bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish
Leucoraja ocellata
(Rajidae)
Authors: Lighten Jackie , Incarnato Danny , Ward Ben J. , van Oosterhout Cock , Bradbury Ian , Hanson Mark , Bentzen Paul
Published: October 2016

The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential (‘K-strategists’), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (
Leucoraja ocellata
), a typical ‘K-strategist’, in Atlantic Canada; an endemic population in the southern Gulf of St Lawrence and a large population on the Scotian Shelf. The endemic population has been able to adapt to a 10°C higher water temperature over short evolutionary time (7000 years), dramatically reducing its body size (by 45%) significantly below the minimum maturation size of Scotian Shelf and other populations of winter skate, as well as exhibiting other adaptations in life history and physiology. We demonstrate that the adaptive response to selection has an epigenetic basis, cataloguing 3653 changes in gene expression that may have enabled this species to rapidly respond to the novel environment. We argue that the epigenetic augmentation of species evolutionary potential (its regulation though gene expression) can enable K-strategists to survive and adapt to different environments, and this mechanism may be particularly important for the persistence of sharks, skates and rays in the light of future climate change.
Towards powerful experimental and statistical approaches to study intraindividual variability in labile traits
Authors: Mitchell David J. , Fanson Benjamin G. , Beckmann Christa , Biro Peter A.
Published: October 2016

There is a long-standing interest in behavioural ecology, exploring the causes and correlates of consistent individual differences in mean behavioural traits (‘personality’) and the response to the environment (‘plasticity’). Recently, it has been observed that individuals also consistently differ in their residual intraindividual variability (rIIV). This variation will probably have broad biological and methodological implications to the study of trait variation in labile traits, such as behaviour and physiology, though we currently need studies to quantify variation in rIIV, using more standardized and powerful methodology. Focusing on activity rates in guppies (Poecilia reticulata), we provide a model example, from sampling design to data analysis, in how to quantify rIIV in labile traits. Building on the doubly hierarchical generalized linear model recently used to quantify individual differences in rIIV, we extend the model to evaluate the covariance between individual mean values and their rIIV. After accounting for time-related change in behaviour, our guppies substantially differed in rIIV, and it was the active individuals that tended to be more consistent (lower rIIV). We provide annotated data analysis code to implement these complex models, and discuss how to further generalize the model to evaluate covariances with other aspects of phenotypic variation.
Hypoxic areas, density-dependence and food limitation drive the body condition of a heavily exploited marine fish predator
Authors: Casini Michele , Käll Filip , Hansson Martin , Plikshs Maris , Baranova Tatjana , Karlsson Olle , Lundström Karl , Neuenfeldt Stefan , Gårdmark Anna , Hjelm Joakim
Published: October 2016

Investigating the factors regulating fish condition is crucial in ecology and the management of exploited fish populations. The body condition of cod (
Gadus morhua
) in the Baltic Sea has dramatically decreased during the past two decades, with large implications for the fishery relying on this resource. Here, we statistically investigated the potential drivers of the Baltic cod condition during the past 40 years using newly compiled fishery-independent biological data and hydrological observations. We evidenced a combination of different factors operating before and after the ecological regime shift that occurred in the Baltic Sea in the early 1990s. The changes in cod condition related to feeding opportunities, driven either by density-dependence or food limitation, along the whole period investigated and to the fivefold increase in the extent of hypoxic areas in the most recent 20 years. Hypoxic areas can act on cod condition through different mechanisms related directly to species physiology, or indirectly to behaviour and trophic interactions. Our analyses found statistical evidence for an effect of the hypoxia-induced habitat compression on cod condition possibly operating via crowding and density-dependent processes. These results furnish novel insights into the population dynamics of Baltic Sea cod that can aid the management of this currently threatened population.
A data-driven model for influenza transmission incorporating media effects
Authors: Mitchell Lewis , Ross Joshua V.
Published: October 2016

Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza; however, quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of ‘big data’ coming from online social media and the like, large volumes of data on a population’s engagement with mass media during an epidemic are becoming available to researchers. In this study, we combine an online dataset comprising millions of shared messages relating to influenza with traditional surveillance data on flu activity to suggest a functional form for the relationship between the two. Using this data, we present a simple deterministic model for influenza dynamics incorporating media effects, and show that such a model helps explain the dynamics of historical influenza outbreaks. Furthermore, through model selection we show that the proposed media function fits historical data better than other media functions proposed in earlier studies.
An
in silico
prediction tool for the expansion culture of human skeletal muscle myoblasts
Authors: Kagawa Yuki , Kino-oka Masahiro
Published: October 2016

Regenerative therapy using autologous skeletal myoblasts requires a large number of cells to be prepared for high-level secretion of cytokines and chemokines to induce good regeneration of damaged regions. However, myoblast expansion culture is hindered by a reduction in growth rate owing to cellular quiescence and differentiation, therefore optimization is required. We have developed a kinetic computational model describing skeletal myoblast proliferation and differentiation, which can be used as a prediction tool for the expansion process. In the model, myoblasts migrate, divide, quiesce and differentiate as observed during
in vitro
culture. We assumed cell differentiation initiates following cell–cell attachment for a defined time period. The model parameter values were estimated by fitting to several predetermined experimental datasets. Using an additional experimental dataset, we confirmed validity of the developed model. We then executed simulations using the developed model under several culture conditions and quantitatively predicted that non-uniform cell seeding had adverse effects on the expansion culture, mainly by reducing the existing ratio of proliferative cells. The proposed model is expected to be useful for predicting myoblast behaviours and in designing efficient expansion culture conditions for these cells.
Fine-scale analysis of an assassin bug's behaviour: predatory strategies to bypass the sensory systems of prey
Authors: Soley Fernando G.
Published: October 2016

Some predators sidestep environments that render them conspicuous to the sensory systems of prey. However, these challenging environments are unavoidable for certain predators.
Stenolemus giraffa
is an assassin bug that feeds on web-building spiders; the web is the environment in which this predator finds its prey, but it also forms part of its preys' sophisticated sensory apparatus, blurring the distinction between environment and sensory systems.
Stenolemus giraffa
needs to break threads in the web that obstruct its path to the spiders, and such vibrations can alert the spiders. Using laser vibrometry, this study demonstrates how
S. giraffa
avoids alerting the spiders during its approach. When breaking threads,
S. giraffa
attenuates the vibrations produced by holding on to the loose ends of the broken thread and causing them to sag prior to release. In addition,
S. giraffa
releases the loose ends of a broken thread one at a time (after several seconds or minutes) and in this way spaces out the production of vibrations in time. Furthermore,
S. giraffa
was found to maximally reduce the amplitude of vibrations when breaking threads that are prone to produce louder vibrations. Finally,
S. giraffa
preferred to break threads in the presence of wind, suggesting that this araneophagic insect exploits environmental noise that temporarily impairs the spiders' ability to detect vibrations. The predatory behaviour of
S. giraffa
seems to be adaptated in intricate manner for bypassing the sophisticated sensory systems of web-building spiders. These findings illustrate how the physical characteristics of the environment, along with the sensory systems of prey can shape the predatory strategies of animals.
Hydration affects the physical and mechanical properties of baleen tissue
Authors: Werth Alexander J. , Harriss Robert W. , Rosario Michael V. , George J. Craig , Sformo Todd L.
Published: October 2016

Baleen, an anisotropic oral filtering tissue found only in the mouth of mysticete whales and made solely of alpha-keratin, exhibits markedly differing physical and mechanical properties between dried or (as in life) hydrated states. On average baleen is 32.35% water by weight in North Atlantic right whales (Eubalaena glacialis) and 34.37% in bowhead whales (Balaena mysticetus). Baleen's wettability measured by water droplet contact angles shows that dried baleen is hydrophobic whereas hydrated baleen is highly hydrophilic. Three-point flexural bending tests of mechanical strength reveal that baleen is strong yet ductile. Dried baleen is brittle and shatters at about 20–30 N mm−2but hydrated baleen is less stiff; it bends with little force and absorbed water is squeezed out when force is applied. Maximum recorded stress was 4× higher in dried (mean 14.29 N mm−2) versus hydrated (mean 3.69 N mm−2) baleen, and the flexural stiffness was >10× higher in dried (mean 633N mm−2) versus hydrated (mean 58 N mm−2) baleen. In addition to documenting hydration's powerful effects on baleen, this study indicates that baleen is far more pliant and malleable than commonly supposed, with implications for studies of baleen's structure and function as well as its susceptibility to oil or other hydrophobic pollutants.
MultispeQ Beta: a tool for large-scale plant phenotyping connected to the open PhotosynQ network
Authors: Kuhlgert Sebastian , Austic Greg , Zegarac Robert , Osei-Bonsu Isaac , Hoh Donghee , Chilvers Martin I. , Roth Mitchell G. , Bi Kevin , TerAvest Dan , Weebadde Prabode , Kramer David M.
Published: October 2016

Large-scale high-throughput plant phenotyping (sometimes called phenomics) is becoming increasingly important in plant biology and agriculture and is essential to cutting-edge plant breeding and management approaches needed to meet the food and fuel needs for the next century. Currently, the application of these approaches is severely limited by the availability of appropriate instrumentation and by the ability to communicate experimental protocols, results and analyses. To address these issues, we have developed a low-cost, yet sophisticated open-source scientific instrument designed to enable communities of researchers, plant breeders, educators, farmers and citizen scientists to collect high-quality field data on a large scale. The MultispeQ provides measurements in the field or laboratory of both, environmental conditions (light intensity and quality, temperature, humidity, CO2levels, time and location) and useful plant phenotypes, including photosynthetic parameters—photosystem II quantum yield (ΦII), non-photochemical exciton quenching (NPQ), photosystem II photoinhibition, light-driven proton translocation and thylakoid proton motive force, regulation of the chloroplast ATP synthase and potentially many others—and leaf chlorophyll and other pigments. Plant phenotype data are transmitted from the MultispeQ to mobile devices, laptops or desktop computers together with key metadata that gets saved to the PhotosynQ platform (https://photosynq.org) and provides a suite of web-based tools for sharing, visualization, filtering, dissemination and analyses. We present validation experiments, comparing MultispeQ results with established platforms, and show that it can be usefully deployed in both laboratory and field settings. We present evidence that MultispeQ can be used by communities of researchers to rapidly measure, store and analyse multiple environmental and plant properties, allowing for deeper understanding of the complex interactions between plants and their environment.
Seven hundred years of human-driven and climate-influenced fire activity in a British Columbia coastal temperate rainforest
Authors: Hoffman Kira M. , Gavin Daniel G. , Starzomski Brian M.
Published: October 2016

While wildland fire is globally most common at the savannah-grassland ecotone, there is little evidence of fire in coastal temperate rainforests. We reconstructed fire activity with aca700-year fire history derived from fire scars and stand establishment from 30 sites in a very wet (up to 4000 mm annual precipitation) temperate rainforest in coastal British Columbia, Canada. Drought and warmer temperatures in the year prior were positively associated with fire events though there was little coherence of climate indices on the years of fires. At the decadal scale, fires were more likely to occur after positive El Niño-Southern Oscillation and Pacific Decadal Oscillation phases and exhibited 30-year periods of synchrony with the negative phase of the Arctic Oscillation. Fire frequency was significantly inversely correlated with the distance from former Indigenous habitation sites and fires ceased following cultural disorganization caused by disease and other European impacts in the late nineteenth century. Indigenous people were likely to have been the primary ignition source in this and many coastal temperate rainforest settings. These data are directly relevant to contemporary forest management and discredit the myth of coastal temperate rainforests as pristine landscapes.
On the use of Bayesian decision theory for issuing natural hazard warnings
Authors: Economou T. , Stephenson D. B. , Rougier J. C. , Neal R. A. , Mylne K. R.
Published: October 2016

Warnings for natural hazards improve societal resilience and are a good example of decision-making under uncertainty. A warning system is only useful if well defined and thus understood by stakeholders. However, most operational warning systems are heuristic: not formally or transparently defined. Bayesian decision theory provides a framework for issuing warnings under uncertainty but has not been fully exploited. Here, a decision theoretic framework is proposed for hazard warnings. The framework allows any number of warning levels and future states of nature, and a mathematical model for constructing the necessary loss functions for both generic and specific end-users is described. The approach is illustrated using one-day ahead warnings of daily severe precipitation over the UK, and compared to the current decision tool used by the UK Met Office. A probability model is proposed to predict precipitation, given ensemble forecast information, and loss functions are constructed for two generic stakeholders: an end-user and a forecaster. Results show that the Met Office tool issues fewer high-level warnings compared with our system for the generic end-user, suggesting the former may not be suitable for risk averse end-users. In addition, raw ensemble forecasts are shown to be unreliable and result in higher losses from warnings.
Flux avalanche in a superconducting film with non-uniform critical current density
Authors: Lu Yurong , Jing Ze , Yong Huadong , Zhou Youhe
Published: October 2016

The flux avalanche in type-II superconducting thin film is numerically simulated in this paper. We mainly consider the effect of non-uniform critical current density on the thermomagnetic stability. The nonlinear electromagnetic constitutive relation of the superconductor is adopted. Then, Maxwell's equations and heat diffusion equation are numerically solved by the fast Fourier transform technique. We find that the non-uniform critical current density can remarkably affect the behaviour of the flux avalanche. The external magnetic field ramp rate and the environmental temperature have been taken into account. The results are compared with a film with uniform critical current density. The flux avalanche first appears at the interface where the critical current density is discontinuous. Under the same environmental temperature or magnetic field, the flux avalanche occurs more easily for the film with the non-uniform critical current density. The avalanche structure is a finger-like pattern rather than a dendritic structure at low environmental temperatures.
Reciprocity, passivity and causality in Willis materials
Authors: Muhlestein Michael B. , Sieck Caleb F. , Alù Andrea , Haberman Michael R.
Published: October 2016

Materials that require coupling between the stress–strain and momentum–velocity constitutive relations were first proposed by Willis (Willis 1981
Wave Motion
3
, 1–11. (
doi:10.1016/0165-2125(81)90008-1
)) and are now known as elastic materials of the Willis type, or simply Willis materials. As coupling between these two constitutive equations is a generalization of standard elastodynamic theory, restrictions on the physically admissible material properties for Willis materials should be similarly generalized. This paper derives restrictions imposed on the material properties of Willis materials when they are assumed to be reciprocal, passive and causal. Considerations of causality and low-order dispersion suggest an alternative formulation of the standard Willis equations. The alternative formulation provides improved insight into the subwavelength physical behaviour leading to Willis material properties and is amenable to time-domain analyses. Finally, the results initially obtained for a generally elastic material are specialized to the acoustic limit.
The evolution of recombination rates in finite populations during ecological speciation
Authors: Reeve James , Ortiz-Barrientos Daniel , Engelstädter Jan
Published: October 2016

Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a divergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill–Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied individually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill–Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations.
Evidence for parasite-mediated selection during short-lasting toxic algal blooms
Authors: Blanquart François , Valero Myriam , Alves-de-Souza Catharina , Dia Aliou , Lepelletier Frédéric , Bigeard Estelle , Jeanthon Christian , Destombe Christophe , Guillou Laure
Published: October 2016

Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellateAlexandrium minutumand two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relativeA. minutumabundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in ‘Red Queen’ dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics.
A compound that directly and selectively stalls PCSK9 translation
Authors: Lintner Nathanael G. , McClure Kim F. , Petersen Donna , Londregan Allyn T. , Piotrowski David W. , Wei Liuqing , Xiao Jun , Bolt Michael , Loria Paula M. , Maguire Bruce , Geoghegan Kieran F. , Huang Austin , Rolph Tim , Liras Spiros , Doudna Jennifer A. , Dullea Robert G. , Cate Jamie H.D.
Published: October 2016

Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) plays a key role in regulating the levels of plasma low density lipoprotein cholesterol (LDL-C). Here we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation. The mechanism of action employed by PF-06446846 reveals a previously unexpected tunability of the human ribosome, which allows small molecules to specifically block translation of individual transcripts.

One Sentence Summary

A small-molecule PCSK9 inhibitor targets the human ribosome and selectively prevents PCSK9 synthesis.
Extremely fast and incredibly close: co-transcriptional splicing in budding yeast
Authors: Wallace Edward W.J. , Beggs Jean D.
Published: October 2016

RNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that quantify co-transcriptional splicing in budding yeast. Splicing in yeast is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3’ splice site. Ribosomal protein mRNAs are spliced particularly fast and co-transcriptionally. Intron-mediated regulation of some genes is also likely to be co-transcriptional. We suggest that intermediates of the splicing reaction, missing from current datasets, may hold key information about splicing kinetics.

Trends

Independent next-generation sequencing methods quantify co-transcriptional splicing in budding yeast

Ribosomal protein mRNAs are spliced particularly fast and co-transcriptionally

Intron-mediated regulation ofDBP2andRPS9Ais likely co-transcriptional

Splicing intermediates, missing from current datasets, may hold key information
Experimental and Computational Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles
Authors: Colangelo Elena , Chen Qiubo , Davidson Adam M. , Paramelle David , Sullivan Michael B. , Volk Martin , Lévy Raphaël
Published: October 2016

The self-assembly and self-organization of small molecules at the surface of nanoparticles constitute a potential route towards the preparation of advanced protein-like nanosystems. However, their structural characterization, critical to the design of bio-nanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles is developed using experimentally characterized CALNN-and CFGAILSS-capped gold nanoparticles as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated by both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on peptide capping density and on nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bio-nanomaterials.
Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells
Authors: Danko Charles G. , Choate Lauren A. , Marks Brooke A. , Rice Edward J. , Wang Zhong , Chu Tinyi , Martins Andre L. , Dukler Noah , Coonrod Scott A. , Wojno Elia D. Tait , Lis John T. , Kraus W. Lee , Siepel Adam
Published: October 2016

Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. This approach allowed us to measure transcription separately from post-transcriptional processes. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. We found evidence that transcription factor binding sites are a primary determinant of transcriptional differences between species, that stabilizing selection maintains gene expression levels despite frequent changes at distal enhancers, and that adaptive substitutions have driven lineage-specific transcription. Finally, we found strong correlations between evolutionary rates and long-range chromatin interactions. These observations clarify the role of primary transcription in regulatory evolution.
An Optimized Approach for Annotation of Large Eukaryotic Genomic Sequences using Genetic Algorithm
Authors: Chowdhury Biswanath , Garai Arnav , Garai Gautam
Published: October 2016

Detection of important functional and/or structural elements and identifying their positions in a large eukaryotic genome is an active research area. Gene is an important functional and structural unit of DNA. The computation of gene prediction is essential for detailed genome annotation. In this paper, we propose a new gene prediction technique based on Genetic Algorithm (GA) for determining the optimal positions of exons of a gene in a chromosome or genome. The correct identification of the coding and non-coding regions are difficult and computationally demanding. The proposed genetic-based method, named Gene Prediction with Genetic Algorithm (GPGA), reduces this problem by searching only one exon at a time instead of all exons along with its introns. The advantage of this representation is that it can break the entire gene-finding problem into a number of smaller subspaces and thereby reducing the computational complexity. We tested the performance of the GPGA with some benchmark datasets and compared the results with the well-known and relevant techniques. The comparison shows the better or comparable performance of the proposed method (GPGA). We also used GPGA for annotating the human chromosome 21 (HS21) using cross species comparison with the mouse orthologs.
Tempo and timing of ecological trait divergence in bird speciation
Authors: McEntee Jay P. , Tobias Joseph A. , Sheard Catherine , Burleigh J. Gordon
Published: October 2016

Summary paragraph

Organismal traits may evolve either gradually or in rapid pulses followed by periods of stasis, but the relative importance of these evolutionary models in generating biodiversity has proven difficult to resolve1,2. In addition, while it is often assumed that pulses of trait evolution are associated with speciation events, few studies have explicitly examined how the tempo of trait divergence varies with respect to different geographical phases of speciation. Thus, we still know little about the trajectories of trait divergence over timescales relevant to speciation, or the extent to which these trajectories are shaped by variation in geographical isolation and overlap (sympatry) among incipient species. Here, we combine divergence time estimates, trait measurements, and geographic range data for avian sister species pairs worldwide to examine the tempo and timing of trait divergence during allopatric speciation. We show that divergence in two important ecological traits—?body mass and beak morphology—is best explained by a model including pulses of divergence and periods of relative stasis. We also infer that trait divergence pulses often precede sympatry, and that pulses leading to greater trait disparity are associated with earlier transitions to sympatry. These findings suggest that early pulses of trait divergence promote subsequent transitions to sympatry, rather than such pulses occurring after sympatry has been established, for example via character displacement3. Incorporating pulsed divergence models into allopatric speciation theory helps to resolve some apparently contradictory observations, including widespread instances of both rapid sympatry and prolonged geographical exclusion4-6.
The Effect of Compositional Context on Synthetic Gene Networks
Authors: Yeung Enoch , Dy Aaron J. , Martin Kyle B. , Ng Andrew H. , Del Vecchio Domitilla , Beck James L. , Collins James J. , Murray Richard M.
Published: October 2016

It is well known that synthetic gene expression is highly sensitive to how comprising genetic elements (promoter structure, spacing regions between promoter and coding sequences, ribosome binding sites, etc.) are spatially configured. An important topic that has received far less attention is how the physical layout of entire genes within a synthetic gene network affects their individual expression levels. In this paper we show, both quantitatively and qualitatively, that compositional context can significantly alter expression levels in synthetic gene networks. We also show that these compositional context effects are pervasive both at the transcriptional and translational level. Further, we demonstrate that key characteristics of gene induction, such as ultra-sensitivity and dynamic range, are heavily dependent on compositional context. We postulate that supercoiling can be used to explain these interference effects and validate this hypothesis through modeling and a series ofin vitrosupercoiling relaxation experiments. On the whole, these results suggest that compositional context introduces feedback in synthetic gene networks. As an illustrative example, we show that a design strategy incorporating compositional context effects can improve threshold detection and memory properties of the toggle switch.
Large-scale meta-analysis suggests low regional modularity in lateral frontal cortex
Authors: de la Vega Alejandro , Yarkoni Tal , Wager Tor D. , Banich Marie T.
Published: October 2016

Extensive fMRI study of human lateral frontal cortex (LFC) has yet to yield a consensus mapping between discrete anatomy and psychological states, partly due to the difficulty of inferring mental states in individual studies. Here, we used a data-driven approach to generate a comprehensive functional-anatomical mapping of LFC from 11,406 neuroimaging studies. We identified putatively separable LFC regions on the basis of whole-brain co-activation, revealing 14 clusters organized into three whole-brain networks. Next, we used multivariate classification to identify the psychological states that best predicted activity in each sub-region, resulting in preferential psychological profiles. We observed large functional differences between networks, suggesting brain networks support distinct modes of processing. Within each network, however, we observed low functional specificity, suggesting discrete psychological states are not modularly organized. Our results are consistent with the view that individual LFC regions work as part of highly parallel, distributed networks to give rise to flexible, adaptive behavior.
Casein Kinase II is Required for Proper Cell Division and Acts as a Negative Regulator of Centrosome Duplication inC. elegansEmbryos
Authors: Medley Jeffrey C. , Kabara Megan M. , Stubenvoll Michael D. , DeMeyer Lauren E. , Song Mi Hye
Published: October 2016

Summary statement

The conserved protein kinase CK2 negatively regulates centrosome assembly and is required for proper cell cycle progression and cytokinesis in earlyC. elegansembryos.

Centrosomes are the primary microtubule-organizing centers that orchestrate microtubule dynamics during the cell cycle. The correct number of centrosomes is pivotal for establishing bipolar mitotic spindles that ensure accurate segregation of chromosomes. Thus, centrioles must duplicate once per cell cycle, one daughter per mother centriole, the process of which requires highly coordinated actions among core factors and modulators. Protein phosphorylation is shown to regulate the stability, localization and activity of centrosome proteins. Here, we report the function of Casein Kinase II (CK2) in earlyC. elegansembryos. The catalytic subunit (KIN-3/CK2α) of CK2 localizes to nuclei, centrosomes and midbodies. Inactivating CK2 leads to cell division defects, including chromosome missegregation, cytokinesis failure and aberrant centrosome behavior. Furthermore, depletion or inhibiting kinase activity of CK2 results in elevated ZYG-1 levels at centrosomes, restoring centrosome duplication and embryonic viability tozyg-1mutants. Our data suggest that CK2 functions in cell division and negatively regulates centrosome duplication in a kinase-dependent manner.
Resolution ofab initioshapes determined from small-angle scattering
Authors: Tuukkanen Anne T. , Kleywegt Gerard J. , Svergun Dmitri I.
Published: October 2016

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment forab initioshape reconstruction from scattering data. The inherent variability of theab initioshapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions ofab initioSAS models.
Creating sustainable cities through knowledge exchange
Authors: Hope Alex
Published: October 2016

Purpose

The purpose of this paper is to examine the use of knowledge transfer partnership (KTP)as a means for universities to generate and exchange knowledge to foster sustainable cities and societies.

Design/methodology/approach

This paper reports on a series of separate yet interrelated KTPs between a university and the local authority in the North East of England, designed to enhance the environmental, social and economic performance of a large-scale urban housing procurement project.

Findings

Results from the partnerships indicate that KTPs may play a crucial role in developing capacity within local authorities tasked with creating sustainable cities and societies, whilst at the same time, enhancing skills and knowledge within the communities whom they represent and their industry partners.

Originality/value

The paper contributes an understanding as to how universities can act as a conduit for the generation and exchange of knowledge for sustainability. It presents a case study which examines how a series of KTPs can provide a useful mechanism for enhancing environmental, social and economic sustainability.
Finding the movement: the geographies of social movement scenes
Authors: Creasap Kimberly
Published: October 2016

Purpose

A social movement scene is “a network of people who share a set of subcultural or countercultural beliefs, values, norms, and convictions as well as a network of physical spaces where members of that group are known to congregate” (Leach and Haunss 2009, p. 260, emphasis in the original). The purpose of this paper is to further develop theories of social movement scenes by examining the spatial dimensions of proximity, centrality, visibility, and accessibility, arguing that different scene configurations are shaped by gentrification processes.

Design/methodology/approach

This is an ethnographic study based on research conducted in Sweden over a five year period (2007-2012), including several summer research trips and a sustained fieldwork period of 14 months. Using snowball sampling, the author conducted semi-structured interviews with 38 activists involved in autonomous movement scenes. The author interviewed both men (n=26) and women (n=12) who ranged in age from 18 to 37, with most interviewees in their late 20s and early 30s.

Findings

Findings suggest that neighborhoods in the early stages of gentrification are most conducive to strong scenes. The author’s findings suggest that, while some of these conditions are locally specific, there were common structural conditions in each city, such as changes in the commercial landscape and housing tenure.

Originality/value

This paper contributes to the specificity of the concept of a social movement scene by presenting three spatial dimensions of scenes: centrality (relative to the Central Business District), concentration (clustering of scene places in one area of the city), and visibility (a visible presence communicated by signs and symbols). A second contribution of this paper is to offer a set of hypotheses about the urban conditions under which social movement scenes thrive (or fizzle).
How can organisations help employees thrive? The development of guidelines for promoting positive mental health at work
Authors: Davenport Lauren J. , Allisey Amanda F. , Page Kathryn M. , LaMontagne Anthony D. , Reavley Nicola J.
Published: October 2016

Purpose

Benefits of positive mental health have been demonstrated across work and non-work domains. Individuals reporting positive mental health experience better work performance, better social relationships and better physical health. Additionally, positive work environments can contribute to employee mental health. The purpose of this paper is to develop “expert” consensus regarding practical, actionable strategies that organisations can implement to promote positive mental health in the workplace.

Design/methodology/approach

A Delphi consensus method was used to establish expert consensus on strategies to promote positive workplace mental health. A 278-item questionnaire was developed and strategies were rated over three survey rounds by two panels comprising 36 workplace mental health practitioners and 36 employer representatives and employees (27 and 9, respectively), employees with experience of promoting positive mental health and well-being in the workplace (total – 72 panellists).

Findings

In total, 220/278 strategies were rated as essential or important by at least 80 per cent of both panels. Endorsed strategies covered the topics of: mental health and well-being strategy, work environment that promotes positive mental health, positive leadership styles, effective communication, designing jobs for positive mental health, recruitment and selection, supporting and developing employees, work-life balance, and positive mental health and well-being initiatives.

Originality/value

The guidelines arising from this study represent expert consensus on what is currently appropriate for promoting positive mental health at work from the perspectives of workplace mental health practitioners, employers and employees, and constitute a resource for translating the growing body of knowledge in this area into policy and practice.
Emotional intelligence and job performance: the role of psychological well-being
Authors: Devonish Dwayne
Published: October 2016

Purpose

The purpose of this paper is to test the mediating roles of two dimensions of psychological well-being (job satisfaction and work-related depression) in the relationship between emotional intelligence (EI) and task performance, individual-targeted citizenship behaviours (OCB-I) and organisation-targeted citizenship behaviours (OCB-O).

Design/methodology/approach

This survey study of 262 employees in a small island territory in the Caribbean captured data on EI, psychological well-being and various dimensions of job performance. Multiple mediation hypotheses were tested using the 95 per cent bootstrapping confidence interval (CI) estimation approach.

Findings

The results revealed that job satisfaction and work-related depression mediated the relationship between EI and task performance; and the relationship between EI and OCB-O, but only work-related depression mediated the relationship between EI and OCB-I.

Research limitations/implications

The study utilised a cross-sectional study design and self-reported measures but still presented significant implications for existing and future theoretical models of EI and job performance.

Practical implications

Organisations should seek to develop high levels of EI in their employees as a means of improving their overall psychological health and well-being and performance behaviours at work.

Originality/value

The study examines multiple mediation of various psychological well-being dimensions in the EI-job performance relationship using the 95 per cent bootstrapping CI approach.
US long-haul truck driver health demands integrated approach
Authors: Hege Adam , Perko Michael , Apostolopoulos Yorghos , Sönmez Sevil , Strack Robert
Published: October 2016

Purpose

The purpose of this paper is to provide a review of both occupational safety and health (OSH) and worksite health promotion (WHP) efforts targeted at long-haul truck drivers (LHTDs) and to identify strengths and weaknesses to inform future interventions and/or policy changes.

Design/methodology/approach

Review of the literature was done to identify theoretical and methodological approaches frequently used for protecting and promoting the health and well-being of LHTDs.

Findings

Health and safety issues impacting LHTDs are complex and naturally interrelated. Historically, the majority of approaches to the health and safety of LHTDs have emphasized the safety side and there has been a lack of comprehensive and integrated WHP/OSH attempts.

Originality/value

The literature pertaining to LHTD health has expanded in recent years, but intervention and policy efforts have had limited success. Several scholars have discussed the need for integrating WHP/OSH efforts for LHTD health, but have not actually provided a description or a framework of what it entails in which the authors provide a conclusion to the review of the literature. The authors provide a critical discussion regarding a collaborative approach focused on National Institute of Occupational Safety and Health’s Total Worker Health model. The integration further promotes an advancement of theoretical and methodological strategies.
Ageing, masculinity and Parkinson's disease: embodied perspectives
Authors: Gibson Grant , Kierans Ciara
Published: October 2016

Parkinson's disease (PD) presents as an illness which predominantly affects older men. However older men's lived experiences ofPD, including how they are influenced by age and gender relations has seen little empirical study. Drawing on Watson's male body schema, this paper explores how men engage with masculinities and ageing in order to make sense and meaning fromPD. Data is presented from 30 narrative and semi structured interviews with 15 men of various ages who were living withPD. Findings suggest thatPDthreatens a visceral embodiment located in the body's basic movements and intimate functions; a pragmatic embodiment expressed through men's everyday occupations and an experiential embodiment concerned with emotions and sensations felt within and through the body. In addition, each dimension of men's embodiment also intersected with the ageing process, a process also shaped in turn by broader social and cultural concerns regarding the positions and possibilities of men's lives as they move through the life course. This paper concludes by discussing the implications of gender and ageing in understanding men's experiences ofPD
‘Let's Talk Autism' –a school‐based project for students to explore and share their experiences of being autistic
Authors: Stevenson Kathryn , Cornell Katie , Hinchcliffe Vivian
Published: October 2016

Understanding what autism means on a personal level can be an important process for young people on the autistic spectrum, and being able to reflect on this and discuss with autistic peers can be particularly helpful. However, opportunities may be restricted by reluctance to talk about diagnosis and because of difficulties in communication inherent in autism. This article describes a therapeutic media project within an ASD school that attempted to support young people to reflect together about what autism meant for them and create resources to share with others. The process is described and main themes of discussions analysed using thematic analysis. Main themes emerged of making sense of diagnosis, experiences of difference and transition to adulthood. Various strategies to manage diagnosis and negotiate identity also emerged. Issues around informed consent and confidentiality and the therapeutic value of such groups are discussed.