bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host circadian clocks do not set the schedule for the within-host replication of malaria parasites
Authors: O’Donnell Aidan J. , Prior Kimberley F. , Reece Sarah E. 
Published: September 2019

SUMMARYCircadian clocks coordinate organisms’ activities with daily cycles in their environment. Parasites are subject to daily rhythms in the within-host environment, resulting from clock-control of host behaviours and physiologies, including immune responses. Parasites also exhibit rhythms in within-host activities; the timing of host feeding sets the timing of the within-host replication of malaria parasites. Why host feeding matters to parasites and how coordination with feeding is achieved are unknown. Determining whether parasites coordinate with clock-driven food-related rhythms of their hosts matters because rhythmic replication underpins disease symptoms and fuels transmission.We find that parasite rhythms became coordinated with the time of day that hosts feed in both wild type and clock-mutant mice, whereas parasite rhythmicity was lost in clock-mutant mice that fed continuously. These patterns occurred regardless of whether infections were initiated with synchronous or with desynchronised parasites.Malaria parasite rhythms are not driven by canonical clock-controlled host rhythms. Instead, we propose parasites coordinate with a temporally-restricted nutrient that becomes available through host digestion or are influenced by a separate clock-independent host process that directly responds to feeding. Thus, interventions could disrupt parasite rhythms to reduce their fitness, without interference by host clock-controlled-homeostasis.
Photosystem II does not convert nascent oxygen to the poisonous singlet form
Authors: Mattila Heta , Tyystjärvi Esa 
Published: September 2019

AbstractIn the light, the Mn4CaO5complex of Photosystem II (PSII) splits water producing O2and the triplet state of the primary donor (3P680) of PSII generates reactive singlet oxygen (1O2). We show that nascent O2is not converted to1O2, but originates exclusively from ambient O2, indicating that the sensitivity of PSII to oxidative damage is not a consequence of the water-splittingper se, and showing that the suggested oxygen channels function nearly perfectly, conveying nascent O2out of the reach of3P680. This may have been crucial during evolution of oxygenic photosynthesis, as3P680cannot be quenched by carotenoids that protect non- oxygenic photosystems. In addition, the data indicate that a1O2-independent mechanism contributes to the light-induced damage of PSII.
Gene capture by transposable elements leads to epigenetic conflict in maize
Authors: Muyle Aline , Seymour Danelle , Darzentas Nikos , Primetis Elias , Gaut Brandon S. , Bousios Alexandros 
Published: September 2019

AbstractPlant transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic cross-talk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. Here, we examined this model by focusing on three TE families in maize: Helitrons, Pack-MULEs and Sirevirus LTR retrotransposons. We documented 1,263 TEs containing exon fragments from 1,629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog vs. translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt cross-talk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing by being highly methylated and less expressed. They were also overrepresented among donor genes, suggesting a link between capture and gene movement. The evidence for an advantage to TEs was less obvious. TEs with captured fragments were older, mapped fewer siRNAs and were slightly less methylated than TEs without captured fragments but showed no evidence of increased copy numbers. Altogether, our results demonstrate that TE capture triggers an epigenetic conflict for important genes, but it may lead to pseudogenization for less constrained genes.
Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon
Authors: Verta Jukka-Pekka , Debes Paul Vincent , Piavchenko Nikolai , Ruokolainen Annukka , Ovaskainen Outi , Moustakas-Verho Jacqueline Emmanuel , Tillanen Seija , Parre Noora , Aykanat Tutku , Erkinaro Jaakko , Primmer Craig Robert 
Published: September 2019

AbstractA major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the early and late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results reveal how regulatory differences can be a central mechanism for the evolution of life history traits.Author summaryAlternative life history strategies are an important source of diversity within populations and promote the maintenance of adaptive capacity and population resilience. However, in many cases the molecular basis of different life history strategies remains elusive. Age at maturity is a key adaptive life history trait in Atlantic salmon and has a relatively simple genetic basis. Using salmon age at maturity as a model, we report a mechanism whereby different transcript isoforms of the key age at maturity gene, vestigial-like 3 (vgll3), associate with variation in the timing of male puberty. Our results show how gene regulatory differences in conjunction with variation in gene transcript structure can encode for complex alternative life histories.
Manipulation of plant primary metabolism by leaf-mining larvae in the race against leaf senescence
Authors: Body Mélanie J.A. , Casas Jérôme , Giron David 
Published: September 2019

AbstractPlants are often considered as suboptimal food for phytophagous insects, requiring them to employ various adaptive mechanisms to overcome food nutritional imbalances. This could include host-plant manipulation and/or symbiotic associations. The extensive reconfiguration of plant primary metabolism upon herbivory, as well as its impact on herbivores, have been largely overlooked, while studies investigating secondary metabolites is extensive. Here, we document how the apple leaf-mining caterpillarPhyllonorycter blancardella, a highly-specialized insect which completes development within a restricted area of a singleMalus domesticaleaf over successive different larval feeding modes, maintains nutrient-rich green tissues in its feeding area on green and senescent leaves. For this purpose, we quantified a large number of compounds involved in plant primary metabolism: starch, total soluble sugars, five individual sugars, twenty protein-bound amino acids and twenty free amino acids. Plant alteration can be observed not only on senescing (photosynthetically inactive) but also normal (photosynthetically active) leaf tissues of its host-plant to compensate for detrimental environmental variations. Our results show a differential control of the primary metabolism depending on the larva developmental stage, itself correlated to the fluid-feeding and tissue-feeding modes. Our results also suggest that leaf amino acid alterations favor a faster insect development. Finally, chemical scores indicate that the most growth-limiting essential amino acids are also common to other phytophagous insects and large herbivores, suggesting that these limitations are a general consequence of using plants as food source. We discuss the possible mechanisms responsible for these different manipulative capacities, as well as their ecological implications.
Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog/Gli Is Required for Tracheoesophageal Separation
Authors: Nasr Talia , Mancini Pamela , Rankin Scott A. , Edwards Nicole A. , Agricola Zachary N. , Kenny Alan P. , Kinney Jessica L. , Daniels Keziah , Vardanyan Jon , Han Lu , Trisno Stephen L. , Cha Sang-Wook , Wells James M. , Kofron Matthew J. , Zorn Aaron M. 
Published: September 2019

SUMMARYThe trachea and esophagus arise from the separation of a common foregut tube during early fetal development. Mutations in key signaling pathways such as Hedgehog (HH)/Gli can disrupt tracheoesophageal (TE) morphogenesis and cause life-threatening birth defects (TEDs), however the underlying cellular mechanisms are unknown. Here we use mouse andXenopusto define the HH/Gli-dependent processes orchestrating TE morphogenesis. We show that downstream of Gli the Foxf1+ splanchnic mesenchyme promotes medial constriction of the foregut at the boundary between the presumptive Sox2+ esophageal and Nkx2-1+ tracheal epithelium. We identify a unique boundary epithelium co-expressing Sox2 and Nkx2-1 that fuses to form a transient septum. Septum formation and resolution into distinct trachea and esophagus requires endosome-mediated epithelial remodeling involving the small GTPase Rab11, and localized extracellular matrix degradation. These are disrupted in Gli-deficient embryos. This work provides a new mechanistic framework for TE morphogenesis and informs the cellular basis of human TEDs.Highlight bullet pointsThe Sox2+ esophagus and Nkx2-1+ trachea arise from the separation of a single foregut tube through a series of cellular events conserved in mouse andXenopusTracheoesophageal morphogenesis initiates with HH/Gli-dependent medial constriction of the gut tube mesenchyme at the Sox2-Nkx2-1 borderThe foregut epithelial walls fuse forming a transient septum co-expressing Sox2 and Nkx2-1Downstream of HH/Gli Rab11-dependent endosome-mediated epithelial remodeling and localized extracellular matrix degradation separate the esophagus and tracheaHH/Gli mutations reveal the cellular basis of tracheoesophageal birth defects
A distinct population of L6 neurons in mouse V1 mediate cross-callosal communication
Authors: Liang Yajie , Sun Wenzhi , Lu Rongwen , Chen Ming , Ji Na 
Published: September 2019

AbstractThrough the corpus callosum, interhemispheric communication is mediated by callosal projection (CP) neurons. Using retrograde labeling, we identified a population of layer 6 (L6) excitatory neurons as the main conveyer of transcallosal information in the monocular zone of the mouse primary visual cortex (V1). Distinct from L6 corticothalamic (CT) population, V1 L6 CP neurons contribute to an extensive reciprocal network across multiple sensory cortices over two hemispheres. Receiving both local and long-range cortical inputs, they encode orientation, direction, and receptive field information, while are also highly spontaneous active. The spontaneous activity of L6 CP neurons exhibits complex relationships with brain states and stimulus presentation, distinct from the spontaneous activity patterns of the CT population. The anatomical and functional properties of these L6 CP neurons enable them to broadcast visual and nonvisual information across two hemispheres, and thus play a major role in regulating and coordinating brain-wide activity events.
Genome-wide synthetic lethal CRISPR screen identifies FIS1 as a genetic interactor of ALS-linked C9ORF72
Authors: Chai Noori , Haney Michael S. , Couthouis Julien , Morgens David W. , Benjamin Alyssa , Wu Kathryn , Ousey James , Fang Shirleen , Finer Sarah , Bassik Michael C. , Gitler Aaron D. 
Published: September 2019

AbstractMutations in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis (ALS). Both toxic gain of function and loss of function pathogenic mechanisms have been proposed. Accruing evidence from mouse knockout studies point to a role for C9ORF72 as a regulator of immune function. To provide further insight into its cellular function, we performed a genome-wide synthetic lethal CRISPR screen in human myeloid cells lacking C9ORF72. We discovered a strong synthetic lethal genetic interaction between C9ORF72 and FIS1, which encodes a mitochondrial membrane protein involved in mitochondrial fission and mitophagy. Mass spectrometry experiments revealed that in C9ORF72 knockout cells, FIS1 strongly bound to a class of immune regulators that activate the receptor for advanced glycation end (RAGE) products and trigger inflammatory cascades. These findings present a novel genetic interactor for C9ORF72 and suggest a compensatory role for FIS1 in suppressing inflammatory signaling in the absence of C9ORF72.
Discovery of genes required for body axis and limb formation by global identification of retinoic acid regulated epigenetic marks
Authors: Berenguer Marie , Meyer Karolin F. , Yin Jun , Duester Gregg 
Published: September 2019

AbstractIdentification of target genes that mediate required functions downstream of transcription factors is hampered by the large number of genes whose expression changes when the factor is removed from a specific tissue and the numerous binding sites for the factor in the genome. Retinoic acid (RA) regulates transcription via RA receptors bound to RA response elements (RAREs) of which there are thousands in vertebrate genomes. Here, we combined ChIP-seq for epigenetic marks and RNA-seq on trunk tissue from wild-type andAldh1a2-/-embryos lacking RA synthesis that exhibit body axis and forelimb defects. We identified a relatively small number of genes with altered expression when RA is missing that also have nearby RA-regulated deposition of H3K27ac (gene activation mark) or H3K27me3 (gene repression mark) associated with conserved RAREs, suggesting they have important downstream functions. RA-regulated epigenetic marks were identified near RA target genes already known to be required for body axis and limb formation, thus validating our approach, plus many other candidate RA target genes were found.Nr2f1,Nr2f2,Meis1, andMeis2gene family members were identified by our approach, and double knockouts of each family demonstrated previously unknown requirements for body axis and/or limb formation. These findings demonstrate that our method for identifying RA-regulated epigenetic marks can be used to discover genes important for development.
A post-ER degradation pathway that relies on protease-dependent internalization from the vacuolar membrane
Authors: Lemus Leticia , Matić Zrinka , Goder Veit 
Published: September 2019

SummaryNewly synthesized proteins of the secretory pathway are quality-controlled inside the endoplasmic reticulum (ER) and, if not properly folded, are retained. An exception are glycosylphosphatidylinositol-anchored proteins (GPI-APs) which can leave the ER even when misfolded and are routed to the vacuole/lysosome for degradation by largely unknown mechanisms linked to post-ER quality control. Using yeast as model organism, we show that Gas1*, an ER-exported misfolded GPI-AP, is diverted from the secretory pathway to endosomes for transport to the vacuole. However, Gas1* is not sorted into endosomal intraluminal vesicles but internalizes directly from the vacuolar membrane. There, the vacuolar protease Pep4, but not any other known vacuolar protease, is required for Gas1* internalization. Our data reveal novel and unexpected mechanisms for invaginations from the vacuolar membrane.HighlightsER-exited misfolded GPI-anchored proteins are routed to the vacuole via endosomes but do not internalize into intraluminal vesiclesInternalization occurs directly from the vacuolar membrane into intravacuolar mobile structuresInternalization from the vacuolar membrane depends on the proteolytic activity of the vacuolar protease Pep4
Personality predicts foraging site fidelity and trip repeatability in a marine predator
Authors: Harris Stephanie M. , Descamps Sébastien , Sneddon Lynne U. , Bertrand Philip , Chastel Olivier , Patrick Samantha C. 
Published: September 2019

Abstract

Animal populations are often comprised of both foraging specialists and generalists. For instance, some individuals show higher foraging site fidelity (spatial specialization) than others. Such individual differences in degree of specialization can persist over time‐scales of months or even years in long‐lived animals, but the mechanisms leading to these different individual strategies are not fully understood.

There is accumulating evidence that individual variation in foraging behaviour is shaped by animal personality traits, such as boldness. Despite this, the potential for boldness to drive differences in the degree of specialization is unknown.

In this study, we used novel object tests to measure boldness in black‐legged kittiwakes (Rissa tridactyla) breeding at four colonies in Svalbard and deployed GPS loggers to examine their at‐sea foraging behaviour. We estimated the repeatability of foraging trips and used a hidden Markov model to identify locations of foraging sites in order to quantify individual foraging site fidelity.

Across the breeding season, bolder birds were more repeatable than shy individuals in the distance and range of their foraging trips, and during the incubation period (but not chick rearing), bolder individuals were more site‐faithful. Birds exhibited these differences while showing high spatial similarity in foraging areas, indicating that site selection was not driven by personality‐dependent spatial partitioning.

We instead suggest that a relationship between boldness and site fidelity may be driven by differences in behavioural flexibility between bold and shy individuals. Together, these results provide a potential mechanism by which widely reported individual differences in foraging specialization may emerge.
The impact of elevated temperature and drought on the ecology and evolution of plant–soil microbe interactions
Authors: Rasmussen Pil U. , Bennett Alison E. , Tack Ayco J. M. 
Published: September 2019

Abstract

Climate change is shifting the distribution of species, and may have a profound impact on the ecology and evolution of species interactions. However, we know little about the impact of increasing temperature and changing rainfall patterns on the interactions between plants and their beneficial and antagonistic root symbionts.

Here, we used a reciprocal multifactorial growth chamber experiment with seeds and soil microbial communities from three origins to investigate the impact of temperature and soil moisture on the growth, arbuscular mycorrhizal (AM) fungal colonization and root‐associated fungal community of a perennial herb. Moreover, we tested whether plants and AM fungi performed better or worse when plants were grown with their local soil biota, for example, due to plant adaptation or changes in the genetic or species composition of the soil microbial community.

Temperature and soil moisture generally increased plant growth, whereas temperature but not soil moisture increased AM fungal colonization. The strength and direction of the plants' response to temperature were dependent on soil moisture and differed among plant populations, and AM fungal colonization was further affected by the origin of the soil microbial community. The root‐associated fungal community structure was impacted by temperature, soil moisture and the soil microbial origin, with interactive effects between the microbial origin and the abiotic environment. Plant biomass was lower when plants were grown with their local soil microbes, potentially due to intraspecific negative plant–soil feedbacks.

Synthesis. Our findings indicate that, beyond a relatively uniform increase of plant growth and arbuscular mycorrhizal (AM) fungal colonization with increasing temperature, plants and root‐associated fungi of different origins will vary in their response to climate change (i.e. elevated temperature and shifts in rainfall). This may create pronounced, but difficult to predict, spatial and temporal variation in the ecology and evolution of plant–microbe interactions with a changing climate.
Art and anthropology for a sustainable world
Authors: Ingold Tim 
Published: September 2019

AbstractBoth art and anthropology, this article proposes, are future‐oriented disciplines, united in the common task of fashioning a world fit for coming generations to inhabit. The first step in establishing this proposition is to show how the objectives of anthropology differ from those of ethnography. Anthropology, it is argued, establishes a relation with the world that is correspondent rather than tangential, that prioritizes difference over alterity, and that places presence before interpretative contextualization. The second step is to rethink the idea of research – to show how, as an open‐ended search for truth and a practice of correspondence, research necessarily overflows the bounds of objectivity. Art and anthropology, then, and not natural science, are exemplary in the pursuit of truth as a way of knowing‐in‐being. The third step is to show that only if it is conceived in this way can research be conducive to the processes of renewal on which our collective futures depend. Thus research as correspondence is a condition for sustainability. But sustainability is nothing if it is not of everything. We have to begin, therefore, with the idea of everything as a plenum, in which each apparent addition is really a reworking. The article concludes with some reflections on the proposed synergy of art and anthropology for education, democracy, and citizenship.