bluuebunny/crossref_metadata_2025 huggingface dataset:
Hitchhiking and Selective Sweeps
Authors: Walsh Bruce , Lynch Michael
Published: September 2018

When a favorable allele increases in frequency, it alters the coalescent structure (the pattern of times back to a common ancestor) at linked sites relative to that under drift. This creates patterns of sequence polymorphism than can be used to potentially detect ongoing, or very recent, selection. This idea of a neutral allele hitchhiking up to high frequency when coupled to a favorable allele is the notion of a selective sweep, and this chapter reviews the considerable body of associated population-genetics theory on sweeps. Different types of sweeps leave different signatures, resulting in the very diverse collection of tests of selection discussed in Chapter 9. Either a history of recurrent sweeps, or of background selection, results in linked genomic regions of reduced effective population size. This implies that more mutations in sich regions are efficiently neutral, which can result in increased substitution rates and lower codon bias. Finally, the chapter examines the theory for when response is expected to start from existing variation, as opposed to waiting for the appearance of new mutations.
Realignment and Beyond
Authors: Dalton Russell J.
Published: September 2018

Affluent democracies have experienced tremendous socio-economic changes since the mid- twentieth century, which has reshaped public opinion, party programs, and electoral choices. This chapter first summarizes the societal changes that have been a driving force behind the political changes described in this study. One pattern involves the longstanding economic issues of contemporary democracies, and shifting social positions on these issues. In addition, an evolving cultural cleavage and its ties to broader attitudes toward social change have altered citizen policy preferences. In most affluent democracies, the parties’ responses to these changing citizen demands have produced a realignment to represent both economic and cultural positions. The chapter concludes by discussing the implications of the findings for the working of electoral systems and the democratic process more broadly.
Against Pastoral
Authors: Heslin Peter J.
Published: September 2018

This chapter picks up the terms of the polemic with Virgilian pastoral that began with Milanion in the first elegy, as Propertius repeatedly revisits the situation of the tenth Eclogue. Propertius refuses to accept the proposition that pastoral love would be an equally satisfying but less painful alternative to his own suffering. He points out that Gallus’ mistress in the tenth eclogue was probably bluffing; that the rustic environment of pastoral is less appealing than the urban context of elegy; and that the whole amatory experience in pastoral is substandard. The polemic climaxes at the end of the first book, when Propertius constructs the Hylas-elegy as an elaborate allegory for the dangerous allurements of the Eclogues. Virgil’s antithesis of Aristaeus and Orpheus is, in part, a response to that allegory, and an adaptation of Propertius’ own antithesis of Amphion and Orpheus.
Hermeneutics
Authors: Forster Michael N.
Published: September 2018

This chapter challenges a reading of Herder’s hermeneutics, or theory of interpretation, that assimilates it to Gadamer’s. For Herder, unlike Gadamer, interpretation is a matter of getting back to a text’s original meaning and avoiding contamination of this by distinctive features of the interpreter’s own viewpoint. Herder’s theory of interpretation rests both on his philosophy of language and on a principle that radical mental differences occur between historical periods, cultures, and even individuals—the latter principle posing the main challenge for accurate interpretation that his theory is designed to address. To that end he develops a whole series of important specific recommendations. These were subsequently taken over by Schleiermacher and Boeckh in their hermeneutic theories, and formed the methodological foundations that enabled the great flowering of the human sciences that occurred in nineteenth-century Germany. Moreover, Herder’s versions of them were in some important ways superior to his successors’.
Aesthetics
Authors: Forster Michael N.
Published: September 2018

Aesthetics, or the philosophy of literature and art, was one of Herder’s main focuses. By valorizing these areas of culture (in comparison with others such as science and religion) and in several other ways he prepared the ground for German Romanticism. He also established many principles of great intrinsic importance: rejecting apriorism and systematization in aesthetics in favor of an empirical, non-systematic approach; insisting that arts such as sculpture and painting express meanings and therefore require interpretation; recognizing the central role of genre not only in literature but also in such arts; perceiving the deep historical, cultural, and even individual variability of literature and art in respect of semantic content, genre, moral values, and aesthetic values, plus the major implications this variability has for both interpretation and evaluation; developing a set of radical views concerning beauty; and emphasizing the importance of literature and art as means of moral pedagogy.
Intellectual Influence
Authors: Forster Michael N.
Published: September 2018

This chapter argues that Herder’s intellectual influence has been enormous, not only encompassing important individual thinkers, such as Goethe, Schleiermacher, Schlegel, Schelling, Hegel, Humboldt, and Nietzsche, but also extending to the founding of whole new disciplines, including linguistics, anthropology, and comparative literature. Moreover, Herder was a sine qua non for both of the two main philosophical movements that arose in the next generation, namely German Romanticism and post-Kantian German Idealism, inspiring not only their neo-Spinozist monism but also much else in them. The failure of his successors to give him proper credit for his astonishing contributions was largely due to a simple fact: as a fiercely independent-minded critic of his contemporaries, by the beginning of the nineteenth century he had managed to alienate both of Germany’s main intellectual power blocs, namely Kant, Fichte, and their followers; and Goethe, Schiller, and theirs.
SAXS Instrumentation
Authors: Lattman Eaton E. , Grant Thomas D. , Snell Edward H.
Published: September 2018

SAXS instrumentation is available for the laboratory, at the synchrotron, and at X-ray free electron laser sources. This chapter deals with SAXS instrumentation. It covers laboratory systems, synchrotron beamlines and newer sources. Multiple synchrotron facilities have SAXS beamlines and the ability to perform SAXS studies on free electron laser sources is growing. Sample handling has adopted automation and in some cases microfluidics to reduce sample volume requirements. Sensitive detectors efficient data collection software and rapid analysis allow real time decisions to be made during data collection. Specialized apparatus enables time resolved studies. Each component is described.
Developments on the Horizon
Authors: Lattman Eaton E. , Grant Thomas D. , Snell Edward H.
Published: September 2018

The field of application for solution scattering is broader than we can cover in detail and with new instrumentation, that field is only growing. XFEL sources offer the potential for time resolved studies exquisitely sensitive to rapid structural biological processes while at the same time potentially extending the information beyond that provided by current solution scattering methods. Cryogenic approaches offer the potential to increase signal and/or improve sample demands opening up the technique to a wider array of studies. Finally, use of the atomic scattering properties reveals biological information in the case of nucleic acids and has the potential to provide molecular rulers able to resolve dynamic structural changes as they occur. This chapter provides a glimpse of what is possible and a starting point for further exploration.
Background matching
Authors: Ruxton Graeme D. , Allen William L. , Sherratt Thomas N. , Speed Michael P.
Published: September 2018

Background matching is perhaps the most obvious phenomenon that falls under the label of crypsis. Stevens & Merilaita (2011) describe background matching as situations where ‘the appearance generally matches the colour, lightness and pattern of one (specialized) or several (compromise) background types’. There are fascinating examples of species that behaviourally select their microhabitat and orientation so as to enhance similarity to features of the background, and species that change aspects of their appearance in ways that enhance background matching. The degree of background matching is often imperfect; this is thought to commonly reflect the fact that organisms are viewed against a range of different backgrounds, and so they have evolved appearance traits that offer some degree of matching against several of these. Understanding background matching addresses important issues in evolutionary biology, such as the maintenance of polymorphisms. We discuss how predation rates that depend on the frequency of morphs in the environment may be a common explanation for polymorphic crypsis, and the role search images might play in this process. Achieving highly effective background matching in a complex environment is difficult and this may create room for other types of crypsis.
Transparency
Authors: Ruxton Graeme D. , Allen William L. , Sherratt Thomas N. , Speed Michael P.
Published: September 2018

We begin this chapter by considering the ecological distribution of transparent organisms and, in particular, how they are found predominantly in one particular habitat type (open waters); we aim to explain this trend. A perfectly transparent organism (or part of an organism) will not absorb or scatter incident light. Superficially, transparent might seem like a synonym for visually undetectable, but this is not quite true: we discuss how transparent organisms can still be visually detected by their predators or prey. Conversely, there are circumstances where a little transparency can go a long way to reducing an organism’s visibility. Some body parts cannot be made transparent, but we argue that opaque body parts need not always significantly increase the detectability of a generally transparent organism. We will then consider the distribution of transparency among natural organisms. The distributional observations we seek to explain are: the greater prevalence of transparency among aquatic than terrestrial organisms, and the particular prevalence among midwater species. An alternative but related strategy to transparency, adopted by some midwater fish, and considered later in this chapter, is silvering of the body to provide crypsis by broadband reflection.
Secondary defences
Authors: Ruxton Graeme D. , Allen William L. , Sherratt Thomas N. , Speed Michael P.
Published: September 2018

In this chapter we consider defences that are usually deployed during, or just before, contact between a prey and its predator: so-called ‘secondary’ defences. Secondary defences are found right across the tree of life and therefore come in very many forms, including: 1.) chemical defences; 2.) mechanical defences; and 3.) behavioural defences. Here we review selected examples that provide useful illustrations of the ecological and evolutionary characteristics associated with secondary defences. We discuss costs of secondary defences, placing emphasis on the consequences of such costs, especially as they relate to forms of social interaction. We show also that the acquisition of secondary defences may modify niche, life history, and habitat range of prey animals and review a well-known and significant study of predator–prey co-evolution of defensive toxins of prey and resistance to those toxins in predators. We include a small selection of examples and ideas from the plant and microbe defence literature where we think a broader perspective is helpful. We begin the chapter by considering the evolutionary mechanisms that favour secondary defence evolution.
Startling predators
Authors: Ruxton Graeme D. , Allen William L. , Sherratt Thomas N. , Speed Michael P.
Published: September 2018

Startling signals are secondary defences that occur after the focal prey individual has been singled out for attack. Startling signals involve stimulation of the predator’s senses that cause it to delay or break off an attack. The assumption is that even a delay in attack can confer a survival advantage to the prey. This might occur because delay gives the prey an added opportunity to flee, or added opportunity for some other event to occur (perhaps the arrival of a predator of the predator) that causes the predator to break off the attack permanently. Startle signals influence the predator’s behaviour primarily through sensory and/or cognitive manipulation and must be separate from other mechanisms that may also influence predators’ behaviour so as to curtail, delay, or diminish an attack. We first consider the empirical evidence for the existence of such signals, before discussing the evolution of startle signals, the ecological aspects of this defence, co-evolutionary considerations, and suggestions for future research.
Deflecting the point of attack
Authors: Ruxton Graeme D. , Allen William L. , Sherratt Thomas N. , Speed Michael P.
Published: September 2018

Deflection involves prey influencing the position of the initial contact of a predator with the prey’s body, in a way that benefits the prey. These traits might be behavioural, involve morphological structures, or pigmentation and other appearance traits, or combinations thereof. The benefit to the prey is normally considered to be an increased likelihood of escaping the attack, and so the benefit to the prey comes at a cost to the predator. The anti-predatory mechanisms covered in this book vary greatly in current understanding of their taxonomic distribution, and deflection is an extreme example of this. It has been postulated to occur in a sparse and eclectic group of organisms, and the evidence for its existence is quite variable among members of this group. We spend the bulk of this chapter exploring this evidence. We argue that the evidence currently available allows some speculation on the evolutionary ecology of this anti-predatory strategy, and we develop hypotheses that aim to broaden the scope of research into deflective traits.
The Majestic Theater of the Air
Authors: Maslon Laurence
Published: September 2018

The advent of radio in the early 1920s allowed for the music of Broadway to penetrate even more households with dance bands, variety shows, and interview programs that exploited the rarified atmosphere of Broadway. In the 1920s, personalities such as Eddie Cantor and Rudy Vallee hawked not only the sponsors’ products, but the latest hit songs of Broadway. Songwriters, such as George Gershwin, as well as Rodgers and Hart, wrote original material for radio and appearing on the air as acclaimed celebrities. The Hit Parade program also codified the hit-making potential of Broadway songs. By the 1940s, Frank Sinatra brought the music of Broadway to avid listeners and used the “bully pulpit” of several popular radio series to disseminate the content and context of Broadway.
Culture’s Constraints
Authors: Gelfand Michele J. , Caluori Nava , Gordon Sarah , Raver Jana , Nishii Lisa , Leslie Lisa , Lun Janetta
Published: September 2018

Research on culture has generally ignored social situations, and research on social situations has generally ignored culture. In bringing together these two traditions, we show that nations vary considerably in the strength of social situations, and this is a key conceptual and empirical bridge between macro and distal cultural processes and micro and proximal psychological processes. The model thus illustrates some of the intervening mechanisms through which distal societal factors affect individual processes. It also helps to illuminate why cultural differences persist at the individual level, as they are adaptive to chronic differences in the strength of social situations. The strength of situations across cultures can provide new insights into cultural differences in a wide range of psychological processes.
Crate Digging Begins at Home
Authors: Stoever Jennifer Lynn
Published: September 2018

Many scholars, music journalists, and hip hop heads have discounted the diversity of ways women helped create the now global art-form known as hip hop. One of these overlooked labors involves the cultivation and passing on of a black and Latina feminist listening praxis through record collecting and selecting. This chapter contributes to black feminist scholarship dedicated to moving hip hop historiography from the critical but critically well-worn streets into the more woman-centric and therefore often marginalized spaces of the South Bronx—those living rooms, kitchens, bedrooms, bathrooms, hallways, stores, and stoops, where black women and Latinas not only participated in early hip hop, but helped to bring it into sonic being. Through archival evidence, rhetorical analysis, and an oral history, “Crate Digging Begins at Home” moves toward the interconnected goals of reconceiving gender in hip hop historiography, rethinking the figure of the “mother” in popular music studies and record collecting culture, and documenting the selecting practices of Black and Latinx women.
Properly Compensating Artists in Academic Hip Hop Research
Authors: Dilday Jess A.
Published: September 2018

Who are hip hop scholars writing for, and how can they write in ways that benefit both artists and their readership? The structure of academia limits the ethical production of knowledge to the elite few who have attained university funding or who have external funding. For instance, independent scholars/practitioners do not have access to the level of funding that tenure-track professors have. Audience access to academic work is likewise restricted to those who can get behind a paywall. In this chapter, I discuss how traditional academic funding models prevent ethical research, why collaborative approaches are preferable and require adequate funding, and how this affects hip hop studies specifically. Finally, I outline some potential interim solutions, with a clarion call for further work in this area.
Epidemiology of Persistent Postsurgical Pain Manifesting as Dry Eye-Like Symptoms After Cataract Surgery
Authors: Sajnani Ravin , Raia Sophia , Gibbons Allister , Chang Victoria , Karp Carol L. , Sarantopoulos Constantine D. , Levitt Roy C. , Galor Anat
Published: September 2018

Purpose:

To evaluate the epidemiology of persistent postsurgical pain (PPP) manifesting as dry eye (DE)-like symptoms 6 months after surgery.

Methods:

This single-center study included 119 individuals whose cataract surgeries were performed by a single surgeon at the Bascom Palmer Eye Institute and who agreed to participate in a phone survey 6 months after surgery. Patients were divided into 2 groups: the PPP group was defined as those with a Dry Eye Questionnaire-5 score ≥6 and without PPP as those with a Dry Eye Questionnaire-5 score <6 at 6 months after cataract surgery.

Results:

Mean age of the study population was 73 ± 8.0 years; 55% (n = 66) were female. PPP was present in 34% (n = 41) of individuals 6 months after surgery. Factors associated with an increased risk of PPP were female sex [odds ratio (OR) = 2.68, 95% confidence interval (CI) = 1.20–6.00, P = 0.01], autoimmune disorder (OR = 13.2, CI = 1.53–114, P = 0.007), nonocular chronic pain disorder (OR = 4.29, CI = 1.01–18.1, P = 0.06), antihistamine use (OR = 6.22, CI = 2.17–17.8, P = 0.0003), antireflux medication use (OR = 2.42, CI = 1.04–5.66, P = 0.04), antidepressant use (OR = 3.17, CI = 1.31–7.68, P = 0.01), anxiolytic use (OR = 3.38, CI = 1.11–10.3, P = 0.03), and antiinsomnia medication use (OR = 5.28, CI = 0.98–28.5, P = 0.047). PPP patients also reported more frequent use of artificial tears (P < 0.0001), higher ocular pain levels (P < 0.0001), and greater neuropathic ocular pain symptoms, including burning (P = 0.001), wind sensitivity (P = 0.001), and light sensitivity (P < 0.0001).

Conclusions:

PPP in the form of persistent DE-like symptoms is present in approximately 34% of individuals 6 months after cataract surgery. The frequency of PPP after cataract surgery is comparable to that of other surgeries including laser refractive surgery, dental implants, and genitourinary procedures.
Fenretinide Inhibits Neutrophil Recruitment and IL-1β Production in Aspergillus fumigatus Keratitis
Authors: Zhao Wenyi , Che Chengye , Liu Kuixiang , Zhang Jie , Jiang Nan , Yuan Kelan , Zhao Guiqiu
Published: September 2018

Purpose:

Fungal keratitis is a major cause of corneal ulcers, resulting in significant visual impairment and blindness. Fenretinide, a derivative of vitamin A, has been shown to suppress inflammation in a multitude of diseases. In this study, we aimed to characterize the effect of fenretinide in Aspergillus fumigatus keratitis of the eye in a mouse model.

Methods:

In vivo and in vitro experiments were performed in mouse models and THP-1 macrophage cell cultures infected with A. fumigatus, respectively. Experimental subjects were first pretreated with fenretinide, and then the effect of the compound was assessed with clinical evaluation, neutrophil staining, myeloperoxidase assay, quantitative polymerase chain reaction (qRT-PCR), and western blot.

Results:

We confirmed that fenretinide contributed to protection of corneal transparency during early mouse A. fumigatus keratitis by reducing neutrophil recruitment, decreasing myeloperoxidase (MPO) levels and increasing apoptosis. Compared with controls, fenretinide impaired proinflammatory cytokine interleukin 1 beta (IL-1β) production in response to A. fumigatus exposure with contributions by lectin-type oxidized LDL receptor 1 (LOX-1) and c-Jun N-terminal kinase (JNK).

Conclusions:

Together, these findings demonstrate that fenretinide may suppress inflammation through reduced neutrophil recruitment and inflammatory cytokine production in A. fumigatus keratitis.
Desikan-Killiany-Tourville Atlas Compatible Version of M-CRIB Neonatal Parcellated Whole Brain Atlas: The M-CRIB 2.0
Authors: Alexander Bonnie , Loh Wai Yen , Matthews Lillian G. , Murray Andrea L. , Adamson Chris , Beare Richard , Chen Jian , Kelly Claire E. , Anderson Peter J. , Doyle Lex W. , Spittle Alicia J. , Cheong Jeanie L.Y. , Seal Marc L. , Thompson Deanne K.
Published: September 2018

Our recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: a) compatibility with this adult cortical atlas, b) greater labelling accuracy due to clearer landmarks, and c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for ten healthy neonates (postmenstrual age at MRI 40-43 weeks, 4 female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and ‘Banks STS’, and modification of boundaries of many other regions. Changes to subcortical regions included the addition of ‘ventral diencephalon’, and deletion of ‘subcortical matter’ labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labelled cortical data and FreeSurfer-labelled subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.
Spatio-temporal structure and reproductive success in a rook (Corvus frugilegus) colony
Authors: Feró Orsolya , Bán Miklós , Barta Zoltán
Published: September 2018

We have studied how individual decisions about timing of breeding and nest location affected the reproductive success of rooks by tracing the formation of a rook breeding colony in Hortobágy NP (Hungary), during the breeding season in 1999.

We have found that birds who built nests earlier also laid eggs earlier and had larger clutch size but had no had more offspring than late nesters. Distance of the nest from the centre or edge of the colony did not affect the reproductive success though rooks generally settled closer to the centre and further from the edge than it can be expected by assuming random distribution. The colony showed high breeding synchrony since date of egg laying varied less than date of nesting but synchrony did not influence the breeding success. Hatchling’s survival rate and number of offspring increased with local nest density and rooks clustered their nests more than it can be expected by random settlement. Nest sites of early and late nesters did not differ regarding the distance from the centre or the edge of the colony but late nesters chose nest sites in more densely populated regions.

The results indicate that individuals may follow different strategies to increase their reproductive success. It is prospectively advantageous to build the nest and lay eggs earlier, in turn, it’s worth nesting in already more densely nested areas for late beginners. We suggest that a game theoretical approach may be useful if we try to understand the adaptive significance of colonial breeding.
eQTL network analysis reveals that regulatory genes are evolutionarily older and bearing more types of PTM sites in Coprinopsis cinerea
Authors: Chang Jinhui , Au Tommy CH , Cheng CK , Kwan HS
Published: September 2018

Understanding the DNA variation in regulation of carbohydrate-active enzymes (CAZymes) is fundamental to the use of wood-decaying basidiomycetes in lignocellulose conversion into renewable energy. Our goal is to identify the regulators of lignocellulolytic enzymes in Coprinopsis cinerea, of which the genome harbors high number of Auxiliary Activities enzymes.

The DNA sequence of C. cinerea family including 46 single spore isolates (SSIs) from crosses of two homozygous strains are used to develop a panel of SNP markers. Then the RNA sequence were used to characterize the gene expression profiles. The RNA were extracted from cultures grown on softwood-enriched sawdust to induce lignocellulolytic enzymes and CCR de-repression genes. To assess the genetic contribution to enzyme expression variations among the 46 SSIs, associations between SNPs and gene expressions were examined genome-widely. 5148 local eQTLs and 7738 distant eQTLs were obtained. By analyzing these eQTLs, the potential regulatory factors of the CAZymes expression and the de-repression of Carbon Catabolism Repression (CCR) were identified,.

The eQTL network is characterized in terms of hotspots, evolutionary age and post-translational modifications (PTMs). In the eQTL network of C. cinerea, the non-regulatory genes are younger than the regulatory genes. The proteins regulated by combinational multiple types of PTMs are more likely to function as super regulatory hotspots in protein-protein interactions. The evolutionary age analysis and the PTMome analysis could serve as alternative methods to identify master regulators from genomic data.

This work demonstrates a comprehensive bioinformatics approach to identify regulatory factors with next-generation sequencing data. The results provide candidate genes for bioengineering to increase the enzyme production, which will practically benefit the bioethanol production from lignocellulose.

Significance

This eQTL analysis is designed to study the fungal CAZymes and carbon catabolism repression, especially during the mycelium stage.

In Coprinopsis cinerea, only the regions near two ends of the chromosomes have high recombination rate, and suitable for family based eQTL analysis.

A sugar transporter is a hotspot controlling many CCR genes.

CAZymes are not regulated by a master regulator, but by individual regulators. This indicates that CAZymes are under specific regulatory pathways, so can response to specific conditions.

In the eQTL network, the rGenes are evolutionarily older, with more types of PTM sites than eGenes.

In the eQTL network, the proteins with more types of PTM sites are more likely associated with Information Storage and Processing, and act as super-hub in the network.
Cex1 is a new component of the COPI Golgi-to-vacuole intracellular trafficking machinery
Authors: Enkler Ludovic , de Craene Johann Owen , Rinaldi Bruno , Hammann Philippe , Nureki Osamu , Senger Bruno , Friant Sylvie , Becker Hubert D.
Published: September 2018

During translational elongation, aminoacylated tRNA are supplied to the ribosome by RNA-interacting proteins. Cex1, a HEAT-containing protein, has been shown to participate to this tRNA channeling by interacting with aminoacylated tRNA during their export from the nucleus. Here, we show that Cex1 is a component of COPI (coatomer complex I) coated vesicles involved in the Golgi-to-vacuole trafficking pathway in Saccharomyces cerevisiae. Cex1 interacts with key components of the COPI coat Sec27, Sec28 and Sec33 proteins. Moreover, fluorescent microscopy indicates that Cex1 is not localized at the nuclear periphery as expected for an effector of nuclear tRNA channeling, but is observed on endosomal trans-Golgi network (TGN) positive structures. This localization relies on the vacuolar protein sorting receptor Vps10. Our data not only resolve the functional ambiguity regarding Cex1 homologues across species, but also point to the possibility to develop yeast-based models to study neurodegenerative disorders linked to the Human Cex1 homologue SCYL1.
Thyroid hormone modulation during zebrafish development recapitulates evolved diversity in danionin jaw protrusion mechanics
Authors: Galindo Demi , Sweet Elly , DeLeon Zoey , Wagner Mitchel , DeLeon Adrian , Carter Casey , McMenamin Sarah , Cooper W. James
Published: September 2018

One of three vertebrates belongs to a fish lineage for which protrusile jaws are a synapomorphy. Identifying the developmental determinants of protrusion ability will improve our understanding of an important area of evolutionary diversification. The high water viscosities experienced by tiny fish larvae inhibit the viability of protrusile jaws. In the zebrafish protrusion does not arise until after metamorphosis. Fish metamorphosis typically includes significant changes in trophic morphology, accompanies a shift in feeding niche and coincides with increased thyroid hormone production. We tested whether thyroid hormone affects the development of zebrafish feeding mechanics. We found that it affected all developmental stages examined, but that these effects were most pronounced after metamorphosis. Thyroid hormone levels affected the development of jaw morphology, feeding mechanics, shape variation and cranial ossification. Adult zebrafish utilize protrusile jaws, but an absence of thyroid hormone eliminated postmetamorphic remodeling of the premaxilla and the premaxillary structure that permits protrusion never formed. The premaxillae of late juvenile and adult zebrafish are similar to those found in the adults of otherDaniospecies. Premaxillae from early juvenile zebrafish and hypothyroid adult zebrafish resemble those from adults in the generaDanionella,DevarioandMicrodevariothat show little to no jaw protrusion.
Candida albicansbiofilms are generally devoid of persister cells
Authors: Denega Iryna , d’Enfert Christophe , Bachellier-Bassi Sophie
Published: September 2018

Candida albicansis known for its ability to form biofilms – communities of microorganisms embedded in an extracellular matrix developing on different surfaces. Biofilms are highly tolerant to antifungal therapy. This phenomenon has been partially explained by the appearance of so-called persister cells, phenotypic variants of wild-type cells, capable of surviving very high concentrations of antimicrobial agents. Persister cells inC. albicanswere found exceptionally in biofilms while none were detected in planktonic cultures of this fungus. Yet, this topic remains controversial as others could not observe persister cells in biofilms formed by theC. albicansSC5314 laboratory strain. Due to ambiguous data in the literature, this work aimed to reevaluate the presence of persister cells inC. albicansbiofilms. We demonstrated that isolation ofC. albicans“persister cells” as described previously was likely to be the result of survival of biofilm cells that were not reached by the antifungal. We tested biofilms of SC5314 and its derivatives, as well as 95 clinical isolates, using an improved protocol, demonstrating that persister cells are not a characteristic trait ofC. albicansbiofilms. Although some clinical isolates are able to yield survivors upon the antifungal treatment of biofilms, this phenomenon is rather stochastic and inconsistent.
Quantifying Heterogeneity in the Genetic Architecture of Complex Traits Between Ethnically Diverse Groups using Random Effect Interaction Models
Authors: Veturi Yogasudha , de los Campos Gustavo , Yi Nengjun , Huang Wen , Vazquez Ana I. , Kühnel Brigitte
Published: September 2018

In humans, most genome-wide association studies have been conducted using data from Caucasians and many of the reported findings have not replicated in other populations. This lack of replication may be due to statistical issues (small sample size, confounding) or perhaps more fundamentally to differences in the genetic architecture of traits between ethnically diverse subpopulations. What aspects of the genetic architecture of traits vary between subpopulations and how can this be quantified? We consider studying effect heterogeneity using random-effect Bayesian interaction models. The proposed methodology can be applied using shrinkage and variable selection methods and produces useful information about effect heterogeneity in the form of whole-genome summaries (e.g., SNP-heritability and the average correlation of effects) as well as SNP-specific attributes. Using simulations, we show that the proposed methodology yields (nearly) unbiased estimates of genomic heritability and of the average correlation of effects between groups when the sample size is not too small relative to the number of SNPs used. Subsequently, we used the proposed methodology for the analyses of four complex human traits (standing height, high-density lipoprotein, low-density lipoprotein, and serum urate levels) in European-Americans (EAs) and African-Americans (AAs). The estimated correlations of effects between the two subpopulations was well below unity for all the traits, ranging from 0.73 to 0.50. The extent of effect heterogeneity varied between traits and SNP-sets. Height showed less differences in SNP effects between AAs and EAs whereas HDL, a trait highly influenced by life-style, exhibited greater extent of effect heterogeneity. For all the traits we observed substantial variability in effect heterogeneity across SNPs, suggesting it varies between regions of the genome.
Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species
Authors: Wells Konstans , Morand Serge , Wardeh Maya , Baylis Matthew
Published: September 2018

Emerging infectious diseases arising from pathogen spillover from mammals to humans comprise a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines. However, the species that share pathogens most widely with other mammals, and the role of different wildlife groups in sharing viruses with humans remain poorly identified. To address this challenge, we applied network analysis and Bayesian hierarchical models to a global database of mammal-virus associations. We show that domesticated mammals and some primates hold the most central positions in networks of known mammal-virus associations. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses, while the frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than DNA viruses. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses with other host species, while network centrality of Primates scored relatively high for sharing DNA viruses. Ungulates hold central positions for sharing both RNA and DNA viruses. Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change.
Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture
Authors: Sweeney Emily G. , Nishida Andrew , Weston Alexandra , Bañuelos Maria S. , Potter Kristin , Conery John , Guillemin Karen
Published: September 2018

Mature bacterial biofilms have elaborate three-dimensional architectures that endow these structures with their durability and resistance to environmental perturbations. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of the human pathogen Helicobacter pylori. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with varying AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger scale emergent properties of biofilms.

Importance

Most bacteria exist in aggregated, three-dimensional structures called biofilms. Biofilms are resistant to antimicrobials and can pose societal problems, for example when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, autoinducer-2 (AI-2) and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.
Single fiber proteomics of respiratory chain defects in mitochondrial disorders
Authors: Murgia Marta , Tan Jing , Geyer Philipp E. , Doll Sophia , Mann Matthias , Klopstock Thomas
Published: September 2018

Mitochondrial DNA mutations progressively compromise the respiratory chain of skeletal muscle, resulting in a mosaic of metabolically healthy and defective fibers. The single fiber investigation of this important diagnostic feature has been beyond the capability of large-scale technologies so far. We used laser capture microdissection (LCM) to excise thin sections of individual muscle fibers from frozen biopsies of patients suffering from chronic progressive external ophthalmoplegia. We then applied a highly sensitive mass spectrometry (MS)-based proteomics workflow to analyze healthy and defective muscle fibers within the same biopsy. We quantified more than 4000 proteins in each patient, covering 75% of all respiratory chain subunits, and compared their expression in metabolically healthy and defective muscle fibers. Our findings show that mitochondrial disease causes extensive proteomic rearrangements, affecting the OPA1-dependent cristae remodeling pathway and mitochondrial translation. We provide fiber type-specific information showing that increased expression of fatty acid oxidation enzymes occurs in defective slow but not fast muscle fibers. Our findings shed light on compensatory mechanisms in muscle fibers that struggle with energy shortage and metabolic stress.
Cationic charge and polyspecificity of an integrin domain regulates infectivity of malaria parasites
Authors: Klug Dennis , Goellner Sarah , Sattler Julia , Strauss Leanne , Kehrer Jessica , Beyer Konrad , Reinig Miriam , Singer Mirko , Lu Chafen , Springer Timothy A. , Frischknecht Friedrich
Published: September 2018

Cell-cell and cell-substrate adhesion is critical for many functions in life. In eukaryotes, I-domains mediate functions as divergent as tissue traversal by malaria-causingPlasmodiumparasites as well as cell adhesion and migration by human leucocytes. The I-domain containing protein TRAP is important forPlasmodiumsporozoite motility and invasion. Here we show that the I-domain of TRAP is required to mediate adhesional properties which can be partially preserved when the native I-domain is replaced by I-domains from human integrins or from an apicomplexan parasite that does not infect insects. By putting in vivo data and structural features in perspective we conclude that polyspecificity and positive charge around the ligand binding site of the I-domain are important for TRAP function. Our data suggest a highly preserved functionality of I-domains across eukaryotic evolution that is used by apicomplexan parasites to invade a broad range of tissues in a variety of hosts.
Policy lessons from spatiotemporal enrollment patterns of Payment for Ecosystem Service Programs in Argentina
Authors: Núñez-Regueiro Mauricio M. , Branch Lyn C. , Hiller Josh , Núñez Godoy Cristina , Siddiqui Sharmin , Volante José , Soto José R.
Published: September 2018

Over the last 50 years, payment for ecosystem services schemes (PES) have been lauded as a market-based solution to curtail deforestation and restore degraded ecosystems. However, PES programs often fail to conserve sites under strong long-term deforestation pressures and allocate financial resources without having a sizeable impact on long-term land use change. Underperformance, in part, is likely due to adverse selection as landowners with land at the lowest threat from conversion or loss may be most likely to enroll or enrollment may be for short time-periods. Improving program performance to overcome adverse selection requires understanding attributes of landowners and their land across large scales to identify spatial and temporal enrollment patterns that drive adverse selection. In this paper, we examine these patterns in Argentina’s PES program in the endangered Chaco forest ecoregion, which was established in 2007 under the National Forest Law. Our study area covers 252,319 km2. Among our most important findings is that large parcels of enrolled land and land owned by absentee landowners show greater evidence of spatiotemporal adverse selection than smaller plots of land and land owned by local actors. Furthermore, lands managed for conservation and restoration are more likely to be associated with adverse selection than lands that provide financial returns such as harvest of non-timber forest products, silviculture, and silvopasture. However, prior to recommending that PES programs focus on land uses with higher potential earnings, a greater understanding is needed of the degree to which these land uses meet ecological and biodiversity goals of PES programs. Because of this, we posit that a PES incorporating a market-based compensation strategy that varies with commodity prices, along with approaches that provide incentives for conservation and restoration land uses and enrollment of local landowners, could promote long-term conservation of endangered lands.
Hierarchical structure and memory retrieval mechanisms in agreement attraction
Authors: Franck Julie , Wagers Matthew
Published: September 2018

Speakers occasionally cause the verb to agree with an element that is not the subject, a so-called ‘attractor’; likewise, comprehenders occasionally fail to notice agreement errors when the attractor agrees with the verb. Cross-linguistic studies converge in showing that attraction is modulated by the hierarchical position of the attractor in the sentence structure. We report two experiments exploring the link between structural position and memory representations in attraction. The method used is innovative in two respects: we used jabberwocky materials to control for semantic influences and focus on structural agreement processing, and we used a Speed-Accuracy Trade-off (SAT) design combined with a memory probe recognition task, as classically used in list memorization tasks. SAT allowed us to investigate the full time-course of processing and it enabled the joint measurement of retrieval speed and retrieval accuracy. Experiment 1 first established that attraction arises in jabberwocky sentences, to a similar extent and following the same structure-dependency as in natural sentences. Experiment 2 showed a close alignment between the attraction profiles found in Experiment 1 and memory parameters. Results support a content-addressable architecture of memory representations for sentences in which nouns’ accessibility depends on their syntactic position, while subjects are kept in the focus of attention.