors: Parise Cesare V. , Knorre Katharina , Ernst Marc O.
Published: April 2014

Significance

Auditory pitch has an intrinsic spatial connotation: Sounds are high or low, melodies rise and fall, and pitch can ascend and descend. In a wide range of cognitive, perceptual, attentional, and linguistic functions, humans consistently display a positive, sometimes absolute, correspondence between sound frequency and perceived spatial elevation, whereby high frequency is mapped to high elevation. In this paper we show that pitch borrows its spatial connotation from the statistics of natural auditory scenes. This suggests that all such diverse phenomena, such as the convoluted shape of the outer ear, the universal use of spatial terms for describing pitch, or the reason why high notes are represented higher in musical notation, ultimately reflect adaptation to the statistics of natural auditory scenes.
Mobile hydrogen carbonate acts as proton acceptor in photosynthetic water oxidation
Authors: Koroidov Sergey , Shevela Dmitriy , Shutova Tatiana , Samuelsson Göran , Messinger Johannes
Published: April 2014

Significance

Photosynthesis by cyanobacteria, algae, and plants sustains life on Earth by oxidizing water to the O
2
we breathe and by converting CO
2
into biomass we eat, burn, or use otherwise. Although O
2
production and CO
2
reduction are functionally and structurally well separated in photosynthetic organisms, there is a long debated role of CO
2
/

in water oxidation. Here we demonstrate that

acts as mobile acceptor and transporter of protons produced by photosystem II, and that depletion of

leads to a reversible down-regulation of O
2
production. These findings add a previously unidentified component to the regulatory networks in higher plants, algae, and cyanobacteria and conclude the long quest for the function of CO
2
/

in photosynthetic water oxidation.
Mating activates the heme peroxidase HPX15 in the sperm storage organ to ensure fertility in
Anopheles gambiae
Authors: Shaw W. Robert , Teodori Eleonora , Mitchell Sara N. , Baldini Francesco , Gabrieli Paolo , Rogers David W. , Catteruccia Flaminia
Published: April 2014

Significance

Successful fertilization requires viable sperm and eggs to meet. Some insects, such as the
Anopheles gambiae
female mosquito, the principal vector of malaria, mate only once and keep sperm received from a male in a specialized sperm storage organ while eggs are developed after taking a blood meal. Sperm are kept functional for several weeks, but the factors and mechanisms that achieve this preservation are unknown in this mosquito. Here we identify a heme peroxidase HPX15 and other mechanisms activated by sex that are important to preserve the functionality of stored sperm and long-term fertility. Disrupting the reproductive cycle in field
Anopheles
would reduce numbers of mosquitoes transmitting malaria, aiding in the fight against one of the world’s deadliest diseases.
Structural basis for the evolution of vancomycin resistance
D
,
D
-peptidases
Authors: Meziane-Cherif Djalal , Stogios Peter J. , Evdokimova Elena , Savchenko Alexei , Courvalin Patrice
Published: April 2014

Significance

Vancomycin is a powerful antibiotic against Gram-positive bacteria that inhibits cell-wall synthesis by binding with high affinity to peptidoglycan precursors. Resistance to vancomycin is due to acquisition of operons encoding, among other enzymes, the zinc-dependent
d
,
d
-peptidases VanX, VanY, or VanXY, which catalyze the removal of the drug targets. Structural characterization of VanXY elucidates the molecular basis of their specificity toward vancomycin-susceptible precursors and explains the dual function of VanXY. These studies highlight the striking plasticity of peptidoglycan-modifying enzymes to evolve to antibiotic resistance proteins. They also provide the molecular framework for development of
d
,
d
-peptidase inhibitors that may help to curb vancomycin resistance.
Glycan variants of a respiratory syncytial virus antibody with enhanced effector function and in vivo efficacy
Authors: Hiatt Andrew , Bohorova Natasha , Bohorov Ognian , Goodman Charles , Kim Do , Pauly Michael H. , Velasco Jesus , Whaley Kevin J. , Piedra Pedro A. , Gilbert Brian E. , Zeitlin Larry
Published: April 2014

Significance

Recently developed plant hosts that have been genetically engineered to produce mammalian glycosylation enzymes are capable of producing mAbs with specific glycans that satisfy effector function or homogeneity requirements. When produced in this type of plant system, an antirespiratory syncytial virus mAb containing nearly homogeneous glycans with N-acetylglucosamine termini was found to significantly enhance the effectiveness of the approved antibody drug palivizumab. The improvement was because of augmented effector function via binding to antibody Fc receptors, suggesting that classic viral neutralization plays a secondary role in the in vivo function of this antibody. We conclude that enhanced antibody-dependent cell-mediated cytotoxicity activity can be a potent contributor to the in vivo efficacy of palivizumab.
Influence of vapor wall loss in laboratory chambers on yields of secondary organic aerosol
Authors: Zhang Xuan , Cappa Christopher D. , Jathar Shantanu H. , McVay Renee C. , Ensberg Joseph J. , Kleeman Michael J. , Seinfeld John H.
Published: April 2014

Significance

Atmospheric secondary organic aerosol (SOA) has important impacts on climate and air quality, yet models continue to have difficulty in accurately simulating SOA concentrations. Nearly all SOA models are tied to observations of SOA formation in laboratory chamber experiments. Here, a comprehensive analysis of new experimental results demonstrates that the formation of SOA in laboratory chambers may be substantially suppressed due to losses of SOA-forming vapors to chamber walls, which leads to underestimates of SOA in air-quality and climate models, especially in urban areas where anthropogenic SOA precursors dominate. This analysis provides a time-dependent framework for the interpretation of laboratory chamber experiments that will allow for development of parameterized models of SOA formation that are appropriate for use in atmospheric models.
Measuring Autobiographical Fluency in the Self-Memory System
Authors: Rathbone Clare J. , Moulin Chris J.A.
Published: April 2014

Autobiographical memory is widely considered to be fundamentally related to concepts of self and identity. However, few studies have sought to test models of self and memory directly using experimental designs. Using a novel autobiographical fluency paradigm, the present study investigated memory accessibility for different levels of self-related knowledge. Forty participants generated 20 “I am” statements about themselves, from which the 1st, 5th, 10th, 15th, and 20th were used as cues in a two-minute autobiographical fluency task. The most salient aspects of the self, measured by both serial position and ratings of personal significance, were associated with more accessible sets of autobiographical memories. This finding supports theories that view the self as a powerful organizational structure in memory. Results are discussed with reference to models of self and memory.
Axon initial segment cytoskeleton comprises a multiprotein submembranous coat containing sparse actin filaments
Authors: Jones Steven L. , Korobova Farida , Svitkina Tatyana
Published: April 2014

The axon initial segment (AIS) of differentiated neurons regulates action potential initiation and axon–dendritic polarity. The latter function depends on actin dynamics, but actin structure and functions at the AIS remain unclear. Using platinum replica electron microscopy (PREM), we have characterized the architecture of the AIS cytoskeleton in mature and developing hippocampal neurons. The AIS cytoskeleton assembly begins with bundling of microtubules and culminates in formation of a dense, fibrillar–globular coat over microtubule bundles. Immunogold PREM revealed that the coat contains a network of known AIS proteins, including ankyrin G, spectrin βIV, neurofascin, neuronal cell adhesion molecule, voltage-gated sodium channels, and actin filaments. Contrary to existing models, we find neither polarized actin arrays, nor dense actin meshworks in the AIS. Instead, the AIS contains two populations of sparse actin filaments: short, stable filaments and slightly longer dynamic filaments. We propose that stable actin filaments play a structural role for formation of the AIS diffusion barrier, whereas dynamic actin may promote AIS coat remodeling.
Adjuvant-specific regulation of long-term antibody responses by ZBTB20
Authors: Wang Yinan , Bhattacharya Deepta
Published: April 2014

The duration of antibody production by long-lived plasma cells varies with the type of immunization, but the basis for these differences is unknown. We demonstrate that plasma cells formed in response to the same immunogen engage distinct survival programs depending on the adjuvant. After alum-adjuvanted immunization, antigen-specific bone marrow plasma cells deficient in the transcription factor ZBTB20 failed to accumulate over time, leading to a progressive loss of antibody production relative to wild-type controls. Fetal liver reconstitution experiments demonstrated that the requirement for ZBTB20 was B cell intrinsic. No defects were observed in germinal center numbers, affinity maturation, or plasma cell formation or proliferation in ZBTB20-deficient chimeras. However, ZBTB20-deficient plasma cells expressed reduced levels of MCL1 relative to wild-type controls, and transgenic expression of BCL2 increased serum antibody titers. These data indicate a role for ZBTB20 in promoting survival in plasma cells. Strikingly, adjuvants that activate TLR2 and TLR4 restored long-term antibody production in ZBTB20-deficient chimeras through the induction of compensatory survival programs in plasma cells. Thus, distinct lifespans are imprinted in plasma cells as they are formed, depending on the primary activation conditions. The durability of vaccines may accordingly be improved through the selection of appropriate adjuvants.
Normalization of metabolomics data with applications to correlation maps
Authors: Jauhiainen Alexandra , Madhu Basetti , Narita Masako , Narita Masashi , Griffiths John , Tavaré Simon
Published: April 2014

Motivation: In metabolomics, the goal is to identify and measure the concentrations of different metabolites (small molecules) in a cell or a biological system. The metabolites form an important layer in the complex metabolic network, and the interactions between different metabolites are often of interest. It is crucial to perform proper normalization of metabolomics data, but current methods may not be applicable when estimating interactions in the form of correlations between metabolites. We propose a normalization approach based on a mixed model, with simultaneous estimation of a correlation matrix. We also investigate how the common use of a calibration standard in nuclear magnetic resonance (NMR) experiments affects the estimation of correlations.

Results : We show with both real and simulated data that our proposed normalization method is robust and has good performance when discovering true correlations between metabolites. The standardization of NMR data is shown in simulation studies to affect our ability to discover true correlations to a small extent. However, comparing standardized and non-standardized real data does not result in any large differences in correlation estimates.

Availability and implementation: Source code is freely available at https://sourceforge.net/projects/metabnorm/

Contact:  alexandra.jauhiainen@ki.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
A modified split Hopkinson torsional bar system for correlated study of
τ
–
γ
relations, shear localization and microstructural evolution
Authors: Yang Rong , Zhang Husheng , Shen Letian , Xu Yongbo , Bai Yilong , Dodd Bradley
Published: April 2014

The conventional split Hopkinson torsional bar (SHTB) system consists of two bars, which can successfully produce the data for the construction of dynamic torsional shear stress and strain relationships. However, the system cannot provide reliable information on the progression of the deformed micro-structure during the test. The reverberation of waves in the bars and the tested specimen can spoil the microstructural pattern formed during the effective loading. This paper briefly reviews a modified version of the SHTB system consisting of four bars that has been developed. This modified system can eliminate the reverberation of waves in the specimen and provide only a single rectangular torsional stress pulse, thus it can properly freeze the microstructure formed during the effective period of loading in the specimen. By using the advantage of the modified SHTB system, together with a new design of specimen, it is possible to perform a correlated study of the dynamic stress–strain response, shear localization and the evolution of the microstructure at a fixed view-field (position) on a given specimen during the sequence of the loading time. The principles, experimental set-up and procedure, calibration and some preliminary results of the correlated study are reported in this paper.
Rate sensitivity and tension–compression asymmetry in AZ31B magnesium alloy sheet
Authors: Kurukuri Srihari , Worswick Michael J. , Ghaffari Tari Dariush , Mishra Raja K. , Carter Jon T.
Published: April 2014

The constitutive response of a commercial magnesium alloy rolled sheet (AZ31B-O) is studied based on room temperature tensile and compressive tests at strain rates ranging from 10−3to 103 s−1. Because of its strong basal texture, this alloy exhibits a significant tension–compression asymmetry (strength differential) that is manifest further in terms of rather different strain rate sensitivity under tensile versus compressive loading. Under tensile loading, this alloy exhibits conventional positive strain rate sensitivity. Under compressive loading, the flow stress is initially rate insensitive until twinning is exhausted after which slip processes are activated, and conventional rate sensitivity is recovered. The material exhibits rather mild in-plane anisotropy in terms of strength, but strong transverse anisotropy (r-value), and a high degree of variation in the measuredr-values along the different sheet orientations which is indicative of a higher degree of anisotropy than that observed based solely upon the variation in stresses. This rather complex behaviour is attributed to the strong basal texture, and the different deformation mechanisms being activated as the orientation and sign of applied loading are varied. A new constitutive equation is proposed to model the measured compressive behaviour that captures the rate sensitivity of the sigmoidal stress–strain response. The measured tensile stress–strain response is fit to the Zerilli–Armstrong hcp material model.
Mucilaginibacter pineti sp. nov., isolated from Pinus pinaster wood from a mixed grove of pines trees
Authors: Paiva Gabriel , Abreu Pedro , Proença Diogo Neves , Santos Susana , Nobre Maria Fernanda , Morais Paula V.
Published: April 2014

Bacterial strain M47C3BT was isolated from the endophytic microbial community of a Pinus pinaster tree branch from a mixed grove of pines. Phylogenetic analysis of 16S rRNA gene sequences showed that this organism represented one distinct branch within the family

Sphingobacteriaceae

, most closely related to the genus

Mucilaginibacter

. Strain M47C3BT formed a distinct lineage, closely related to

Mucilaginibacter dorajii

KACC 14556T, with which it shared 97.2 % 16S rRNA gene sequence similarity. The other members of the genus

Mucilaginibacter

included in the same clade were

Mucilaginibacter lappiensis

ATCC BAA-1855T sharing 97.0 % similarity and

Mucilaginibacter composti

TR6-03T that had a lower similarity (95.7 %). The novel strain was Gram-staining-negative, formed rod-shaped cells, grew optimally at 26 °C and at pH 7, and was able to grow with up to 0.3 % (w/v) NaCl. The respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids of the strain were summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH, representing 73.5 % of the total fatty acids. The major components of the polar lipid profile of strain M47C3BT consisted of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The G+C content of the DNA was 40.6 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics we propose the name Mucilaginibacter pineti sp. nov. for the novel species represented by strain M47C3BT ( = CIP 110632T = LMG 28160T).
Alicyclobacillus cellulosilyticus sp. nov., a thermophilic, cellulolytic bacterium isolated from steamed Japanese cedar chips from a lumbermill
Authors: Kusube Masataka , Sugihara Asami , Moriwaki Yoshito , Ueoka Takahiro , Shimane Yasuhiro , Minegishi Hiroaki
Published: April 2014

A thermophilic bacterium, strain SueokaT, was isolated from steamed Japanese cedar chips from a lumber mill in Gobo, Japan. The strain was able to grow on carboxymethyl cellulose at 60 °C, was Gram-stain-negative, and grew between 40.0 and 67.5 °C (optimum at 55 °C) and between pH 3.5 and 6.5 (optimum at pH 4.8). Comparative analysis of 16S rRNA gene sequences revealed 91.9 , 90.9 , and 90.8 % similarity toAlicyclobacillus macrosporangiidusT,Alicyclobacillus pomorumT, andAlicyclobacillus acidocaldariusT, respectively. The major quinone was MK-7 and the predominant cellular fatty acids wereω-cyclohexane C19 : 0andω-cyclohexane C17 : 0. The DNA G+C content was 60.8 mol%. Based on the results of this study, strain SueokaTis a novel species of the genusAlicyclobacillus, and the namehttp://dx.doi.org/10.1601/nm.5071Alicyclobacilluscellulosilyticussp. nov. (type strain SueokaT = JCM 18487T = KCTC 33007T) is proposed.
Spirosoma arcticum sp. nov., isolated from high Arctic glacial till
Authors: Chang Xulu , Jiang Fan , Wang Tao , Kan Wenjing , Qu Zhihao , Ren Lvzhi , Fang Chengxiang , Peng Fang
Published: April 2014

A novel orange-pigmented strain, designated R2-35T, was isolated from a glacier till near Ny-Alesund, Svalbard Archipelago, Norway. The cells were aerobic, Gram-negative, rod-shaped and sometimes filamentous. Growth occurred at 4–28 °C (optimum, 20 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–1 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-35T belonged to the genus

Spirosoma

with sequence similarity to related species ranging from 91.65 to 95.19 %. Strain R2-35T contained C16 : 0 (10.7 %), C18 : 0 (9.2 %), C16 : 1ω5c (16.5 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (24.6 %) as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain R2-35T was 54.9 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-35T is considered to represent a novel species of the genus

Spirosoma

, for which the name Spirosoma arcticum sp. nov., is proposed, The type strain is R2-35T ( = CCTCC AB 2012849T = LMG 28141T).
Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre
Authors: Zhang Zenghu , Fan Xiaoyang , Gao Xin , Zhang Xiao-Hua
Published: April 2014

A Gram-stain-negative, facultatively anaerobic, rod-shaped, motile bacterium with a subpolar or lateral flagellum, designated strain XH089T, was isolated from deep-sea sediment sample collected from the South Pacific Gyre (41°51′ S 153°06′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH089T belonged to the genus

Achromobacter

and showed the highest 16S rRNA gene sequence similarities with

Achromobacter ruhlandii

ATCC 15749T (96.95 %),

Achromobacter denitrificans

DSM 30026T (96.70 %) and

Achromobacter marplatensis

B2T (96.66 %). The DNA G+C content of strain XH089T was 66.5 mol%. The major fatty acids were C16 : 0 and C17 : 0 cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, three unknown phospholipids and four unknown polar lipids. On the basis of data from the polyphasic analysis, strain XH089T is considered to represent a novel species of the genus

Achromobacter

, for which the name

Achromobacter

sediminum sp. nov. is proposed. The type strain is XH089T ( = DSM 27279T = JCM 19223T).
Brachyury cooperates with Wnt/β-Catenin signalling to elicit Primitive Streak like behaviour in differentiating mouse ES cells.
Authors: Turner David Andrew , Rué Pau , Mackenzie Jonathan P , Davies Eleanor , Martinez Arias Alfonso
Published: April 2014

The formation of the Primitive Streak is the first visible sign of gastrulation, the process by which the three germ layers are formed from a single epithelium during early development. Embryonic Stem Cells (ESCs) provide a good system to understand the molecular and cellular events associated with these processes. Previous work, both in embryos and in culture, has shown how converging signals from both Nodal/TGFβR and Wnt/β-Catenin signalling pathways specify cells to adopt a Primitive Streak like fate and direct them to undertake an epithelial to mesenchymal transition (EMT). However, many of these approaches have relied on genetic analyses without taking into account the temporal progression of events within single cells. In addition, it is still unclear as to what extent events in the embryo are able to be reproduced in culture. Here, we combine flow-cytometry and a quantitative live single-cell imaging approach to demonstrate how the controlled differentiation of mouse ESCs (mESCs) towards a Primitive Streak fate in culture results in cells displaying many of the characteristics observed during early mouse development including transient Brachyury expression, EMT and increased motility. We also find that the EMT initiates the process, and this is both fuelled and terminated by the action of Bra, whose expression is dependent on the EMT and β-Catenin activity. As a consequence of our analysis, we propose that a major output of Brachyury expression is in controlling the velocity of the cells that are transiting out of the Primitive Streak.
Recurrent epimutations activate gene body promoters in primary glioblastoma
Authors: Nagarajan Raman P. , Zhang Bo , Bell Robert J.A. , Johnson Brett E. , Olshen Adam B. , Sundaram Vasavi , Li Daofeng , Graham Ashley E. , Diaz Aaron , Fouse Shaun D. , Smirnov Ivan , Song Jun , Paris Pamela L. , Wang Ting , Costello Joseph F.
Published: April 2014

Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MRE-seq, adjusting for copy number differences, in a small set of non-glioma CpG island methylator phenotype (non-G-CIMP) primary tumors. Recurrent hypomethylated loci were enriched within a region of chromosome 5p15 that is specified as a cancer amplicon and also encompasses TERT, encoding telomerase reverse transcriptase, which plays a critical role in tumorigenesis. Overall, 76 gene body promoters were recurrently hypomethylated, including TERT and the oncogenes GLI3 and TP73. Recurring hypomethylation also affected previously unannotated alternative promoters, and luciferase reporter assays for three of four of these promoters confirmed strong promoter activity in GBM cells. Histone H3 lysine 4 trimethylation (H3K4me3) ChIP-seq on tissue from the GBMs uncovered peaks that coincide precisely with tumor-specific decrease of DNA methylation at 200 loci, 133 of which are in gene bodies. Detailed investigation of TP73 and TERT gene body hypomethylation demonstrated increased expression of corresponding alternate transcripts, which in TP73 encodes a truncated p73 protein with oncogenic function and in TERT encodes a putative reverse transcriptase-null protein. Our findings suggest that recurring gene body promoter hypomethylation events, along with histone H3K4 trimethylation, alter the transcriptional landscape of GBM through the activation of a limited number of normally silenced promoters within gene bodies, in at least one case leading to expression of an oncogenic protein.
Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
Authors: Bonhoure Nicolas , Bounova Gergana , Bernasconi David , Praz Viviane , Lammers Fabienne , Canella Donatella , Willis Ian M. , Herr Winship , Hernandez Nouria , Delorenzi Mauro ,   The CycliX Consortium
Published: April 2014

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This “spike” chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes.
Quantifying Shape Changes and Tissue Deformation in Leaf Development
Authors: Rolland-Lagan Anne-Gaëlle , Remmler Lauren , Girard-Bock Camille
Published: April 2014

The analysis of biological shapes has applications in many areas of biology, and tools exist to quantify organ shape and detect shape differences between species or among variants. However, such measurements do not provide any information about the mechanisms of shape generation. Quantitative data on growth patterns may provide insights into morphogenetic processes, but since growth is a complex process occurring in four dimensions, growth patterns alone cannot intuitively be linked to shape outcomes. Here, we present computational tools to quantify tissue deformation and surface shape changes over the course of leaf development, applied to the first leaf of Arabidopsis (Arabidopsis thaliana). The results show that the overall leaf shape does not change notably during the developmental stages analyzed, yet there is a clear upward radial deformation of the leaf tissue in early time points. This deformation pattern may provide an explanation for how the Arabidopsis leaf maintains a relatively constant shape despite spatial heterogeneities in growth. These findings highlight the importance of quantifying tissue deformation when investigating the control of leaf shape. More generally, experimental mapping of deformation patterns may help us to better understand the link between growth and shape in organ development.
(μ-Dihydrogen pyrazine-2,3,5,6-tetracarboxylato-κ6O2,N1,O6;O3,N4,O5)bis(diaqualithium) monohydrate
Authors: Starosta Wojciech , Leciejewicz Janusz
Published: April 2014

The structure of the title compound, [Li2(C8H2N2O8)(H2O)4]·H2O, is composed of dinuclear molecules in which the ligand bridges two symmetry-related LiIions, each coordinated also by two water O atoms, in anO,N,O′-manner. The Li and N atoms occupy special positions on twofold rotation axes, whereas a crystal water molecule is located at the intersection of three twofold rotation axes. The LiIcation shows a distorted trigonal–bipyramidal coordination. Two carboxylate groups remain protonated and form short interligand hydrogen bonds. The molecules are held together by a network of hydrogen bonds in which the coordinating and solvation water molecules act as donors and carboxylate O atoms as acceptors, forming a three-dimensional architecture.
A reversed genetic approach reveals the coenzyme specificity and other catalytic properties of three enzymes putatively involved in anaerobic oxidation of methane with sulfate
Authors: Kojima Hisaya , Moll Johanna , Kahnt Jörg , Fukui Manabu , Shima Seigo
Published: April 2014

Consortia of anaerobic methanotrophic (ANME) archaea and delta‐proteobacteria anaerobically oxidize methane coupled to sulfate reduction to sulfide. The metagenome of ANME‐1 archaea contains genes homologous to genes otherwise only found in methanogenic archaea, and transcription of some of these genes in ANME‐1 cells has been shown. We now have heterologously expressed three of these genes in Escherichia coli, namely those homologous to genes for formylmethanofuran : tetrahydromethanopterin formyltransferase, methenyltetrahydromethanopterin cyclohydrolase (Mch) and coenzyme F420‐dependent methylenetetrahydromethanopterin dehydrogenase (Mtd), and have characterized the overproduced enzymes with respect to their coenzyme specificity and other catalytic properties. The three enzymes from ANME‐1 were found to catalyse the same reactions and with similar specific activities using identical coenzymes as the respective enzymes in methanogenic archaea, the apparent Km for their substrates being in the same concentration range. The results support the proposal that anaerobic oxidation of methane to CO2 in ANME involves the same enzymes and coenzymes as CO2 reduction to methane in methanogenic archaea. Interestingly, the activity of Mch and the stability of Mtd from ANME‐1 were found to be dependent on the presence of 0.5–1.0 M potassium phosphate, which suggested that ANME‐1 archaea contain high concentrations of lyotropic salts, presumably as compatible solutes.
The nitrate‐ammonifying andnosZ‐carrying bacteriumBacillus viretiis a potent source and sink for nitric and nitrous oxide under high nitrate conditions
Authors: Mania Daniel , Heylen Kim , van Spanning Rob J. M. , Frostegård Åsa
Published: April 2014

SeveralGram‐positive bacteria carry genes for anaerobic reduction of NO3−via NO2−to NH4+or gaseous nitrogen compounds, but the processes are understudied for these organisms. Here, we present results from a whole‐genome analysis of the soil bacteriumBacillus viretiand a phenotypic characterization of intermediate and end‐products, formed under anoxic conditions in the presence of NO3−.Bacillus viretihas a versatile metabolism. It produces acetate, formate, succinate and lactate from fermentation and performs dissimilatory nitrate reduction via NO2−to ammonium (DNRA) usingNrfA, whileNirBmay detoxifyNO2−in the cytoplasm. Moreover, it producesNOfrom an unknown source and reduces it viaN2OtoN2using two enzymes connected to denitrification: an unusual NO reductase,qCuANorencoded bycbaA, and a z‐typeN2Oreductase, encoded bynosZ. In batch cultures,B. viretireduced allNO3−toNO2−before theNO2−was reduced further. The quantities of all products varied with the initialNO3−concentration. With 5 mMNO3−, 90% was reduced toNH4+while with ≥ 20 mMNO3−, 50% was reduced toNO,N2OandN2. This organism is thus an aggressiveNO2−accumulator and may act as a net source and sink ofNOandN2O.
Optimising seed portfolios to cope ex ante with risks from bad weather: evidence from a recent maize farmer survey in China
Authors: Bai Junfei , Xu Zhigang , Qiu Huanguang , Liu Haiyan
Published: April 2014

Using 4‐year panel data collected from surveying 640 farmers from leading maize producing provinces in China, this study analyses how maize farmers cope with anticipated risks from bad weather by strategically adjusting variety portfolios, with particular interest in farmers' strategies in choosing and combining new and old varieties. While diversification was commonly demonstrated to be an effective means to reduce risk in most previous studies, our empirical results indicate that, in facing anticipated risks from bad weather, Chinese maize farmers tend to use fewer new varieties and allocate more land to old varieties. The lack of knowledge about weather tolerance of new varieties might be the major reason for this practice. As new varieties often have higher yield potential relative to old varieties due to technological progress, this finding suggests that Chinese maize farmers might be trading yield potential against risk reduction from bad weather. Furthermore, this study shows that maize farmers' variety adoption is significantly related to farmers' land conditions as well as their access to credit markets and technique extensions, suggesting that a well‐designed policy intervention could offset or partially offset the anticipation of adverse weather impacts on farmers' variety choices and therefore on maize production.
Inactivation of Bacillus spores in batch vs continuous heating systems at sterilisation temperatures
Authors: Stoeckel Marina , Abduh Setya B M , Atamer Zeynep , Hinrichs Jörg
Published: April 2014

This study was performed to assess the heat resistance of spores of Bacillus species in batch and continuous heating systems under commercial sterilisation conditions. Spores of thermophilic Bacillus smithii and mesophilic Bacillus amyloliquefaciens were found to be highly heat resistant in the batch system. They were able to withstand typical sterilisation temperatures. B. amyloliquefaciens showed tailing in the batch system and, before the onset of the tailing, a higher inactivation rate than in the continuous system at low temperatures. The reason for the tailing might be the presence of spore aggregates which are disrupted in the continuous system.
Accounting Standards Harmonization and Financial Statement Comparability: Evidence from Transnational Information Transfer
Authors: WANG CLARE
Published: April 2014

This paper investigates whether accounting standards harmonization enhances the comparability of financial information across countries. I hypothesize that a firm yet to announce earnings reacts more strongly to the earnings announcement of a foreign firm when both report under the same rather than different accounting standards. My analysis of abnormal price reactions for a global sample of firms supports the prediction. Next, in an attempt to control for the underlying economic comparability and the effects of changes in reporting quality, I use a difference‐in‐differences design around the mandatory introduction of International Financial Reporting Standards. I find that mandatory adopters experience a significant increase in market reactions to the release of earnings by voluntary adopters compared to the period preceding mandatory adoption. This increase is not observed for nonadopters. Taken together, the results show that accounting standards harmonization facilitates transnational information transfer and suggest financial statement comparability as a direct mechanism.
Paracetamol toxicity: What would be the implications of a change in Australian treatment guidelines?
Authors: Wong Anselm , Graudins Andis , Kerr Fergus , Greene Shaun L
Published: April 2014

Objectives

The present study aims to study the implications for resource utilisation if Australia adopted recent revised UK treatment guidelines for paracetamol poisoning.

Methods

Retrospective database review of paracetamol toxicity presentations and calls from the Victorian Poisons Information Centre (VPIC) and Austin Hospital, Victoria, Australia, from 1 January 2010 to 31 December 2011. There were 200 presentations at the Austin Hospital, and the VPIC received 4272 calls regarding paracetamol toxicity. An analytical model was designed to estimate the cost of this additional treatment and referral to hospital. The main outcome measures were the potential increase in number of admissions requiring treatment with N‐acetylcysteine (NAC), costs involved and increased number of referrals to hospitals by the VPIC.

Results

Twenty‐five (12.5%, 95% confidence interval 8.4–17.6%, P < 0.01) patients in our study who did not qualify for NAC therapy based upon the current Australasian paracetamol treatment guideline would have received it if the revised UK guideline was followed. Eighteen (72%) of these presented with acute single ingestions of paracetamol. No patients re‐presented to our hospital with acute liver injury or required admission to the liver transplant unit.

Conclusions

Alignment of current Australian paracetamol treatment guidelines with those in the UK would result in an increase in ED attendances as directed by Poisons Information Centres and hospital admissions for antidotal treatment. This would be associated with increased health expenditure and inpatient bed utilisation. The present study does not support the clinical need for adoption of UK paracetamol treatment guidelines in Australia.
Improvement in emergency department length of stay using a nurse‐led ‘emergency journey coordinator’: A before/after study
Authors: Asha Stephen E , Ajami Allan
Published: April 2014

Objective

Australian EDs are required to conform to the National Emergency Access Target (NEAT): patients must depart within 4 h of arrival. The study's aim was to determine if a nursing role called the ‘Emergency Journey Coordinator’ (EJC) improved NEAT through resolving delays in patient processing.

Methods

The proportion of patients achieving NEAT before and after the EJC role started were compared with adjustment for confounding variables. All data were obtained from the ED computer management system.

Results

There were 23 848 patients over a 128 day period before and 20 884 over a 115 day period after the introduction of the EJC role. The proportion of patients meeting NEAT after the EJC role started was 64.4% compared with 59.6% before, an absolute improvement of 4.9% (95% confidence interval [CI] 4.0–5.8, P < 0.001). This benefit persisted after controlling for confounding effects. For patients admitted NEAT was 38.1% after the EJC role started compared with 32.5% before, an absolute improvement of 5.6% (95% CI 4.1–7.1, P < 0.001). For patients discharged, NEAT was 80.2% after the EJC role started compared with 74.6% before, an absolute improvement of 5.6% (95% CI 4.7–6.6, P < 0.001). Mean ED occupancy decreased from 34.3 patients before to 32.4 after, a decrease of 2.0 patients (95% CI 1.2–2.8, P < 0.001). There was no clinically important difference in the proportion of patient who did not wait to be seen or in ambulance transfer of care time.

Conclusion

NEAT targets were improved in the ED of a tertiary referral hospital after the introduction of the EJC role.
Determination of Trace Elements in Honey from Different Regions in Rio de Janeiro State (Brazil) by Total Reflection X‐Ray Fluorescence
Authors: Ribeiro Roberta de Oliveira Resende , Mársico Eliane Teixeira , de Jesus Edgar Francisco Oliveira , da Silva Carneiro Carla , Júnior Carlos Adam Conte , de Almeida Eduardo , Filho Virgílio Franco do Nascimento
Published: April 2014

Trace and minor elements in Brazilian honey were analyzed by total reflection X‐ray fluorescence spectroscopy. Up to 12 elements (K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Se, Br, and Sr) were detected in 160 samples of honey from 4 regions of Rio de Janeiro State (Barra Mansa, Teresópolis, northern and southern Nova Friburgo). The results showed the samples from Teresópolis had higher rates of essential and nonessential elements than samples from the other regions, except for Ni. K and Ca were the most abundant elements in all samples, in the range of 116.5 to 987.0 μg g−1. Ni, Cu, Zn, Se, and Sr were identified in small concentrations (0.01 to 12.08 μg g−1) in all samples, indicating a low level of contamination in all the regions.
Amylose–Potassium Oleate Inclusion Complex in Plain Set‐Style Yogurt
Authors: Singh Mukti , Byars Jeffrey A. , Kenar James A.
Published: April 2014

Health and wellness aspirations of U.S. consumers continue to drive the demand for lower fat from inherently beneficial foods such as yogurt. Removing fat from yogurt negatively affects the gel strength, texture, syneresis, and storage of yogurt. Amylose–potassium oleate inclusion complexes (AIC) were used to replace skim milk solids to improve the quality of nonfat yogurt. The effect of AIC on fermentation of yogurt mix and strength of yogurt gel was studied and compared to full‐fat samples. Texture, storage modulus, and syneresis of yogurt were observed over 4 weeks of storage at 4 °C. Yogurt mixes having the skim milk solids partially replaced by AIC fermented at a similar rate as yogurt samples with no milk solids replaced and full‐fat milk. Initial viscosity was higher for yogurt mixes with AIC. The presence of 3% AIC strengthened the yogurt gel as indicated by texture and rheology measurements. Yogurt samples with 3% AIC maintained the gel strength during storage and resulted in low syneresis after storage for 4 wk.
Predicting Bacillus coagulans Spores Inactivation in Tomato Pulp under Nonisothermal Heat Treatments
Authors: Zimmermann Morgana , Longhi Daniel A. , Schaffner Donald W. , Aragão Gláucia M. F.
Published: April 2014

The knowledge and understanding of Bacillus coagulans inactivation during a thermal treatment in tomato pulp, as well as the influence of temperature variation during thermal processes are essential for design, calculation, and optimization of the process. The aims of this work were to predict B. coagulans spores inactivation in tomato pulp under varying time–temperature profiles with Gompertz‐inspired inactivation model and to validate the model's predictions by comparing the predicted values with experimental data. B. coagulans spores in pH 4.3 tomato pulp at 4 °Brix were sealed in capillary glass tubes and heated in thermostatically controlled circulating oil baths. Seven different nonisothermal profiles in the range from 95 to 105 °C were studied. Predicted inactivation kinetics showed similar behavior to experimentally observed inactivation curves when the samples were exposed to temperatures in the upper range of this study (99 to 105 °C). Profiles that resulted in less accurate predictions were those where the range of temperatures analyzed were comparatively lower (inactivation profiles starting at 95 °C). The link between fail prediction and both lower starting temperature and magnitude of the temperature shift suggests some chemical or biological mechanism at work. Statistical analysis showed that overall model predictions were acceptable, with bias factors from 0.781 to 1.012, and accuracy factors from 1.049 to 1.351, and confirm that the models used were adequate to estimate B. coagulans spores inactivation under fluctuating temperature conditions in the range from 95 to 105 °C.

Practical Application

How can we estimate Bacillus coagulans inactivation during sudden temperature shifts in heat processing? This article provides a validated model that can be used to predict B. coagulans under changing temperature conditions. B. coagulans is a spore‐forming bacillus that spoils acidified food products. The mathematical model developed here can be used to predict the spoilage risk following thermal process deviations for tomato products.
Dipyrone metabolite 4‐MAA induces hypothermia and inhibits PGE2‐dependent and ‐independent fever while 4‐AA only blocks PGE2‐dependent fever
Authors: Malvar David do C , Aguiar Fernando A , Vaz Artur de L L , Assis Débora C R , de Melo Miriam C C , Jabor Valquíria A P , Kalapothakis Evanguedes , Ferreira Sérgio H , Clososki Giuliano C , de Souza Glória E P
Published: April 2014

Background and Purpose

The antipyretic and hypothermic prodrug dipyrone prevents PGE2‐dependent and ‐independent fever induced by LPS from Escherichia coli and Tityus serrulatus venom (Tsv) respectively. We aimed to identify the dipyrone metabolites responsible for the antipyretic and hypothermic effects.

Experimental Approach

Male Wistar rats were treated i.p. with indomethacin (2 mg·kg−1), dipyrone, 4‐methylaminoantipyrine (4‐MAA), 4‐aminoantipyrine (4‐AA) (60–360 mg·kg−1), 4‐formylaminoantipyrine, 4‐acethylaminoantipyrine (120–360 mg·kg−1) or vehicle 30 min before i.p. injection of LPS (50 μg·kg−1), Tsv (150 μg·kg−1) or saline. Rectal temperatures were measured by tele‐thermometry and dipyrone metabolite concentrations determined in the plasma, CSF and hypothalamus by LC‐MS/MS. PGE2 concentrations were determined in the CSF and hypothalamus by elisa.

Key Results

In contrast to LPS, Tsv‐induced fever was not followed by increased PGE2 in the CSF or hypothalamus. The antipyretic time‐course of 4‐MAA and 4‐AA on LPS‐induced fever overlapped with the period of the highest concentrations of 4‐MAA and 4‐AA in the hypothalamus, CSF and plasma. These metabolites reduced LPS‐induced fever and the PGE2 increase in the plasma, CSF and hypothalamus. Only 4‐MAA inhibited Tsv‐induced fever. The higher doses of dipyrone and 4‐MAA also induced hypothermia.

Conclusions and Implications

The presence of 4‐MAA and 4‐AA in the CSF and hypothalamus was associated with PGE2 synthesis inhibition and a decrease in LPS‐induced fever. 4‐MAA was also shown to be an antipyretic metabolite for PGE2‐independent fever induced by Tsv suggesting that it is responsible for the additional antipyretic mechanism of dipyrone. Moreover, 4‐MAA is the hypothermic metabolite of dipyrone.