bluuebunny/crossref_metadata_2025 huggingface dataset:
Disease causing mutants of TDP-43 nucleic acid binding domains are resistant to aggregation and have increased stability and half-life
Authors: Austin James A. , Wright Gareth S. A. , Watanabe Seiji , Grossmann J. Günter , Antonyuk Svetlana V. , Yamanaka Koji , Hasnain S. Samar
Published: March 2014

Significance

Adult onset neurodegenerative diseases are viewed as protein destabilization, misfolding, and aggregation diseases. TAR DNA binding protein-43 (TDP-43) protein is strongly associated with many neurological disorders, particularly amyotrophic lateral sclerosis and frontotemporal lobar degeneration. All of the disease-associated TDP-43 mutants tested have been shown to increase TDP-43 half-life and this correlates inversely with the age at which the sufferer first becomes aware of symptoms. Here we show that disease mutations in two TDP-43 nucleic acid binding domains also increase the protein’s half-life and this is commensurate with increased structural stability and resistance to aggregation. Our results are an unusual contrast to other neurodegenerative diseases and provide a potential link between the molecular characteristics of mutant TDP-43 and the symptoms of these debilitating diseases.
Electric double-layer transistor using layered iron selenide Mott insulator TlFe
1.6
Se
2
Authors: Katase Takayoshi , Hiramatsu Hidenori , Kamiya Toshio , Hosono Hideo
Published: March 2014

Significance

One of the key strategies to obtaining higher superconducting critical temperature is to dope carriers into an antiferromagnetic Mott insulator with a high Néel temperature. Fe-vacancy-ordered
A

1–
x

Fe

2–
y

Se
2
(
A
= K, Cs, Rb, Tl) is only one Mott insulator phase with extremely high Néel temperature among recently discovered iron-based superconductors. Here, we examined electrostatic carrier doping of the TlFe
1.6
Se
2
insulator using an electric double-layer transistor structure. Three orders of magnitude modulation of channel conductance was observed, and the phase transition was induced by gate voltage, which indicates that delocalized carrier generation by electrostatic doping is its origin. This result opens a way to explore high critical temperature superconductivity in iron-based layered materials, where carrier doping by conventional chemical means is difficult.
Two distinct neural mechanisms underlying indirect reciprocity
Authors: Watanabe Takamitsu , Takezawa Masanori , Nakawake Yo , Kunimatsu Akira , Yamasue Hidenori , Nakamura Mitsuhiro , Miyashita Yasushi , Masuda Naoki
Published: March 2014

Significance

Humans help strangers even if the strangers will not directly help them in the future. The so-called indirect reciprocity seems to support large-scale cooperation in human society. We revealed functional and anatomical neural bases of two types of indirect reciprocity by combining group and neuroimaging experiments. Reputation-based indirect reciprocity activated the precuneus, a brain region associated with self-centered cognition. Indirect reciprocity occurring as a succession of pay-it-forward behaviors specifically recruited the anterior insula, a region related to affective empathy. Furthermore, task-irrelevant neural fingerprints of these brain regions are predictive of the individual’s tendency of cooperation. These results in particular explain why we often conduct seemingly irrational cooperation such as pay-it-forward reciprocity.
Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus
Authors: Reker Daniel , Rodrigues Tiago , Schneider Petra , Schneider Gisbert
Published: March 2014

Significance

New chemical entities (NCEs) with desired pharmacological and biological activity spectra fuel drug discovery and provide tools for chemical biologists. Computer-assisted molecular design generates novel chemotypes with predictable polypharmacologies. We present the successful application of fully automated de novo drug design coupled with a pioneering approach for target panel prediction to obtain readily synthesizable bioactive compounds. This innovative concept enabled the identification of relevant macromolecular targets of computationally designed NCEs and led to the discovery of previously unknown off-targets of approved drugs.
Redesign of extensive protein–DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization
Authors: Takeuchi Ryo , Choi Michael , Stoddard Barry L.
Published: March 2014

Significance

Specific gene-targeting nucleases are critical for genetic engineering and therapy. Meganucleases have been shown to harbor many properties, including small monomeric folds and high cleavage specificities, that are appropriate for this purpose. However, they are rarely used for genome modification because their DNA specificity requires an extensive network of up to 50 amino acids, making redesign difficult. Because extensively reprogramming molecular recognition across such a complex interface is a fundamental biotechnology challenge, meganucleases are used here as a model system for the development of an efficient approach to alter their specificity. The nucleases produced by this method, when tethered to transcription activator-like effector domains, resulted in highly active DNA targeting reagents with notable recognition properties.
Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode
Authors: Agrawal Praveen , Kurcon Tomasz , Pilobello Kanoelani T. , Rakus John F. , Koppolu Sujeethraj , Liu Zhongyin , Batista Bianca S. , Eng William S. , Hsu Ku-Lung , Liang Yaxuan , Mahal Lara K.
Published: March 2014

Significance

Carbohydrates (glycans) are complex cell surface molecules that control multiple aspects of cell biology, including cell–cell communication, cancer metastasis, and inflammation. Glycan biosynthesis requires the coordination of many enzymes, but how this is regulated is not well understood. Herein we show that microRNA (miRNA), small noncoding RNA, are a major regulator of cell surface glycosylation. We map miRNA expression onto carbohydrate signatures obtained by using lectin microarrays, a glycan analysis method. We identify and validate several miRNA–glycan networks, including a major decision point in
N
-linked glycan biosynthesis. Overall, our work provides insights into the “black box” of carbohydrate control mechanisms.
Individual letters of the RNA polymerase II CTD code govern distinct gene expression programs in fission yeast
Authors: Schwer Beate , Bitton Danny Asher , Sanchez Ana M. , Bähler Jürg , Shuman Stewart
Published: March 2014

Significance

The carboxyl-terminal domain (CTD) code encrypted within the YSPTSPS heptad repeats of RNA polymerase II is deeply rooted in eukaryal biology. This paper exploits fission yeast CTD mutants in which single coding cues (or combinations of cues) are subtracted from all consensus heptads to gauge the roles of the Tyr1, Ser2, Thr4, and Ser7 phosphoacceptors in gene expression. Transcriptome profiling revealed distinctive signatures for the CTD phosphoacceptors that were verified by cell-based activity assays. The results highlight (
i
) the role of Tyr1 and Ser2 in repressing the iron uptake regulon and (
ii
) the distinctive roles of Thr4 and Ser7 in the phosphate starvation response, whereby Thr4 facilitates and Ser7 represses the induction of Pho1 acid phosphatase.
Parkinson disease-associated mutation R1441H in LRRK2 prolongs the “active state” of its GTPase domain
Authors: Liao Jingling , Wu Chun-Xiang , Burlak Christopher , Zhang Sheng , Sahm Heather , Wang Mu , Zhang Zhong-Yin , Vogel Kurt W. , Federici Mark , Riddle Steve M. , Nichols R. Jeremy , Liu Dali , Cookson Mark R. , Stone Todd A. , Hoang Quyen Q.
Published: March 2014

Significance

Mutations in the gene encoding for leucine-rich-repeat kinase 2 (LRRK2) are a common cause of Parkinson disease (PD). To understand how LRRK2 causes PD, we need to understand its normal functions and how they are altered by disease-causing mutations. This effort has been hampered by the lack of appropriate samples, which led to some confusion in the field. This study shows the construction of a stably folded domain of LRRK2 called Ras of complex proteins (Roc). We use the study to resolve two conflicting models of Roc oligomerization by quantitatively demonstrating its GTPase activity in both monomeric and dimeric states. We further show that a PD-causing mutation affects both GTP binding and GTPase activity of Roc.
Individual I
Ks
channels at the surface of mammalian cells contain two KCNE1 accessory subunits
Authors: Plant Leigh D. , Xiong Dazhi , Dai Hui , Goldstein Steve A. N.
Published: March 2014

Significance

I
Kslow
(I
Ks
) channels allow heartbeats and hearing. The channels contain two types of subunits: Q1 and E1. Both are required. While four Q1 subunits are known to form the pore, the number of E1 subunits has been controversial for over a decade. The answer is critical to understanding cardiac function, diseases, including life-threatening arrhythmias, and for drug development. Here, we describe an improved method to study the composition and surface density of single I
Ks
channels—simultaneous, two-color, subunit counting for channels on the surface of live mammalian cells. We show that I
Ks
channels contain two E1 subunits and four Q1 subunits. This subunit ratio does not vary even when levels of E1 are raised or lowered 10-fold as found in tissues.
Real-time analysis of composite magnetic nanoparticle disassembly in vascular cells and biomimetic media
Authors: Tengood Jillian E. , Alferiev Ivan S. , Zhang Kehan , Fishbein Ilia , Levy Robert J. , Chorny Michael
Published: March 2014

Significance

Disassembly rates and patterns of nanoparticles used as drug carriers or diagnostic tools are important determinants of their performance and biocompatibility. Thus, understanding them is essential for the design and optimization of nanoparticle formulations for clinical use. Currently available strategies are not applicable to real-time, quantitative nanoparticle disassembly analysis directly in environments of interest, such as the cell interior or biomimetic media. In the present study, a quantitative strategy using Förster resonance energy transfer for monitoring integrity status of nanoparticles in situ was developed and applied for characterizing disassembly of biodegradable polymer-based magnetic nanoparticles in vascular cells and different types of model milieu. This methodology and study results may be relevant for a broad range of biomedical and analytical applications.
Hic-5 is a transcription coregulator that acts before and/or after glucocorticoid receptor genome occupancy in a gene-selective manner
Authors: Chodankar Rajas , Wu Dai-Ying , Schiller Benjamin J. , Yamamoto Keith R. , Stallcup Michael R.
Published: March 2014

Significance

Transcription factors (TFs) and their coregulators constitute two components of transcriptional regulatory complexes. TFs are thought to mediate genomic site selection, whereas coregulators appear to modulate the assembly/disassembly of the regulatory complex, which in turn specifies mechanisms of regulation. Here we show that coregulator hydrogen peroxide-inducible clone-5 (Hic-5) acts gene selectively in both modes. On some glucocorticoid receptor (GR) target genes it contributes to the assembly of transcription complexes. However, on other GR target genes it acts before genome occupancy by GR and thereby influences the set of sites occupied by GR. Because genomic occupancy by GR and other TFs varies in different cell types and regulatory contexts, Hic-5 represents an alternative mechanism for regulating DNA binding by TFs, complementing the influence of chromatin and pioneer factors.
Transcriptional divergence and conservation of human and mouse erythropoiesis
Authors: Pishesha Novalia , Thiru Prathapan , Shi Jiahai , Eng Jennifer C. , Sankaran Vijay G. , Lodish Harvey F.
Published: March 2014

Significance

Mouse models have been instrumental in advancing our understanding of blood cell production. Although many studies have suggested specific differences between human and mouse red cell production (erythropoiesis), a global study of such similarities and differences has been lacking. By computationally comparing global gene expression data from adult human and mouse erythroid precursors representing the distinct stages of maturation, we showed that, while the overall transcriptional landscape has changed, critical erythroid gene signatures and transcriptional regulators have remained conserved. Importantly, these analyses can serve as a tool to integrate data between human and mouse erythropoiesis research, explain why certain human blood diseases are not faithfully recapitulated in mouse models, and highlight hurdles in translating therapeutic findings from mice to humans.
Clioquinol promotes the degradation of metal-dependent amyloid-β (Aβ) oligomers to restore endocytosis and ameliorate Aβ toxicity
Authors: Matlack Kent E. S. , Tardiff Daniel F. , Narayan Priyanka , Hamamichi Shusei , Caldwell Kim A. , Caldwell Guy A. , Lindquist Susan
Published: March 2014

Significance

Identifying disease-modifying therapies for Alzheimer’s disease (AD) has been an insurmountable challenge. To provide a new discovery tool for high-throughput compound screening, we used a simple yeast model that makes toxic amounts of β-amyloid (Aβ), a peptide central to AD pathology. Previous genetic analysis established that Aβ compromises yeast biology in a manner relevant to human AD. We screened 140,000 compounds for reversal of toxicity and identified a class of protective metal-binding compounds related to clioquinol (CQ), a compound that alleviates Aβ toxicity in mouse AD models. Treating yeast with CQ promoted rapid degradation of Aβ oligomers, rescuing cellular processes perturbed by this insidious peptide and restoring viability. Our approach provides a method for identifying compounds that may eventually help treat AD.
Cross-linguistic register studies
Authors: Neumann Stella
Published: March 2014

This paper discusses register as a meaningful unit of contrastive linguistics and translation studies. Drawing on systemic functional register theory, it categorizes different approaches to register-oriented cross-linguistic studies emphasizing either the comparison of contrasted features organized by register or that of registers using features as operationalizations. The approach is exemplified with the help of sample analyses of the English-German CroCo Corpus, a corpus containing originals and translations from eight different registers. In order to account for the systematic contrastive differences in frequencies of compared features, the magnitude of difference between register-specific and register-neutral frequencies is contrasted. The paper finally discusses complex register-specific combinations of indicators and shows how these help to identify translation properties.
A lexical bundle approach to comparing languages
Authors: Granger Sylviane
Published: March 2014

Contrastive studies of phraseology have tended to focus on figurative units, such as idioms and metaphors, and paid comparatively less attention to less colourful types of units such as collocations and lexical bundles, which are equally, if not more, worthy of study. This article tries to fill this gap by exploring the potential contribution of a lexical bundle approach to language comparison. Some guidelines are presented to help solve some of the methodological challenges posed by a cross-linguistic comparison of lexical bundles. The approach is illustrated with a study of lexical bundles in English and French with a particular focus on units that have a metadiscursive function. Two different genres are compared — parliamentary debates and newspaper editorials — in an attempt to tease out systemic differences between languages and genre effects.
Discourse-structuring functions of initial adverbials in English and Norwegian news and fiction
Authors: Hasselgård Hilde
Published: March 2014

This paper explores the discourse-structuring functions of initial adverbial adjuncts in English and Norwegian news and fiction. Such discourse functions have to do with discourse linking and information management. The corpus study reveals frequency differences in the use of initial adjuncts across the languages, which are to some extent connected with an overall greater frequency of adjuncts in Norwegian. While initial adjuncts in fiction often signal cohesive relations, those in news are more typically due to backgrounding of less important information or to framing/scene-setting for the clause message. Norwegian initial adjuncts are even less likely than English ones to convey new information; on the other hand, initial position is to a lesser extent associated with contrastive focus in Norwegian. This, together with the higher frequency of initial adjuncts in Norwegian, suggests that initial placement of adjuncts carries a lower degree of markedness in Norwegian than in English.
Canonical tag questions in English, Spanish and Portuguese
Authors: Gómez González María de los Ángeles
Published: March 2014

This paper compares and contrasts the patterns of variation exhibited by canonical tag questions ((C)TQs) in English (e.g. ‘That’s enough, isn’t it?’) with those presented by their analogous constructions in Spanish (Es suficiente, ¿no?/ ¿verdad?) and Portuguese (É suficiente, não é?/não?) across a variety of spoken genres that represent the monologic-dialogic, formal-informal and private-public oppositions. The aim is to provide previously lacking comparative statistics that emerge from this trilingual comparison along four parameters: (i) frequencies, (ii) formal features, (iii) distribution across genres, and (iv) functional characteristics. It will be observed that English CTQs are less frequent than analogous constructions in Spanish and particularly in Portuguese. A tag/polarity-based scale will also be proposed in which Portuguese situates itself at one extreme in displaying the widest array of variant and invariant tag types; at the other extreme is Spanish allowing for invariant tags only, whereas English occupies a middle position as it admits both invariant and variant tags but the latter exhibit less variability in kind than their Portuguese counterparts. Lastly, it will be shown that English CTQs display less distributional and functional flexibility than the analogous constructions in the two Romance languages under analysis.
Loving and hating the movies in English, German and Spanish
Authors: Taboada Maite , Carretero Marta , Hinnell Jennifer
Published: March 2014

We present a quantitative analysis of evaluative language in a genre in which it is particularly prominent, that of movie reviews. The data chosen are non-professional consumer-generated reviews written in English, German and Spanish. The reviews are analysed in terms of the categories of Attitude and Graduation within the Appraisal framework (Martin and White, 2005). A number of similarities in the distribution of the Appraisal subcategories were found across the three languages, such as the high frequency of Appreciation and the narrow relationship between the global polarity of the reviews and the individual polarity of the spans. More importantly, the analysis uncovers a number of cross-linguistic distributional differences, which may be explained in terms of a wide array of factors, such as lexicogrammar, word order, argumentative style or sociocultural reasons.
The Old English adjectival affixes ful- and -ful
Authors: Mendaza Raquel Mateo
Published: March 2014

The aim of this article is to measure the indexes of productivity of the prefix ful- and the suffix -ful in Old English adjective formation. This analysis is based on Baayen’s framework, which comprises different measures on productivity. The major sources of the analysis are The Dictionary of Old English Corpus and the lexical database of Old English Nerthus. This study of productivity allows for a diachronic perspective on the evolution of these affixes from the Old English period to the present. The main conclusion drawn from this analysis is that the suffix -ful is more productive than its prefixal counterpart, which implies that more productive patterns are still maintained in Present-day English in contradistinction to the less productive ones.
Early physical maturation of female common bottlenose dolphin Tursiops truncatus in the eastern Levantine Basin
Authors: Kerem Dan , Kent Rafi , Roditi-Elasar Mia , Goffman Oz , Scheinin Aviad , Gol’din Pavel
Published: March 2014

Regional resource limitation in the eastern Levantine Basin was predicted to protract the growth of members of the Israeli sub-population of the common bottlenose dolphin (CBD), compared to CBD sub-populations of similar adult size. Growth curves were fitted to length-at-age data available for 24 male and 26 female CBD stranded or incidentally caught along the Israeli coastline between 2000 and 2009. The obtained model growth constants were compared to those of other CBD sub-populations from the southeastern coast of the United States and a correlation to regional seawater primary productivity was sought. As in other sub-populations, local CBD females initially grow faster than males for approximately 3–4 years and remain longer until around eight years old, after which males surpass them in length. Yet the steep early growth of females as well as its high rate of decay was found to be extreme compared to other CBD sub-populations, with 99% of the asymptotic length being reached at the age of six years. A positive correlation between seawater primary productivity and early growth rate as well as growth decay constants could be demonstrated for CBD males from Texas, Florida and Israeli coasts. Females of the same sub-population presented a non-monotonic relationship to primary productivity. Early female attainment of physical maturity in an ultra-oligotrophic region was unpredicted and is not readily explained. It may accompany early reproductive maturation, selected for as partial compensation for lower lifelong reproductive success.
Blimp-1 represses CD8 T cell expression of PD-1 using a feed-forward transcriptional circuit during acute viral infection
Authors: Lu Peiyuan , Youngblood Benjamin A. , Austin James W. , Rasheed Mohammed Ata Ur , Butler Royce , Ahmed Rafi , Boss Jeremy M.
Published: March 2014

Programmed cell death 1 (PD-1) is an inhibitory immune receptor that regulates T cell function, yet the molecular events that control its expression are largely unknown. We show here that B lymphocyte–induced maturation protein 1 (Blimp-1)–deficient CD8 T cells fail to repress PD-1 during the early stages of CD8 T cell differentiation after acute infection with lymphocytic choriomeningitis virus (LCMV) strain Armstrong. Blimp-1 represses PD-1 through a feed-forward repressive circuit by regulating PD-1 directly and by repressing NFATc1 expression, an activator of PD-1 expression. Blimp-1 binding induces a repressive chromatin structure at the PD-1 locus, leading to the eviction of NFATc1 from its site. These data place Blimp-1 at an important phase of the CD8 T cell effector response and provide a molecular mechanism for its repression of PD-1.
Follicular regulatory T cells control humoral autoimmunity via NFAT2-regulated CXCR5 expression
Authors: Vaeth Martin , Müller Gerd , Stauss Dennis , Dietz Lena , Klein-Hessling Stefan , Serfling Edgar , Lipp Martin , Berberich Ingolf , Berberich-Siebelt Friederike
Published: March 2014

Maturation of high-affinity B lymphocytes is precisely controlled during the germinal center reaction. This is dependent on CD4+CXCR5+ follicular helper T cells (TFH) and inhibited by CD4+CXCR5+Foxp3+ follicular regulatory T cells (TFR). Because NFAT2 was found to be highly expressed and activated in follicular T cells, we addressed its function herein. Unexpectedly, ablation of NFAT2 in T cells caused an augmented GC reaction upon immunization. Consistently, however, TFR cells were clearly reduced in the follicular T cell population due to impaired homing to B cell follicles. This was TFR-intrinsic because only in these cells NFAT2 was essential to up-regulate CXCR5. The physiological relevance for humoral (auto-)immunity was corroborated by exacerbated lupuslike disease in the presence of NFAT2-deficient TFR cells.
BicOverlapper 2.0: visual analysis for gene expression
Authors: Santamaría Rodrigo , Therón Roberto , Quintales Luis
Published: March 2014

Motivation: Systems biology demands the use of several point of views to get a more comprehensive understanding of biological problems. This usually leads to take into account different data regarding the problem at hand, but it also has to do with using different perspectives of the same data. This multifaceted aspect of systems biology often requires the use of several tools, and it is often hard to get a seamless integration of all of them, which would help the analyst to have an interactive discourse with the data.

Results: Focusing on expression profiling, BicOverlapper 2.0 visualizes the most relevant aspects of the analysis, including expression data, profiling analysis results and functional annotation. It also integrates several state-of-the-art numerical methods, such as differential expression analysis, gene set enrichment or biclustering.

Availability and implementation: BicOverlapper 2.0 is available at: http://vis.usal.es/bicoverlapper2

Contact:  rodri@usal.es
The Sinorhizobium meliloti EmrR Regulator Is Required for Efficient Colonization of Medicago sativa Root Nodules
Authors: Santos Mário R. , Marques Andreia T. , Becker Jörg D. , Moreira Leonilde M.
Published: March 2014

The nitrogen-fixing bacterium Sinorhizobium meliloti must adapt to diverse conditions encountered during its symbiosis with leguminous plants. We characterized a new symbiotically relevant gene, emrR (SMc03169), whose product belongs to the TetR family of repressors and is divergently transcribed from emrAB genes encoding a putative major facilitator superfamily–type efflux pump. An emrR deletion mutant produced more succinoglycan, displayed increased cell-wall permeability, and exhibited higher tolerance to heat shock. It also showed lower tolerance to acidic conditions, a reduced production of siderophores, and lower motility and biofilm formation. The simultaneous deletion of emrA and emrR genes restored the mentioned traits to the wild-type phenotype, except for survival under heat shock, which was lower than that displayed by the wild-type strain. Furthermore, the ΔemrR mutant as well as the double ΔemrAR mutant was impaired in symbiosis with Medicago sativa; it formed fewer nodules and competed poorly with the wild-type strain for nodule colonization. Expression profiling of the ΔemrR mutant showed decreased expression of genes involved in Nod-factor and rhizobactin biosynthesis and in stress responses. Expression of genes directing the biosynthesis of succinoglycan and other polysaccharides were increased. EmrR may therefore be involved in a regulatory network targeting membrane and cell wall modifications in preparation for colonization of root hairs during symbiosis.
Singlet oxygen-mediated and EXECUTER-dependent signalling and acclimation of
Arabidopsis thaliana
exposed to light stress
Authors: Zhang Shengrui , Apel Klaus , Kim Chanhong
Published: March 2014

Plants respond to environmental changes by acclimation that activates defence mechanisms and enhances the plant's resistance against a subsequent more severe stress. Chloroplasts play an important role as a sensor of environmental stress factors that interfere with the photosynthetic electron transport and enhance the production of reactive oxygen species (ROS). One of these ROS, singlet oxygen (
1
O
2
), activates a signalling pathway within chloroplasts that depends on the two plastid-localized proteins EXECUTER 1 and 2. Moderate light stress induces acclimation protecting photosynthetic membranes against a subsequent more severe high light stress and at the same time activates
1
O
2
-mediated and EXECUTER-dependent signalling. Pre-treatment of
Arabidopsis
seedlings with moderate light stress confers cross-protection against a virulent
Pseudomonas syringae
strain. While non-pre-acclimated seedlings are highly susceptible to the pathogen regardless of whether
1
O
2
- and EXECUTER-dependent signalling is active or not, pre-stressed acclimated seedlings without this signalling pathway lose part of their pathogen resistance. These results implicate
1
O
2
- and EXECUTER-dependent signalling in inducing acclimation but suggest also a contribution by other yet unknown signalling pathways during this response of plants to light stress.
Putative role of the malate valve enzyme NADP–malate dehydrogenase in H
2
O
2
signalling in
Arabidopsis
Authors: Heyno Eiri , Innocenti Gilles , Lemaire Stéphane D. , Issakidis-Bourguet Emmanuelle , Krieger-Liszkay Anja
Published: March 2014

In photosynthetic organisms, sudden changes in light intensity perturb the photosynthetic electron flow and lead to an increased production of reactive oxygen species. At the same time, thioredoxins can sense the redox state of the chloroplast. According to our hypothesis, thioredoxins and related thiol reactive molecules downregulate the activity of H
2
O
2
-detoxifying enzymes, and thereby allow a transient oxidative burst that triggers the expression of H
2
O
2
responsive genes. It has been shown recently that upon light stress, catalase activity was reversibly inhibited in
Chlamydomonas reinhardtii
in correlation with a transient increase in the level of H
2
O
2
. Here, it is shown that
Arabidopsis thaliana
mutants lacking the NADP–malate dehydrogenase have lost the reversible inactivation of catalase activity and the increase in H
2
O
2
levels when exposed to high light. The mutants were slightly affected in growth and accumulated higher levels of NADPH in the chloroplast than the wild-type. We propose that the malate valve plays an essential role in the regulation of catalase activity and the accumulation of a H
2
O
2
signal by transmitting the redox state of the chloroplast to other cell compartments.
Abscisic acid signalling determines susceptibility of bundle sheath cells to photoinhibition in high light-exposed
Arabidopsis
leaves
Authors: Gorecka Magdalena , Alvarez-Fernandez Ruben , Slattery Katie , McAusland Lorna , Davey Phillip A. , Karpinski Stanislaw , Lawson Tracy , Mullineaux Philip M.
Published: March 2014

The rapid induction of the bundle sheath cell (BSC)-specific expression of
ASCORBATE PEROXIDASE2
(
APX2
) in high light (HL)-exposed leaves of
Arabidopsis thaliana
is, in part, regulated by the hormone abscisic acid (ABA) produced by vascular parenchyma cells. In this study, we provide more details of the ABA signalling that regulates
APX2
expression and consider its importance in the photosynthetic responses of BSCs and whole leaves. This was done using a combination of analyses of gene expression and chlorophyll
a
fluorescence of both leaves and individual BSCs and mesophyll cells. The regulation of
APX2
expression occurs by the combination of the protein kinase SnRK2.6 (OST1):protein phosphatase 2C ABI2 and a Gα (GPA1)-regulated signalling pathway. The use of an
ost1-1/gpa1-4
mutant established that these signalling pathways are distinct but interact to regulate
APX2
. In HL-exposed leaves, BSC chloroplasts were more susceptible to photoinhibition than those of mesophyll cells. The activity of the ABA-signalling network determined the degree of susceptibility of BSCs to photoinhibition by influencing non-photochemical quenching. By contrast, in HL-exposed whole leaves, ABA signalling did not have any major influence on their transcriptomes nor on their susceptibility to photoinhibition, except where guard cell responses were observed.
Relaxation of the non-photochemical chlorophyll fluorescence quenching in diatoms: kinetics, components and mechanisms
Authors: Roháček Karel , Bertrand Martine , Moreau Brigitte , Jacquette Boris , Caplat Christelle , Morant-Manceau Annick , Schoefs Benoît
Published: March 2014

Diatoms are especially important microorganisms because they constitute the larger group of microalgae. To survive the constant variations of the light environment, diatoms have developed mechanisms aiming at the dissipation of excess energy, such as the xanthophyll cycle and the non-photochemical chlorophyll (Chl) fluorescence quenching. This contribution is dedicated to the relaxation of the latter process when the adverse conditions cease. An original nonlinear regression analysis of the relaxation of non-photochemical Chl fluorescence quenching, qN, in diatoms is presented. It was used to obtain experimental evidence for the existence of three time-resolved components in the diatom
Phaeodactylum tricornutum
: qNf, qNi and qNs. qNf (s time-scale) and qNs (h time-scale) are exponential in shape. By contrast, qNi (min time-scale) is of sigmoidal nature and is dominant among the three components. The application of metabolic inhibitors (dithiothreitol, ammonium chloride, cadmium and diphenyleneiodonium chloride) allowed the identification of the mechanisms on which each component mostly relies. qNi is linked to the relaxation of the ΔpH gradient and the reversal of the xanthophyll cycle. qNs quantifies the stage of photoinhibition caused by the high light exposure, qNf seems to reflect fast conformational changes within thylakoid membranes in the vicinity of the photosystem II complexes.
Aggregicoccus edonensis gen. nov., sp. nov., an unusually aggregating myxobacterium isolated from a soil sample
Authors: Sood Sakshi , Awal Ram Prasad , Wink Joachim , Mohr Kathrin I. , Rohde Manfred , Stadler Marc , Kämpfer Peter , Glaeser Stefanie P. , Schumann Peter , Garcia Ronald , Müller Rolf
Published: March 2014

A novel myxobacterium, MCy1366T (Ar1733), was isolated in 1981 from a soil sample collected from a region near Tokyo, Japan. It displayed general myxobacterial features like Gram-negative-staining, rod-shaped vegetative cells, gliding on solid surfaces, microbial lytic activity, fruiting-body-like aggregates and myxospore-like structures. The strain was mesophilic, aerobic and showed a chemoheterotrophic mode of nutrition. It was resistant to many antibiotics such as cephalosporin C, kanamycin, gentamicin, hygromycin B, polymyxin and bacitracin, and the key fatty acids of whole cell hydrolysates were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 0 2-OH. The genomic DNA G+C content of the novel strain was 65.6 mol%. The 16S rRNA gene sequence showed highest similarity (97.60 %) to ‘Stigmatella koreensis’ strain KYC-1019 (GenBank accession no. EF112185). Phylogenetic analysis based on 16S rRNA gene sequences and MALDI-TOF MS data revealed a novel branch in the family

Myxococcaceae

. DNA–DNA hybridization showed only 28 % relatedness between the novel strain and the closest recognized species,

Corallococcus exiguus

DSM 14696T (97 % 16S rRNA gene sequence similarity). A recent isolate from a soil sample collected in Switzerland, MCy10622, displayed 99.9 % 16S rRNA gene sequence similarity with strain MCy1366T and showed almost the same characteristics. Since some morphological features like fruiting-body-like aggregates were barely reproducible in the type strain, the newly isolated strain, MCy10622, was also intensively studied. On the basis of a comprehensive taxonomic study, we propose a novel genus and species, Aggregicoccus edonensis gen. nov., sp. nov., for strains MCy1366T and MCy10622. The type strain of the type species is MCy1366T ( = DSM 27872T = NCCB 100468T).
Oral Candida carriage and immune status in Thai human immunodeficiency virus-infected individuals
Authors: Thanyasrisung Panida , Kesakomol Piyanate , Pipattanagovit Patchara , Youngnak-Piboonratanakit Pornpan , Pitiphat Waranuch , Matangkasombut Oranart
Published: March 2014

Oral candidiasis is a common opportunistic infection among human immunodeficiency virus (HIV)-infected individuals, with growing concerns about the emergence of non-albicans species with resistance to antifungal agents. This cross-sectional study determined the prevalence of oral Candida species in Thai HIV-infected adults and factors affecting their colonization. Candida species were identified from oral rinse samples of 60 HIV-infected participants of the MTCT-Plus initiative and 49 healthy controls by culture-based and molecular assays. The prevalence of oral Candida carriage was similar in HIV-infected patients (56.6 %) and in controls (55.1 %, P = 0.87). Candida albicans was the most predominant species in both groups (94.1 % of Candida carriers in HIV, 88.9 % in control). Interestingly, Candida dubliniensis was the second most common species in controls (29.6 %) and the third in HIV-infected patients (11.8 %, P = 0.08). Multivariate analysis showed that, amongst HIV-infected individuals, CD4 count <200 cells mm–3 was associated with increased prevalence of oral carriage of both C. albicans (P = 0.03) and non-albicans species (P = 0.03). Moreover, patients with tuberculosis infection had a higher prevalence of the non-albicans species than those without (P = 0.03). Intriguingly, contraceptive use was also associated positively with non-albicans and multi-species carriage (P = 0.04 for both). However, use of antiretroviral drugs protected the patients from Candida carriage (P = 0.03), especially from C. albicans (P = 0.02). In conclusion, while HIV-infected individuals had a similar prevalence of oral Candida carriage to that of the control group, host immune status, tuberculosis infection, and contraceptive use may influence oral colonization of Candida, especially of the non-albicans species.
DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent
Authors: Jones Graham , Oxelman Bengt
Published: March 2014

Motivation

The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the species tree. None of the available approaches so far have simultaneously co-estimated all the relevant parameters in the model, without restricting the parameter space by requiring a guide tree and/or prior assignment of individuals to clusters or species.

Results

We present DISSECT, which explores the full space of possible clusterings of individuals and species tree topologies in a Bayesian framework. It uses an approximation to avoid the need for reversible-jump MCMC, in the form of a prior that is a modification of the birth-death prior for the species tree. It incorporates a spike near zero in the density for node heights. The model has two extra parameters: one controls the degree of approximation, and the second controls the prior distribution on the numbers of species. It is implemented as part of BEAST and requires only a few changes from a standard *BEAST analysis. The method is evaluated on simulated data and demonstrated on an empirical data set. The method is shown to be insensitive to the degree of approximation, but quite sensitive to the second parameter, suggesting that large numbers of sequences are needed to draw firm conclusions.

Availability

http://code.google.com/p/beast-mcmc/,http://www.indriid.com/dissectinbeast.html

Contact

art@gjones.name,http://www.indriid.com

Supplementary information

Supplementary material is available.
Molecular basis underlying histone H3 lysine–arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1
Authors: Su Xiaonan , Zhu Guixin , Ding Xiaozhe , Lee Shirley Y. , Dou Yali , Zhu Bing , Wu Wei , Li Haitao
Published: March 2014

Histone modification patterns and their combinatorial readout have emerged as a fundamental mechanism for epigenetic regulation. Here we characterized Spindlin1 as a histone effector that senses a cis-tail histone H3 methylation pattern involving trimethyllysine 4 (H3K4me3) and asymmetric dimethylarginine 8 (H3R8me2a) marks. Spindlin1 consists of triple tudor-like Spin/Ssty repeats. Cocrystal structure determination established concurrent recognition of H3K4me3 and H3R8me2a by Spin/Ssty repeats 2 and 1, respectively. Both H3K4me3 and H3R8me2a are recognized using an “insertion cavity” recognition mode, contributing to a methylation state-specific layer of regulation. In vivo functional studies suggest that Spindlin1 activates Wnt/β-catenin signaling downstream from protein arginine methyltransferase 2 (PRMT2) and the MLL complex, which together are capable of generating a specific H3 “K4me3–R8me2a” pattern. Mutagenesis of Spindlin1 reader pockets impairs activation of Wnt target genes. Taken together, our work connects a histone “lysine–arginine” methylation pattern readout by Spindlin1-to-Wnt signaling at the transcriptional level.
Rice Fertilization-Independent Endosperm1 Regulates Seed Size under Heat Stress by Controlling Early Endosperm Development
Authors: Folsom Jing J. , Begcy Kevin , Hao Xiaojuan , Wang Dong , Walia Harkamal
Published: March 2014

Although heat stress reduces seed size in rice (Oryza sativa), little is known about the molecular mechanisms underlying the observed reduction in seed size and yield. To elucidate the mechanistic basis of heat sensitivity and reduced seed size, we imposed a moderate (34°C) and a high (42°C) heat stress treatment on developing rice seeds during the postfertilization stage. Both stress treatments reduced the final seed size. At a cellular level, the moderate heat stress resulted in precocious endosperm cellularization, whereas severe heat-stressed seeds failed to cellularize. Initiation of endosperm cellularization is a critical developmental transition required for normal seed development, and it is controlled by Polycomb Repressive Complex2 (PRC2) in Arabidopsis (Arabidopsis thaliana). We observed that a member of PRC2 called Fertilization-Independent Endosperm1 (OsFIE1) was sensitive to temperature changes, and its expression was negatively correlated with the duration of the syncytial stage during heat stress. Seeds from plants overexpressing OsFIE1 had reduced seed size and exhibited precocious cellularization. The DNA methylation status and a repressive histone modification of OsFIE1 were observed to be temperature sensitive. Our data suggested that the thermal sensitivity of seed enlargement could partly be caused by altered epigenetic regulation of endosperm development during the transition from the syncytial to the cellularized state.
5-Bromo-2,4,6-trimethyl-3-(4-methylphenylsulfinyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: March 2014

In the title compound, C18H17BrO2S, the dihedral angle between the methylphenyl ring and the mean plane of the benzofuran rung system is 87.0 (2)°. In the crystal, molecules related by inversion are paired into dimersviaC—H...O and C—H...π interactions. These dimers are further linked by C—H...O hydrogen bonds and π–π interactions between the benzene and furan rings of neighbouring molecules [centroid–centroid distance = 3.555 (5) Å], resulting in a three-dimensional supramolecular network.
2-{2,4,6-Tris(bromomethyl)-3,5-bis[(1,3-dioxoisoindolin-2-yl)methyl]benzyl}isoindoline-1,3-dione toluene monosolvate
Authors: Koch Niklas , Seichter Wilhelm , Mazik Monika
Published: March 2014

In the title compound, C36H24Br3N3O6·C7H8, the toluene solvent molecule is associated with the receptor moleculeviaC—H...π bonding. The planes of the phthalimido groups are inclined at 77.0 (1), 63.0 (1) and 77.8 (1)° with respect to the benzene ring. The molecular conformation is stabilized by C—H...O and C—H...Br hydrogen bonds. The crystal structure features non-classical hydrogen bonds of the C—H...N, C—H...O and C—H...Br type, leading to a three-dimensional cross-linking of molecules. The pattern of non-covalent intermolecular bonding is completed by O...Br halogen bonds [3.306 (3) Å], which link the receptor molecules into infinite strands extending along thea-axis direction.
(Z)-5-(3,4,5-Trimethoxystyryl)-2,3-dihydrothieno[3,4-b][1,4]dioxine
Authors: Liu Yu-Tao , Chu Gang
Published: March 2014

In the title compound, C17H18O5S, an analogue of the potent anticancer agent combretastatin A-4, the alkene C=C bond has acisconformation and the C—C=C—C torsion angle is 9.0 (3)°. The dihedral angle between the benzene and thiophene rings is 54.07 (4)°. The dioxene ring adopts a half-chair conformation, with the C atoms of the methylene groups displaced by −0.325 (2) and 0.341 (3) Å from the plane of the other atoms. The C atoms of the twometa-methoxy groups are close to being coplanar with their attached benzene ring [displacements = −0.025 (2) and −0.196 (2) Å], whereas the C atom of thepara-methoxy group is significantly displaced [by −1.107 (2) Å]. In the crystal, C—H...O hydrogen bonds link the molecules into [0-11] chains, which feature two different types ofR22(6) loops.
Dimethylammonium tetraaqua(hydrogensulfato)sulfatocuprate(II)
Authors: Held Peter
Published: March 2014

In the title salt, [(CH3)2NH2][Cu(HSO4)(SO4)(H2O)4], one type of cation and anion is present in the asymmetric unit. The CuIIatom in the complex anion, [Cu(HSO4)(SO4)(H2O)4]−, has a tetragonal bipyramidal [4 + 2] coordination caused by a Jahn–Teller distortion, with the aqua ligands in equatorial and two O atoms of tetrahedral HSO4and SO4units in apical positions. Both types of ions form sheets parallel to (010). The interconnection within and between the sheets is reinforced by O—H...O and N—H...O hydrogen bonds, respectively, involving the water molecules, the two types of sulfate anions and the ammonium groups.
Glycinium 3-carboxy-4-hydroxybenzenesulfonate
Authors: Thirunavukkarasu A. , Silambarasan A. , Kumar R. Mohan , Umarani P. R. , Chakkaravarthi G.
Published: March 2014

In the anion of the title salt, C2H6NO2+·C7H5O6S−, the dihedral angle between the carboxylic acid group and the benzene ring is 5.02 (12)°. In the crystal, the anions are linked into inversion dimers through pairs of O—H...O hydrogen bonds between the carboxylic acid groups and sulfonate O atoms. A pair of C—H...O interactions is also observed within each dimer. The anion dimers and the cations are linked into a three-dimensional network by N—H...O, O—H...O and C—H...O hydrogen bonds.
Unaccompanied children living in transitional houses – voices from Sweden
Authors: Malmsten Jenny
Published: March 2014

Purpose

– The purpose of this paper is to show how unaccompanied minors perceive the time they spend in transitional houses in Malmö in southern Sweden. An important outlook when presenting the empiric data is to provide the perspective of the child, not just to have a child perspective (i.e. an adult perspective on children's experiences).

Design/methodology/approach

– The paper is the result of interviews with 11 unaccompanied boys living in transitional houses, i.e., group homes. The theoretical section has two purposes, to describe the Swedish context and the ambivalent discourse regarding immigrants in Sweden and to give a background on aspects that are relevant to understand unaccompanied minors situation.

Findings

– Even though many unaccompanied minors suffer from psychological difficulties and worries about the asylum process, the interviews show that the children in this study are generally content with the transitional houses. The staff strives to support them in coping with daily life, and strengthen their sense of coherence.

Research limitations/implications

– Since unaccompanied minors do not have family close by, the interviews shows the importance in different sorts of activities to promote wellbeing. A stronger focus on participation could also be a way of reinforcing the children's sense of coherence.

Originality/value

– This paper gives an insight to life in transitional houses from unaccompanied minors point of view.