bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Orientation Change during Environmental Learning on Age-Related Difference in Spatial Memory
Authors: Yamamoto Naohide , Fox Michael J. , Boys Ellen , Ord Jodi 
Published: September 2018

AbstractIt has been suggested that older adults suffer a greater degree of decline in environmental learning when navigating in an environment than when reading a map of the environment. However, the two types of spatial learning differ not only in perspectives (i.e., navigation is done with a ground-level perspective; a map is read from an aerial perspective) but also in orientations (i.e., orientations vary during navigation; spatial information is drawn from a single orientation in a map), making it unclear which factor critically affects older adults’ spatial learning. The present study addressed this issue by having younger and older participants learn the layout of a large-scale environment through an aerial movie that contained changes in orientations from which the environment was depicted. Results showed that older participants’ memories for the environmental layout were as distorted as those created through a ground-level movie (which involved the same orientation changes), whereas they formed more accurate memories through another aerial movie in which an orientation was fixed. By contrast, younger participants learned the environment equally well from the three movies. Taken together, these findings suggest that there is age-related alteration specifically in the ability to process multiple orientations of an environment while encoding its layout in memory. It is inferred that this alteration stems from functional deterioration of the medial temporal lobe, and possibly that of posterior cingulate areas as well (e.g., the retrosplenial cortex), in late adulthood.
The genomic view of diversification
Authors: Marin Julie , Achaz Guillaume , Crombach Anton , Lambert Amaury 
Published: September 2018

AbstractEvolutionary relationships between species are traditionally represented in the form of a tree, the species tree. Its reconstruction from molecular data is hindered by frequent conflicts between gene genealogies. Usually, these disagreements are explained by incomplete lineage sorting (ILS) due to random coalescences of gene lineages inside the edges of the species tree. This paradigm, the multi-species coalescent (MSC), is constantly violated by the ubiquitous presence of gene flow, leading to incongruences between gene trees that cannot be explained by ILS alone. Here we argue instead in favor of a vision acknowledging the importance of gene flow and where gene histories shape the species tree rather than the opposite. We propose a new framework for modeling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees. We implement this framework in two mathematical models called the gene-based diversification models (GBD): 1) GBD-forward following all evolving genomes and 2) GBD-backward based on coalescent theory. They feature four parameters tuning colonization, gene flow, genetic drift and genetic differentiation. We propose a quick inference method based on differences between gene trees. Applied to two empirical data-sets prone to gene flow, we find a better support for the GBD model than for the MSC model. Along with the increasing awareness of the extent of gene flow, this work shows the importance of considering the richer signal contained in genomic histories, rather than in the mere species tree, to better apprehend the complex evolutionary history of species.
Very few sites can reshape a phylogenetic tree
Authors: Francis Warren R. , Canfield Donald E. 
Published: September 2018

AbstractThe history of animal evolution, and the relative placement of extant animal phyla in this history is, in principle, testable from phylogenies derived from molecular sequence data. Though datasets have increased in size and quality in the past years, the contribution of individual genes (and ultimately amino acid sites) to the final phylogeny is unequal across genes. Here we demonstrate that by removing a small fraction of sites that strongly favor one topology, it is possible produce a highly-supported tree of an alternate topology. We explore this approach using a dataset for animal phylogeny, and create a highly-supported tree with a monophyletic group of sponges and ctenophores, a topology not usually recovered. As nearly all gene sets are neither standardized nor representative of the entire genome, we conclude that there are only two possible ways to remedy this problem. One solution would need to use a fixed set of genes, which though not representative, is at least standardized. The other would be to construct phylogenies using all genes, thus limiting analysis to species with sequenced genomes.
Cortical control of locomotor muscle activity through muscle synergies in humans: a neural decoding study
Authors: Yokoyama Hikaru , Kaneko Naotsugu , Ogawa Tetsuya , Kawashima Noritaka , Watanabe Katsumi , Nakazawa Kimitaka 
Published: September 2018

AbstractWalking movements are orchestrated by the activation of a large number of muscles. The control of numerous muscles during walking is believed to be simplified by flexible activation of groups of muscles called muscle synergies. Although significant corticomuscular connectivity during walking has been reported, the level at which the cortex controls locomotor muscle activity (i.e., muscle synergy or individual muscle level) remains unclear. Here, we examined cortical involvement in muscle control during walking by brain decoding of the activation of muscle synergies and individual muscles from electroencephalographic (EEG) signals using linear decoder models. First, we demonstrated that activation of locomotor muscle synergies was decoded from slow cortical waves with significant accuracy. In addition, we found that decoding accuracy for muscle synergy activation was greater than that for individual muscle activation and that decoding of individual muscle activation was based on muscle synergy-related cortical information. Taken together, these results provide indirect evidence that the cerebral cortex hierarchically controls multiple muscles through a few muscle synergies during walking. Our findings extend the current understanding of the role of the cortex in muscular control during walking and could accelerate the development of effective brain-machine interfaces for people with locomotor disabilities.
Spatial and temporal organization of RecA in theEscherichia coliDNA-damage response
Authors: Ghodke Harshad , Paudel Bishnu P , Lewis Jacob S , Jergic Slobodan , Gopal Kamya , Romero Zachary J , Wood Elizabeth A , Woodgate Roger , Cox Michael M , van Oijen Antoine M 
Published: September 2018

SummaryThe RecA protein orchestrates the cellular response to DNA damage via its multiple roles in the bacterial SOS response. Lack of tools that provide unambiguous access to the various RecA states within the cell have prevented understanding of the spatial and temporal changes in RecA structure/function that underlie control of the damage response. Here, we develop a monomeric C-terminal fragment of the λ repressor as a novel fluorescent probe that specifically interacts with RecA filaments on single-stranded DNA (RecA*). Single-molecule imaging techniques in live cells demonstrate that RecA is largely sequestered in storage structures during normal metabolism. Upon DNA damage, the storage structures dissolve and the cytosolic pool of RecA rapidly nucleates to form early SOS-signaling complexes, maturing into DNA-bound RecA bundles at later time points. Both before and after SOS induction, RecA* largely appears at locations distal from replisomes. Upon completion of repair, RecA storage structures reform.
Autophagy regulates hyaluronan synthase 2 levels in vascular endothelial cells
Authors: Chen Carolyn G. , Gubbiotti Maria A. , Han Xiaorui , Yu Yanglei , Linhardt Robert J. , Iozzo Renato V. 
Published: September 2018

AbstractHyaluronan is emerging as a key player regulating wound repair, inflammation, and angiogenesis. Of the three hyaluronan synthases (HAS1-3), HAS2 is the main driver of tumorigenicity by enhancing hyaluronan deposition. We discovered that HAS2 was degraded in vascular endothelial cells via autophagy, a catabolic process evoked by endorepellin and endostatin, two angiostatic and pro-autophagic effectors, and by Torin 1, a specific mTOR inhibitor. Protracted autophagy increased co-localization of HAS2 with three core components of the autophagosome, LC3, p62, and ATG9A, and binding of HAS2 to ATG9A. Importantly, autophagic induction led to an exclusive and marked suppression of secreted hyaluronan with no significant effects on either heparan or chondroitin sulfate levels. Thus, we have unveiled autophagy as a key catabolic mechanism regulating the production of hyaluronan in endothelial cells. Moreover, our study provides a biological link between autophagy and angiogenesis that could lead to potential targets for tumor neovascularization.SummaryHyaluronan is pro-angiogenic and pro-tumorigenic. We report a novel mechanism through which three autophagic inducers―endorepellin, endostatin, and Torin 1―regulate the levels of hyaluronan synthase-2. Protracted autophagy results in suppression of extracellular hyaluronan, thereby implicating autophagy in the regulation hyaluronan production.
The Perceptual Neural Trace of Memorable Unseen Scenes
Authors: Mohsenzadeh Yalda , Mullin Caitlin , Oliva Aude , Pantazis Dimitrios 
Published: September 2018

ABSTRACTSome scenes are more memorable than others: they cement in minds with consistencies across observers and time scales. While memory mechanisms are traditionally associated with the end stages of perception, recent behavioral studies suggest that the features driving these memorability effects are extracted early on, and in an automatic fashion. This raises the question: is the neural signal of memorability detectable during early perceptual encoding phases of visual processing? Using the high temporal resolution of magnetoencephalography (MEG), during a rapid serial visual presentation (RSVP) task, we traced the neural temporal signature of memorability across the brain. We found an early and prolonged memorability related signal recruiting a network of regions in both dorsal and ventral streams, detected outside of the constraints of subjective awareness. This enhanced encoding could be the key to successful storage and recognition.
Spatial variation in the biochemical and isotopic composition of corals during bleaching and recovery
Authors: Wall Christopher B , Ritson-Williams Raphael , Popp Brian N , Gates Ruth D 
Published: September 2018

AbstractOcean warming and the increased prevalence of coral bleaching events threaten coral reefs. However, the biology of corals during and following bleaching events under field conditions is poorly understood. We examined bleaching and post-bleaching recovery inMontipora capitataandPorites compressacorals that either bleached or did not bleach during a 2014 bleaching event at three reef locations in Kāne‘ohe Bay, O‘ahu. We measured changes in chlorophylls, biomass, and nutritional plasticity using stable isotopes (δ13C, δ15N). Coral traits showed significant variation among bleaching conditions, reef sites, time periods, and their interactions. Bleached colonies of both species had lower chlorophyll and total biomass. WhileM. capitatachlorophyll and biomass recovered three months later,P. compressachlorophyll recovery was location-dependent and total biomass of previously bleached colonies remained low. Biomass energy reserves were not affected by bleaching, insteadM. capitataproteins andP. compressabiomass energy declined over time, andP. compressalipid biomass was site-specific. Stable isotope analyses of host and symbiont tissues did not indicate increased heterotrophic nutrition in bleached colonies of either species, during or after thermal stress. Instead, mass balance calculations revealed variance in δ13C values was best explained by augmented biomass composition, whereas δ15N values reflected spatial and temporal variability in nitrogen sources in addition to bleaching effects on symbiont nitrogen demand. These results emphasize total biomass quantity may change substantially during bleaching and recovery. Consequently, there is a need to consider the influence of biomass composition in the interpretation of isotopic values in corals.
Bacterial clearance enhanced by α2, 3- and α2, 6-sialyllactose via receptor-mediated endocytosis and phagocytosis
Authors: Kim Jimin , Kim Yong Jae , Kim Jae Wha 
Published: September 2018

AbstractSialyllactose (SL) is a representative human milk oligosaccharide (HMO) of human breast milk. The roles of SL in infant brain development and immunity have been reported in previous studies. In this study, we identified the impact of SL on innate immunity. Our results showed that the administration of SL had significant efficacy on bacterial clearance in Pseudomonas aeruginosa K-infected mice. We also examined the role of SL in the human THP-1 macrophage-like cell line. SL effectively promoted receptor-mediated endocytosis and phagocytosis. Furthermore, SL accelerated the recruitment of Rac1 to the cell membrane, leading to the generation of reactive oxygen species for the elimination of phagocytosed bacteria. Our findings provide a new perspective on the role of SL in breast milk and suggest its potential application as a therapeutic agent to treat bacterial and viral infections.
Genome-wide admixture is common across the Heliconius radiation
Authors: Kozak Krzysztof M. , McMillan W. Owen , Joron Mathieu , Jiggins Christopher D. 
Published: September 2018

ABSTRACTHow frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, implying that speciation is a series of splits between lineages. Yet gene flow between good species is increasingly recognized as an important mechanism in the diversification of radiations, often spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied in cases involving few species, or geographically restricted to spaces like islands, but not on the scale of a continental radiation. Previous studies have documented gene flow, adaptive introgression and hybrid speciation in a small subsection of the charismatic Neotropical butterflies Heliconius. Using genome-wide resequencing of 40 out of 45 species in the genus we demonstrate for the first time that admixture has played a role throughout the evolution of Heliconius and the sister genus Eueides. Modelling of phylogenetic networks based on 6848 orthologous autosomal genes (Maximum Pseudo-Likelihood Networks) or 5,483,419 high quality SNPs (Ancestral Recombination Graph) uncovers nine new cases of interspecific gene flow at up to half of the genome. However, f4 statistics of admixture show that the extent of the process has varied between subgenera. Evidence for introgression is found at all five loci controlling the colour and shape of the mimetic wing patterns, including in the putative hybrid species H. hecalesia, characterised by an unusual hindwing. Due to hybridization and incomplete coalescence during rapid speciation, individual gene trees show rampant discordance. Although reduced gene flow and faster coalescence are expected at the Z chromosome, we discover high levels of conflict between the 416 sex-linked loci. Despite this discordant pattern, both concatenation and multispecies coalescent approaches yield surprisingly consistent and fully supported genome-wide phylogenies. We conclude that the imposition of the bifurcating tree model without testing for interspecific gene flow may distort our perception of adaptive radiations and thus the ability to study trait evolution in a comparative framework.
Pleistocene climate changes explain large-scale genetic variation in a dominant grassland species, Lolium perenne L
Authors: Blanco-Pastor J.L. , Manel S. , Barre P. , Roschanski A.M. , Willner E. , Dehmer K.J. , Hegarty M. , Muylle H. , Ruttink T. , Roldán-Ruiz I. , Ledauphin T. , Escobar-Gutierrez A. , Sampoux J.P. 
Published: September 2018

AbstractAimGrasslands have been pivotal in the development of herbivore breeding since the Neolithic and are still nowadays the most widespread agricultural land-use across Europe. However, it remains unclear whether the current large-scale genetic variation of plant species found in natural grasslands of Europe is the result of human activities or natural processes.LocationEurope.TaxonLolium perenne L (perennial ryegrass).MethodsWe reconstructed the phylogeographic history of L. perenne, a dominant grassland species, using 481 natural populations including 11 populations from closely related taxa. We combined the Genotyping-by-Sequencing (GBS) and Pool-sequencing (Pool-seq) methods to obtain high-quality allele frequency calls of ~ 500 k SNP loci. We performed genetic structure analyses and demographic reconstructions based on the site frequency spectrum (SFS). We additionally used the same genotyping protocol to assess the genomic diversity of a set of 32 cultivars representative of the L. perenne cultivars widely used for forage purposes.ResultsExpansion across Europe took place during the Würm glaciation (12-110 kya), a cooling period that decreased the dominance of trees in favour of grasses. Splits and admixtures in L. perenne fit historical sea level changes in the Mediterranean basin. The development of agriculture in Europe (7-3.5 kya), that caused an increase in the abundance of grasslands, did not have an effect on the demographic patterns of L. perenne. We found little differentiation between modern cultivars and certain natural variants. However, modern cultivars do not represent the wide genetic variation found in natural populations.Main conclusionsDemographic events in L. perenne can be explained by the changing climatic conditions during the Pleistocene. Natural populations maintain a wide genomic variability at continental scale that has been underused by recent breeding activities. This variability constitutes valuable standing genetic variation for future adaptation of grasslands to climate change, safeguarding the agricultural services they provide.
Myh10deficiency leads to defective extracellular matrix remodeling and pulmonary disease
Authors: Kim Hyun-Taek , Yin Wenguang , Jin Young-June , Panza Paolo , Gunawan Felix , Grohmann Beate , Buettner Carmen , Sokol Anna M. , Preussner Jens , Guenther Stefan , Kostin Sawa , Ruppert Clemens , Bhagwat Aditya M. , Ma Xuefei , Graumann Johannes , Looso Mario , Guenther Andreas , Adelstein Robert S. , Offermanns Stefan , Stainier Didier Y.R. 
Published: September 2018

AbstractImpaired alveolar formation and maintenance are features of many pulmonary diseases that are associated with significant morbidity and mortality. In a forward genetic screen for modulators of mouse lung development, we identified the non-muscle myosin II heavy chain gene,Myh10.Myh10mutant pups exhibit cyanosis and respiratory distress, and die shortly after birth from differentiation defects in alveolar epithelium and mesenchyme. From omics analyses and follow up studies, we find decreased Thrombospondin expression accompanied with increased matrix metalloproteinase activity in both mutant lungs and cultured mutant fibroblasts, as well as disrupted extracellular matrix (ECM) remodeling. Loss ofMyh10specifically in mesenchymal cells results in ECM deposition defects and alveolar simplification. Notably, MYH10 expression is down-regulated in the lung of emphysema patients. Altogether, our findings reveal critical roles forMyh10in alveologenesis at least in part via the regulation of ECM remodeling, which may contribute to the pathogenesis of emphysema.
Structural basis of light-induced redox regulation in the Calvin cycle
Authors: McFarlane Ciaran , Shah Nita R. , Kabasakal Burak V. , Cotton Charles A.R. , Bubeck Doryen , Murray James W. 
Published: September 2018

AbstractIn plants, carbon dioxide is fixed via the Calvin cycle in a tightly regulated process. Key to this regulation is the conditionally disordered protein CP12. CP12 forms a complex with two Calvin cycle enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), inhibiting their activities. The mode of CP12 action was unknown. By solving crystal structures of CP12 bound to GAPDH, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide pre-orders CP12 prior to binding the PRK active site. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our model explains how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation.One Sentence SummaryHow plants turn off carbon fixation in the dark.
Oct1/Pou2f1 is selectively required for gut regeneration and regulates gut malignancy
Authors: Vázquez-Arreguín Karina , Bensard Claire , Schell John C. , Swanson Eric , Chen Xinjian , Rutter Jared , Tantin Dean 
Published: September 2018

AbstractThe transcription factor Oct1/Pou2f1 promotes poised gene expression states, mitotic stability, glycolytic metabolism and other characteristics of stem cell potency. To determine the effect of Oct1 loss on stem cell maintenance and malignancy, we deleted Oct1 in two different mouse gut stem cell compartments. Oct1 deletion preserved homeostasis in vivo and the ability to generate cultured organoids in vitro, but blocked the ability to regenerate after treatment with dextran sodium sulfate, and the ability to maintain organoids after passage. In a chemical model of colon cancer, loss of Oct1 in the colon severely restricted tumorigenicity. In contrast, loss of one or bothOct1alleles progressively increased tumor burden in a colon cancer model driven by loss of heterozygosity of the tumor suppressor geneApc.The different outcomes are consistent with prior findings that Oct1 promotes mitotic stability, and consistent with different gene expression signatures associated with the two models. These results reveal that Oct1 is selectively required for gut regeneration, and has potent effects in colon malignancy, with outcome (pro-oncogenic or tumor suppressive) dictated by tumor etiology.Author summaryColorectal cancer is the second leading cause of cancer death in the United States. Approximately 35% of diagnosed patients eventually succumb to disease. The high incidence and mortality due to colon cancer demand a better understanding of factors controlling the physiology and pathophysiology of the gastrointestinal tract. Previously, we and others showed that the widely expressed transcription factor is expressed at higher protein levels in stem cells, including intestinal stem cells. In this study we use a conditional mouseOct1(Pou2f1) allele deleted in two different intestinal stem cell compartments. The results indicate that Oct1 loss is dispensable for maintenance of the mouse gut, but required for regeneration. We also tested Oct1 loss in the context of two different mouse colon cancer models. We find that Oct1 loss has opposing effects in the two models, and further that the two models are associated with different gene expression signatures. The differentially expressed genes are enriched for previously identified Oct1 targets, suggesting that differential gene control by Oct1 is one mechanism underlying different outcomes.