bluuebunny/crossref_metadata_2025 huggingface dataset:
A controlling role for the air−sea interface in the chemical processing of reactive nitrogen in the coastal marine boundary layer
Authors: Kim Michelle J. , Farmer Delphine K. , Bertram Timothy H.
Published: March 2014

Significance

Reactions occurring at the air−sea interface have the potential to alter the chemical composition of the atmosphere. However, our knowledge of the extent to which these reactions impact the concentration of oxidants and their precursors is derived from laboratory measurements using systems that mimic the chemical, biological, and physical complexity of the surface ocean. Here, we present direct measurements of the vertical fluxes of a reactant−product pair using eddy covariance coupled with chemical ionization time-of-flight mass spectrometry to directly assess the role of the ocean surface in the exchange of reactive nitrogen and halogens. Our observations suggest that the ocean surface plays a critical role in controlling the lifetime of N
2
O
5
, a primary nocturnal reservoir for tropospheric reactive nitrogen.
Molecular mechanism and structure of the
Saccharomyces cerevisiae
iron regulator Aft2
Authors: Poor Catherine B. , Wegner Seraphine V. , Li Haoran , Dlouhy Adrienne C. , Schuermann Jonathan P. , Sanishvili Ruslan , Hinshaw James R. , Riggs-Gelasco Pamela J. , Outten Caryn E. , He Chuan
Published: March 2014

Significance

Iron is essential for eukaryotic cell survival but toxic at higher concentrations. In yeast, iron levels are tightly regulated by the transcriptional activators Aft1 and Aft2 (
a
ctivators of
f
errous
t
ransport), which activate iron-uptake genes when iron levels are low. We report the first crystal structure of DNA-bound Aft2 and show that Aft2 senses cellular iron levels via direct [2Fe-2S]-cluster binding, which promotes Aft2 dimerization and deactivation of the regulated genes. We further demonstrate that Aft2 acquires a [2Fe-2S] cluster from glutaredoxin-3 and Fe repressor of activation-2, two [2Fe-2S]-binding proteins with homologs in higher eukaryotes. This study unveils the molecular mechanism of the Aft family of iron-regulatory proteins and emphasizes the importance of Fe-S clusters in cellular iron sensing in eukaryotes.
Quantifying the atomic-level mechanics of single long physisorbed molecular chains
Authors: Kawai Shigeki , Koch Matthias , Gnecco Enrico , Sadeghi Ali , Pawlak Rémy , Glatzel Thilo , Schwarz Jutta , Goedecker Stefan , Hecht Stefan , Baratoff Alexis , Grill Leonhard , Meyer Ernst
Published: March 2014

Significance

Mechanical properties of biopolymers such as DNA and proteins have been studied to understand the details of complex processes in living systems via systematic statistical analyses of repeated measurements. However, the mechanical behavior of a single molecular chain pulled off a surface has never been investigated with atomic-scale resolution. Herein, we present such a study on in situ polymerized fluorene chains by pulling individual chains with the tip of an atomic force microscope at 4.8 K. The measured variations of the force gradient provide detailed insights into the detachment process of fluorene units and the role of near-incommensurability with the substrate structure.
Memory loss in a nonnavigational spatial task after hippocampal inactivation in monkeys
Authors: Forcelli Patrick A. , Palchik Guillermo , Leath Taylor , DesJardin Jacqueline T. , Gale Karen , Malkova Ludise
Published: March 2014

Significance

Although the hippocampus has a well-documented role for spatial navigation across species, its role for spatial memory in nonnavigational tasks is uncertain. Thus, when monkeys are tested in tasks that do not require navigation through space, spatial memory seems unaffected by hippocampal lesions. However, the interpretation of these results is compromised by long-term compensatory adaptation occurring in the days and weeks after lesions. To preclude long-term compensation, we transiently inactivated hippocampus at the time of testing. Hippocampal inactivation reduced performance on a nonnavigational spatial memory task to chance levels. These data align the role of hippocampus for spatial memory in monkeys with the broader literature while simultaneously demonstrating the efficacy of inactivation of hippocampus in monkeys.
A soil actinobacterium scavenges atmospheric H
2
using two membrane-associated, oxygen-dependent [NiFe] hydrogenases
Authors: Greening Chris , Berney Michael , Hards Kiel , Cook Gregory M. , Conrad Ralf
Published: March 2014

Significance

Molecular hydrogen is present in trace concentrations in the Earth’s lower atmosphere and is rapidly turned over through a biogeochemical cycle. Microbial soil processes are responsible for the majority of net uptake of H
2
from the atmosphere, but the enzymes involved have remained elusive. In this communication, we use genetic dissection and GC measurements to show that the soil actinobacterium
Mycobacterium smegmatis
can oxidize trace concentrations of H
2
. This process depends on two oxygen-dependent, membrane-associated [NiFe] hydrogenases with picomolar thresholds. Activity is most pronounced during carbon limitation, suggesting that mycobacteria oxidize a dependable trace gas to survive starvation. We propose that these enzymes and their homologs in other actinobacteria and soil phyla constitute the principal sink of global atmospheric H
2
.
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology
Authors: Legendre Matthieu , Bartoli Julia , Shmakova Lyubov , Jeudy Sandra , Labadie Karine , Adrait Annie , Lescot Magali , Poirot Olivier , Bertaux Lionel , Bruley Christophe , Couté Yohann , Rivkina Elizaveta , Abergel Chantal , Claverie Jean-Michel
Published: March 2014

Significance

Giant DNA viruses are visible under a light microscope and their genomes encode more proteins than some bacteria or intracellular parasitic eukaryotes. There are two very distinct types and infect unicellular protists such as
Acanthamoeba
. On one hand, Megaviridae possess large pseudoicosahedral capsids enclosing a megabase-sized adenine–thymine-rich genome, and on the other, the recently discovered Pandoraviruses exhibit micron-sized amphora-shaped particles and guanine–cytosine-rich genomes of up to 2.8 Mb. While initiating a survey of the Siberian permafrost, we isolated a third type of giant virus combining the Pandoravirus morphology with a gene content more similar to that of icosahedral DNA viruses. This suggests that pandoravirus-like particles may correspond to an unexplored diversity of unconventional DNA virus families.
Circulating hematopoietic stem and progenitor cells are myeloid-biased in cancer patients
Authors: Wu Wen-Chao , Sun Hong-Wei , Chen Hai-Tian , Liang Jing , Yu Xing-Juan , Wu Chong , Wang Zilian , Zheng Limin
Published: March 2014

Significance

Hematopoietic stem and progenitor cells (HSPCs) cannot only replace depleted progeny pools, but act as the primary immune response to various pathological conditions. Here we show that the circulating HSPCs from various patients with solid tumors exhibit a generalized myeloid bias with a skew toward granulocytic differentiation. Importantly, circulating hematopoietic precursors were highly enriched in tumor tissues and positively correlated with disease progression. We developed an in vitro short-term culture model to effectively induce the rapid generation of myeloid-derived suppressor cells (MDSCs), defined as cord blood-derived MDSCs. In addition, we suggest that the altered circulating HSPCs may serve as an important link between dysregulated hematopoiesis and accumulated immunosuppressive MDSCs in patients with cancer.
Contextual effect of positive intergroup contact on outgroup prejudice
Authors: Christ Oliver , Schmid Katharina , Lolliot Simon , Swart Hermann , Stolle Dietlind , Tausch Nicole , Al Ramiah Ananthi , Wagner Ulrich , Vertovec Steven , Hewstone Miles
Published: March 2014

Significance

Although mixed social environments can provoke conflict, where this diversity promotes positive intergroup contact, prejudice is reduced. Seven multilevel studies demonstrate that the benefits of intergroup contact are broader than previously thought. Contact not only changes attitudes for individuals experiencing direct positive intergroup contact, their attitudes are also influenced by the behavior (and norms) of fellow ingroup members in their social context. Even individuals experiencing no direct, face-to-face intergroup contact can benefit from living in mixed settings where fellow ingroup members do engage in such contact. Two longitudinal studies rule out selection bias as an explanation for these findings on the contextual level. Prejudice is a function not only of whom you interact with, but also of where you live.
Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog
Authors: Kodan Atsushi , Yamaguchi Tomohiro , Nakatsu Toru , Sakiyama Keita , Hipolito Christopher J. , Fujioka Akane , Hirokane Ryo , Ikeguchi Keiji , Watanabe Bunta , Hiratake Jun , Kimura Yasuhisa , Suga Hiroaki , Ueda Kazumitsu , Kato Hiroaki
Published: March 2014

Significance

P-glycoprotein exports various hydrophobic chemicals in an ATP-dependent manner, determines their absorption and distribution in the body, and is involved in multidrug resistance (MDR) in tumors. Understanding the mechanism of the multidrug transport is important for designing drugs of good bioavailability and efficient cancer chemotherapy. We determined the high-resolution crystal structures of a eukaryotic P-glycoprotein homolog and revealed the detailed architecture of its transmembrane domains, which contain an exit gate for substrates that opens to the extracellular side and two entrance gates that open to the intramembranous region and the cytosolic side. We propose a motion of the transmembrane domains powered by the association of two nucleotide-binding domains on ATP binding that is different from other transporters.
Fine mapping of genome activation in bovine embryos by RNA sequencing
Authors: Graf Alexander , Krebs Stefan , Zakhartchenko Valeri , Schwalb Björn , Blum Helmut , Wolf Eckhard
Published: March 2014

Significance

Gene expression profiling is widely used to get insight into mechanisms of early embryonic development and to characterize embryos generated by various techniques or exposed to different culture conditions. Transcripts in early embryos may be of maternal or embryonic origin, which is difficult to distinguish by conventional techniques. RNA sequencing in bovine oocytes and embryos facilitated mapping of the onset of embryonic expression for almost 7,400 genes. The timing of embryonic gen(om)e activation offers an additional level of information for embryo biosystems research and for detecting disturbances of early development due to genetic, epigenetic, and environmental factors.
Marine fish may be biochemically constrained from inhabiting the deepest ocean depths
Authors: Yancey Paul H. , Gerringer Mackenzie E. , Drazen Jeffrey C. , Rowden Ashley A. , Jamieson Alan
Published: March 2014

Significance

Fish appear to be absent from the ocean's greatest depths, the trenches from 8,400–11,000 m. The reason is unknown, but hydrostatic pressure is suspected. We propose that the answer is the need for high levels of trimethylamine oxide (TMAO, common in many marine animals), a potent stabilizer capable of counteracting the destabilization of proteins by pressure. TMAO is known to increase with depth in bony fishes (teleosts) down to 4,900 m. By capturing the world's second-deepest known fish, the hadal snailfish
Notoliparis kermadecensis
from 7,000 m, we find that they have the highest recorded TMAO contents, which, moreover, yield an extrapolated maximum for fish at about 8,200 m. This is previously unidentified evidence that biochemistry may constrain depth for a large taxonomic group.
Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts
Authors: Liu Yu , Tan Yun Lei , Zhang Xin , Bhabha Gira , Ekiert Damian C. , Genereux Joseph C. , Cho Younhee , Kipnis Yakov , Bjelic Sinisa , Baker David , Kelly Jeffery W.
Published: March 2014

Significance

Historically, the folding of individual proteins in buffers has been studied spectroscopically. The majority of spectroscopic methods (NMR and fluorescence excluded) cannot be used in a cell, because the protein of interest (POI) cannot be distinguished from the background proteome. Herein, we introduce folding probes, which when used in cell lysates with sufficient holdase activity, faithfully quantify the folded and functional fraction of a POI at a time point of interest in a cell by selectively reacting with that state to afford a fluorescent signal. This work provides a blueprint for how to convert enzyme inhibitors, ligands for nonenzyme proteins, etc. into folding probes to efficiently and specifically investigate how intracellular function is controlled by the proteostasis network as a function of cellular perturbations.
BMP signaling is required for the generation of primordial germ cells in an insect
Authors: Donoughe Seth , Nakamura Taro , Ewen-Campen Ben , Green Delbert A. , Henderson Lory , Extavour Cassandra G.
Published: March 2014

Significance

Many model organisms specify germ cells using maternally supplied germ-line determinants. In contrast, mice rely on embryonic cell–cell signaling to induce cells to become germ cells. Molecular evidence for inductive germ-line specification had previously been provided only for the mouse. Here we provide functional evidence for inductive germ cell specification in an invertebrate, by showing that bone morphogenetic protein (BMP) signaling, which induces mouse germ cell specification, is required for establishment of embryonic germ cells in a cricket. BMP pathway knockdown causes reduction or loss of germ cells, and elevated levels of BMP signaling cause supernumerary and ectopic germ cells. BMP-based germ cell induction in mice and crickets suggests that this may be a shared ancestral mechanism in animals.
Fatty acid-inducible ANGPTL4 governs lipid metabolic response to exercise
Authors: Catoire Milène , Alex Sheril , Paraskevopulos Nicolas , Mattijssen Frits , Evers-van Gogh Inkie , Schaart Gert , Jeppesen Jacob , Kneppers Anita , Mensink Marco , Voshol Peter J. , Olivecrona Gunilla , Tan Nguan Soon , Hesselink Matthijs K. C. , Berbée Jimmy F. , Rensen Patrick C. N. , Kalkhoven Eric , Schrauwen Patrick , Kersten Sander
Published: March 2014

Significance

Physical exercise causes profound changes in energy metabolism in humans. In this study we show that resting skeletal muscle has a crucial role in the metabolic response to acute exercise. During endurance exercise, selective induction of the protein angiopoietin-like 4 (ANGPTL4) in nonexercising muscle reduces local fatty acid uptake, presumably to prevent fat overload, while directing fatty acids to the active skeletal muscle as fuel. Our data thus suggest that nonexercising muscle has a key role in governing lipid homeostasis during exercise.
Amazonian functional diversity from forest canopy chemical assembly
Authors: Asner Gregory P. , Martin Roberta E. , Tupayachi Raul , Anderson Christopher B. , Sinca Felipe , Carranza-Jiménez Loreli , Martinez Paola
Published: March 2014

Significance

Canopy trees are keystone organisms that create habitat for an enormous array of flora and fauna and dominate carbon storage in tropical forests. Determining the functional diversity of tree canopies is, therefore, critical to understanding how tropical forests are assembled and predicting ecosystem responses to environmental change. Across the megadiverse Andes-to-Amazon corridor of Peru, we discovered a large-scale nested pattern of canopy chemical assembly among thousands of trees. This nested geographic and phylogenetic pattern within and among forest communities provides a different perspective on current and future alterations to the functioning of western Amazonian forests resulting from land use and climate change.
Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery
Authors: Geertsema Hylkje J. , Kulczyk Arkadiusz W. , Richardson Charles C. , van Oijen Antoine M.
Published: March 2014

Significance

The DNA replication machinery is a multiprotein assembly that is responsible for a rapid and faithful duplication of the genome. Based on biochemical, structural, and genetic studies, we have obtained a very detailed picture of its different enzymatic activities that underlie unwinding of the parental duplex DNA and incorporation of nucleotides into daughter DNA. However, little is known about the dynamic changes in composition of the complex during replication. Here, we use single-molecule fluorescence methods to visualize the dynamics with which individual DNA polymerases, the replication protein responsible for DNA synthesis, associate with and dissociate from the replication machinery. Our results show that the DNA polymerase remains associated with the replication complex for a much shorter time than our previous models suggested.
Harvesting renewable energy from Earth’s mid-infrared emissions
Authors: Byrnes Steven J. , Blanchard Romain , Capasso Federico
Published: March 2014

Significance

Renewable energy can be generated whenever heat flows from a hotter to a colder body. One such flow is from the warm surface of Earth to cold outer space, via infrared thermal radiation. An emissive energy harvester (EEH) is a device that can generate energy from emitting thermal radiation into the clear sky. We calculate how much power is thermodynamically available, using a location in Oklahoma as a case study. We discuss two possible ways to make such a device: A thermal EEH (analogous to solar thermal power generation) and an optoelectronic EEH (analogous to photovoltaic power generation). For the latter, we propose using a rectifying antenna, and we discuss its operating principles, efficiency limits, system design considerations, and possible technological implementations.
Differential regulation of S-region hypermutation and class-switch recombination by noncanonical functions of uracil DNA glycosylase
Authors: Yousif Ashraf S. , Stanlie Andre , Mondal Samiran , Honjo Tasuku , Begum Nasim A.
Published: March 2014

Significance

Uracil DNA glycosylase (UNG) has been known as a critical base excision repair protein required for class switch recombination (CSR) and somatic hypermutation (SHM). On the other hand, its precise function in both CSR and SHM is extremely debatable and elusive. Here, we showed that UNG suppresses S region SHM (s-SHM) by recruiting the faithful DNA repair complex and, in the absence of UNG, the error-prone repair complex that induces s-SHM overrides. Moreover, UNG promotes activation-induced cytidine deaminase-induced CSR by regulating S-S synapse and DNA end repair. Interestingly, the enzymatic activity of UNG is dispensable for s-SHM suppression and CSR promotion.
Evidence of a common mechanism of disassembly of adherens junctions through Gα13 targeting of VE-cadherin
Authors: Gong Haixia , Gao Xiaopei , Feng Shaoting , Siddiqui M. Rizwan , Garcia Alexander , Bonini Marcelo G. , Komarova Yulia , Vogel Stephen M. , Mehta Dolly , Malik Asrar B.
Published: March 2014

The heterotrimeric G protein Gα13 transduces signals from G protein–coupled receptors (GPCRs) to induce cell spreading, differentiation, migration, and cell polarity. Here, we describe a novel GPCR-independent function of Gα13 in regulating the stability of endothelial cell adherens junctions (AJs). We observed that the oxidant H2O2, which is released in response to multiple proinflammatory mediators, induced the interaction of Gα13 with VE-cadherin. Gα13 binding to VE-cadherin in turn induced Src activation and VE-cadherin phosphorylation at Tyr 658, the p120-catenin binding site thought to be responsible for VE-cadherin internalization. Inhibition of Gα13–VE-cadherin interaction using an interfering peptide derived from the Gα13 binding motif on VE-cadherin abrogated the disruption of AJs in response to inflammatory mediators. These studies identify a unique role of Gα13 binding to VE-cadherin in mediating VE-cadherin internalization and endothelial barrier disruption and inflammation.
Nontriviality of the 𝑀-degree of the 𝐴-polynomial
Authors: Boden Hans
Published: March 2014

This note gives a proof that the

A
A

-polynomial of any nontrivial knot in

S
3

S^3

has nontrivial

M
M

-degree.
Additive schemes (splitting schemes) for some systems of evolutionary equations
Authors: Vabishchevich Petr
Published: March 2014

On the basis of additive schemes (splitting schemes) we construct efficient numerical algorithms to solve approximately the initial-boundary value problems for systems of time-dependent partial differential equations (PDEs). In many applied problems the individual components of the vector of unknowns are coupled together and then splitting schemes are applied in order to get a simple problem for evaluating components at a new time level. Typically, the additive operator-difference schemes for systems of evolutionary equations are constructed for operators coupled in space. In this paper we investigate more general problems where coupling of derivatives in time for components of the solution vector takes place. Splitting schemes are developed using an additive representation for both the primary operator of the problem and the operator at the time derivative. Splitting schemes are based on a triangular two-component representation of the operators.
Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013
Authors:   MS-SIG 2013 Organizers, Ryu So Young , Payne Samuel H. , Schaab Christoph , Xiao Wenzhong
Published: March 2014

Contact:  wenzhong.xiao@mgh.harvard.edu
Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region
Authors: Clabbers Max T. B. , Olsthoorn Rene C. L. , Gultyaev Alexander P.
Published: March 2014

Summary: The intergenic regions of the ambisense RNA segments of viruses from the Tospovirus genus form large extended RNA structures that regulate virus replication. Using comparative structure analysis, we show the presence of conserved alternative conformations at the apical parts of these structures. In one conformation, a branched Y-shape, the 5′-proximal hairpin arms are mostly capped by exceptionally stable tetraloop motifs. The tetraloop hairpins are folded in both virus and virus-complementary sense RNAs, and different tetraloops can functionally replace each other. Folding simulations show that the branched Y-shape structures can undergo a conformational transition to alternative extended rod-like conformations. Functional importance of both alternatives is supported by nucleotide covariations. The balanced equilibrium between alternative structures is evidenced by native gel electrophoresis of mutant RNA transcripts with shifted equilibria. The tetraloops play a role in the stability and dynamics of structures but may also be recognized by proteins involved in translation and/or replication.

Contact:  goultiaevap2@chem.leidenuniv.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
New Insights into the Regulation of Aquaporins by the Arbuscular Mycorrhizal Symbiosis in Maize Plants Under Drought Stress and Possible Implications for Plant Performance
Authors: Bárzana Gloria , Aroca Ricardo , Bienert Gerd Patrick , Chaumont François , Ruiz-Lozano Juan Manuel
Published: March 2014

The relationship between modulation by arbuscular mycorrhizae (AM) of aquaporin expression in the host plant and changes in root hydraulic conductance, plant water status, and performance under stressful conditions is not well known. This investigation aimed to elucidate how the AM symbiosis modulates the expression of the whole set of aquaporin genes in maize plants under different growing and drought stress conditions, as well as to characterize some of these aquaporins in order to shed further light on the molecules that may be involved in the mycorrhizal responses to drought. The AM symbiosis regulated a wide number of aquaporins in the host plant, comprising members of the different aquaporin subfamilies. The regulation of these genes depends on the watering conditions and the severity of the drought stress imposed. Some of these aquaporins can transport water and also other molecules which are of physiological importance for plant performance. AM plants grew and developed better than non-AM plants under the different conditions assayed. Thus, for the first time, this study relates the well-known better performance of AM plants under drought stress to not only the water movement in their tissues but also the mobilization of N compounds, glycerol, signaling molecules, or metalloids with a role in abiotic stress tolerance. Future studies should elucidate the specific function of each aquaporin isoform regulated by the AM symbiosis in order to shed further light on how the symbiosis alters the plant fitness under stressful conditions.
The relationship between maximum tolerated light intensity and photoprotective energy dissipation in the photosynthetic antenna: chloroplast gains and losses
Authors: Ruban Alexander V. , Belgio Erica
Published: March 2014

The principle of quantifying the efficiency of protection of photosystem II (PSII) reaction centres against photoinhibition by non-photochemical energy dissipation (NPQ) has been recently introduced by Ruban & Murchie (2012
Biochim. Biophys. Acta
1817
, 977–982 (
doi:10.1016/j.bbabio.2012.03.026
)). This is based upon the assessment of two key parameters: (i) the relationship between the PSII yield and NPQ, and (ii) the fraction of intact PSII reaction centres in the dark after illumination. In this paper, we have quantified the relationship between the amplitude of NPQ and the light intensity at which all PSII reaction centres remain intact for plants with different levels of PsbS protein, known to play a key role in the process. It was found that the same, nearly linear, relationship exists between the levels of the protective NPQ component (pNPQ) and the tolerated light intensity in all types of studied plants. This approach allowed for the quantification of the maximum tolerated light intensity, the light intensity at which all plant leaves become photoinhibited, the fraction of (most likely) unnecessary or ‘wasteful’ NPQ, and the fraction of photoinhibited PSII reaction centres under conditions of prolonged illumination by full sunlight. It was concluded that the governing factors in the photoprotection of PSII are the level and rate of protective pNPQ formation, which are often in discord with the amplitude of the conventional measure of photoprotection, the quickly reversible NPQ component, qE. Hence, we recommend pNPQ as a more informative and less ambiguous parameter than qE, as it reflects the effectiveness and limitations of the major photoprotective process of the photosynthetic membrane.
Thioredoxin-dependent regulatory networks in chloroplasts under fluctuating light conditions
Authors: Nikkanen Lauri , Rintamäki Eevi
Published: March 2014

Plants have adopted a number of mechanisms to restore redox homeostasis in the chloroplast under fluctuating light conditions in nature. Chloroplast thioredoxin systems are crucial components of this redox network, mediating environmental signals to chloroplast proteins. In the reduced state, thioredoxins control the structure and function of proteins by reducing disulfide bridges in the redox active site of a protein. Subsequently, an oxidized thioredoxin is reduced by a thioredoxin reductase, the two enzymes together forming a thioredoxin system. Plant chloroplasts have versatile thioredoxin systems, including two reductases dependent on ferredoxin and NADPH as reducing power, respectively, several types of thioredoxins, and the system to deliver thiol redox signals to the thylakoid membrane and lumen. Light controls the activity of chloroplast thioredoxin systems in two ways. First, light reactions activate the thioredoxin systems via donation of electrons to oxidized ferredoxin and NADP
+
, and second, light induces production of reactive oxygen species in chloroplasts which deactivate the components of the thiol redox network. The diversity and partial redundancy of chloroplast thioredoxin systems enable chloroplast metabolism to rapidly respond to ever-changing environmental conditions and to raise plant fitness in natural growth conditions.
The functions of WHIRLY1 and REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 in cross tolerance responses in plants: a hypothesis
Authors: Foyer Christine H. , Karpinska Barbara , Krupinska Karin
Published: March 2014

Chloroplasts are important sensors of environment change, fulfilling key roles in the regulation of plant growth and development in relation to environmental cues. Photosynthesis produces a repertoire of reductive and oxidative (redox) signals that provide information to the nucleus facilitating appropriate acclimation to a changing light environment. Redox signals are also recognized by the cellular innate immune system allowing activation of non-specific, stress-responsive pathways that underpin cross tolerance to biotic–abiotic stresses. While these pathways have been intensively studied in recent years, little is known about the different components that mediate chloroplast-to-nucleus signalling and facilitate cross tolerance phenomena. Here, we consider the properties of the WHIRLY family of proteins and the REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) in relation to chloroplast redox signals that facilitate the synergistic co-activation of gene expression pathways and confer cross tolerance to abiotic and biotic stresses. We propose a new hypothesis for the role of WHIRLY1 as a redox sensor in chloroplast-to-nucleus retrograde signalling leading to cross tolerance, including acclimation and immunity responses. By virtue of its association with chloroplast nucleoids and with nuclear DNA, WHIRLY1 is an attractive candidate coordinator of the expression of photosynthetic genes in the nucleus and chloroplasts. We propose that the redox state of the photosynthetic electron transport chain triggers the movement of WHIRLY1 from the chloroplasts to the nucleus, and draw parallels with the regulation of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1).
Light-harvesting mutants show differential gene expression upon shift to high light as a consequence of photosynthetic redox and reactive oxygen species metabolism
Authors: Tikkanen Mikko , Gollan Peter J. , Mekala Nageswara Rao , Isojärvi Janne , Aro Eva-Mari
Published: March 2014

The amount of light energy that is harvested and directed to the photosynthetic machinery is regulated in order to control the production of reactive oxygen species (ROS) in leaf tissues. ROS have important roles as signalling factors that instigate and mediate a range of cellular responses, suggesting that the mechanisms regulating light-harvesting and photosynthetic energy transduction also affect cell signalling. In this study, we exposed wild-type (WT)
Arabidopsis
and mutants impaired in the regulation of photosynthetic light-harvesting (
stn7
,
tap38
and
npq4
) to transient high light (HL) stress in order to study the role of these mechanisms for up- and downregulation of gene expression under HL stress. The mutants, all of which have disturbed regulation of excitation energy transfer and distribution, responded to transient HL treatment with surprising similarity to the WT in terms of general ‘abiotic stress-regulated’ genes associated with hydrogen peroxide and 12-oxo-phytodienoic acid signalling. However, we identified distinct expression profiles in each genotype with respect to induction of singlet oxygen and jasmonic acid-dependent responses. The results of this study suggest that the control of excitation energy transfer interacts with hormonal regulation. Furthermore, the photosynthetic pigment–protein complexes appear to operate as receptors that sense the energetic balance between the photosynthetic light reactions and downstream metabolism.
Influence of plastids on light signalling and development
Authors: Larkin Robert M.
Published: March 2014

In addition to their contribution to metabolism, chloroplasts emit signals that influence the expression of nuclear genes that contribute to numerous plastidic and extraplastidic processes. Plastid-to-nucleus signalling optimizes chloroplast function, regulates growth and development, and affects responses to environmental cues. An incomplete list of plastid signals is available and particular plastid-to-nucleus signalling mechanisms are partially understood. The plastid-to-nucleus signalling that depends on theGENOMES UNCOUPLED(GUN) genes couples the expression of nuclear genes to the functional state of the chloroplast. Analyses ofgunmutants provided insight into the mechanisms and biological functions of plastid-to-nucleus signalling.GUNgenes contribute to chloroplast biogenesis, the circadian rhythm, stress tolerance, light signalling and development. Some have criticized thegunmutant screen for employing inhibitors of chloroplast biogenesis and suggested thatgunalleles do not disrupt significant plastid-to-nucleus signalling mechanisms. Here, I briefly reviewGUN-dependent plastid-to-nucleus signalling, explain the flaws in the major criticisms of thegunmutant screen and review the influence of plastids on light signalling and development.
Photosynthesis under artificial light: the shift in primary and secondary metabolism
Authors: Darko Eva , Heydarizadeh Parisa , Schoefs Benoît , Sabzalian Mohammad R.
Published: March 2014

Providing an adequate quantity and quality of food for the escalating human population under changing climatic conditions is currently a great challenge. In outdoor cultures, sunlight provides energy (through photosynthesis) for photosynthetic organisms. They also use light quality to sense and respond to their environment. To increase the production capacity, controlled growing systems using artificial lighting have been taken into consideration. Recent development of light-emitting diode (LED) technologies presents an enormous potential for improving plant growth and making systems more sustainable. This review uses selected examples to show how LED can mimic natural light to ensure the growth and development of photosynthetic organisms, and how changes in intensity and wavelength can manipulate the plant metabolism with the aim to produce functionalized foods.
Multiple feedbacks between chloroplast and whole plant in the context of plant adaptation and acclimation to the environment
Authors: Demmig-Adams Barbara , Stewart Jared J. , Adams William W.
Published: March 2014

This review focuses on feedback pathways that serve to match plant energy acquisition with plant energy utilization, and thereby aid in the optimization of chloroplast and whole-plant function in a given environment. First, the role of source–sink signalling in adjusting photosynthetic capacity (light harvesting, photochemistry and carbon fixation) to meet whole-plant carbohydrate demand is briefly reviewed. Contrasting overall outcomes, i.e. increased plant growth versus plant growth arrest, are described and related to respective contrasting environments that either do or do not present opportunities for plant growth. Next, new insights into chloroplast-generated oxidative signals, and their modulation by specific components of the chloroplast's photoprotective network, are reviewed with respect to their ability to block foliar phloem-loading complexes, and, thereby, affect both plant growth and plant biotic defences. Lastly, carbon export capacity is described as a newly identified tuning point that has been subjected to the evolution of differential responses in plant varieties (ecotypes) and species from different geographical origins with contrasting environmental challenges.
Kinetics of retrograde signalling initiation in the high light response of
Arabidopsis thaliana
Authors: Alsharafa Khalid , Vogel Marc Oliver , Oelze Marie-Luise , Moore Marten , Stingl Nadja , König Katharina , Friedman Haya , Mueller Martin J. , Dietz Karl-Josef
Published: March 2014

High light acclimation depends on retrograde control of nuclear gene expression. Retrograde regulation uses multiple signalling pathways and thus exploits signal patterns. To maximally challenge the acclimation system,
Arabidopsis thaliana
plants were either adapted to 8 (low light (L-light)) or 80 µmol quanta m
−2
s
−1
(normal light (N-light)) and subsequently exposed to a 100- and 10-fold light intensity increase, respectively, to high light (H-light, 800 µmol quanta m
−2
s
−1
), for up to 6 h. Both L → H- and N → H-light plants efficiently regulated CO
2
assimilation to a constant level without apparent damage and inhibition. This experimental set-up was scrutinized for time-dependent regulation and efficiency of adjustment. Transcriptome profiles revealed that N-light and L-light plants differentially accumulated 2119 transcripts. After 6 h in H-light, only 205 remained differently regulated between the L → H- and N → H-light plants, indicating efficient regulation allowing the plants to reach a similar transcriptome state. Time-dependent analysis of transcripts as markers for signalling pathways, and of metabolites and hormones as possibly involved transmitters, suggests that oxylipins such as oxophytodienoic acid and jasmonic acid, metabolites and redox cues predominantly control the acclimation response, whereas abscisic acid, salicylic acid and auxins play an insignificant or minor role.
Natural variation in phosphorylation of photosystem II proteins in
Arabidopsis thaliana
: is it caused by genetic variation in the STN kinases?
Authors: Flood Pádraic J. , Yin Lan , Herdean Andrei , Harbinson Jeremy , Aarts Mark G. M. , Spetea Cornelia
Published: March 2014

Reversible phosphorylation of photosystem II (PSII) proteins is an important regulatory mechanism that can protect plants from changes in ambient light intensity and quality. We hypothesized that there is natural variation in this process in
Arabidopsis
(
Arabidopsis thaliana
), and that this results from genetic variation in the
STN7
and
STN8
kinase genes. To test this,
Arabidopsis
accessions of diverse geographical origins were exposed to two light regimes, and the levels of phospho-D1 and phospho-light harvesting complex II (LHCII) proteins were quantified by western blotting with anti-phosphothreonine antibodies. Accessions were classified as having high, moderate or low phosphorylation relative to Col-0. This variation could not be explained by the abundance of the substrates in thylakoid membranes. In genotypes with atrazine-resistant forms of the D1 protein, low D1 and LHCII protein phosphorylation was observed, which may be due to low PSII efficiency, resulting in reduced activation of the STN kinases. In the remaining genotypes, phospho-D1 levels correlated with STN8 protein abundance in high-light conditions. In growth light, D1 and LHCII phosphorylation correlated with longitude and in the case of LHCII phosphorylation also with temperature variability. This suggests a possible role of natural variation in PSII protein phosphorylation in the adaptation of
Arabidopsis
to diverse environments.
Conditions for the validity of SNP-based heritability estimation
Authors: Lee James J. , Chow Carson C.
Published: March 2014

The heritability of a trait (h2) is the proportion of its population variance caused by genetic differences, and estimates of this parameter are important for interpreting the results of genome-wide association studies (GWAS). In recent years, researchers have adopted a novel method for estimating a lower bound on heritability directly from GWAS data that uses realized genetic similarities between nominally unrelated individuals. The quantity estimated by this method is purported to be the contribution to heritability that could in principle be recovered from association studies employing the given panel of SNPsThus far the validity of this approach has mostly been tested empirically. Here, we provide a mathematical explication and show that the method should remain a robust means of obtainingunder circumstances wider than those under which it has so far been derived.
Metabolic Flux Analysis of Plastidic Isoprenoid Biosynthesis in Poplar Leaves Emitting and Nonemitting Isoprene
Authors: Ghirardo Andrea , Wright Louwrance Peter , Bi Zhen , Rosenkranz Maaria , Pulido Pablo , Rodríguez-Concepción Manuel , Niinemets Ülo , Brüggemann Nicolas , Gershenzon Jonathan , Schnitzler Jörg-Peter
Published: March 2014

The plastidic 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway is one of the most important pathways in plants and produces a large variety of essential isoprenoids. Its regulation, however, is still not well understood. Using the stable isotope 13C-labeling technique, we analyzed the carbon fluxes through the MEP pathway and into the major plastidic isoprenoid products in isoprene-emitting and transgenic isoprene-nonemitting (NE) gray poplar (Populus × canescens). We assessed the dependence on temperature, light intensity, and atmospheric [CO2]. Isoprene biosynthesis was by far (99%) the main carbon sink of MEP pathway intermediates in mature gray poplar leaves, and its production required severalfold higher carbon fluxes compared with NE leaves with almost zero isoprene emission. To compensate for the much lower demand for carbon, NE leaves drastically reduced the overall carbon flux within the MEP pathway. Feedback inhibition of 1-deoxy-d-xylulose-5-phosphate synthase activity by accumulated plastidic dimethylallyl diphosphate almost completely explained this reduction in carbon flux. Our data demonstrate that short-term biochemical feedback regulation of 1-deoxy-d-xylulose-5-phosphate synthase activity by plastidic dimethylallyl diphosphate is an important regulatory mechanism of the MEP pathway. Despite being relieved from the large carbon demand of isoprene biosynthesis, NE plants redirected only approximately 0.5% of this saved carbon toward essential nonvolatile isoprenoids, i.e. β-carotene and lutein, most probably to compensate for the absence of isoprene and its antioxidant properties.
2-(3-{(3R,4R)-4-Methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}oxetan-3-yl)acetonitrile monohydrate
Authors: Gehringer Matthias , Pfaffenrot Ellen , Keck Peter R. W. E. F. , Schollmeyer Dieter , Laufer Stefan A.
Published: March 2014

In the title compound, C18H24N6O·H2O, the piperidine ring adopts a chair conformation with an N—C—C—C torsion angle of 39.5 (5)° between thecis-related substituents. The pyrrole N—H group forms a water-mediated intermolecular hydrogen bond to one of the N atoms of the annelated pyrimidine ring. The water molecule connects two organic molecules and is disorderd over two positions (occupancies of 0.48 and 0.52). The crystal packing shows zigzag chains of alternating organic and water molecules running parallel to theaaxis.
6,6′-Dinitro-1,1′-(ethane-1,2-diyl)di(1H-indazole)
Authors: Kouakou Assoman , Rakib El Mostapha , El Malki Abdelghani , Saadi Mohamed , El Ammari Lahcen
Published: March 2014

The molecule of the title compound, C16H12N6O4, is built up from two fused five- and six-membered rings linked by an ethylene group. The dihedral angle between the planes through the indazole ring systems is 39.74 (5)°. The nitro groups are tilted by 7.2 (2) and 8.5 (2)° with respect to planes of the fused-ring systems. In the crystal, molecules are linked by C—H...N and C—H...O hydrogen bonds into chains running parallel to thecaxis.
3,3′-Bis(chloromethyl)-4,4′-diethoxy-1,1′-biphenyl
Authors: Trad Hager , Belkhiria Mohamed Salah , Majdoub Mustapha
Published: March 2014

The asymmetric unit of the title compound, C18H20Cl2O2, consists of a half-molecule, the other half being generated by an inversion center, located at the mid-point of the benzene–benzene bond. Except for the two Cl atoms, all other atoms of the compound are nearly coplanar, with the atomic displacements from the molecular mean plane ranging from 0.0037 (19) to 0.071 (2) Å. The two Cl atoms are intranspositions and are displaced with respect to the mean plane by 1.687 (2) and −1.693 (3) Å. The crystal packing is governed by van der Waals interactions.
7-Chloro-4-(2-hydroxyethylamino)quinolin-1-ium chloride
Authors: Gama Ivson L. , Souza Marcus V. N. de , Wardell James L. , Tiekink Edward R. T.
Published: March 2014

In the title salt, C11H12ClN2O+·Cl−, the ten non-H atoms comprising the quinolinium residue are coplanar (r.m.s. deviation = 0.041 Å) and the hydroxyethyl group is approximately perpendicular to this plane [Cring—N—Cmethylene—C torsion angle = −74.61 (18)°]. A supramolecular chain aligned along [101] mediated by charge-assisted O/N—H...Cl−hydrogen bonds features in the crystal packing. Chains are connected into a three-dimensional architecture by C—H...O(hydroxy) interactions.
(E)-2-[4-(Diethylamino)styryl]-1-methylquinolin-1-ium 4-chlorobenzenesulfonate monohydrate
Authors: Chantrapromma Suchada , Kaewmanee Narissara , Boonnak Nawong , Quah Ching Kheng , Fun Hoong-Kun
Published: March 2014

The asymmetric unit of the title hydrated salt, C22H25N2+·C6H4ClO3S−·H2O, comprises two 2-[4-(diethylamino)styryl]-1-methylquinolin-1-ium cations, two 4-chlorobenzenesulfonate anions and two solvent water molecules. One ethyl group of both cations displays disorder over two positions in a 0.659 (2):0.341 (2) ratio in one molecule and in a 0.501 (2):0.499 (2) ratio in the other. The sulfonate group of one anion is also disordered over two positions in a 0.893 (7):0.107 (7) ratio. The dihedral angle between the mean plane of the quinolinium ring system and that of benzene ring is 10.57 (18)° in one cation and 14.4 (2)° in the other. In the crystal, cations, anions and water molecules are linked into chains along the [010] direction by O—H...Osulfonatehydrogen bonds, together with weak C—H...Osulfonateand C—H...Cl interactions. The cations are stacked by π–π interactions, with centroid–centroid distances in the range 3.675 (2)–4.162 (3) Å.
The religious imperative of cost accounting in the early industrial revolution
Authors: Funnell Warwick , Williams Robert
Published: March 2014

Purpose

– The paper aims to extend research which has sought to explain Britain's early success as an industrial power by identifying the influence of religious doctrine of the Dissenting Protestant churches on the development of accounting practices in the factory. The concern is not with specific accounting practices but with the social and moral environment which provided the incentives and permissions that encouraged late eighteenth century English industrialists to develop the practices that they used.

Design/methodology/approach

– The paper draws on the highly influential writings of social theorists such Weber, Sombart and Tawney to identify the religious doctrines that both motivated and justified the rational, ideological business practices of prominent businessmen.

Findings

– The rise of accounting as a powerful tool of control and discipline was significantly assisted by the teaching of the Dissenting Protestant churches on “calling”. Religious beliefs provided permissions, justifications and incentives which underpinned the entrepreneurial energies, opportunities and successes of the early industrialists. Accounting could be seen to assume almost the aura and nascent legitimacy of a religious practice, a means of sanctifying practices which were otherwise reviled by social elites.

Originality/value

– Despite encouragement from accounting researchers for histories of accounting which give greater credence to the reflexivity between accounting and society, this has yet to find a significant presence amongst the searches for beginnings in cost accounting where economic and management factors remain the overwhelming focus. Religious beliefs are shown to have been especially influential in the adoption of accounting practices by early industrialists who were frequently members of the Dissenting Protestant churches.