bluuebunny/crossref_metadata_2025_split huggingface dataset:
ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK–RSK pathway
Authors: Adachi Shungo , Homoto Masae , Tanaka Rikou , Hioki Yusaku , Murakami Hiroshi , Suga Hiroaki , Matsumoto Masaki , Nakayama Keiichi I. , Hatta Tomohisa , Iemura Shun-ichiro , Natsume Tohru 
Published: August 2014

Abstract
Low-density lipoprotein receptor (LDLR) mRNA is unstable, but is stabilized upon extracellular signal-regulated kinase (ERK) activation, possibly through the binding of certain proteins to the LDLR mRNA 3′-untranslated region (UTR), although the detailed mechanism underlying this stability control is unclear. Here, using a proteomic approach, we show that proteins ZFP36L1 and ZFP36L2 specifically bind to the 3′-UTR of LDLR mRNA and recruit the CCR4-NOT-deadenylase complex, resulting in mRNA destabilization. We also show that the C-terminal regions of ZFP36L1 and ZFP36L2 are directly phosphorylated by p90 ribosomal S6 kinase, a kinase downstream of ERK, resulting in dissociation of the CCR4-NOT-deadenylase complex and stabilization of LDLR mRNA. We further demonstrate that targeted disruption of the interaction between LDLR mRNA and ZFP36L1 and ZFP36L2 using antisense oligonucleotides results in upregulation of LDLR mRNA and protein. These results indicate that ZFP36L1 and ZFP36L2 regulate LDLR protein levels downstream of ERK. Our results also show the usefulness of our method for identifying critical regulators of specific RNAs and the potency of antisense oligonucleotide-based therapeutics.
ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe
Authors: Sastre-Moreno Guillermo , Sánchez Arancha , Esteban Verónica , Blanco Luis 
Published: August 2014

Abstract7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique PolX in fission yeast, incorporates ATP opposite 8oxodG almost exclusively when all nucleotides (ribos and deoxys) are provided at physiological concentrations. Remarkably, this SpPol4-specific reaction could also occur during the NHEJ of DSBs. In cell extracts, misincorporation of ATP opposite 8oxodG was shown to be SpPol4-specific, although RNase H2 efficiently recognized the 8oxodG:AMP mispair to remove AMP and trigger error-free incorporation of dCTP. These data are the first evidence that ribonucleotides can be used safely for 8oxodG tolerance, suggesting that insertion of the highly abundant ATP substrate could be beneficial to promote efficient and error-free repair of 8oxodG-associated DSBs. Moreover, we demonstrate that purified SpPol4 uses 8oxo-dGTP and 8oxo-GTP as substrates for DNA polymerization, although with poor efficiency compared to the incorporation of undamaged nucleotides opposite either 8oxodG or undamaged templates. This suggests that SpPol4 is specialized in tolerating 8oxodG as a DNA template, without contributing significantly to the accumulation of this lesion in the DNA.
Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development
Authors: Singer Ruth , Atar Shimshi , Atias Osnat , Oron Efrat , Segal Daniel , Hirsch Joel A. , Tuller Tamir , Orian Amir , Chamovitz Daniel A. 
Published: August 2014

AbstractThe COP9 signalosome protein complex has a central role in the regulation of development of multicellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control. In accord, loss of CSN7 function leads to cell-cycle delay and altered wing development. These results indicate that CSN7, and by extension the entire COP9 signalosome, functions directly in transcriptional control. While the COP9 signalosome protein complex has long been known to regulate protein degradation, here we expand the role of this complex by showing that subunit 7 binds DNA in vitro and functions directly in vivo in transcriptional control of developmentally important pathways that are relevant for human health.
Number Representations and their Relation with Mathematical Ability
Authors: Gebuis Titia , Reynvoet Bert 
Published: August 2014

Abstract
In this chapter we review research on the processes that underlie the development of mathematical abilities. It is proposed that numerical deficiencies might arise from domain specific problems. The approximate number system that supports reasoning with non-symbolic numbers, on the one hand, and the symbolic number system on the other hand were put forth as possible candidates. To gain insight into the two different systems, we will describe the development of non-symbolic and symbolic number processing and introduce the two main theories about numerical deficiencies: the approximate number system and the access deficit hypothesis. The paradigms used to study both accounts differ in several ways and are of importance for research on the relation between non-symbolic and symbolic number and mathematical abilities. Then, we will review how the studies investigating both accounts relate to two different sets of developmental models that describe the neural representation of number.
Mapping the Brain for Math
Authors: Salillas Elena , Semenza Carlo 
Published: August 2014

Abstract
Brain stimulation techniques allow for the search of crucial areas for a given function. Not always convergent with neuroimaging, TMS studies have targeted parietal areas critical for quantity representation, spatio-numerical links, numerical and non-numerical quantity, finger gnosis and calculation. TMS data indicate the intraparietal sulcus and surrounding areas in the left and right hemisphere as crucial for quantity processing, although left hemisphere might be dominant. Bilateral parietal loci are essential for calculation and bilateral parietal areas are behind the spatio-numerical link, which extends to frontal and posterior parietal sites. DCE studies to date have focused on the dominant hemisphere, have used calculation tasks and have found both dissociation and overlap between operations. An integrative view of positive findings and a focus on convergence and possible improvement is proposed. Although regularities are found between these techniques, more research is needed before arriving at conclusions that will have basic and clinical importance.
Impact of the Anesthetic Conserving Device on Respiratory Parameters and Work of Breathing in Critically Ill Patients under Light Sedation with Sevoflurane
Authors: Chabanne Russell , Perbet Sebastien , Futier Emmanuel , Said Nordine Ait Ben , Jaber Samir , Bazin Jean-Etienne , Pereira Bruno , Constantin Jean-Michel 
Published: August 2014

Abstract

Background:
Sevoflurane sedation in the intensive care unit is possible with a special heat and moisture exchanger called the Anesthetic Conserving Device (ACD) (AnaConDa®; Sedana Medical AB, Uppsala, Sweden). The ACD, however, may corrupt ventilatory mechanics when used during the weaning process of intensive care unit patients. The authors compared the ventilatory effects of light-sedation with sevoflurane administered with the ACD and those of classic management, consisting of a heated humidifier and intravenous sedation, in intensive care unit patients receiving pressure-support ventilation.

Methods:
Fifteen intensive care unit patients without chronic pulmonary disease were included. A target Richmond Agitation Sedation Scale level of −1/−2 was obtained with intravenous remifentanil (baseline 1-condition). Two successive interventions were tested: replacement of the heated humidifier by the ACD without sedation change (ACD-condition) and sevoflurane with the ACD with an identical target level (ACD-sevoflurane-condition). Patients finally returned to baseline (baseline 2-condition). Work of breathing, ventilatory patterns, blood gases, and tolerance were recorded. A steady state of 30 min was achieved for each experimental condition.

Results:
ACD alone worsened ventilatory parameters, with significant increases in work of breathing (from 1.7 ± 1.1 to 2.3 ± 1.2 J/l), minute ventilation, P0,1, intrinsic positive end-expiratory pressure (from 1.3 ± 2.6 to 4.7 ± 4.2 cm H2O), inspiratory pressure swings, and decreased patient comfort. Sevoflurane normalized work of breathing (from 2.3 ± 1.2 to 1.8 ± 1 J/l), intrinsic positive end-expiratory pressure (from 4.7 ± 4.2 to 1.8 ± 2 cm H2O), inspiratory pressure swings, other ventilatory parameters, and patient tolerance.

Conclusions:
ACD increases work of breathing and worsens ventilatory parameters. Sevoflurane use via the ACD (for a light-sedation target) normalizes respiratory parameters. In this patient’s population, light-sedation with sevoflurane and the ACD may be possible during the weaning process.
NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases
Authors: Costa Marta , Manton James D. , Ostrovsky Aaron D. , Prohaska Steffen , Jefferis Gregory S. X. E. 
Published: August 2014

AbstractNeural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches.We validated NBLAST on a published dataset of 16,129 singleDrosophilaneurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) withouta prioriinformation. Cluster analysis of extensively studied neuronal classes identified new types and un-reported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.
Seasonality dynamics of avian influenza occurrences in Central and West Africa
Authors: Fuller T. L. , Ducatez M. F. , Njabo K. Y. , Couacy-Hymann E. , Chasar T. , Aplogan G. L. , Lao S. , Awoume F. , Téhou A. , Langeois Q. , Krauss S. , Smith T. B. 
Published: August 2014

SUMMARYUnderstanding seasonal cycles of viruses originating in wildlife can provide insight into their likelihood of persistence in animal populations and inform policies to limit spillover to human populations. Avian influenza virus (AIV) is an important zoonotic agent causing seasonal occurrence of avian influenza (AI) in wild birds in temperate areas. Although the seasonality of AIV transmission in tropical birds is largely unknown, peaks of influenza activity in human populations in the tropics coincide with the rainy season. To assess the seasonality of AI in tropical birds, from 2010-14, we sampled 40,099 birds at 32 sites in Central Africa (Cameroon, Central African Republic, Congo-Brazzaville, and Gabon) and West Africa (Benin, Côte d’Ivoire, and Togo). Although AIV was not isolated by egg culture, in Central Africa, detection rates by real-time RT-PCR were 3.57% for passerine songbirds and 8.74% for Anatid ducks. RT-PCR positivity in resident birds increased when Palearctic migrants arrived in Central Africa. At sampling sites with two annual wet seasons, the positive rate in wild birds was greatest during the big rainy season in September – October. This study provides the first evidence that AI is present in Central African birds and identifies environmental factors associated with cases.
Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels
Authors: Li Xin , Yu Vivian Yaci , Lin Yuping , Chomvong Kulika , Estrela Raíssa , Liang Julie M. , Znameroski Elizabeth A. , Feehan Joanna , Kim Soo Rin , Jin Yong-Su , Glass N. Louise , Cate Jamie H. D. 
Published: August 2014

AbstractSustainable biofuel production from renewable biomass will require the efficient and complete use of all abundant sugars in the plant cell wall. Using the cellulolytic fungusNeurospora crassaas a model, we identified a xylodextrin transport and consumption pathway required for its growth on hemicellulose. Successful reconstitution of this xylodextrin utilization pathway inSaccharomyces cerevisiaerevealed that fungal xylose reductases act as xylodextrin reductases, and together with two hydrolases, generate intracellular xylose and xylitol. Xylodextrin consumption using xylodextrin reductases and tandem intracellular hydrolases greatly expands the capacity of yeasts to use plant cell wall-derived sugars, and should be adaptable to increase the efficiency of both first-generation and next-generation biofuel production.
Metabolism-Based Herbicide Resistance and Cross-Resistance in Crop Weeds: A Threat to Herbicide Sustainability and Global Crop Production
Authors: Yu Qin , Powles Stephen 
Published: August 2014

Abstract
Weedy plant species that have evolved resistance to herbicides due to enhanced metabolic capacity to detoxify herbicides (metabolic resistance) are a major issue. Metabolic herbicide resistance in weedy plant species first became evident in the 1980s in Australia (in Lolium rigidum) and the United Kingdom (in Alopecurus myosuroides) and is now increasingly recognized in several crop-weed species as a looming threat to herbicide sustainability and thus world crop production. Metabolic resistance often confers resistance to herbicides of different chemical groups and sites of action and can extend to new herbicide(s). Cytochrome P450 monooxygenase, glycosyl transferase, and glutathione S-transferase are often implicated in herbicide metabolic resistance. However, precise biochemical and molecular genetic elucidation of metabolic resistance had been stalled until recently. Complex cytochrome P450 superfamilies, high genetic diversity in metabolic resistant weedy plant species (especially cross-pollinated species), and the complexity of genetic control of metabolic resistance have all been barriers to advances in understanding metabolic herbicide resistance. However, next-generation sequencing technologies and transcriptome-wide gene expression profiling are now revealing the genes endowing metabolic herbicide resistance in plants. This Update presents an historical review to current understanding of metabolic herbicide resistance evolution in weedy plant species.
Unraveling the Mechanism Underlying the Glycosylation and Methylation of Anthocyanins in Peach
Authors: Cheng Jun , Wei Guochao , Zhou Hui , Gu Chao , Vimolmangkang Sornkanok , Liao Liao , Han Yuepeng 
Published: August 2014

AbstractModification of anthocyanin plays an important role in increasing its stability in plants. Here, six anthocyanins were identified in peach (Prunus persica), and their structural diversity is attributed to glycosylation and methylation. Interestingly, peach is quite similar to the wild species Prunus ferganensis but differs from both Prunus davidiana and Prunus kansueasis in terms of anthocyanin composition in flowers. This indicates that peach is probably domesticated from P. ferganensis. Subsequently, genes responsible for both methylation and glycosylation of anthocyanins were identified, and their spatiotemporal expression results in different patterns of anthocyanin accumulation in flowers, leaves, and fruits. Two tandem-duplicated genes encoding flavonoid 3-O-glycosyltransferase (F3GT) in peach, PpUGT78A1 and PpUGT78A2, showed different activity toward anthocyanin, providing an example of divergent evolution of F3GT genes in plants. Two genes encoding anthocyanin O-methyltransferase (AOMT), PpAOMT1 and PpAOMT2, are expressed in leaves and flowers, but only PpAOMT2 is responsible for the O-methylation of anthocyanins at the 3′ position in peach. In addition, our study reveals a novel branch of UGT78 genes in plants that lack the highly conserved intron 2 of the UGT gene family, with a great variation of the amino acid residue at position 22 of the plant secondary product glycosyltransferase box. Our results not only provide insights into the mechanisms underlying anthocyanin glycosylation and methylation in peach but will also aid in future attempts to manipulate flavonoid biosynthesis in peach as well as in other plants.
Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C3 and C4 Plant Species
Authors: Külahoglu Canan , Denton Alisandra K. , Sommer Manuel , Maß Janina , Schliesky Simon , Wrobel Thomas J. , Berckmans Barbara , Gongora-Castillo Elsa , Buell C. Robin , Simon Rüdiger , De Veylder Lieven , Bräutigam Andrea , Weber Andreas P.M. 
Published: August 2014

Abstract
C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C4) and Tarenaya hassleriana (C3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C3 and C4 species. We found that known C4 genes were recruited to photosynthesis from different expression domains in C3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C4 leaf.
TheArabidopsis14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation
Authors: Catalá Rafael , López-Cobollo Rosa , Mar Castellano M. , Angosto Trinidad , Alonso José M. , Ecker Joseph R. , Salinas Julio 
Published: August 2014

AbstractIn plants, the expression of 14-3-3 genes reacts to various adverse environmental conditions, including cold, high salt, and drought. Although these results suggest that 14-3-3 proteins have the potential to regulate plant responses to abiotic stresses, their role in such responses remains poorly understood. Previously, we showed that the RARE COLD INDUCIBLE 1A (RCI1A) gene encodes the 14-3-3 psi isoform. Here, we present genetic and molecular evidence implicating RCI1A in the response to low temperature. Our results demonstrate that RCI1A functions as a negative regulator of constitutive freezing tolerance and cold acclimation in Arabidopsis thaliana by controlling cold-induced gene expression. Interestingly, this control is partially performed through an ethylene (ET)-dependent pathway involving physical interaction with different ACC SYNTHASE (ACS) isoforms and a decreased ACS stability. We show that, consequently, RCI1A restrains ET biosynthesis, contributing to establish adequate levels of this hormone in Arabidopsis under both standard and low-temperature conditions. We further show that these levels are required to promote proper cold-induced gene expression and freezing tolerance before and after cold acclimation. All these data indicate that RCI1A connects the low-temperature response with ET biosynthesis to modulate constitutive freezing tolerance and cold acclimation in Arabidopsis.
Identification of a Sphingolipid α-Glucuronosyltransferase That Is Essential for Pollen Function inArabidopsis
Authors: Rennie Emilie A. , Ebert Berit , Miles Godfrey P. , Cahoon Rebecca E. , Christiansen Katy M. , Stonebloom Solomon , Khatab Hoda , Twell David , Petzold Christopher J. , Adams Paul D. , Dupree Paul , Heazlewood Joshua L. , Cahoon Edgar B. , Scheller Henrik Vibe 
Published: August 2014

AbstractGlycosyl inositol phosphorylceramide (GIPC) sphingolipids are a major class of lipids in fungi, protozoans, and plants. GIPCs are abundant in the plasma membrane in plants, comprising around a quarter of the total lipids in these membranes. Plant GIPCs contain unique glycan decorations that include a conserved glucuronic acid (GlcA) residue and various additional sugars; however, no proteins responsible for glycosylating GIPCs have been identified to date. Here, we show that the Arabidopsis thaliana protein INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE1 (IPUT1) transfers GlcA from UDP-GlcA to GIPCs. To demonstrate IPUT1 activity, we introduced the IPUT1 gene together with genes for a UDP-glucose dehydrogenase from Arabidopsis and a human UDP-GlcA transporter into a yeast mutant deficient in the endogenous inositol phosphorylceramide (IPC) mannosyltransferase. In this engineered yeast strain, IPUT1 transferred GlcA to IPC. Overexpression or silencing of IPUT1 in Nicotiana benthamiana resulted in an increase or a decrease, respectively, in IPC glucuronosyltransferase activity in vitro. Plants in which IPUT1 was silenced accumulated IPC, the immediate precursor, as well as ceramides and glucosylceramides. Plants overexpressing IPUT1 showed an increased content of GIPCs. Mutations in IPUT1 are not transmitted through pollen, indicating that these sphingolipids are essential in plants.