bluuebunny/crossref_metadata_2025_split huggingface dataset:
Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots
Authors: Yu Peng , Wang Chao , Baldauf Jutta A. , Tai Huanhuan , Gutjahr Caroline , Hochholdinger Frank , Li Chunjian 
Published: October 2017

Key findingOur data illustrates for the first time that root type identity and phosphate availability determine the community composition of colonizing fungi and shape the transcriptomic response of the maize root system.SummaryPlant root systems consist of different root types colonized by a myriad of soil microorganisms including fungi, which influence plant health and performance. The distinct functional and metabolic characteristics of these root types may influence root type inhabiting fungal communities.We performed internal transcribed spacer (ITS) DNA profiling to determine the composition of fungal communities in field-grown axial and lateral roots of maize (Zea maysL.) and in response to two different soil phosphate (P) regimes. In parallel, these root types were subjected to transcriptome profiling by RNA-Seq.We demonstrated that fungal communities were influenced by soil P levels in a root type-specific manner. Moreover, maize transcriptome sequencing revealed root type-specific shifts in cell wall metabolism and defense gene expression in response to high phosphate. Furthermore, lateral roots specifically accumulated defense related transcripts at high P levels. This observation was correlated with a shift in fungal community composition including a reduction of colonization by arbuscular mycorrhiza fungi as observed in ITS sequence data and microscopic evaluation of root colonization.Our findings point towards a diversity of functional niches within root systems, which dynamically change in response to soil nutrients. Our study provides new insights for understanding root-microbiota interactions of individual root types to environmental stimuli aiming to improve plant growth and fitness.
NDC80 clustering modulates microtubule dynamics under force
Authors: Volkov Vladimir A. , Huis in't Veld Pim J. , Dogterom Marileen , Musacchio Andrea 
Published: October 2017

AbstractMultivalency, the presence of multiple interfaces for intermolecular interactions, underlies many biological phenomena, including receptor clustering and cytosolic condensation. One of its ultimate purposes is to increase binding affinity, but systematic analyses of its role in complex biological assemblies have been rare. Presence of multiple copies of the microtubule-binding NDC80 complex is an evolutionary conserved but poorly characterized feature of kinetochores, the points of attachment of chromosomes to spindle microtubules. To address its significance, we engineered modules allowing incremental addition of NDC80 complexes. The modules’ residence time on microtubules increased exponentially with the number of NDC80 complexes. While modules containing a single NDC80 complex were unable to track depolymerizing microtubules, modules with two or more complexes tracked depolymerizing microtubules and stiffened the connection with microtubules under force. Cargo-conjugated modules of divalent or trivalent NDC80 stalled and rescued microtubule depolymerization in a force-dependent manner. Thus, multivalent microtubule binding through NDC80 clustering is crucial for force-induced modulation of kinetochore-microtubule attachments.
SWEET11 and 15 as key players in seed filling in rice
Authors: Yang Jungil , Luo Dangping , Yang Bing , Frommer Wolf B. , Eom Joon-Seob 
Published: October 2017

SummaryDespite the relevance of seed filling mechanisms for crop yield, we still have only a rudimentary understanding of the pathways and transport processes for supplying the caryopsis with sugars. We hypothesized that the recently identified SWEET sucrose transporters may play important roles in nutrient import pathways in the rice caryopsis.We used a combination of mRNA quantification, histochemical analyses, translational promoter-reporter fusions and analysis ofknock outmutants created by genomic editing to evaluate the contribution of SWEET transporters to seed filling.In rice caryopses,SWEET11and15had the highest mRNA levels and proteins localized to four key sites: the nucellus proper at early stages, the nucellar projection close to the dorsal vein, the nucellar epidermis that surrounds the endosperm, and the aleurone.ossweet11;15doubleknock-outlines accumulated starch in the pericarp while caryopses did not contain a functional endosperm.Jointly, SWEET11 and 15 show all hallmarks of being responsible for seed filling with sucrose efflux function at the nucellar projection and transfer across the nucellar epidermis/aleurone interface, delineating two major steps for apoplasmic seed filling, observations that are discussed in relation to observations made in rice and barely on the relative prevalence of these two potential import routes.
Identification of Cancer–associated Metabolic Vulnerabilities by Modeling Multi-objective Optimality in Metabolism
Authors: Dai Ziwei , Xu Liyan , Hu Hongrong , Liao Kun , Deng Shuye , Chen Qiyi , Yang Shiyu , Wang Qian , Gao Shuaishi , Li Bo , Lai Luhua 
Published: October 2017

AbstractComputational modeling of the genome-wide metabolic network is essential for designing new therapeutics targeting cancer-associated metabolic disorder, which is a hallmark of human malignancies. However, previous studies generally assumed that metabolic fluxes of cancer cells are subjected to the maximization of biomass production, despite the wide existence of trade-offs among multiple metabolic objectives. To address this issue, we developed a multi-objective model of cancer metabolism with algorithms depicting approximate Pareto surfaces and incorporating multiple omics datasets. To validate this approach, we built individualized models for NCI-60 cancer cell lines, and accurately predicted cell growth rates and other biological consequences of metabolic perturbations in these cells. By analyzing the landscape of approximate Pareto surface, we identified a list of metabolic targets essential for cancer cell proliferation and the Warburg effect, and further demonstrated their close association with cancer patient survival. Finally, metabolic targets predicted to be essential for tumor progression were validated by cell-based experiments, confirming this multi-objective modelling method as a novel and effective strategy to identify cancer-associated metabolic vulnerabilities.
Allosteric Modulation of Conformational Dynamics in Human Hsp90α: A Computational Study
Authors: Penkler David L. , Atilgan Canan , Bishop Özlem Tastan 
Published: October 2017

AbstractCentral to Hsp90’s biological function is its ability to interconvert between various conformational states. Drug targeting of Hsp90’s regulatory mechanisms, including its modulation by co-chaperone association, presents as an attractive therapeutic strategy for Hsp90 associated pathologies. Here, we utilize homology modeling techniques to calculate full-length structures of human Hsp90α in closed and partially-open conformations. Atomistic simulations of these structures demonstrated that bound ATP stabilizes the dimer by ‘tensing’ each protomer, while ADP and apo configurations ‘relax’ the complex by increasing global flexibility. Dynamic residue network analysis revealed regions of the protein involved in intra-protein communication, and identified several overlapping key communication hubs that correlate with known functional sites. Perturbation response scanning analysis identified several potential residue sites capable of modulating conformational change in favour of interstate conversion. For the ATP-bound open conformation, these sites were found to overlap with known Aha1 and client binding sites, demonstrating how naturally occurring forces associated with co-factor binding could allosterically modulate conformational dynamics.
A Multimodal Strategy Used By A Large c-di-GMP Network
Authors: Dahlstrom Kurt M. , Collins Alan J. , Doing Georgia , Taroni Jacyln N , Gauvin Timothy J. , Greene Casey S. , Hogan Deborah A. , O’Toole George A. 
Published: October 2017

AbstractThePseudomonas fluorescensgenome encodes for 50+ proteins involved in -di-GMP signaling. Here, we demonstrate that when tested across 188 nutrients, these enzymes and effectors appear capable of impacting biofilm formation. Transcriptional analysis of network members across ∼50 nutrient conditions indicates that altered gene expression can explain a subset, but not all, of biofilm-formation responses to the nutrients. Additional organization of the network is likely achieved through physical interaction, as determined via probing ∼2000 interactions by bacterial two-hybrid assays. Our analysis revealed a multimodal regulatory strategy, using combinations of ligand-mediated signals, protein-protein interaction and/or transcriptional regulation to further fine-tune c-di-GMP-mediated responses. These results create a profile of a large c-di-GMP network that is used to make important cellular decisions, opening the door to future model building and the ability to engineer this complex circuitry in other bacteria.Abstract ImportanceCyclic diguanylate (c-di-GMP) is a key signalling molecule regulating bacterial biofilm formation, and many microbes have up to dozens of proteins that make, break or bind this dinucleotide. Thus, a major open question in the field is how signalling specificity is conferred in this context with a soluble signalling molecule. Here, we take a systems approach, using mutational analysis, transcriptional studies and bacterial two-hybrid analysis to interrogate this network. We find that the network typically combines two or more modes of regulation (i.e., transcriptional control with protein-protein interaction) to generate an observed output.
Introducing prescribed biases in out of equilibrium Markov models
Authors: Dixit Purushottam D. 
Published: October 2017

AbstractMarkov models are often used in modeling complex out of equilibrium chemical and biochemical systems. However, many times their predictions do not agree with experiments. We need a systematic framework to update Markov models to make them consistent with constraints that are derived from experiments. Here, we present a framework based on the principle of maximum path entropy to update Markov models using stationary state and dynamical trajectory-based constraints. We illustrate the framework using a biochemical model network of growth factors-based signaling. We also show how to find the closest detailed balanced Markov model to a given Markov model. Further applications and generalizations are discussed.
Targeting of Photoreceptor Genes inChlamydomonas reinhardtiivia Zinc-Finger Nucleases and CRISPR/Cas9
Authors: Greiner Andre , Kelterborn Simon , Evers Heide , Kreimer Georg , Sizova Irina , Hegemann Peter 
Published: October 2017

AbstractThe fast-growing biflagellated single-celled chlorophyte Chlamydomonas reinhardtii is the most widely used alga in basic research. The physiological functions of the 18 sensory photoreceptors are of particular interest with respect to Chlamydomonas development and behavior. Despite the demonstration of gene editing in Chlamydomonas in 1995, the isolation of mutants lacking easily ascertained newly acquired phenotypes remains problematic due to low DNA recombination efficiency. We optimized gene-editing protocols for several Chlamydomonas strains (including wild-type CC-125) using zinc-finger nucleases (ZFNs), genetically encoded CRISPR/associated protein 9 (Cas9) from Staphylococcus aureus and Streptococcus pyogenes, and recombinant Cas9 and developed protocols for rapidly isolating nonselectable gene mutants. Using this technique, we disrupted the photoreceptor genes COP1/2, COP3 (encoding channelrhodopsin 1 [ChR1]), COP4 (encoding ChR2), COP5, PHOT, UVR8, VGCC, MAT3, and aCRY and created the chr1 chr2 and uvr8 phot double mutants. Characterization of the chr1, chr2, and mat3 mutants confirmed the value of photoreceptor mutants for physiological studies. Genes of interest were disrupted in 5 to 15% of preselected clones (∼1 out of 4000 initial cells). Using ZFNs, genes were edited in a reliable, predictable manner via homologous recombination, whereas Cas9 primarily caused gene disruption via the insertion of cotransformed DNA. These methods should be widely applicable to research involving green algae.
Approaching the wicked problem of obesity: an introduction to the food system compass
Authors: Parkinson Joy , Dubelaar Chris , Carins Julia , Holden Stephen , Newton Fiona , Pescud Melanie 
Published: October 2017

Purpose
The purpose of this paper is to focus on food consumption as part of the wicked problem of obesity. Specifically, the authors seek to explore the complex interplay between stakeholders such as food producers, marketers, health and medical practitioners and policymakers and their influence on the ways in which individuals consume food and also chart a course forward using a systems approach, social marketing techniques and social enterprise to develop solutions to effect change.

Design/methodology/approach
This is a conceptual paper that proposes the food system compass to understand the complex interplay between stakeholders.

Findings
This new tool will provide social marketers with an improved understanding of the complexity of interactions between stakeholders and outcomes and integrating the necessity for coordination within and across micro, meso, exo and macro levels of the system as well as across sectors, institutions and stakeholders.

Research limitations/implications
This is a conceptual paper and proposes the food system compass which offers a foundation for future research to expand upon.

Originality/value
This paper seeks to advance the theoretical base of social marketing by providing new insights into the trans-disciplinary and dynamic circumstances surrounding food consumption and obesity and highlights leverage points where joint actions can be facilitated with actors across and between micro, meso, exo and macro levels.
Exploring value destruction in social marketing services
Authors: Leo Cheryl , Zainuddin Nadia 
Published: October 2017

Purpose
This paper seeks to draw from services marketing theory as an alternative and under-used pathway to social and behaviour change for the achievement of societal well-being. Social marketing services are an important part of social change programmes as they contribute towards service users’ health, well-being, and the fulfilment of social marketing goals. However, value destruction can occur in users’ service experiences, leading to a decline rather than improvement of their well-being. The purpose of this paper is to understand the nature of the value destruction process and identify the outcomes in social marketing services from a consumer’s perspective.

Design/methodology/approach
A qualitative exploratory study using a focus group (n = 4) and individual depth interview (n = 4) methods was undertaken. The discussions were guided by a semi-structured interview guide and were audio recorded and transcribed verbatim.

Findings
Thematic analysis of the data revealed two value destruction processes: incongruent resource application and misuse of firm resources. The value destruction processes suggest three types of outcomes: reduced usage of the service, termination of service and strategic behavioural actions.

Originality/value
This study is the first to examine value destruction processes and outcomes in social marketing services from a consumer’s perspective. This study contributes towards the small but growing body of research on value destruction in both commercial and social marketing by challenging the assumption that value creation is always positively valenced and responding to critique that there is currently insufficient focus on value destruction in service research and its impact on well-being.
Fair play
Authors: Faullant Rita , Fueller Johann , Hutter Katja 
Published: October 2017

PurposeCompanies are discovering the power of crowdsourcing as a source of new ideas for products and services. It is assumed that the personal engagement and the continuous involvement with a company’s products or services over a period of several weeks positively affect participants’ loyalty intentions toward the host companies. The research leads the authors to challenge this assumption. In addition to mere participation in crowdsourcing initiatives, the authors argue that perceptions of fairness will explain changes in customer relationship-related consequences such as loyalty, perceived innovativeness and product interest. The paper aims to discuss these issues.Design/methodology/approachThe authors analyzed a real-life crowdsourcing contest launched by a leading lighting manufacturer and investigated the impact of two fairness dimensions (distributive and procedural) on participants’ future behavioral and attitudinal intentions (n=121). The analysis was performed with SEM.FindingsThe results suggest that fairness perceptions are significantly related to evoked product interest, perceived innovativeness and loyalty intentions. The analysis reveals that the influence of the fairness dimensions is asymmetric: while distributive fairness can be considered as a basic factor that must be fulfilled in order to avoid negative behavioral consequences, procedural fairness instead is an excitement factor that causes truly positive behavioral consequences.Research limitations/implicationsThe results are particularly relevant for companies launching a crowdsourcing competition under their own brand name, and for broadcasting platforms. For companies with no relations to end-users, these findings may not be as relevant.Practical implicationsOrganizers of crowdsourcing contests should be aware that such initiatives can be a double-edged sword. Fair Play is a must to gain the positive effects from crowdsourcing initiatives for both new product development and the customer relationship. For companies lacking the capabilities to manage crowdsourcing initiatives professionally it is advisable to rely on intermediary broadcasting platforms.Originality/valueThe research is the first to investigate systematically the consequences of fairness perceptions in a real-life crowdsourcing idea contest. The authors demonstrate the asymmetric nature of fairness perceptions on three different outcome variables that are important for the customer relationship.
Earthworms increase plant biomass more in soil with no earthworm legacy than in earthworm‐mediated soil, and favour late successional species in competition
Authors: Mudrák Ondřej , Frouz Jan 
Published: October 2017

AbstractAs ecosystem engineers, earthworms greatly affect plant communities. They create persistent soil structures enriched by nutrients that improve the conditions for plant growth and modify competition between plant species. We therefore hypothesized that earthworm activity would be more important in early stages of the primary succession, when the soil is not modified by earthworms, than in the late stages of the succession, when the soil is already improved by earthworms. On the other hand, earthworms also affect plants via many other effects such as seed predation or excreting hormone‐like compounds, which could make earthworm presence important in late successional soil.To explore earthworm effects on plant community succession, we performed a laboratory microcosm experiment without and with earthworms (Lumbricus rubellusandAporrectodea caliginosa), with early successional plants (Poa compressa,Medicago lupulinaandDaucus carota) and late successional plants (Arrhenatherum elatius,Lotus corniculatusandPlantago lanceolata) and with soil previously unaffected by earthworms (young soil) and soil substantially affected by earthworms (developed soil). These soils were taken from the early and late successional post‐mining sites of the Sokolov coal mining district (northwest Czech Republic).When both early and late successional plants were grown separately, earthworms increased plant biomass proportionally more in the young soil than in the developed soil, indicating that earthworm activity is more important in undeveloped than in developed soil.When early and late successional plants were competing each other, the biomass of the early successional plants was reduced. In the young soil, the reduction was independent of earthworm presence. In the developed soil, the reduction was promoted by the earthworms. Late successional plants profited from the reduction of early successional plants and increased their biomass. This increase was promoted by the earthworm presence.Our results indicate that the direct effects of earthworm presence on plants decrease during succession because of the cumulative effects of earthworm activity on soil conditions. Such ecosystem engineering effects favour late successional competitors and therefore promote the replacement of species during succession.Aplain language summaryis available for this article.
Reduced CBF recovery detected by longitudinal 3D‐SSP SPECT analyses predicts outcome of postoperative patients after subarachnoid haemorrhage
Authors: Mutoh Tatsushi , Totsune Tomoko , Takenaka Shunsuke , Tatewaki Yasuko , Nakagawa Manabu , Suarez Jose I , Taki Yasuyuki , Ishikawa Tatsuya 
Published: October 2017

SummaryThe aim of this study was to evaluate the impact of cerebral blood flow (CBF) recovery obtained from brain single‐photon emission computed tomography (SPECT) images on postoperative outcome after aneurysmal subarachnoid haemorrhage (SAH). Twenty‐nine patients who had undergone surgical clipping for ruptured anterior communicating artery aneurysms were analyzed prospectively. Routine measurements of CBF were performed using technetium‐99 m hexamethyl propyleneamine oxine SPECT on days 4 and 14 after SAH. Regional voxel data analyzed by three dimensional stereotactic surface projection (3D‐SSP) were compared between patients and age‐matched normal database (NDB). In 3D‐SSP analysis of all patients, cortical hypoperfusion around the surgical site in bilateral frontal lobes was evident on day 4 (P < .05 vs NDB), which was improved significantly on day 14. However, the recovery was less complete in patients with poor clinical grades (P < .05) and presenting symptoms attributable to delayed cerebral ischaemia (DCI) (P < .05) than those without. Multivariate analysis showed that patients with mild to moderate CBF recovery (relative Z‐score differences of <4) (P = .014; odds ratio, 2.5; 95% confidence interval, 1.93–3.31) was independently associated with poor functional outcome at 3 months. We conclude that reduced CBF recovery detected by serial 3D‐SSP SPECT image analyses can be a potential predictor of poor prognosis in postoperative patients after SAH.