bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization
Authors: Roberts Brock , Haupt Amanda , Tucker Andrew , Grancharova Tanya , Arakaki Joy , Fuqua Margaret A. , Nelson Angelique , Hookway Caroline , Ludmann Susan A. , Mueller Irina A. , Yang Ruian , Horwitz Alan R. , Rafelski Susanne M. , Gunawardane Ruwanthi N. 
Published: April 2017

AbstractWe present a CRISPR/Cas9 genome editing strategy to systematically tag endogenous proteins with fluorescent tags in human inducible pluripotent stem cells. To date we have generated multiple human iPSC lines with GFP tags for 10 proteins representing key cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, lamin B1, non-muscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome editing methodology using Cas9 ribonuclear protein electroporation and fluorescence-based enrichment of edited cells resulted in <0.1-24% HDR across all experiments. Clones were generated from each edited population and screened for precise editing. ∼25% of the clones contained precise mono-allelic edits at the targeted locus. Furthermore, 92% (36/39) of expanded clonal lines satisfied key quality control criteria including genomic stability, appropriate expression and localization of the tagged protein, and pluripotency. Final clonal lines corresponding to each of the 10 cellular structures are now available to the research community. The data described here, including our editing protocol, genetic screening, quality control assays, and imaging observations, can serve as an initial resource for genome editing in cell biology and stem cell research.
Members of the abscisic acid co-receptor PP2C protein family mediate salicylic acid-abscisic acid crosstalk
Authors: Manohar Murli , Wang Dekai , Manosalva Patricia M. , Choi Hyong Woo , Kombrink Erich , Klessig Daniel F. 
Published: April 2017

AbstractThe interplay between abscisic acid (ABA) and salicylic acid (SA) influences plant responses to various (a)biotic stresses; however, the underlying mechanism(s) for this crosstalk is largely unknown. Here we report that type 2C protein phosphatases (PP2Cs), some of which are negative regulators of ABA signaling, bind SA. SA binding suppressed the ABA-enhanced interaction between these PP2Cs and various ABA receptors belonging to the PYR/PYL/RCAR protein family. Additionally, SA suppressed ABA-enhanced degradation of PP2Cs and ABA-induced stabilization of SnRK2s. Supporting SA’s role as a negative regulator of ABA signaling, exogenous SA suppressed ABA-induced gene expression, whereas SA-deficientsid2-1mutants displayed heightened PP2C degradation and hypersensitivity to ABA-induced suppression of seed germination. Together, these results suggest a new molecular mechanism through which SA antagonizes ABA signaling. A better understanding of the crosstalk between these hormones is important for improving the sustainability of agriculture in the face of climate change.
A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia
Authors: Kuncha Santosh Kumar , Mazeed, Mohd , Singh, Raghvendra , Kattula, Bhavita , Brata Routh, Satya , Sankaranarayanan Rajan 
Published: April 2017

ABSTRACTD-aminoacyl-tRNA deacylase (DTD), atrans-editing factor found in bacteria and eukaryotes, removes D-amino acids mischarged on tRNAs as well as achiral glycine mischarged on tRNAAla. An invariant cross-subunit Gly-cisPro motif forms the mechanistic basis of strict L-amino acid rejection from the catalytic site. Here, we present the identification of a DTD variant, named ATD (Animalia-specifictRNAdeacylase), that harbors a Gly-transPro motif. Thecis-to-transswitch causes a “gain of function” through L-chiral selectivity in ATD resulting in the clearing of L-alanine mischarged on tRNAThr(G4•U69) by eukaryotic AlaRS. The biochemical proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNAThr(G4•U69) genes are in strict association with the presence of ATD, underlining the mandatory requirement of a dedicated factor to proofread tRNA misaminoacylation. The study highlights the emergence of ATD during genome expansion as a key event associated with the evolution of Animalia.
Multiple sources of slow activity fluctuations in a bacterial chemosensory network
Authors: Colin R. , Rosazza C. , Vaknin A. , Sourjik V. 
Published: April 2017

AbstractCellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis ofEscherichia coliprovides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway. We observed surprisingly large methylation-independent thermal fluctuations of receptor activity, which contribute to noise comparably to the energy-consuming methylation dynamics. Interactions between clustered receptors involved in amplification of chemotactic signals are also necessary to produce the observed large activity fluctuations. Our work thus shows that the high response sensitivity of this cellular pathway also increases its susceptibility to noise, from thermal and out-of-equilibrium processes.
Extensions of BLUP models for genomic prediction in heterogeneous populations: Application in a diverse switchgrass sample
Authors: Ramstein Guillaume P. , Casler Michael D. 
Published: April 2017

ABSTRACTGenomic prediction is a useful tool to accelerate genetic gain in selection using DNA marker information. However, this technology usually relies on models that are not designed to accommodate population heterogeneity, which results from differences in marker effects across genetic backgrounds. Previous studies have proposed to cope with population heterogeneity using diverse approaches: (i) either ignoring it, therefore relying on the robustness of standard approaches; (ii) reducing it, by selecting homogenous subsets of individuals in the sample; or (iii) modelling it by using interactive models. In this study we assessed all three possible approaches, applying existing and novel procedures for each of them. All procedures developed are based on deterministic optimizations, can account for heteroscedasticity, and are applicable in contexts of admixed populations. In a case study on a diverse switchgrass sample, we compared the procedures to a control where predictions rely on homogeneous subsamples. Ignoring heterogeneity was often not detrimental, and sometimes beneficial, to prediction accuracy, compared to the control. Reducing heterogeneity did not result in further increases in accuracy. However, in scenarios of limited subsample sizes, a novel procedure, which accounted for redundancy within subsamples, outperformed the existing procedure, which only considered relationships to selection candidates. Modelling heterogeneity resulted in substantial increases in accuracy, in the cases where accounting for population heterogeneity yielded a highly significant improvement in fit. Our study exemplifies advantages and limits of the various approaches that are promising in various contexts of population heterogeneity, e.g. prediction based on historical datasets or dynamic breeding.
Sleep-dependent modulation of metabolic rate inDrosophila
Authors: Stahl Bethany A. , Slocumb Melissa E. , Chaitin Hersh , DiAngelo Justin R. , Keene Alex C. 
Published: April 2017

AbstractDysregulation of sleep is associated with metabolic diseases, and metabolic rate is acutely regulated by sleep-wake behavior. In humans and rodent models, sleep loss is associated with obesity, reduced metabolic rate, and negative energy balance, yet little is known about the neural mechanisms governing interactions between sleep and metabolism. We have developed a system to simultaneously measure sleep and metabolic rate in individualDrosophila, allowing for interrogation of neural systems governing interactions between sleep and metabolic rate. Like mammals, metabolic rate in flies is reduced during sleep and increased during sleep deprivation suggesting sleep-dependent regulation of metabolic rate is conserved across phyla. The reduction of metabolic rate during sleep is not simply a consequence of inactivity because metabolic rate is reduced ∼30 minutes following the onset of sleep, raising the possibility that CO2production provides a metric to distinguish different sleep states in the fruit fly. To examine the relationship between sleep and metabolism, we determined basal and sleep-dependent changes in metabolic rate is reduced in starved flies, suggesting that starvation inhibits normal sleep-associated effects on metabolic rate. Further,translinmutant flies that fail to suppress sleep during starvation demonstrate a lower basal metabolic rate, but this rate was further reduced in response to starvation, revealing that regulation of starvation-induced changes in metabolic rate and sleep duration are genetically distinct. Therefore, this system provides the unique ability to simultaneously measure sleep and oxidative metabolism, providing novel insight into the physiological changes associated with sleep and wakefulness in the fruit fly.Significance statementMetabolic disorders are associated with sleep disturbances, yet our understanding of the mechanisms underlying interactions between sleep and metabolism remain limited. Here, we describe a novel system to simultaneously record sleep and metabolic rate in singleDrosophila. Our findings reveal that uninterrupted sleep bouts of 30 minutes or greater are associated with a reduction in metabolic rate providing a physiological readout of sleep. Use of this system, combined with existing genetic tools inDrosophila, will facilitate identification of novel sleep genes and neurons, with implications for understanding the relationship between sleep loss and metabolic disease.
Client requirement representations and transformations in construction project design
Authors: Collinge William Henry 
Published: April 2017

Purpose
This paper aims to examine how client requirements undergo representational and transformational shifts and changes in the design process and explore the consequence of such changes.

Design/methodology/approach
A series of design resources relating to hospital departmental configurations are examined and analysed using a social semiotic framework. The findings are supplemented by practitioner opinion.

Findings
Construction project requirements are represented and transformed through semiotic resource use; such representations deliver specific meanings, make new meanings and affect project relationships. Requirement representations may be understood as socially motivated meaning-making resources.

Research limitations/implications
The paper focuses on one set of project requirements: hospital departmental configurations from a National Health Service hospital construction project in the UK.

Practical implications
The use of semiotic resources in briefing work fundamentally affects the briefing and design discourse between client and design teams; their significance should be noted and acknowledged as important.

Social implications
The findings of the paper indicate that briefing and design work may be understood as a social semiotic practice.

Originality/value
This original paper builds upon scholarly work in the area of construction project communications. Its fine-grained analysis of briefing communications around representations of specific requirements is novel and valuable.
Towards a functional understanding of species coexistence: ecomorphological variation in relation to whole‐organism performance in two sympatric lizards
Authors: Žagar Anamarija , Carretero Miguel A. , Vrezec Al , Drašler Katarina , Kaliontzopoulou Antigoni 
Published: April 2017

SummaryWe examined intra‐ and interspecific variation in functional morphology and whole‐organism performance in a sympatric lizard species pair,Iberolacerta horvathiandPodarcis muralis, in the area with a high potential for competition.The biggest variation between species was found in two functional traits, bite force and climbing speed, linked with corresponding morphological traits.The species with larger and taller heads,P. muralis, exhibited correspondingly stronger bite forces. The other species exhibited smaller and flatter head. Both traits may potentially promote segregation between species in trophic niche (stronger bites relate to harder prey) and in refuge use (flatter heads allow using narrower crevices, hence, influencing escaping from common predators). Stronger bites and larger heads also provide one species with a dominant position in interspecific agonistic interactions.Females had longer trunks that impacted negatively on climbing speed, which may lower anti‐predator escape abilities of the more trunk‐dimorphic species, but positively influence reproductive effort.Our results exemplify how the joint examination of morphological and functional traits of ecologically similar and sympatric species can provide a mechanistic background for understanding their coexistence, namely, syntopic populations that are frequent in the study area.The identified roles of functional morphology in this system of sympatric rock lizards support the contribution of functional diversification for the complexity of community structure via coexistence.Alay summaryis available for this article.
Resting vs. active: a meta‐analysis of the intra‐ and inter‐specific associations between minimum, sustained, and maximum metabolic rates in vertebrates
Authors: Auer Sonya K. , Killen Shaun S. , Rezende Enrico L. 
Published: April 2017

Summary

Variation in aerobic capacity has far reaching consequences for the physiology, ecology, and evolution of vertebrates. Whether at rest or active, animals are constrained to operate within the energetic bounds determined by their minimum (minMR) and sustained or maximum metabolic rates (upperMR). MinMR and upperMR can differ considerably among individuals and species but are often presumed to be mechanistically linked to one another. Specifically, minMR is thought to reflect the idling cost of the machinery needed to support upperMR. However, previous analyses based on limited datasets have come to conflicting conclusions regarding the generality and strength of their association.

Here we conduct the first comprehensive assessment of their relationship, based on a large number of published estimates of both the intra‐specific (n = 176) and inter‐specific (n = 41) phenotypic correlations between minMR and upperMR, estimated as either exercise‐induced maximum metabolic rate (VO2max), cold‐induced summit metabolic rate (Msum), or daily energy expenditure (DEE).

Our meta‐analysis shows that there is a general positive association between minMR and upperMR that is shared among vertebrate taxonomic classes. However, there was stronger evidence for intra‐specific correlations between minMR and Msum and between minMR and DEE than there was for a correlation between minMR and VO2max across different taxa. As expected, inter‐specific correlation estimates were consistently higher than intra‐specific estimates across all traits and vertebrate classes.

An interesting exception to this general trend was observed in mammals, which contrast with birds and exhibit no correlation between minMR and Msum. We speculate that this is due to the evolution and recruitment of brown fat as a thermogenic tissue, which illustrates how some species and lineages might circumvent this seemingly general association.

We conclude that, in spite of some variability across taxa and traits, the contention that minMR and upperMR are positively correlated generally holds true both within and across vertebrate species. Ecological and comparative studies should therefore take into consideration the possibility that variation in any one of these traits might partly reflect correlated responses to selection on other metabolic parameters.

A lay summary is available for this article.
Beyond troubled waters: the influence of eutrophication on host–parasite interactions
Authors: Budria Alexandre 
Published: April 2017

Summary

Recent research in biomedicine and in ecology has linked disease emergence and resurgence with human‐induced environmental change. Water bodies, in particular, have dramatically changed during the past century due to artificial enrichment of nutrients from diverse sources (e.g. agriculture, forestry, waste discharges). A growing number of studies, reviewed in this synthesis, highlights how these alterations are tightly linked to changes in host–parasite interactions and impact wildlife health.

Direct responses of aquatic ecosystems to the disturbance include changes in the community of primary producers and cause indirect responses such as turbidity, oxygen depletion and foodweb alteration; a phenomenon known as anthropogenic eutrophication. Ultimately, eutrophication causes a wide range of effects on host–parasite interactions which should all be considered to predict infection probability and outcome in disturbed areas.

Future research should encompass a more fundamental and holistic view of eutrophication, considering altogether the multitude of environmental changes encountered in eutrophied sites. Stronger collaborations among disease biologists and aquatic ecologists are necessary to better understand and manage wildlife health at impacted water bodies.

A lay summary is available for this article.
The causes of dispersal and the cost of carry‐over effects for an endangered bird in a dynamic wetland landscape
Authors: Robertson Ellen P. , Fletcher Robert J. , Austin James D. 
Published: April 2017

Summary

The decision to disperse or remain philopatric between breeding seasons has important implications for both ecology and evolution, including the potential for carry‐over effects, where an individual's previous history affects its current performance. Carry‐over effects are increasingly documented although underlying mechanisms remain unclear.

Here we test for potential carry‐over effects and their mechanisms by uniting hypotheses for the causes and consequences of habitat selection and dispersal across space and time. We linked hypotheses regarding different types of factors and information (environmental conditions, personal and public information) predicted to impact reproductive success and dispersal for an endangered, wetland‐dependent bird, the snail kite (Rostrhamus sociabilis plumbeus). To do so, we coupled structural equation modelling with 20 years of mark–recapture and nesting data across the breeding range of this species to isolate potential direct and indirect effects of these factors.

We found that water depth at nest sites explained subsequent emigration rates via an indirect path through the use of personal, not public, information. Importantly, we found that these dispersers tended to initiate nests later the following breeding season. This pattern explained a phenological mismatch of nesting with hydrological conditions, whereby immigrants tended to nest later, late nesters tended to experience lower water depths, higher nest failure occurred at lower water depths and higher nest failure explained subsequent breeding dispersal.

These results identified a novel potential mechanism for carry‐over effects: a phenological mismatch with environmental conditions (water depth) that occurred potentially due to time costs of dispersal. Our results also highlighted a substantial benefit of philopatry – earlier initiation of reproduction – which allows philopatric individuals to better coincide with environmental conditions that are beneficial for successful reproduction.

These results have implications for our mechanistic understanding and prediction of carryover effects, and emphasize that local conservation strategies, such as water management, can explain future demography at distant sites connected through dispersal.
C‐reactive protein and ageing
Authors: Tang Ying , Fung Erik , Xu Anping , Lan Hui‐Yao 
Published: April 2017

SummaryIncreasing evidence shows that C‐reactive protein (CRP) is not only an inflammatory biomarker but also an important risk factor associated with ageing‐related diseases including cardiovascular disease, hypertension, diabetes mellitus, and kidney disease. Recent studies have demonstrated thatCRPis pathogenic in a number of diseases including hypertensive cardiovascular and kidney complications, diabetic nephropathy, and acute and chronic kidney diseases. It is well known thatCRPbinds its receptor,CD32/CD64, to induce the process of inflammation by activating theNF‐κB signalling pathway. In addition,CRPmediates tissue fibrosis in a number of cardiovascular and kidney diseases by activatingTGF‐β/Smad signalling viaTGF‐β1‐dependent and independent mechanisms. Furthermore,CRPis able to activatemTORsignalling in the diabetic conditions. Our recent studies also revealed thatCRPimpairs cell regeneration by causing the G1 cell cycle arrest and promotes ageing via a Smad3‐dependent p21/p27 mechanism. In this review, we discuss the roles ofCRPin ageing, with a focus on its function and mechanisms in physiological or “healthy” ageing, in ageing‐related diseases, and in cell signalling.
Compared effects on cerebral oxygenation of ephedrine vs phenylephrine to treat hypotension during carotid endarterectomy
Authors: Aliane Jugurtha , Dualé Christian , Guesmi Nader , Baud Charlotte , Rosset Eugenio , Pereira Bruno , Bouvier Damien , Schoeffler Pierre 
Published: April 2017

SummaryWhile both ephedrine and phenylephrine are currently used to treat hypotension occurring during carotid endarterectomy (CEA) under general anaesthesia, phenylephrine may have deleterious effects on the cerebral watershed, due to its exclusively vasoconstrictive action. In this controlled, double‐blind randomised trial, we compared the effects of ephedrine and phenylephrine administered in a standardised algorithm to treat the first hypotensive event occurring since induction of anaesthesia until carotid cross‐clamping. The algorithm consisted of 1‐to‐3 boluses of 6 mg of ephedrine or 50 μg of phenylephrine, after a goal‐directed fluid therapy. In case of failure, the treatment switched to the other study drug. Cerebral tissue oxygen saturation (SctO2) was monitored by near infrared spectroscopy (NIRS), and the primary outcome was the restoring effect of SctO2 (ipsilateral to surgery) to baseline values. Secondary postoperative outcomes were: contralateral SctO2, neurological outcomes, and plasma S100B protein measured at discharge from post‐anaesthesia care unit. Ephedrine treatment provided a higher rate of restoration of ipsilateral SctO2 than phenylephrine (93.2% vs 85.1%, P=.034); this was also noted for contralateral SctO2 (93.5% vs 90.7%, P=.026). The gain in SctO2 on the lowest value during hypotension was also higher under ephedrine than phenylephrine (6.4% vs 4.3% ipsilateral, 5.1% vs 4% contralateral), but not significantly so. Clinical outcomes were unaffected by the treatment, but S100B protein plasma concentration was higher in the phenylephrine group. To conclude, this pilot trial, focusing on intermediate outcomes, suggests that ephedrine should be preferred to phenylephrine to treat hypotension during CEA.