bluuebunny/crossref_metadata_2025 huggingface dataset:
Aerodynamics of manoeuvring flight in brown long-eared bats (Plecotus auritus)
Authors: Henningsson Per , Jakobsen Lasse , Hedenström Anders
Published: November 2018

In this study, we explicitly examine the aerodynamics of manoeuvring flight in animals. We studied brown long-eared bats flying in a wind tunnel while performing basic sideways manoeuvres. We used particle image velocimetry in combination with high-speed filming to link aerodynamics and kinematics to understand the mechanistic basis of manoeuvres. We predicted that the bats would primarily use the downstroke to generate the asymmetries for the manoeuvre since it has been shown previously that the majority of forces are generated during this phase of the wingbeat. We found instead that the bats more often used the upstroke than they used the downstroke for this. We also found that the bats used both drag/thrust-based and lift-based asymmetries to perform the manoeuvre and that they even frequently switch between these within the course of a manoeuvre. We conclude that the bats used three main modes: lift asymmetries during downstroke, thrust/drag asymmetries during downstroke and thrust/drag asymmetries during upstroke. For future studies, we hypothesize that lift asymmetries are used for fast turns and thrust/drag for slow turns and that the choice between up- and downstroke depends on the timing of when the bat needs to generate asymmetries.
Stability trophic cascades in food chains
Authors: Shanafelt David W. , Loreau Michel
Published: November 2018

While previous studies have evaluated the change in stability for the addition or removal of individual species from trophic food chains and food webs, we know of no study that presents a general theory for how stability changes with the addition or removal of trophic levels. In this study, we present a simple model of a linear food chain and systematically evaluate how stability—measured as invariability—changes with the addition or removal of trophic levels. We identify the presence of trophic cascades in the stability of species. Owing to top-down control by predation and bottom-up regulation by prey, we find that stability of a species is highest when it is at the top of the food chain and lowest when it is just under the top of the food chain. Thus, stability shows patterns identical to those of mean biomass with the addition or removal of trophic levels in food chains. Our results provide a baseline towards a general theory of the effect of adding or removing trophic levels on stability, which can be used to inform empirical studies.
Promoting information technology for the sustainable development of the phosphate fertilizer industry: a case study of Guizhou Province, China
Authors: Ma Shujie , Luo Zhibo , Hu Shanying , Chen Dingjiang
Published: November 2018

The information technology revolution has brought unprecedented opportunities to the sustainable development of the traditional phosphate fertilizer industry. In this paper, the changes in characteristic indexes during this technological progress and business innovation are investigated at the industrial level and for different stakeholders using scenario simulation analysis based on system dynamics. The results show that information technology will have a significant impact on the traditional fertilizer industry. The popularity of information technology represents a win–win situation for industries, farmers, enterprises and governments. The sustainable development of the phosphate fertilizer industry promoted by information technology means that agrochemical services are a new growth point for the industry, and farmers will be the largest beneficiaries. Enterprises will adjust their product structures to achieve the relevant phosphate reduction goals before 2020. At the government level, the indirect benefits from energy savings, water conservation and reductions in non-point source pollution control treatment also increase significantly. In the new production and sales model, the development of the phosphate fertilizer industry is completely decoupled from resource consumption. In the future, this technological progress will eventually form a sustainable network of industrial innovation patterns. Our finding suggests that the application of information technology in the phosphate fertilizer industry can stimulate the vitality of each entity in the industry and achieve a win–win situation.
Supersaturation with water explains the unusual adhesion of aggregate glue in the webs of the moth-specialist spider,Cyrtarachne akirai
Authors: Diaz Candido , Tanikawa Akio , Miyashita Tadashi , Amarpuri Gaurav , Jain Dharamdeep , Dhinojwala Ali , Blackledge Todd A.
Published: November 2018

Orb webs produced by araneoid spiders depend upon aggregate glue-coated capture threads to retain their prey. Moths are challenging prey for most spiders because their scales detach and contaminate the glue droplets, significantly decreasing adhesion.Cyrtarachneare moth-specialist orb-weaving spiders whose capture threads adhere well to moths. We compare the adhesive properties and chemistry ofCyrtarachneaggregate glue to other orb-weaving spiders to test hypotheses about their structure, chemistry and performance that could explain the strength ofCyrtarachneglue. We show that the unusually large glue droplets onCyrtarachnecapture threads make them approximately 8 times more adhesive on glass substrate than capture threads from typical orb-weaving species, butCyrtarachneadhesion is similar to that of other species after normalization by glue volume. Glue viscosity reversibly changes over 1000-fold in response to atmospheric humidity, and the adhesive strength of many species of orb spiders is maximized at a viscosity of approximately 105–106cst where the contributions of spreading and bulk cohesion are optimized. By contrast, viscosity ofCyrtarachneaggregate glue droplets is approximately 1000 times lower at maximum adhesive humidity, likely facilitating rapid spreading across moth scales. Water uptake by glue droplets is controlled, in part, by hygroscopic low molecular weight compounds. NMR showed evidence thatCyrtarachneglue contains a variety of unknown low molecular weight compounds. These compounds may help explain howCyrtarachneproduces such exceptionally large and low viscosity glue droplets, and also why these glue droplets rapidly lose water volume after brief ageing or exposure to even slightly dry (e.g. < 80% RH) conditions, permanently reducing their adhesion. We hypothesize that the combination of large glue droplet size and low viscosity helpsCyrtarachneglue to penetrate the gaps between moth scales.
An evaluation of the failure modes transition and the Christensen ductile/brittle failure theory using molecular dynamics
Authors: Christensen Richard , Li Zhi , Gao Huajian
Published: November 2018

The Christensen ductile/brittle failure theory can be interpreted in terms of the associated failure modes, those of shear bands and voids nucleation. Their conjunction is then termed as the failure modes transition and it is studied here using molecular dynamics. The test material is taken as a particular metallic glass, CuZr. First the theoretical failure criteria are evaluated and then the theoretical failure modes transition is evaluated. Both are found to perform extremely well. The overall failure theory contains three modes of failure, the two already mentioned plus a fracture criterion. A general conclusion from the work is that the voids nucleation criterion is of unusually broad relevance. Voids nucleation leads to voids growth and then further deteriorating mechanisms and ultimately failure. But the voids nucleation is the precipitating event of all that subsequently occurs in this process. Access to these capabilities is gained through the failure theory for all homogeneous, full density, isotropic materials. Only two standard testing measurements are needed to calibrate the entire failure theory, including the transitions.
Optoacoustic image reconstruction: the full inverse problem with variable bases
Authors: Schoeder S. , Olefir I. , Kronbichler M. , Ntziachristos V. , Wall W. A.
Published: November 2018

Optoacoustic imaging was for a long time concerned with the reconstruction of energy density or optical properties. In this work, we present the full inverse problem with respect to optical absorption and diffusion as well as speed of sound and mass density. The inverse problem is solved by an iterative gradient-based optimization procedure. Since the ill-conditioning increases with the number of sought parameters, we propose two approaches to improve the conditioning. The first approach is based on the reduction of the size of the basis for the parameter spaces, that evolves according to the particular characteristics of the solution, while maintaining the flexibility of element-wise parameter selection. The second approach is a material identification technique that incorporates prior knowledge of expected material types and uses the acoustical gradients to identify materials uniquely. We present numerical studies to illustrate the properties and functional principle of the proposed methods. Significant convergence speed-ups are gained by the two approaches countering ill-conditioning. Additionally, we show results for the reconstruction of a mouse brain from
in vivo
measurements.
Locomotor constraints favour the evolution of the human pygmy phenotype in tropical rainforests
Authors: Venkataraman Vivek V. , Yegian Andrew K. , Wallace Ian J. , Holowka Nicholas B. , Tacey Ivan , Gurven Michael , Kraft Thomas S.
Published: November 2018

The convergent evolution of the human pygmy phenotype in tropical rainforests is widely assumed to reflect adaptation in response to the distinct ecological challenges of this habitat (e.g. high levels of heat and humidity, high pathogen load, low food availability, and dense forest structure), yet few precise adaptive benefits of this phenotype have been proposed. Here, we describe and test a biomechanical model of how the rainforest environment can alter gait kinematics such that short stature is advantageous in dense habitats. We hypothesized that environmental constraints on step length in rainforests alter walking mechanics such that taller individuals are expected to walk more slowly due to their inability to achieve preferred step lengths in the rainforest. We tested predictions from this model with experimental field data from two short-statured populations that regularly forage in the rainforest: the Batek of Peninsular Malaysia and the Tsimane of the Bolivian Amazon. In accordance with model expectations, we found stature-dependent constraints on step length in the rainforest and concomitant reductions in walking speed that are expected to compromise foraging efficiency. These results provide the first evidence that the human pygmy phenotype is beneficial in terms of locomotor performance and highlight the value of applying laboratory-derived biomechanical models to field settings for testing evolutionary hypotheses.
Marginal sinks or potential refuges? Costs and benefits for coral-obligate reef fishes at deep range margins
Authors: MacDonald Chancey , Jones Geoffrey P. , Bridge Tom
Published: November 2018

Escalating climate-related disturbances and asymmetric habitat losses will increasingly result in species living in more marginal habitats. Marginal habitats may represent important refuges if individuals can acquire adequate resources to survive and reproduce. However, resources at range margins are often distributed more sparsely; therefore, increased effort to acquire resources can result in suboptimal performance and lead to marginal populations becoming non-self-sustaining sink-populations. Shifting resource availability is likely to be particularly problematic for dietary specialists. Here, we use extensivein situbehavioural observations and physiological condition measurements to examine the costs and benefits of resource-acquisition along a depth gradient in two obligate corallivore reef fishes with contrasting levels of dietary specialization. As expected, the space used to secure coral resources increased towards the lower depth margin. However, increased territory sizes resulted in equal or greater availability of resources within deeper territories. In addition, we observed decreased competition and no differences in foraging distance, pairing behaviour, body condition or fecundity at greater depths. Contrary to expectation, our results demonstrate that coral-obligate fishes can select high-quality coral patches on the deeper-reef to access equal or greater resources than their shallow-water counterparts, with no extra costs. This suggests depth offers a viable potential refuge for some at-risk coral-specialist fishes.
Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)
Authors: Moodley Yoshan , Russo Isa-Rita M. , Robovský Jan , Dalton Desiré L. , Kotzé Antoinette , Smith Steve , Stejskal Jan , Ryder Oliver A. , Hermes Robert , Walzer Chris , Bruford Michael W.
Published: November 2018

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results.
Sexual dimorphism in a top predator (
Notophthalmus viridescens
) drives aquatic prey community assembly
Authors: Start Denon , De Lisle Stephen
Published: November 2018

Intraspecific variation can have important consequences for the structure and function of ecological communities, and serves to link community ecology to evolutionary processes. Differences between the sexes are an overwhelmingly common form of intraspecific variation, but its community-level consequences have never been experimentally investigated. Here, we manipulate the sex ratio of a sexually dimorphic predacious newt in aquatic mesocosms, then track their impact on prey communities. Female and male newts preferentially forage in the benthic and pelagic zones, respectively, causing corresponding reductions in prey abundances in those habitats. Sex ratio differences also explained a large proportion (33%) of differences in the composition of entire pond communities. Ultimately, we demonstrate the impact of known patterns of sexual dimorphism in a predator on its prey, uncovering overlooked links between evolutionary adaptation and the structure of contemporary communities. Given the extreme prevalence of sexual dimorphism, we argue that the independent evolution of the sexes will often have important consequences for ecological communities.
Elements of time and place: manganese and barium in shark vertebrae reflect age and upwelling histories
Authors: Mohan John A. , Miller Nathan R. , Herzka Sharon Z. , Sosa-Nishizaki Oscar , Kohin Suzanne , Dewar Heidi , Kinney Michael , Snodgrass Owyn , Wells R. J. David
Published: November 2018

As upper-level predators, sharks are important for maintaining marine food web structure, but populations are threatened by fishery exploitation. Sustainable management of shark populations requires improved understanding of migration patterns and population demographics, which has traditionally been sought through physical and/or electronic tagging studies. The application of natural tags such as elemental variations in mineralized band pairs of elasmobranch vertebrae cartilage could also reveal endogenous and exogenous processes experienced by sharks throughout their life histories. Here, elemental profiles were characterized in vertebrae encompassing complete life histories (birth-to-death) of shortfin mako (
Isurus oxyrinchus
), common thresher (
Alopias vulpinus
) and blue shark (
Prionace glauca
) of known tag and recapture locations in the eastern North Pacific Ocean. All sharks were injected with oxytetracycline at initial capture, released and subsequently recaptured, with individual liberty times ranging from 215 days to 6 years. Vertebral band pairs forming over the liberty intervals were verified by counting the number of band pairs deposited since the oxytetracycline band. Regular oscillations in vertebrae manganese (Mn) content corresponded well with the number of validated band pairs, suggesting that Mn variation could be used to age sharks. Increases in vertebrae barium concentration were correlated with times when individuals occupied areas with high coastal upwelling indices, the timing and spatial intensity of which varied from year to year. Interspecific relationships were probably influenced by behavioural differences in horizontal and vertical habitat use, feeding habits and thermoregulatory physiology. These results indicate that vertebral sclerochronology has the potential to advance our knowledge of elasmobranch life history including age and growth estimation and environmental reconstruction.
Dental ontogeny in extinct synapsids reveals a complex evolutionary history of the mammalian tooth attachment system
Authors: LeBlanc Aaron R. H. , Brink Kirstin S. , Whitney Megan R. , Abdala Fernando , Reisz Robert R.
Published: November 2018

The mammalian dentition is uniquely characterized by a combination of precise occlusion, permanent adult teeth and a unique tooth attachment system. Unlike the ankylosed teeth in most reptiles, mammal teeth are supported by a ligamentous tissue that suspends each tooth in its socket, providing flexible and compliant tooth attachment that prolongs the life of each tooth and maintains occlusal relationships. Here we investigate dental ontogeny through histological examination of a wide range of extinct synapsid lineages to assess whether the ligamentous tooth attachment system is unique to mammals and to determine how it evolved. This study shows for the first time that the ligamentous tooth attachment system is not unique to crown mammals within Synapsida, having arisen in several non-mammalian therapsid clades as a result of neoteny and progenesis in dental ontogeny. Mammalian tooth attachment is here re-interpreted as a paedomorphic condition relative to the ancestral synapsid form of tooth attachment.
Tropical tree diversity mediates foraging and predatory effects of insectivorous birds
Authors: Nell Colleen S. , Abdala-Roberts Luis , Parra-Tabla Victor , Mooney Kailen A.
Published: November 2018

Biodiversity affects the structure of ecological communities, but little is known about the interactive effects of diversity across multiple trophic levels. We used a large-scale forest diversity experiment to investigate the effects of tropical tree species richness on insectivorous birds, and the subsequent indirect effect on predation rates by birds. Diverse plots (four tree species) had higher bird abundance (61%), phylogenetic diversity (61%), and functional diversity (55%) than predicted based on single-species monocultures, which corresponded to higher attack rates on artificial caterpillars (65%). Tree diversity effects on attack rate were driven by complementarity among tree species, with increases in attack rate observed on all tree species in polycultures. Attack rates on artificial caterpillars were higher in plots with higher bird abundance and diversity, but the indirect effect of tree species richness was mediated by bird diversity, providing evidence that diversity can interact across trophic levels with consequences tied to ecosystem services and function.
Non-stationary climate–salmon relationships in the Gulf of Alaska
Authors: Litzow Michael A. , Ciannelli Lorenzo , Puerta Patricia , Wettstein Justin J. , Rykaczewski Ryan R. , Opiekun Michael
Published: November 2018

Studies of climate effects on ecology often account for non-stationarity in individual physical and biological variables, but rarely allow for non-stationary relationships among variables. Here, we show that non-stationary relationships among physical and biological variables are central to understanding climate effects on salmon (
Onchorynchus
spp.) in the Gulf of Alaska during 1965–2012. The relative importance of two leading patterns in North Pacific climate, the Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO), changed around 1988/1989 as reflected by changing correlations with leading axes of sea surface temperature variability. Simultaneously, relationships between the PDO and Gulf of Alaska environmental variables weakened, and long-standing temperature–salmon and PDO–salmon covariance declined to zero. We propose a mechanistic explanation for changing climate–salmon relationships in terms of non-stationary atmosphere–ocean interactions coinciding with changing PDO–NPGO relative importance. We also show that regression models assuming stationary climate–salmon relationships are inappropriate over the multidecadal time scale we consider. Relaxing assumptions of stationary relationships markedly improved modelling of climate effects on salmon catches and productivity. Attempts to understand the implications of changing climate patterns in other ecosystems might also be aided by the application of models that allow associations among environmental and biological variables to change over time.
Isogamy in large and complex volvocine algae is consistent with the gamete competition theory of the evolution of anisogamy
Authors: da Silva Jack , Drysdale Victoria L.
Published: November 2018

Although the gamete competition theory remains the dominant explanation for the evolution of anisogamy, well-known exceptions to its predictions have raised doubts about the completeness of the theory. One of these exceptions is isogamy in large or complex species of green algae. Here, we show that this exception may be explained in a manner consistent with a game-theoretic extension of the original theory: a constraint on the minimum size of a gamete may prevent the evolution of continuously stable anisogamy. We show that in the volvocine algae, both gametes of isogamous species retain an intact chloroplast, whereas the chloroplast of the microgamete in anisogamous species is invariably degenerate. The chloroplast, which functions in photosynthesis and starch storage, may be necessary to provision a gamete for an extended period when gamete encounter rates are low. The single chloroplast accounts for most of the volume of a typical gamete, and thus may constrain the minimum size of a gamete, preventing the evolution of anisogamy. A prediction from this hypothesis, that isogametes should be larger than the microgametes of similar-size species, is confirmed for the volvocine algae. Our results support the gamete competition theory.
Intraspecific brain size variation between coexisting sunfish ecotypes
Authors: Axelrod Caleb J. , Laberge Frédéric , Robinson Beren W.
Published: November 2018

Variation in spatial complexity and foraging requirements between habitats can impose different cognitive demands on animals that may influence brain size. However, the relationship between ecologically related cognitive performance and brain size is not well established. We test whether variation in relative brain size and brain region size is associated with habitat use within a population of pumpkinseed sunfish composed of different ecotypes that inhabit either the structurally complex shoreline littoral habitat or simpler open-water pelagic habitat. Sunfish using the littoral habitat have on average 8.3% larger brains than those using the pelagic habitat. We found little difference in the proportional sizes of five brain regions between ecotypes. The results suggest that cognitive demands on sunfish may be reduced in the pelagic habitat given no habitat-specific differences in body condition. They also suggest that either a short divergence time or physiological processes may constrain changes to concerted, global modifications of brain size between sunfish ecotypes.
Acute drivers influence recent inshore Great Barrier Reef dynamics
Authors: Lam Vivian Y. Y. , Chaloupka Milani , Thompson Angus , Doropoulos Christopher , Mumby Peter J.
Published: November 2018

Understanding the dynamics of habitat-forming organisms is fundamental to managing natural ecosystems. Most studies of coral reef dynamics have focused on clear-water systems though corals inhabit many turbid regions. Here, we illustrate the key drivers of an inshore coral reef ecosystem using 10 years of biological, environmental, and disturbance data. Tropical cyclones, crown-of-thorns starfish, and coral bleaching are recognized as the major drivers of coral loss at mid- and offshore reefs along the Great Barrier Reef (GBR). In comparison, little is known about what drives temporal trends at inshore reefs closer to major anthropogenic stress. We assessed coral cover dynamics using state-space models within six major inshore GBR catchments. An overall decline was detected in nearly half (46%) of the 15 reefs at two depths (30 sites), while the rest exhibited fluctuating (23%), static (17%), or positive (13%) trends. Inshore reefs responded similarly to their offshore counterparts, where contemporary trends were predominantly influenced by acute disturbance events. Storms emerged as the major driver affecting the inshore GBR, with the effects of other drivers such as disease, juvenile coral density, and macroalgal and turf per cent cover varying from one catchment to another. Flooding was also associated with negative trends in live coral cover in two southern catchments, but the mechanism remains unclear as it is not reflected in available metrics of water quality and may act through indirect pathways.
A host immune hormone modifies parasite species interactions and epidemics: insights from a field manipulation
Authors: Halliday Fletcher W. , Umbanhowar James , Mitchell Charles E.
Published: November 2018

Parasite epidemics can depend on priority effects, and parasite priority effects can result from the host immune response to prior infection. Yet we lack experimental evidence that such immune-mediated priority effects influence epidemics. To address this research gap, we manipulated key host immune hormones, then measured the consequences for within-host parasite interactions, and ultimately parasite epidemics in the field. Specifically, we applied plant immune-signalling hormones to sentinel plants, embedded into a wild host population, and tracked foliar infections caused by two common fungal parasites. Within-host individuals, priority effects were altered by the immune-signalling hormone, salicylic acid (SA). Scaling up from within-host interactions, hosts treated with SA experienced a lower prevalence of a less aggressive parasite, increased burden of infection by a more aggressive parasite, and experienced fewer co-infections. Together, these results indicate that by altering within-host priority effects, host immune hormones can drive parasite epidemics. This study therefore experimentally links host immune hormones to within-host priority effects and parasite epidemics, advancing a more mechanistic understanding of how interactions among parasites alter their epidemics.
Prey abundance and urbanization influence the establishment of avian predators in a metropolitan landscape
Authors: McCabe Jennifer D. , Yin He , Cruz Jennyffer , Radeloff Volker , Pidgeon Anna , Bonter David N. , Zuckerberg Benjamin
Published: November 2018

Urbanization causes the simplification of natural habitats, resulting in animal communities dominated by exotic species with few top predators. In recent years, however, many predators such as hawks, and in the US coyotes and cougars, have become increasingly common in urban environments. Hawks in the
Accipiter
genus, especially, are recovering from widespread population declines and are increasingly common in urbanizing landscapes. Our goal was to identify factors that determine the occupancy, colonization and persistence of
Accipiter
hawks in a major metropolitan area. Through a novel combination of citizen science and advanced remote sensing, we quantified how urban features facilitate the dynamics and long-term establishment of
Accipiter
hawks. Based on data from Project FeederWatch, we quantified 21 years (1996–2016) of changes in the spatio-temporal dynamics of
Accipiter
hawks in Chicago, IL, USA. Using a multi-season occupancy model, we estimated Cooper's (
Accipiter cooperii
) and sharp-shinned (
A. striatus
) hawk occupancy dynamics as a function of tree canopy cover, impervious surface cover and prey availability. In the late 1990s, hawks occupied 26% of sites around Chicago, but after two decades, their occupancy fluctuated close to 67% of sites and they colonized increasingly urbanized areas. Once established, hawks persisted in areas with high levels of impervious surfaces as long as those areas supported high abundances of prey birds. Urban areas represent increasingly habitable environments for recovering predators, and understanding the precise urban features that drive colonization and persistence is important for wildlife conservation in an urbanizing world.
Mechanisms driving endosperm-based hybrid incompatibilities: insights from hybrid monkeyflowers
Authors: Kinser Taliesin J. , Smith Ronald D. , Lawrence Amelia H. , Cooley Arielle M. , Vallejo-Marin Mario , Conradi-Smith G.D. , Puzey Joshua R.
Published: November 2018

Angiosperm endosperm requires genomic and epigenomic interactions between maternal and paternal genomes for proper seed development. Genomic imprinting, an epigenetic phenomenon where the expression of certain genes is predominantly contributed by one parent, is an essential part of this process and unique to endosperm. Perturbation of imprinting can be fatal to developing seeds, and can be caused by interspecific or interploidy hybridization. However, underlying mechanisms driving these endosperm-based hybridization barriers are not well understood or described. Here we investigate the consequences of genomic imprinting in a naturally occurring interploidy and interspecies hybrid between the diploid,Mimulus guttatus,and the allotetraploid (with two subgenomes),M. luteus(Phrymaceae). We find that the two parental species differ in patterns of DNA methylation, gene expression, and imprinting. Hybrid crosses in both directions, which suffer from endosperm abnormalities and decreased germination rates, display altered methylation patterns compared to parent endosperm. Furthermore, imprinting and expression patterns appear perturbed in hybrid endosperm, where we observe global expression dominance of each of the twoM. luteussubgenomes, which share similar expression patterns, over theM. guttatusgenome, regardless of crossing direction. We suggest that epigenetic repatterning within the hybrid may drive global shifts in expression patterns and be the result of diverged epigenetic/regulatory landscapes between parental genomes. This may either establish or exacerbate dosage-based epistatic incompatibilities between the specific imprinting patterns that have diverged between parental species, thus driving potentially rapid endosperm-based hybridization barriers.
BIN1 recovers tauopathy-induced long-term memory deficits in mice and interacts with Tau through Thr348 phosphorylation
Authors: Sartori Maxime , Mendes Tiago , Desai Shruti , Lasorsa Alessia , Herledan Adrien , Malmanche Nicolas , Mäkinen Petra , Marttinen Mikael , Malki Idir , Chapuis Julien , Flaig Amandine , Vreulx Anaïs-Camille , Amouyel Philippe , Leroux Florence , Déprez Benoit , Cantrelle François-Xavier , Maréchal Damien , Pradier Laurent , Hiltunen Mikko , Landrieu Isabelle , Kilinc Devrim , Herault Yann , Laporte Jocelyn , Lambert Jean-Charles
Published: November 2018

The bridging integrator 1 gene (BIN1) is a major genetic risk factor for Alzheimer’s disease (AD). In this report, we investigated how BIN1-dependent pathophysiological processes might be associated with Tau. We first generated a cohort of control and transgenic mice either overexpressing human MAPT (TgMAPT) or both human MAPT and BIN1 (TgMAPT;TgBIN1), which we followed-up from 3 to 15 months. In TgMAPT;TgBIN1 mice short-term memory deficits appeared earlier than in TgMAPT mice; however – unlike TgMAPT mice – TgMAPT;TgBIN1 mice did not exhibit any long-term or spatial memory deficits for at least 15 months. After sacrifice of the cohort at 18 months, immunohistochemistry revealed that BIN1 overexpression prevents both Tau mislocalization and somatic inclusion in the hippocampus, where an increase in BIN1-Tau interaction was also observed. We then sought mechanisms controlling the BIN1-Tau interaction. We developed a high-content screening approach to characterize modulators of the BIN1-Tau interaction in an agnostic way (1,126 compounds targeting multiple pathways), and we identified – among others – an inhibitor of Calcineurin, a Ser/Thr phosphatase. We determined that Calcineurin dephosphorylates BIN1 on a Cyclin-dependent kinase phosphorylation site at T348, promoting the open conformation of the neuronal BIN1 isoform. Phosphorylation of this site increases the availability of the BIN1 SH3 domain for Tau interaction, as demonstrated by nuclear magnetic resonance experiments and in primary neurons. Finally, we observed that the levels of the neuronal BIN1 isoform were decreased in AD brains, whereas phospho-BIN1(T348):BIN1 ratio was increased, suggesting a compensatory mechanism. In conclusion, our data support the idea that BIN1 modulates the AD risk through an intricate regulation of its interaction with Tau. Alteration in BIN1 expression or activity may disrupt this regulatory balance with Tau and have direct effects on learning and memory.
A novel link between Cell Wall Integrity pathway and Flocculation, regulated by yeast Sen1 dependent interplay between Rlm1 and Tup1
Authors: Sariki Santhosh Kumar , Kumawat Ramesh , Singh Vikash , Tomar Raghuvir Singh
Published: November 2018

The budding yeast,Saccharomyces cerevisiaeis one of the most studied organisms used for the synthesis of products, to explore the human diseases and eukaryotic gene expression mechanisms. The yeast cells with flocculation property are in high demand for industrial applications. However, the pathogenic yeast becomes drug-resistant due to flocculation/biofilm phenotype. The flocculation property of yeast depends on the expression of specificFLOgenes. Genetic and epigenetic factors have been suggested to induce the expression ofFLOs and flocculation, an evolutionarily conserved process. The present study was undertaken to identify a molecular link between stress caused by genetic and epigenetic factors and expression ofFLOs. We utilized flocculating yeast strains to study the regulation ofFLOgenes and flocculation phenotype. We found rough surface morphology and constitutive activation of Slt2 in flocculating cells. The external cell wall stress factors as well as specific mutations in Sen1 and histone proteins strongly correlated with the induction ofFLOgenes whereas deletion ofSLT2/RLM1, suppressed the expression and flocculation phenotype. We detected constitutive binding of Rlm1 and eviction of Tup1 from the promoters ofFLO1andFLO5genes in flocculating cells. Thus we provide evidence for the CWI pathway dependent flocculation of yeast, regulated by Sen1 mediated interplay between Tup1 and Rlm1.
ARF5/MONOPTEROS directly regulates miR390 expression in theArabidopsis thalianaprimary root meristem
Authors: Dastidar Mouli Ghosh , Scarpa Andrea , Mägele Ira , Ruiz-Duarte Paola , von Born Patrick , Bald Lotte , Jouannet Virginie , Maizel Alexis
Published: November 2018

The root meristem is organized around a quiescent centre surrounded by stem cells that generate all cell types of the root. In the transit amplifying compartment progeny of stem cells further divide prior to differentiation. Auxin controls the size of this transit-amplifying compartment via Auxin Response Factors (ARF) that interact with Auxin Response Elements (AuxRE) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3 and ARF4 by triggering the production of trans-acting (ta)-siRNA fromTAS3. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to auxin. A single AuxRE bound by ARF5/MONOPTEROS (MP) in miR390 promoter is necessary for miR390 expression in this compartment. We show that interfering withARF5/MPdependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment. Our results show that ARF5/MP regulates directly the expression of miR390 in the basal root meristem. We propose that ARF5, miR390 and the ta-siRNAs-regulated ARFs are necessary to maintain the size of the transit-amplifying region of the meristem.

One sentence summary

The expression of miR390 in the Arabidopsis basal root meristem is controlled by ARF5/MONOPTEROS.
Impacts of Deep-Sea Mining on Microbial Ecosystem Services
Authors: Orcutt Beth N. , Bradley James , Brazelton William J. , Estes Emily R. , Goordial Jacqueline M. , Huber Julie A. , Jones Rose M. , Mahmoudi Nagissa , Marlow Jeffrey J. , Murdock Sheryl , Pachiadaki Maria
Published: November 2018

Interest in extracting mineral resources from the seafloor through deep-sea mining has accelerated substantially in the past decade, driven by increasing consumer demand for various metals like copper, zinc, manganese, cobalt and rare earth elements. While there are many on-going discussions and studies evaluating potential environmental impacts of deep-sea mining activities, these focus primarily on impacts to animal biodiversity. The microscopic spectrum of life on the seafloor and the services that this microbial realm provides in the deep sea are rarely considered explicitly. In April 2018, a community of scientists met to define the microbial ecosystem services that should be considered when assessing potential impacts of deep-sea mining, and to provide recommendations for how to evaluate these services. Here we show that the potential impacts of mining on microbial ecosystem services in the deep sea vary substantially, from minimal expected impact to complete loss of services that cannot be remedied by protected area offsets. We conclude by recommending that certain types of ecosystems should be “off limits” until initial characterizations can be performed, and that baseline assessments of microbial diversity, biomass, and biogeochemical function need to be considered in environmental impact assessments of all potential instances of deep-sea mining.
Promoter-intrinsic and local chromatin features determine gene repression in lamina-associated domains
Authors: Leemans Christ , van der Zwalm Marloes , Brueckner Laura , Comoglio Federico , van Schaik Tom , Pagie Ludo , van Arensbergen Joris , van Steensel Bas
Published: November 2018

It is largely unclear whether genes that are naturally embedded in lamina associated domains (LADs) are inactive due to their chromatin environment, or whether LADs are merely secondary to the lack of transcription. We show that hundreds of human promoters become active when moved from their native LAD position to a neutral context in the same cells, indicating that LADs form a repressive environment. Another set of promoters inside LADs is able to "escape" repression, although their transcription elongation is attenuated. By inserting reporters into thousands of genomic locations, we demonstrate that these escaper promoters are intrinsically less sensitive to LAD repression. This is not simply explained by promoter strength, but by the interplay between promoter sequence and local chromatin features that vary strongly across LADs. Enhancers also differ in their sensitivity to LAD chromatin. This work provides a general framework for the systematic understanding of gene regulation by repressive chromatin.

Highlights

Two promoter transplantation strategies elucidate the regulatory role of LAD chromatin

LADs are generally repressive, but also highly heterogeneous

LADs can impede both promoter activity and transcription elongation

Promoters vary intrinsically in their sensitivity to LAD repression
Photoperiod-dependent expression of MicroRNA in Drosophila
Authors: Pegoraro Mirko , Tauber Eran
Published: November 2018

Like many other insects in temperate regions, Drosophila melanogaster exploits the photoperiod shortening that occurs during the autumn as an important cue to trigger a seasonal response. Flies survives the winter by entering a state of reproductive arrest (diapause), which drives relocation of resources from reproduction to survival. Here, we profiled the expression of microRNA (miRNA) in long and short photoperiods and identified seven differentially expressed miRNAs (dme-mir-2b, dme-mir-11, dme-mir-34, dme-mir-274, dme-mir-184, dme-mir-184* and dme-mir-285). Misexpression of dme-mir-2b, dme-mir-184 and dme-mir-274 in pigment-dispersing factor-expressing neurons largely disrupted the normal photoperiodic response, suggesting that these miRNAs play functional roles in photoperiodic timing. We also analyzed the targets of photoperiodic miRNA by both computational predication and by Argonaute-1- mediated immunoprecipitation of long- and short-day RNA samples. Together with global transcriptome profiling, our results expand existing data on other Drosophila species, identifying genes and pathways that are differentially regulated in different photoperiods and reproductive status. Our data suggest that post-transcriptional regulation by miRNA is an important facet of photoperiodic timing.
Exome sequencing identifies high-impact trait-associated alleles enriched in Finns
Authors: Locke Adam E , Meltz Steinberg Karyn , Chiang Charleston WK , Service Susan K , Havulinna Aki S , Stell Laurel , Pirinen Matti , Abel Haley J , Chiang Colby C , Fulton Robert S , Jackson Anne U , Kang Chul Joo , Kanchi Krishna L , Koboldt Daniel C , Larson David E , Nelson Joanne , Nicholas Thomas J , Pietilä Arto , Ramensky Vasily , Ray Debashree , Scott Laura J , Stringham Heather M , Vangipurapu Jagadish , Welch Ryan , Yajnik Pranav , Yin Xianyong , Eriksson Johan G , Ala-Korpela Mika , Järvelin Marjo-Riitta , Männikkö Minna , Laivuori Hannele ,   FinnGen Project, Dutcher Susan K , Stitziel Nathan O , Wilson Richard K , Hall Ira M , Sabatti Chiara , Palotie Aarno , Salomaa Veikko , Laakso Markku , Ripatti Samuli , Boehnke Michael , Freimer Nelson B
Published: November 2018

As yet undiscovered rare variants are hypothesized to substantially influence an individual’s risk for common diseases and traits, but sequencing studies aiming to identify such variants have generally been underpowered. In isolated populations that have expanded rapidly after a population bottleneck, deleterious alleles that passed through the bottleneck may be maintained at much higher frequencies than in other populations. In an exome sequencing study of nearly 20,000 cohort participants from northern and eastern Finnish populations that exemplify this phenomenon, most novel trait-associated deleterious variants are seen only in Finland or display frequencies more than 20 times higher than in other European populations. These enriched alleles underlie 34 novel associations with 21 disease-related quantitative traits and demonstrate a geographical clustering equivalent to that of Mendelian disease mutations characteristic of the Finnish population. Sequencing studies in populations without this unique history would require hundreds of thousands to millions of participants for comparable power for these variants.
Desmoplakin is required for epidermal integrity and morphogenesis in theXenopus laevisembryo
Authors: Bharathan Navaneetha Krishnan , Dickinson Amanda J.G.
Published: November 2018

Desmoplakin (Dsp) is a unique and critical desmosomal protein, however, it is unclear whether this protein and desmosomes themselves are required for epidermal morphogenesis. Using morpholinos or Crispr/Cas9 mutagenesis we decreased the function of Dsp in frog embryos to better understand its role during epidermal development. Dsp morphant and mutant embryos had developmental defects that mimicked what has been reported in mammals. Such defects included epidermal fragility which correlated with reduction in cortical keratin and junctional e-cadherin in the developing epidermis. Dsp protein sequence and expression are also highly similar with mammals and suggest shared function across vertebrates. Most importantly, we also uncovered a novel function for Dsp in the morphogenesis of the epidermis inX. laevis. Specifically, Dsp is required during the process of radial intercalation where basally located cells move into the outer epidermal layer. Once inserted these newly intercalated cells expand their apical surface and then they differentiate into specific epidermal cell types. Decreased levels of Dsp resulted in the failure of the radially intercalating cells to expand their apical surface, thereby reducing the number of differentiated multiciliated and secretory cells. Dsp is also required in the development of other ectodermally derived structures such as the mouth, eye and fin that utilize intercalating-like cell movements. We have developed a novel system, in the frog, to demonstrate for the first time that desmosomes not only protect against mechanical stress but are also critical for epidermal morphogenesis.

Summary Statement

Critical desmosomal protein, desmoplakin, is required for proper distribution and levels of cytoskeletal elements and e-cadherin. Thus embryos with decreased desmoplakin have defects in epidermal integrity and morphogenesis.