bluuebunny/crossref_metadata_2025 huggingface dataset:
LITE microscopy: a technique for high numerical aperture, low photobleaching fluorescence imaging
Authors: Fadero Tanner C , Gerbich Therese M , Rana Kishan , Suzuki Aussie , DiSalvo Matthew , Schaefer Kristina N , Heppert Jennifer K , Boothby Thomas C , Goldstein Bob , Peifer Mark , Allbritton Nancy L , Gladfelter Amy S , Maddox Amy S , Maddox Paul S
Published: October 2017

Fluorescence microscopy is a powerful approach for studying sub-cellular dynamics at high spatiotemporal resolution; however, conventional fluorescence microscopy techniques are light-intensive and introduce unnecessary photodamage. Light sheet fluorescence microscopy (LSFM) mitigates these problems by selectively illuminating the focal plane of the detection objective using orthogonal excitation. Orthogonal excitation requires geometries that physically limit the detection objective numerical aperture (NA), thereby limiting both light-gathering efficiency (brightness) and native spatial resolution. We present a novel LSFM method: Lateral Interference Tilted Excitation (LITE), in which a tilted light sheet illuminates the detection objective focal plane without a sterically-limiting illumination scheme. LITE is thus compatible with any detection objective, including oil immersion, without an upper NA limit. LITE combines the low photodamage of LSFM with high resolution, high brightness, coverslip-based objectives. We demonstrate the utility of LITE for imaging animal, fungal, and plant model organisms over many hours at high spatiotemporal resolution.
Genetic study links components of the autonomous nervous system to heart-rate profile during exercise
Authors: Verweij Niek , de Vegte Yordi van , der Harst Pim van
Published: October 2017

Heart rate (HR) response to exercise, as defined by HR-increase upon exercise and HR-recovery after exercise, is an important predictor of mortality and believed to be modulated by the autonomic nervous system. However, the mechanistic basis underlying inter-individual differences remains to be elucidated. To investigate this, we performed a large-scale genome wide analysis of HR-increase and HR-recovery in 58,818 individuals. A total of 25 significant independent SNPs in 23 loci (P<8.3×10−9) were associated with HR-increase or HR-recovery, and 36 candidate causal genes were prioritized that were enriched for pathways related to neuron biology. There was no evidence of a causal relationship with mortality or cardiovascular diseases, however, a nominal association with parental lifespan was observed (5.5×10−4) that requires further study. In conclusion, our findings provide new biological and clinical insight into the mechanistic under-pinning of HR response to exercise, underscoring the role of the autonomous nervous system in HR-recovery.

ABBREVIATIONS

BMI

Body mass index

ECG

Electrocardiography

HR

Heart rate

HRR

Heart rate recovery

GWAS

Genome-wide association study

LD

Linkage disequilibrium

MAF

Minor allele frequency

SE

Standard error

CI

Confidence interval
A circadian clock in the blood-brain barrier regulates xenobiotic efflux from the brain
Authors: Zhang Shirley L. , Yue Zhifeng , Arnold Denice M. , Sehgal Amita
Published: October 2017

Highlights

TheDrosophilaBBB displays a circadian rhythm of permeability

Cyclic efflux driven by a clock in the BBB underlies the permeability rhythm

Circadian control is non-cell-autonomous via gap junction regulation of [Mg2+]i

An anti-seizure drug is more effective when administered at night

Endogenous circadian rhythms are thought to modulate responses to external factors, but mechanisms that confer time-of-day differences in organismal responses to environmental insults / therapeutic treatments are poorly understood. Using a xenobiotic, we find that permeability of theDrosophila“blood”-brain barrier (BBB) is higher at night. The permeability rhythm is driven by circadian regulation of efflux and depends upon a molecular clock in the perineurial glia of the BBB, although efflux transporters are restricted to subperineurial glia (SPG). We show that transmission of circadian signals across the layers requires gap junctions, which are expressed cyclically. Specifically, during nighttime gap junctions reduce intracellular magnesium ([Mg2+]i), a positive regulator of efflux, in SPG. Consistent with lower nighttime efflux, nighttime administration of the anti-epileptic phenytoin is more effective at treating aDrosophilaseizure model. These findings identify a novel mechanism of circadian regulation and have therapeutic implications for drugs targeted to the central nervous system.
Non-predictive online spatial coding in the posterior parietal cortex when aiming ahead for catching
Authors: Reid Sinéad A. , Dessing Joost C.
Published: October 2017

Catching movements must be aimed ahead of the moving ball, which may require predictions of when and where to catch. Here, using Transcranial Magnetic Stimulation we show for the first time that, although interception movements were clearly aimed at the predicted final target position, the Superior Parietal Occipital Cortex (SPOC) displayed non-predictive online spatial coding. The ability to aim ahead for catching must thus arise downstream within the parietofrontal network for reaching.
Association theory: a new framework for analyzing social evolution
Authors: Gilbert Owen M.
Published: October 2017

The dominant social-evolutionary paradigm implicitly equates social actions and behaviors causing associations by extrapolating from models of social actions to explain behaviors affecting association. This extrapolation occurs when models of helping behavior are applied to explain aggregation or fusion, and when models of discriminatory helping behavior are applied to explain discriminatory segregation or discriminatory rejection. Here, I outline an alternative theoretical approach that explicitly distinguishes a social action as a helping or harming behavior, and an association as the context for a social action. Based on this distinction, I define a list of terms that allows a classification of association phenomena and the conceptual framework necessary to explain their evolution. I apply the resulting theory, which I call “association theory,” to identify a series of steps common to major and minor transitions in social evolution. These steps include the evolution of association, the evolution of differential treatment, the evolution of association preference, and the evolution of genetic kin recognition. I explain how to measure the parameters of association theory and I apply the theory to test Hamilton’s rule. I evaluate the evidence for association theory, including how it resolves anomalies of a former paradigm. Finally, I discuss association theory’s assumptions, and I explain why it may become the dominant framework for analyzing social evolution.
Clogging-free continuous operation with whole blood in a radial pillar device (RAPID)
Authors: Mehendale Ninad , Sharma Oshin , Pandey Shilpi , Paul Debjani
Published: October 2017

Pillar-based passive microfluidic devices combine the advantages of simple designs, low device footprint, and high selectivity for size-based separation of blood cells. Most of these device designs have been validated with dilute blood samples. Handling whole blood in pillar-based devices is extremely challenging due to clogging. The high proportion of cells (particularly red blood cells) in blood, the varying sizes and stiffness of the different blood cells, and the tendency of the cells to aggregate lead to clogging of the pillars within a short period. We recently reported aradialpillardevice (RAPID) design for contin-uous and high throughput separation of multi-sized rigid polystyrene particles in a single experiment. In this manuscript, we have given detailed guidelines to modify the design of RAPID for any application with deformable objects (e.g. cells). We have adapted RAPID to work with blood samples directly without any pre-processing steps. We were successful in operating the device with whole blood for almost 6 hours, which is difficult to achieve with most pillar-based devices. Finally, we demonstrated up to ~ 60-fold enrichment of platelets as an illustration of the improved device design. Whole blood pillar-based platelet clog-free RAPID
A set informative multiple autosomal markers for human identification: forensic research and population genetics analysis in a Chinese Xinjiang Hui group
Authors: Xie Tong , Guo Yuxin , Chen Ling , Fang Yating , Tai Yunchun , Zhou Yongsong , Qiu Pingming , Zhu Bofeng
Published: October 2017

In recent years, insertion/deletion (InDel) markers became a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 24 previously studied populations using varies methods such as forensic statistical parameter analysis, phylogenetic reconstruction, STRUCTURE analysis, multi-dimensional scaling, and principal component analysis. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD 92), 0.2222 (HLD 114) to 0.5000 (HLD 6), respectively. Besides, after Bonferroni correction, no deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in Xinjiang Hui group. The cumulative probability of exclusion and combined discrimination power were 0.988849 and 0.99999999999378, respectively, which indicated that the 30 loci could be used as complementary genetic markers for paternity test and be qualified for personal identification in forensic cases. In this study, we found that Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations, and all the results based on different genetic methods we used had a strong support for this finding. The 30 InDel loci has important significance in forensic identification research, in spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, molecular genetic genotyping at various genetic markers is necessary in future studies.

Summary Statement

We report here, a promising Individual identification and population differentiation maker which could be used in forensic cases.
ZMPSTE24Missense Mutations that Cause Progeroid Diseases Decrease Prelamin A Cleavage Activity and/or Protein Stability
Authors: Spear Eric D. , Hsu Ehr-Ting , Nie Laiyin , Carpenter Elisabeth P. , Hrycyna Christine A. , Michaelis Susan
Published: October 2017

The human zinc metalloprotease ZMPSTE24 is an integral membrane protein critical for the final step in the biogenesis of the nuclear scaffold protein lamin A, encoded byLMNA. After farnesylation and carboxyl methylation of its C-terminal CAAX motif, the lamin A precursor, prelamin A, undergoes proteolytic removal of its modified C-terminal 15 amino acids by ZMPSTE24. Mutations inLMNAorZMPSTE24that impede this prelamin A cleavage step cause the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS) and the related progeroid disorders mandibuloacral dysplasia-type B (MAD-B) and restrictive dermopathy (RD). Here we report a “humanized yeast” system to assay ZMPSTE24-dependent cleavage of prelamin A and examine the eight known disease-associatedZMPSTE24missense mutations. All show diminished prelamin A processing and fall into three classes, with defects in activity, protein stability, or both. Notably, some ZMPSTE24 mutants can be rescued by deleting the E3 ubiquitin ligase Doa10, involved in ER-associated degradation of misfolded membrane proteins, or by treatment with the proteasome inhibitor bortezomib, which may have important therapeutic implications for some patients. We also show that ZMPSTE24-mediated prelamin A cleavage can be uncoupled from the recently discovered role of ZMPSTE24 in clearance of ER membrane translocon-clogged substrates. Together with the crystal structure of ZMPSTE24, this “humanized yeast system” can guide structure-function studies to uncover mechanisms of prelamin A cleavage, translocon unclogging, and membrane protein folding and stability.
Identification of a Small Molecule Inhibitor of the Aminoglycoside 6’-N-Acetyltransferase Type Ib [AAC(6’)-Ib] Using Mixture-Based Combinatorial Libraries
Authors: Tran Tung , Chiem Kevin , Jani Saumya , Arivett Brock A. , Lin David , Lad Rupali , Jimenez Verónica , Farone Mary B. , Debevec Ginamarie , Santos Radleigh , Giulianotti Marc , Pinilla Clemencia , Tolmasky Marcelo E.
Published: October 2017

The aminoglycoside 6′-N-acetyltransferase type Ib [AAC(6’)-Ib] is the most widely distributed enzyme among AAC(6’)-I-producing Gram-negative pathogens and confers resistance to clinically relevant aminoglycosides including amikacin. This enzyme is therefore ideal to target with enzymatic inhibitors that could overcome resistance to aminoglycosides. The search for inhibitors was carried out using mixture-based combinatorial libraries, the scaffold ranking approach, and the positional scanning strategy. A library with high inhibitory activity had pyrrolidine pentamine scaffold and was selected for further analysis. This library contained 738,192 compounds with functionalities derived from 26 different amino acids (R1, R2 and R3) and 42 different carboxylic acids (R4) in four R group functionalities. The most active compounds all contained S-phenyl (R1 and R3) and S-hydromethyl (R2) functionalities at three locations and differed at the R4 position. The compound containing 3-phenylbutyl at R4 (compound206) was a robust enzymatic inhibitor in vitro, in combination with amikacin potentiated the inhibition of growth of three resistant bacteria in culture, and improved survival when used as treatment ofGalleria mellonellainfected withaac(6’)-Ib-harboringKlebsiella pneumoniaeandAcinetobacter baumanniistrains.
On a ‘failed’ attempt to manipulate conscious perception with transcranial magnetic stimulation to prefrontal cortex
Authors: Ruby Eugene , Maniscalco Brian , Lau Hakwan , Peters Megan A.K.
Published: October 2017

It has been reported that continuous theta burst transcranial magnetic stimulation (TMS) to the dorsolateral prefrontal cortex (DLPFC) impairs metacognitive awareness in visual perception (Rounis et al., 2010). Bor et al. (2017) recently attempted to replicate this result. However, the authors modified the experimental design of the original study considerably, meaning that this was not strictly a replication. In some cases, the changes area prioriexpected to lower the chance of obtaining positive findings. Despite these changes, the researchers in fact still found an effect similar to Rounis et al.’s, but they claimed that it was necessary to adopt certain criteria to discard ∽30% of their subjects, after which a null result was reported. Using computer simulations, we evaluated whether the subject exclusion criteria Bor et al. adopted was appropriate or beneficial. We found that, contrary to their intended purpose, excluding subjects by their criteria does not actually reduce false positive rates. Taking into account both their positive result (without subject exclusion) and negative result (after exclusion) in a Bayesian framework, we further found that their results suggest a 75% or greater likelihood that TMS to DLPFC does in fact impair metacognition, directly contradicting their claim of replication failure. That lesion and chemical inactivation studies are known to demonstrate positive effects in similar paradigms further suggests that Bor et al.’s alleged negative finding cannot be taken as evidence against the role of the prefrontal cortex in conscious perception in general.
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 finding

Our 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.

Plant 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

Multivalency, 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

Summary

Despite 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

Computational 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

Central 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

ThePseudomonas 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 Importance

Cyclic 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.
R-spondins can potentiate WNT signaling without LGR receptors
Authors: Lebensohn Andres M. , Rohatgi Rajat
Published: October 2017

The WNT signaling pathway regulates patterning and morphogenesis during embryonic development and promotes tissue renewal and regeneration in adults. Some WNT responses in vertebrates depend on a second signal provided by the R-spondin family of four secreted proteins (RSPO1-4) that drive the renewal of stem cells in many tissues. RSPOs markedly amplify target cell sensitivity to WNT ligands by neutralizing two transmembrane E3 ligases, ZNRF3 and RNF43, which reduce cell-surface levels of WNT receptors. Chromosomal translocations that increase RSPO expression or that inactivate ZNRF3/RNF43 can drive human cancers. RSPOs contain tandem furin-like repeats (FU1 and FU2), a thrombospondin type I (TSP) domain, and a basic region (BR). RSPOs simultaneously engage ZNRF3/RNF43 through their FU1 domain and one of three leucine-rich repeat-containing G-protein coupled receptors (LGR4-6) through their FU2 domain, triggering the clearance of ZNRF3/RNF43 and the consequent rise in WNT receptor levels. LGRs are selectively expressed in various tissue stem cells and are considered the primary high-affinity receptors for RSPOs. Using purified mutant and chimeric RSPOs and cell lines lacking various receptors, we show that RSPO2 and RSPO3, but not RSPO1 and RSPO4, can potentiate WNT/β-catenin signaling in the absence of all three LGRs. The ZNRF3/RNF43-interacting FU1 domain was necessary for LGR-independent signaling, while the LGR-interacting FU2 domain was dispensable. The FU1 domain of RSPO3 was also sufficient to confer LGR-independence when transplanted to RSPO1, demonstrating that its interaction with ZNRF3/RNF43 dictates LGR-independent signaling. The enigmatic TSP/BR domains of RSPOs and their interaction with heparan sulfate proteoglycans (HSPGs), previously considered dispensable for WNT/β-catenin signaling, became essential in the absence of LGRs. These results define two alternative modes of RSPO-mediated signaling that share a common dependence on ZNRF3/RNF43, but differ in their use of either LGRs or HSPGs, with implications for understanding their mechanism of action, biological functions and evolutionary origins.
Introducing prescribed biases in out of equilibrium Markov models
Authors: Dixit Purushottam D.
Published: October 2017

Markov 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.
Integrator orchestrates RAS/ERK1/2 signaling transcriptional programs
Authors: Yue Jingyin , Lai Fan , Beckedorff Felipe , Zhang Anda , Pastori Chiara , Shiekhattar Ramin
Published: October 2017

Activating mutations in the mitogen-activated protein kinase (MAPK) cascade, also known as the RAS–MEK–extracellular signal-related kinase (ERK1/2) pathway, are an underlying cause of >70% of human cancers. While great strides have been made toward elucidating the cytoplasmic components of MAPK signaling, the key downstream coactivators that coordinate the transcriptional response have not been fully illustrated. Here, we demonstrate that the MAPK transcriptional response in human cells is funneled through Integrator, an RNA polymerase II-associated complex. Integrator depletion diminishes ERK1/2 transcriptional responsiveness and cellular growth in human cancers harboring activating mutations in MAPK signaling. Pharmacological inhibition of the MAPK pathway abrogates the stimulus-dependent recruitment of Integrator at immediate early genes and their enhancers. Following epidermal growth factor (EGF) stimulation, activated ERK1/2 is recruited to immediate early genes and phosphorylates INTS11, the catalytic subunit of Integrator. Importantly, in contrast to the broad effects of Integrator knockdown on MAPK responsiveness, depletion of a number of critical subunits of the coactivator complex Mediator alters only a few MAPK-responsive genes. Finally, human cancers with activating mutations in the MAPK cascade, rendered resistant to targeted therapies, display diminished growth following depletion of Integrator. We propose Integrator as a crucial transcriptional coactivator in MAPK signaling, which could serve as a downstream therapeutic target for cancer treatment.
A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency
Authors: Xie Liangqi , Torigoe Sharon E. , Xiao Jifang , Mai Daniel H. , Li Li , Davis Fred P. , Dong Peng , Marie-Nelly Herve , Grimm Jonathan , Lavis Luke , Darzacq Xavier , Cattoglio Claudia , Liu Zhe , Tjian Robert
Published: October 2017

Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during animal development. Despite decades of study, we know little about the dynamics or order of events animating TF assembly at cis-regulatory elements in living cells and the long-range molecular “dialog” between enhancers and promoters. Here, combining genetic, genomic, and imaging approaches, we characterize a complex long-range enhancer cluster governing Krüppel-like factor 4 (Klf4) expression in naïve pluripotency. Genome editing by CRISPR/Cas9 revealed that OCT4 and SOX2 safeguard an accessible chromatin neighborhood to assist the binding of other TFs/cofactors to the enhancer. Single-molecule live-cell imaging uncovered that two naïve pluripotency TFs, STAT3 and ESRRB, interrogate chromatin in a highly dynamic manner, in which SOX2 promotes ESRRB target search and chromatin-binding dynamics through a direct protein-tethering mechanism. Together, our results support a highly dynamic yet intrinsically ordered enhanceosome assembly to maintain the finely balanced transcription program underlying naïve pluripotency.
Another case for diet restriction: TAp73-expressing medulloblastomas are stunted by glutamine withdrawal
Authors: Napoli Marco , Flores Elsa R.
Published: October 2017

Medulloblastomas are among the most common malignant brain cancers in the pediatric population and consist of at least four distinct subgroups with unique molecular and genetic features and clinical outcomes. In this issue of Genes & Development, Niklison-Chirou and colleagues (pp. 1738–1753) identify the p53 family member and p73 isoform TAp73 as a crucial factor causing glutamine addiction in aggressive medulloblastomas. Their findings pave the way for the use of glutamine restriction as an adjuvant treatment for TAp73-expressing medulloblastomas.
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

The 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

Purpose

Companies 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/approach

The 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.

Findings

The 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/implications

The 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 implications

Organizers 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/value

The 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

As 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.

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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

The 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.
Alternatives to austerity
Authors: Bear Laura , Knight Daniel M.
Published: October 2017

We are in the age of austerity. Across the globe, there have recently been calls from both the left and the right to rethink policies of austerity and to rein in the forces of globalization. Over the past two years, anti‐austerity sentiment has been a major factor in public votes in Europe and the US. Anti‐globalization, anti‐debt and anti‐PPP movements are gaining broad support. Claiming to speak for ordinary families hit by the effects of austerity, parties across the political spectrum are scrambling to improvise new policies. Some alternatives to austerity are simply old ideas repackaged or reappropriated and help to legitimize the current status quo, yet others seem to offer genuine respite from the established order, claiming new forms of social relations and redistribution. The authors argue that only through an analysis of the longer‐term origins and multiple guises of austerity can we move towards proposals for social change. They challenge established understandings of austerity and ask readers to imagine seemingly utopian alternatives. Overall, they ask: how can we give a new critical meaning to the concept of the public good?
The concept of chronicity in action: everyday classification practices and the shaping of mental health care
Authors: Bister Milena D.
Published: October 2017

For almost half a century social scientists have explored the phenomenon of chronic illness. In this paper, I examine how the concept of chronicity participates in present‐day mental health care settings. Using ethnomethodology and material‐semiotic theory within science and technology studies, I investigate how the classification ‘chronically mentally ill’ interacts with the everyday socio‐material shaping of public mental health care in the context of professional institutions. Drawing on ethnographic fieldwork in a psychiatric day hospital and in a community day care centre in Berlin, Germany, I demonstrate how the classification of chronicity acts as a tool of description (of people or their conditions), regulation (of therapy, health care or administration), and connection to infrastructures of care (practised technologies or standards of various kinds). In these ways, I argue, the classification engages in actions of producing treatability, arranging resources, demarcating responsibilities, practicing accountability, and doing presence. Notably, community mental health care has developed into a designated territory of the concept: explicitly arranged for ‘the chronically mentally ill’ as a human kind, we can take everyday life in these institutions as instructive of how chronicity is defined in daily practice.