bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nectar-dwelling microbes of common tansy are attractive to its mosquito pollinator,Culex pipiensL
Authors: Peach D. A. H. , Carroll C. , Meraj S. , Gomes S. , Galloway E. , Balcita A. , Coatsworth H. , Young N. , Uriel Y. , Gries R. , Lowenberger C. , Moore M. , Gries G. 
Published: April 2020

AbstractBackgroundThere is widespread interkingdom signalling between insects and microbes. For example, microbes found in floral nectar may modify its nutritional composition and produce odorants that alter the floral odor bouquet which may attract insect pollinators. Mosquitoes consume nectar and can pollinate flowers. We identified microbes isolated from nectar of common tansy,Tanacetum vulgare,elucidated the microbial odorants, and tested their ability to attract the common house mosquito,Culex pipiens.ResultsWe collected 18 microbial isolates fromT. vulgarenectar, representing at least 12 different taxa which we identified with 16S or 26S rDNA sequencing as well as by biochemical and physiological tests. Three microorganisms(Lachancea thermotolerans, Micrococcus lactis, Micrococcus luteus)were grown on culture medium and tested in bioassays. Only the yeastL. thermotoleransgrown on nectar, malt extract agar, or in synthetic nectar broth significantly attractedC. pipiensfemales. The odorant profile produced byL. thermotoleransvaried with the nutritional composition of the culture medium. Surprisingly, all three microbes grown separately, but presented concurrently, attracted fewerC. pipiensfemales thanL. thermotoleransby itself.ConclusionsFloral nectar ofT. vulgarecontains various microbes whose odorants contribute to the odor profile of inflorescences. In addition,L. thermotoleransproduced odorants that attractCx. pipiensfemales. As the odor profile ofL. thermotoleransvaried with the composition of the culture medium, we hypothesize that microbe odorants inform nectar-foraging mosquitoes about the availability of certain macro-nutrients which, in turn, affect foraging decisions by mosquitoes.
Engineering multiple species-like genetic incompatibilities in insects
Authors: Maselko Maciej , Feltman Nathan , Upadhyay Ambuj , Hayward Amanda , Das Siba , Myslicki Nathan , Peterson Aidan J. , O’Connor Michael B. , Smanski Michael J. 
Published: April 2020

AbstractSpeciation constrains the flow of genetic information between populations of sexually reproducing organisms. Gaining control over mechanisms of speciation would enable new strategies to manage wild populations of disease vectors, agricultural pests, and invasive species. Additionally, such control would provide safe biocontainment of transgenes and gene drives. Natural speciation can be driven by pre-zygotic barriers that prevent fertilization or by post-zygotic genetic incompatibilities that render the hybrid progeny inviable or sterile. Here we demonstrate a general approach to create engineered genetic incompatibilities (EGIs) in the model insectDrosophila melanogaster. Our system couples a dominant lethal transgene with a recessive resistance allele. EGI strains that are homozygous for both elements are fertile and fecund when they mate with similarly engineered strains, but incompatible with wild-type strains that lack resistant alleles. We show that EGI genotypes can be tuned to cause hybrid lethality at different developmental life-stages. Further, we demonstrate that multiple orthogonal EGI strains ofD. melanogastercan be engineered to be mutually incompatible with wild-type and with each other. Our approach to create EGI organisms is simple, robust, and functional in multiple sexually reproducing organisms.
The spectral sensitivity ofDrosophilaphotoreceptors
Authors: Sharkey Camilla R. , Blanco Jorge , Leibowitz Maya M. , Pinto-Benito Daniel , Wardill Trevor J. 
Published: April 2020

AbstractDrosophila melanogasterhas long been a popular model insect species, due in large part to the availability of genetic tools and is fast becoming the model for insect colour vision. Key to understanding colour reception inDrosophilais in-depth knowledge of spectral inputs and downstream neural processing. While recent studies have sparked renewed interest in colour processing inDrosophila, photoreceptor spectral sensitivity measurements have yet to be carried outin vivo. We have fully characterised the spectral input to the motion and colour vision pathways, and directly measured the effects of spectral modulating factors, screening pigment density and carotenoid-based ocular pigments. All receptor sensitivities had significant shifts in spectral sensitivity compared to previous measurements. Notably, the spectral range of the Rh6 visual pigment is substantially broadened and its peak sensitivity is shifted by 92 nm from 508 to 600 nm. We propose that this deviation can be explained by transmission of long wavelengths through the red screening pigment and by the presence of the blue-absorbing filter in the R7y receptors. Further, we tested direct interactions between photoreceptors and found evidence of interactions between inner and outer receptors, in agreement with previous findings of cross-modulation between receptor outputs in the lamina.
The role of Kabuki Syndrome genesKMT2DandKDM6Ain development: Analysis in Human sequencing data and compared to mice and zebrafish
Authors: Sen Rwik , Lencer Ezra , Geiger Elizabeth A. , Jones Kenneth , Shaikh Tamim H. , Artinger Kristin Bruk 
Published: April 2020

AbstractKMT2DandKDM6Aare epigenetic regulators that have been implicated in Kabuki Syndrome, a rare congenital birth defect with multiple tissue and organ abnormalities, including craniofacial and heart defects. Our previous study identified human families with mutations in the epigenetic modifiers KMT2D and KDM6A, which is implicated in 32% and 10% of Kabuki Syndrome patients respectively. To understand the connection to Kabuki syndrome patients, and the transcriptional targets of KMT2D and KDM6A in humans, we performed RNA sequencing (seq) of lymphoblastoid cells from Kabuki Syndrome patients carrying mutations inKMT2DandKDM6A. We identified 1995 significant changes in transcriptional targets forKMT2Dand 1917 forKDM6A, as compared to control. When compared with RNA-seq datasets obtained from other mouse and zebrafish studies, our analysis revealedKMT2Dmutations affect the expression of 76 orthologous genes across all three datasets. Similarliy,KDM6Aafftects the expprssion of 7 orthologous genes across three datasets. Despite the differences in cell types, stages, and species in the comparison between the transcriptomic datasets, there are common gene expression changes associated with KMT2D and KDM6A mutations. qPCR on novel zebrafish mutants confirmed the differentially expression in KMT2D or KDM6A mutant backgrounds. Taken together, our results show thatKMT2DandKDM6Aregulate common and unique genes across humans, mice, and zebrafish for early craniofacial and cardiac development and this information contributes to the understanding of epigenetic dysregulation during development of Kabuki syndrome.
From simplicity to complexity: The gain or loss of spot rows underlies the morphological diversity of threeDrosophilaspecies
Authors: Dion William A. , Shittu Mujeeb O. , Steenwinkel Tessa E. , Raja Komal K. B. , Kokate Prajakta P. , Werner Thomas 
Published: April 2020

AbstractTo understand how novel animal patterning emerged, one needs to ask how the development of color patterns has changed among diverging species. Here we examine three species of fruit flies –Drosophila guttifera(D. guttifera),Drosophila palustris(D. palustris), andDrosophila subpalustris(D. subpalustris) – displaying a varying number of abdominal spot rows that were either gained or lost throughout evolutionary time. Throughin situhybridization, we examine the mRNA expression patterns for the pigmentation genesDopa decarboxylase(Ddc),tan(t), andyellow(y) during pupal development. Our results show thatDdc,t, andyare co-expressed in identical patterns, each foreshadowing the adult abdominal spots inD. guttifera,D. palustris, andD. subpalustris.
Cell culture system to efficiently test candidate genes and molecular pathways implicated in congenital diaphragmatic hernias
Authors: Bogenschutz Eric L. , Sefton Elizabeth M. , Kardon Gabrielle 
Published: April 2020

ABSTRACTThe mammalian muscularized diaphragm is essential for respiration and defects in the developing diaphragm cause a common and frequently lethal birth defect, congenital diaphragmatic hernia (CDH). Human genetic studies have implicated more than 150 genes and multiple molecular pathways in CDH, but few of these have been validated because of the expense and time to generate mouse mutants. The pleuroperitoneal folds (PPFs) are transient embryonic structures in diaphragm development and a critical cellular source of CDH. We have developed a system to culture PPF fibroblasts from E12.5 mouse embryos and show that these fibroblasts, in contrast to the commonly used NIH 3T3 fibroblasts, maintain expression of key genes in normal diaphragm development. Using pharmacological and genetic manipulations that result in CDHin vivo, we also demonstrate that differences in proliferation provide a rapid means of distinguishing healthy and impaired PPF fibroblasts. Thus, the PPF fibroblast cell culture system is an efficient tool for testing the functional significance of CDH candidate genes and molecular pathways and will be an important resource for elucidating the complex etiology of CDH.SUMMARY STATEMENTMultiple candidate genes and molecular pathways have been identified as potentially contributing to the etiology of congenital diaphragmatic hernias. We describe a cell culture system to efficiently functionally test these candidates.
Intrinsically disordered linkers control tethered kinases via effective concentration
Authors: Dyla Mateusz , Kjaergaard Magnus 
Published: April 2020

AbstractKinase specificity is crucial to the fidelity of signalling pathways, yet many pathways use the same kinases to achieve widely different effects. Specificity arises in part from the enzymatic domain, but also from the physical tethering of kinases to their substrates. Such tethering can occur via protein interaction domains in the kinase or via anchoring and scaffolding proteins, and can drastically increase the kinetics of phosphorylation. However, we do not know how such intra-complex reactions depend on the link between enzyme and substrate. Here we show that the kinetics of tethered kinases follow a Michaelis-Menten like dependence on effective concentration. We find that phosphorylation kinetics scale with the length of the intrinsically disordered linkers that join the enzyme and substrate, but that the scaling differs between substrates. Steady-state kinetics can only partially predict rates of tethered reactions as product release may obscure the rate of phospho-transfer. Our results suggest that changes in signalling complex architecture not only enhance the rates of phosphorylation reactions, but may also alter the relative substrate usage. This suggests a mechanism for how scaffolding proteins can allosterically modify the output from a signalling pathway.
From winter to summer and back: Lessons from the parameterization of a seasonal food web model for the Białowieża forest
Authors: Sauve Alix M. C. , Barraquand Frederic 
Published: April 2020

AbstractDynamic food web models describe how species abundances change over time as a function of trophic and life‐history parameters. They are essential to predicting the response of ecosystems to perturbations. However, they are notoriously difficult to parameterize, so that most models rely heavily either on allometric scaling of parameters or inverse estimation of biomass flows. The allometric approach makes species of comparable body mass have near‐identical parameters which can generate extinctions within a trophic level. The biomass flow approach is more precise, but is restricted to steady‐states, which is not appropriate for time‐varying environments.Adequately parameterizing large food webs of temperate and arctic environments requires dealing both with many species of similar sizes and a strongly seasonal environment. Inspired by the rich empirical knowledge on the vertebrate food web of the Białowieża forest, we parameterize a bipartite food web model comprising 21 predators and 124 prey species. Our model is a non‐autonomous coupled ordinary differential equations system that allows for seasonality in life‐history and predation parameters.Birth and death rates, seasonal descriptions of diet for each species, food requirements and biomass information are combined into a seasonal parameterization of a dynamic food web model. Food web seasonality is implemented with time‐varying intrinsic growth rate and interaction parameters, while predation is modelled with both type I and type II functional responses.All our model variants allow for >80% persistence in spite of massive apparent competition, and a quantitative match to observed (seasonal) biomasses. We also identify trade‐offs between maximizing persistence, reproducing observed biomasses, and ensuring model robustness to sampling errors. Although multi‐annual cycles are expected with type II functional responses, they are here prevented by a strong predator self‐regulation. We discuss these results and possible improvements on the model.We provide a general workflow to parameterize dynamic food web models in seasonal environments, based on a real case study. This may help to better predict how biodiverse food webs respond to changing environments.
Applying the core microbiome to understand host–microbe systems
Authors: Risely Alice 
Published: April 2020

Abstract

The host‐associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability or ecological influence, as well as their contribution to host function and fitness.

A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal and ecological core microbiomes can together generate insights into ecological processes that act independently of host function, while functional and host‐adapted cores distinguish between facultative and near‐obligate symbionts that differ in their effects on host fitness.

This commentary summarizes five broad definitions of the core microbiome that have been applied across the literature, highlighting their strengths and limitations for advancing our understanding of host–microbe systems, noting where they are likely to overlap, and discussing their potential relevance to host function and fitness.

No one definition of the core microbiome is likely to capture the range of key microbes across a host population. Applied together, they have the potential to reveal different layers of microbial organization from which we can begin to understand the ecological and evolutionary processes that govern host–microbe interactions.
Long‐term research and hierarchical models reveal consistent fitness costs of being the last egg in a clutch
Authors: Acevedo Cheyenne R. , Riecke Thomas V. , Leach Alan G. , Lohman Madeleine G. , Williams Perry J. , Sedinger James S. 
Published: April 2020

Abstract

Maintenance of phenotypic heterogeneity in the face of strong selection is an important component of evolutionary ecology, as are the consequences of such heterogeneity. Organisms may experience diminishing returns of increased reproductive allocation as clutch or litter size increases, affecting current and residual reproductive success. Given existing uncertainty regarding trade‐offs between the quantity and quality of offspring, we sought to examine the potential for diminishing returns on increased reproductive allocation in a long‐lived species of goose, with a particular emphasis on the effect of position in the laying sequence on offspring quality.

To better understand the effects of maternal allocation on offspring survival and growth, we estimated the effects of egg size, timing of breeding, inter‐ and intra‐annual variation, and position in the laying sequence on gosling survival and growth rates of black brant Branta bernicla nigricans breeding in western Alaska from 1987 to 2007.

We found that gosling growth rates and survival decreased with position in the laying sequence, regardless of clutch size. Mean egg volume of the clutch a gosling originated from had a positive effect on gosling survival (β = 0.095, 95% CRI: 0.024, 0.165) and gosling growth rates (β = 0.626, 95% CRI: 0.469, 0.738). Gosling survival (β = −0.146, 95% CRI: −0.214, −0.079) and growth rates (β = −1.286, 95% CRI: −1.435, −1.132) were negatively related to hatching date.

These findings indicate substantial heterogeneity in offspring quality associated with their position in the laying sequence. They also potentially suggest a trade‐off mechanism for females whose total reproductive investment is governed by pre‐breeding state.
Associational resistance to both insect and pathogen damage in mixed forests is modulated by tree neighbour identity and drought
Authors: Field Elsa , Castagneyrol Bastien , Gibbs Melanie , Jactel Hervé , Barsoum Nadia , Schönrogge Karsten , Hector Andrew 
Published: April 2020

Abstract

Tree health declines can be caused by interactions between pests and pathogens and many studies have shown a reduction in their damage in mixed species forests compared to monocultures. Yet few authors have considered tree diversity effects on both groups simultaneously. Moreover, it is unclear whether diversity effects on tree pests and pathogens are robust to changes in abiotic conditions, such as drought.

We addressed tree diversity effects on foliar insect herbivory, oak powdery mildew and their interaction under contrasting water regimes in a large-scale tree diversity experiment in SW France. Using an irrigation treatment that alleviated drought conditions, we were able to experimentally assess the effects of tree diversity under contrasting abiotic environments. We surveyed plots along a richness gradient from one to four tree species, in which a focal study species of oak (Quercus robur) was mixed with other oak species (Q. pyrenaica and Q. ilex) and a taller, broadleaved species (Betula pendula).

Increasing tree species richness lowered leaf miner abundance, leaf chewer damage and oak powdery mildew infection, consistent with a protective effect of resource dilution. However, richness effects on leaf miners were stronger in irrigated compared to non-irrigated blocks, indicating that environmental conditions can modulate diversity effects. Separate from the effect of tree species richness, the presence of birch in a plot increased damage by leaf chewers and powdery mildew, but lowered leaf miner damage, suggesting additional tree neighbour identity effects potentially linked to modulation of microclimate. We found a negative association between leaf miner abundance and oak powdery mildew, consistent with antagonism between oak damage agents.

Synthesis. Overall, our study illustrates the importance of considering both tree diversity and composition (neighbour identity) in designing forests more resistant to pest and pathogen damage.
Patterns of pollen dispersal and mating in a population of the clonal plant Sagittaria latifolia
Authors: Stephens Samantha , van Kleunen Mark , Dorken Marcel E. 
Published: April 2020

Abstract

Increased plant size is generally expected to have negative consequences for mating by increasing pollen transfer between flowers of the same plant. Such geitonogamous self‐pollination would then reduce sexual fitness through both female and male function. However, recent theoretical work has indicated that when plants grow clonally, the outward expansion of plants caused by clonal growth might have positive effects on siring without substantially increasing rates of self‐pollination.

We investigated patterns of pollen dispersal, selfing and siring in a monoecious population of the clonal plant Sagittaria latifolia, in which clones varied in size and the extent of intermingling with other clones. A spatially explicit statistical model based on the inferred pollen dispersal kernel was constructed to examine the mechanisms underlying observed mating patterns.

Pollen dispersal typically occurred over distances that exceeded the spatial extent of clones. There was a positive association between clone size (measured as the number of ramets per genet) and the likelihood that clones were intermingled with the shoots of other clones. Together, these patterns of pollen dispersal and clonal intermingling resulted in a weak positive association between clone size and selfing rates and a strong positive association between clone size and outcross siring success. These patterns were replicated in the spatially explicit model, indicating that the intermingling of clones is an important determinant of mating patterns in this population.

Synthesis. Our study provides the first examination of the pollen dispersal kernel for a clonal plant. It is the first study providing empirical support for model predictions that potentially negative effects of increased selfing in large clones might be offset by increased siring success. This implies that the negative consequences of becoming large do not necessarily apply to clonal plants.
MiR‐342 attenuates lipopolysaccharide‐induced acute lung injury via inhibiting MAPK1 expression
Authors: Zhu Siliang , Song Wenke , Sun Yanqi , Zhou Yongqin , Kong Fanpo 
Published: April 2020

AbstractMicro RNA (miRNA) and mitogen‐activated protein kinase (MAPK) are reported as the crucial regulators of inflammatory responses in acute lung injury (ALI). This study will explore the role of the miR‐342/MAPK1 axis in regulation of lipopolysaccharide (LPS)‐induced ALI. We found that miR‐342 was down‐regulated in LPS‐induced A549 cells compared with the control group with DMSO, accompanied by elevated inflammatory cytokines and apoptosis. Over‐expression of miR‐342 reduced LPS‐induced inflammatory responses and apoptosis in LPS‐stimulated A549 cells, and had a protective role in LPS‐treated mice with ALI by decreasing levels of inflammatory cytokines, improving survival of mice with ALI, and ameliorating the lung permeability. Dual‐luciferase reporter gene assay demonstrated that miR‐342 regulated the expression of MAPK1 by directly targeting its 3′ untranslated region (3′‐UTR). Mechanistically, MAPK1 silencing abrogated LPS‐induced inflammatory injury in A549 cells, and partially enhanced the protective effect of miR‐342. Therefore, miR‐342 attenuates LPS‐induced ALI by targeting MAPK1 expression, thereby protecting against A549 cell injury induced by LPS and lung injury of mice with ALI.