bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA‐guided transcriptional regulation in planta via synthetic dCas9‐based transcription factors
Authors: Piatek Agnieszka , Ali Zahir , Baazim Hatoon , Li Lixin , Abulfaraj Aala , Al‐Shareef Sahar , Aouida Mustapha , Mahfouz Magdy M. 
Published: November 2014

SummaryTargeted genomic regulation is a powerful approach to accelerate trait discovery and development in agricultural biotechnology. Bacteria and archaea use clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR‐associated (Cas) regulatory systems for adaptive molecular immunity against foreign nucleic acids introduced by invading phages and conjugative plasmids. The type II CRISPR/Cas system has been adapted for genome editing in many cell types and organisms. A recent study used the catalytically inactive Cas9 (dCas9) protein combined with guide‐RNAs (gRNAs) as a DNA‐targeting platform to modulate gene expression in bacterial, yeast, and human cells. Here, we modified this DNA‐targeting platform for targeted transcriptional regulation in planta by developing chimeric dCas9‐based transcriptional activators and repressors. To generate transcriptional activators, we fused the dCas9 C‐terminus with the activation domains of EDLL and TAL effectors. To generate a transcriptional repressor, we fused the dCas9 C‐terminus with the SRDX repression domain. Our data demonstrate that dCas9 fusion with the EDLL activation domain (dCas9:EDLL) and the TAL activation domain (dCas9:TAD), guided by gRNAs complementary to selected promoter elements, induce strong transcriptional activation on Bs3::uidA targets in plant cells. Further, the dCas9:SRDX‐mediated transcriptional repression of an endogenous gene. Thus, our results suggest that the synthetic transcriptional repressor (dCas9:SRDX) and activators (dCas9:EDLL and dCas9:TAD) can be used as endogenous transcription factors to repress or activate transcription of an endogenous genomic target. Our data indicate that the CRISPR/dCas9 DNA‐targeting platform can be used in plants as a functional genomics tool and for biotechnological applications.
Transgenic soya bean seeds accumulating β‐carotene exhibit the collateral enhancements of oleate and protein content traits
Authors: Schmidt Monica A. , Parrott Wayne A. , Hildebrand David F. , Berg R. Howard , Cooksey Amanda , Pendarvis Ken , He Yonghua , McCarthy Fiona , Herman Eliot M. 
Published: November 2014

SummaryTransgenic soya bean (Glycine max) plants overexpressing a seed‐specific bacterial phytoene synthase gene from Pantoea ananatis modified to target to plastids accumulated 845 μg β carotene g−1 dry seed weight with a desirable 12:1 ratio of β to α. The β carotene accumulating seeds exhibited a shift in oil composition increasing oleic acid with a concomitant decrease in linoleic acid and an increase in seed protein content by at least 4% (w/w). Elevated β‐carotene accumulating soya bean cotyledons contain 40% the amount of abscisic acid compared to nontransgenic cotyledons. Proteomic and nontargeted metabolomic analysis of the mid‐maturation β‐carotene cotyledons compared to the nontransgenic did not reveal any significant differences that would account for the altered phenotypes of both elevated oleate and protein content. Transcriptomic analysis, confirmed by RT‐PCR, revealed a number of significant differences in ABA‐responsive transcripton factor gene expression in the crtB transgenics compared to nontransgenic cotyledons of the same maturation stage. The altered seed composition traits seem to be attributed to altered ABA hormone levels varying transcription factor expression. The elevated β‐carotene, oleic acid and protein traits in the β‐carotene soya beans confer a substantial additive nutritional quality to soya beans.
Identification and overexpression of gibberellin 2‐oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance
Authors: Wuddineh Wegi A. , Mazarei Mitra , Zhang Jiyi , Poovaiah Charleson R. , Mann David G. J. , Ziebell Angela , Sykes Robert W. , Davis Mark F. , Udvardi Michael K. , Stewart Charles Neal 
Published: November 2014

SummaryGibberellin 2‐oxidases (GA2oxs) are a group of 2‐oxoglutarate‐dependent dioxygenases that catalyse the deactivation of bioactive GA or its precursors through 2β‐hydroxylation reaction. In this study, putatively novel switchgrass C20 GA2ox genes were identified with the aim of genetically engineering switchgrass for improved architecture and reduced biomass recalcitrance for biofuel. Three C20 GA2ox genes showed differential regulation patterns among tissues including roots, seedlings and reproductive parts. Using a transgenic approach, we showed that overexpression of two C20 GA2ox genes, that is PvGA2ox5 and PvGA2ox9, resulted in characteristic GA‐deficient phenotypes with dark‐green leaves and modified plant architecture. The changes in plant morphology appeared to be associated with GA2ox transcript abundance. Exogenous application of GA rescued the GA‐deficient phenotypes in transgenic lines. Transgenic semi‐dwarf lines displayed increased tillering and reduced lignin content, and the syringyl/guaiacyl lignin monomer ratio accompanied by the reduced expression of lignin biosynthetic genes compared to nontransgenic plants. A moderate increase in the level of glucose release in these transgenic lines might be attributed to reduced biomass recalcitrance as a result of reduced lignin content and lignin composition. Our results suggest that overexpression of GA2ox genes in switchgrass is a feasible strategy to improve plant architecture and reduce biomass recalcitrance for biofuel.
The Perception of Activity
Authors: Crowther Thomas 
Published: November 2014

AbstractThere is a much‐discussed form of argument the conclusion of which is that we do not directly perceive space‐filling material objects themselves, only parts of their surfaces. Donald Davidson's view that events are temporal particulars invites a structurally similar argument about the direct perception of events. In this paper, I spell out such an argument and consider a number of possible solutions to it. I explore the idea that a satisfactory response to this problem in the philosophy of perception can be grounded in a temporal ontology that includes temporal stuff as well as temporal particulars. I discuss different ways of developing this idea, and I go on to identify what I take to be the most promising version of an approach of this kind.
Perceptual Guidance
Authors: Watzl Sebastian 
Published: November 2014

AbstractProponents of an intentionalist theory of perceptual experience have taken for granted that perceptual experience is an informing form of intentionality. Hence they often speak of the way an experience represents the environment to be, or what there is. In this respect perceptual experience is thus assumed to resemble a speech act like assertion or a mental state like belief. There is another important form of intentionality though that concerns not what there is, but what to do. I call this a guiding form of intentionality. In speech, there are – for example – imperatives and among intentional mental states there are desires and intentions. In this paper I argue that perceptual experience is at least sometimes characterized by such a guiding form of intentionality. Perception does not just inform, it is sometimes intrinsically action‐guiding. I call this the perceptual guidance claim. I distinguish the perceptual guidance claim from related, but importantly distinct claims (such as claims concerning the perception of affordances or concerning whether perception is normative), and argue that perceptual action guidance occurs not just in an unconscious vision‐for‐action system, but also within conscious perceptual experience.
Distinct relict fringing reefs in the northern shelf of the Gulf of Elat/Aqaba: Markers of Quaternary eustatic and climatic episodes
Authors: Hartman Gal , Niemi Tina M. , Ben‐Avraham Zvi , Tibor Gideon , Al‐Zoubi Abdallah , Sade Ronnie A. , Hall John K. , Akawi Emad , Abueladas Abd , Al‐Ruzouq Rami , Makovsky Yizhaq 
Published: November 2014

AbstractQuaternary reef development and demise have been shown to correspond to worldwide sea‐level fluctuations and related environmental changes, yet the mechanisms and rates affecting this relationship are not well resolved. A set of high‐resolution seismic reflection and multibeam bathymetric data were interpreted. Six distinct systems of relict fringing reefs embedded within the sedimentary cover of the northern shelf of the Gulf of Elat/Aqaba were identified. The two uppermost relict fringing reefs are also exposed on the sea floor in water depths of ca 20 m and ca 60 m, along the north‐western corner of the northern Gulf of Elat/Aqaba and sub‐parallel to the current northern coast, respectively. Two other relict fringing reefs are laterally correlated to each of the last two transgressive cycles, and are inferred to have formed during decelerations in sea‐level rise during the last two deglaciations. These reefs and the units to which they are laterally correlated portray a repeating stratigraphic pattern of reef development during deposition of seismically homogeneous sediment and an ensuing demise during deposition of heterogeneous sediment. Correlation of the reef stratigraphy with rates of Late Quaternary sea‐level rise and a sediment accumulation rate from one shelf core provide age estimations for the seismic stratigraphy. Two phases of fringing reef generation occurred during the last deglaciation (since ca 18 ka); the older reef probably developed between 12·8 ka and 11·5 ka at ca 60 m below present sea‐level and the younger reef after 8·4 to 8·0 ka at ca 20 m below present sea‐level. These last two phases of reef generation are separated by a lobate seismic unit that is interpreted as fluvial‐deltaic deposits that backstepped across the shelf during the Early Holocene transgression. Results suggest that fringing reefs evolved along the northern shelf of the Gulf of Elat/Aqaba only during relative decelerations in sea‐level rise, contemporaneous with low input of terrigenous sediment and probably during a period of aridity. At present, no fringing reef grows along the northern coast of the Gulf of Elat/Aqaba, suggesting that these relatively arid periods may have been drier than Recent. The pattern of slowdown in sea‐level rise contemporaneous with conditions of increased aridity seems to have repeated during the last two sea‐level rises, approximately at the same sea‐levels, suggesting a common mechanism of short (millennium‐scale) phases of eustatic and climatic alteration during deglaciations.
The receptor kinase CERK1 has dual functions in symbiosis and immunity signalling
Authors: Zhang Xiaowei , Dong Wentao , Sun Jongho , Feng Feng , Deng Yiwen , He Zuhua , Oldroyd Giles E.D. , Wang Ertao 
Published: November 2014

SummaryThe establishment of symbiotic interactions between mycorrhizal fungi, rhizobial bacteria and their legume hosts involves a common symbiosis signalling pathway. This signalling pathway is activated by Nod factors produced by rhizobia and these are recognised by the Nod factor receptors NFR1/LYK3 and NFR5/NFP. Mycorrhizal fungi produce lipochitooligosaccharides (LCOs) similar to Nod factors, as well as short‐chain chitin oligomers (CO4/5), implying commonalities in signalling during mycorrhizal and rhizobial associations. Here we show that NFR1/LYK3, but not NFR5/NFP, is required for the establishment of the mycorrhizal interaction in legumes. NFR1/LYK3 is necessary for the recognition of mycorrhizal fungi and the activation of the symbiosis signalling pathway leading to induction of calcium oscillations and gene expression. Chitin oligosaccharides also act as microbe associated molecular patterns that promote plant immunity via similar LysM receptor‐like kinases. CERK1 in rice has the highest homology to NFR1 and we show that this gene is also necessary for the establishment of the mycorrhizal interaction as well as for resistance to the rice blast fungus. Our results demonstrate that NFR1/LYK3/OsCERK1 represents a common receptor for chitooligosaccharide‐based signals produced by mycorrhizal fungi, rhizobial bacteria (in legumes) and fungal pathogens. It would appear that mycorrhizal recognition has been conserved in multiple receptors across plant species, but additional diversification in certain plant species has defined other signals that this class of receptors can perceive.
In Arabidopsis thaliana two co‐adapted cyto‐nuclear systems correlate with distinct ccmC transcript sizes
Authors: Stoll Katrin , Jonietz Christian , Binder Stefan 
Published: November 2014

SummaryPlant mitochondrial transcripts undergo maturation processes at both termini. Although frequently observed, the post‐transcriptional formation of mature 5′ ends is still poorly understood. We now analyzed the processing of transcripts derived from the mitochondrial ccmC gene, coding for a component of the cytochrome c maturation system. In Arabidopsis thaliana (Arabidopsis) there are two mitochondrial ccmC configurations, discriminated by a 66‐bp sequence segment located approximately 500 bp upstream of the ccmC gene. In Arabidopsis accessions these divergent mitochondrial genotypes correlate with the generation of two different 5′ termini that map to positions around −484 in accession Columbia (Col ccmC genotype) or −390 in accession C24 relative to the translation start codon (C24 ccmC genotype). Previously we identified RNA PROCESSING FACTOR 3 (RPF3), a pentatricopeptide repeat (PPR) protein required for the maturation of ccmCmRNAs with −484 5′ ends transcribed from the Col ccmC genotype. Now we identified several accessions defective in maturation of ccmC transcripts. Taking advantage of this natural genetic variation we identified RNA PROCESSING FACTOR 6 (RPF6), a PPR protein necessary for the generation of ccmCmRNAs with −390 5′ ends transcribed from the C24 ccmC genotype. Both Col‐type and C24‐type accessions encode RPF3 and RPF6 so that they can process ccmC transcripts derived from the two different mitochondrial genotypes. These factors and their cognate RNA recognition sites in the different ccmC genotypes are an intriguing example for the evolution of two co‐adapted cyto‐nuclear systems required for the same process i.e. 5′ maturation of ccmC transcripts.
Effect of uraemia on endothelial cell damage is mediated by the integrin linked kinase pathway
Authors: García‐Jérez Andrea , Luengo Alicia , Carracedo Julia , Ramírez‐Chamond Rafael , Rodriguez‐Puyol Diego , Rodriguez‐Puyol Manuel , Calleros Laura 
Published: November 2014

Key points
Patients with chronic kidney disease have a higher risk of developing cardiovascular diseases than the general population. Their vascular endothelium is dysfunctional, among other things, because it is permanently exposed to uraemic toxins, several of which have poor clearance by conventional dialysis.
Recent studies have demonstrated the important role of integrin‐linked kinase (ILK) in the maintenance of endothelial integrity and in this study we investigate the involvement of ILK in the mechanism underlying vascular endothelial damage that occurs in uraemia.
For the first time, we demonstrate the implication of ILK in the protection against endothelial cell damage (inhibition of proliferation, toxicity, oxidative stress and programed cell death) induced by uraemic serum from chronic kidney disease patients and uraemic toxins.
This molecular mechanism may have clinical relevance because it highlights the importance of maintaining high levels of ILK activity to help preserve endothelial integrity, at least in early stages of chronic kidney disease.
AbstractPatients with chronic kidney disease (CKD) have a higher risk of developing cardiovascular diseases. Their vascular endothelium is dysfunctional, among other things, because it is permanently exposed to uraemic toxins, several of which, mostly protein‐bound compounds such as indoxyl sulfate (IS) and p‐cresyl sulphate, having poor clearance by conventional dialysis, induce endothelial toxicity. However, the molecular mechanism by which uraemic toxins regulate early stages of endothelial dysfunction remains unclear. Recent studies have demonstrated the important role of integrin‐linked kinase (ILK) in the maintenance of endothelial integrity. In this study, we investigate the involvement of ILK in the mechanism underlying vascular endothelial damage that occurs in uraemia. First, we show that incubation of EA.hy926 cells with human uraemic serum from CKD patients upregulates ILK activity. This ILK activation also occurs when the cells are exposed to IS (25–100 μg ml−1), p‐cresol (10–100 μg ml−1) or both combined, compared to human serum control. Next, we observed that high doses of both toxins together induce a slight decrease in cell proliferation and increase apoptosis and reactive oxygen species production. Interestingly, these toxic effects displayed a strong increase when the ILK protein is knocked down by small interfering RNA, even at low doses of uraemic toxins. Abrogation of AKT has demonstrated the ILK/AKT signalling pathway involved in these processes. This study has demonstrated the implication of ILK in the protection against endothelial cell damage induced by uraemic toxins, a molecular mechanism that could play a protective role in the early stages of endothelial dysfunction observed in uraemic patients.
Experimental Study on Lithium Leakage Behavior
Authors: Furukawa Tomohiro , Ohtaka Masahiko , Hirakawa Yasushi 
Published: November 2014

In the Japanese engineering validation activities on the target facility of the International Fusion Materials Irradiation Facility, two studies on the advanced lithium leak detection system and the fire-extinguishing behavior of lithium were performed.
In the former study, the fluorescence was distinguishable from the background using the difference of decay curves from the results of the lithium fluorescence measurement under two lithium concentration (256 ng/L and 4.58 ng/L) in argon. This result shows the basic applicability of the laser based lithium measuring technique as the lithium detector could be confirmed.
In the latter study, fire-extinguishing behavior of two kinds of carbon base fire extionguishishants — MITEX and GRAPHEX — to lithium was examined. The both extinguishants showed excellent fire-extinguishing performance, and there were equivalent to that of Natlex-L obtained in the previous study. Since the bulk densities of the both carbon based extinguishants were about equal to the density of lithium, the subsidence of the fire-extinguishings which was observed in the Natlex-L was not observed. In fact, it was considered that no dependency of lithium pool depth on the required thickness of the fire extinguishants was observed for the carbon based extinguishants.
Development of Prediction Technology of Two-Phase Flow Dynamics Under Earthquake Acceleration: (14) Numerical Simulation of Two-Phase Flow in Subchannels Under Accelerating Condition
Authors: Yoshida Hiroyuki , Nagatake Taku , Takase Kazuyuki , Kaneko Akiko , Monji Hideaki , Abe Yutaka 
Published: November 2014

An earthquake is one of the most serious phenomena to consider for the safety of a nuclear reactor in Japan. Therefore, structural safety of nuclear reactors has been studied and nuclear reactors were contracting with structural safety for a big earthquake. However, it is not enough for safety operation of nuclear reactors because thermal-fluid safety is not confirmed under the earthquake. For instance, behavior of gas-liquid two-phase flow is unknown in seismic conditions. Especially, fluctuation of void fraction is an important factor for the safety operation of the nuclear reactor. In previous work, fluctuation of void faction in bubbly flow was studied experimentally and theoretically to investigate the stability of the bubbly flow. In such studies, flow rate or void fraction fluctuations were given to the steady bubbly flow. In case of the earthquake, the fluctuation is not only the flow rate, but also a body force on the two-phase flow and shear force through the pipe wall. Interactions of gas and liquid through their interface also act on the behavior of the two-phase flow. The fluctuation of the void fraction is not clear for such complicated situation during the earthquake.
Therefore, the behavior of gas-liquid two-phase flow is investigated experimentally and numerically in a series of studies. In this study, to develop the predictive technology of two-phase flow dynamics under earthquake acceleration, a detailed two-phase flow simulation code with an advanced interface tracking method TPFIT (Two-Phase Flow simulation code with Interface Tracking) was expanded to two-phase flow simulation in seismic conditions. In a previous study, we performed a numerical simulation of a two-phase bubbly flow in a horizontal pipe and a vertical bubble motion in a water tank in seismic conditions. And it was confirmed that the modified TPFIT can be applicable to the bubbly flow in seismic conditions.
In this paper, the two-phase bubbly flow in a simulated single-subchannel excited by oscillation acceleration was simulated by using the expanded TPFIT. A calculation domain used in this simulation was a simplified subchannel in a BWR core. And time-series of void fraction distributions were evaluated based on predicted bubble distributions. When no oscillation acceleration was added, void fraction concentrated in a region near the wall. When oscillation acceleration was added, void fraction distribution was changed by time. And coalesces of bubbles occurred in the numerical simulation, and bubbles with relatively large diameter were observed. In the results, complicated void fraction distribution was observed, because the response of void fraction distribution on the oscillation acceleration was dependent on not only imposed acceleration, but also the bubble diameter.
Water/Pb-Bi Interaction Experiments in LIFUS5/Mod2 Facility Modelled by SIMMER Code
Authors: Pesetti Alessio , Forgione Nicola , Del Nevo Alessandro 
Published: November 2014

The new generation Heavy Liquid Metal Reactors (HLMRs) are characterized by a pool type configuration having high pressure steam generators set inside the reactor vessel. The primary (hot low pressure LBE melt) and secondary (high pressure sub-cooled water) coolant could come into contact as consequence of Steam Generator Tube Rupture (SGTR) phenomenon, that cannot be considered negligible. The structural integrity of the reactor internals, steam generators in particular, could be affected by the SGTR scenario consequences. The pressure wave propagation, cover gas pressurization, domino effect on the surrounding tubes, reactivity feedback due to steam dragged into the core, primary system pollution and slug formation constitute the most hazardous effects of the SGTR accident. Therefore, this accidental scenario constitutes a safety issue in the design and in the preliminary safety analysis. A key issue in the SGTR analysis for HLMRs is constituted by the availability of qualified experimental data, suitable to be extrapolated to full scale plant and to support the computer code development and demonstrating the code reliability in the phenomena prediction (qualified code).
In this paper, part of the experimental campaign performed in the LIFUS5/Mod2 facility at ENEA CR Brasimone (in the frame of the THINS project), investigating the water-LBE interaction, is reported. The experimental activity aimed to provide high-quality measurement data for supporting the development and validation phase of computer codes for SGTR numerical simulation. The reported experimental test has been numerically simulated by SIMMER III code. The pressure, temperature and injected water mass flow rate time trends have been computed during the water-LBE interaction in the reaction vessel. The work aims to evaluate the prediction capability of the two-dimensional SIMMER III code and to determine the suitability of the SIMMER code physical models.