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PLoS Biology

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https://www.readbyqxmd.com/read/30005073/decoding-the-chromatin-proteome-of-a-single-genomic-locus-by-dna-sequencing
#1
Tessy Korthout, Deepani W Poramba-Liyanage, Ila van Kruijsbergen, Kitty F Verzijlbergen, Frank P A van Gemert, Tibor van Welsem, Fred van Leeuwen
Transcription, replication, and repair involve interactions of specific genomic loci with many different proteins. How these interactions are orchestrated at any given location and under changing cellular conditions is largely unknown because systematically measuring protein-DNA interactions at a specific locus in the genome is challenging. To address this problem, we developed Epi-Decoder, a Tag-chromatin immunoprecipitation-Barcode-Sequencing (TAG-ChIP-Barcode-Seq) technology in budding yeast. Epi-Decoder is orthogonal to proteomics approaches because it does not rely on mass spectrometry (MS) but instead takes advantage of DNA sequencing...
July 13, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30005062/highly-diverged-novel-subunit-composition-of-apicomplexan-f-type-atp-synthase-identified-from-toxoplasma-gondii
#2
Rahul Salunke, Tobias Mourier, Manidipa Banerjee, Arnab Pain, Dhanasekaran Shanmugam
The mitochondrial F-type ATP synthase, a multisubunit nanomotor, is critical for maintaining cellular ATP levels. In T. gondii and other apicomplexan parasites, many subunit components necessary for proper assembly and functioning of this enzyme appear to be missing. Here, we report the identification of 20 novel subunits of T. gondii F-type ATP synthase from mass spectrometry analysis of partially purified monomeric (approximately 600 kDa) and dimeric (>1 MDa) forms of the enzyme. Despite extreme sequence diversification, key FO subunits a, b, and d can be identified from conserved structural features...
July 13, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30005061/species-in-ecosystems-and-all-that-jazz
#3
Oswald J Schmitz
Ecosystem ecologists explore how different kinds of species fit together to drive ecosystem processes such as nutrient cycling and productivity. This research is motivated by theories that assume that the suite of traits that characterize a species' form determines its function, that these traits have become fixed over evolutionary time, and that ensuing ecosystem process are not resilient to environmental change. Here, I explore new research that re-evaluates this theory. Recent results suggest that functional traits are malleable, enabling species to rapidly respond and adapt to each other as environmental conditions change with predictable effects on ecosystem processes...
July 13, 2018: PLoS Biology
https://www.readbyqxmd.com/read/30001335/the-noisy-basis-of-morphogenesis-mechanisms-and-mechanics-of-cell-sheet-folding-inferred-from-developmental-variability
#4
Pierre A Haas, Stephanie S M H Höhn, Aurelia R Honerkamp-Smith, Julius B Kirkegaard, Raymond E Goldstein
Variability is emerging as an integral part of development. It is therefore imperative to ask how to access the information contained in this variability. Yet most studies of development average their observations and, discarding the variability, seek to derive models, biological or physical, that explain these average observations. Here, we analyse this variability in a study of cell sheet folding in the green alga Volvox, whose spherical embryos turn themselves inside out in a process sharing invagination, expansion, involution, and peeling of a cell sheet with animal models of morphogenesis...
July 12, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29985916/the-actin-remodeling-protein-cofilin-is-crucial-for-thymic-%C3%AE-%C3%AE-but-not-%C3%AE-%C3%AE-t-cell-development
#5
Isabel Seeland, Ying Xiong, Christian Orlik, Daniel Deibel, Sandra Prokosch, Günter Küblbeck, Beate Jahraus, Daniela De Stefano, Sonja Moos, Florian C Kurschus, Bernd Arnold, Yvonne Samstag
Cofilin is an essential actin remodeling protein promoting depolymerization and severing of actin filaments. To address the relevance of cofilin for the development and function of T cells in vivo, we generated knock-in mice in which T-cell-specific nonfunctional (nf) cofilin was expressed instead of wild-type (WT) cofilin. Nf cofilin mice lacked peripheral αβ T cells and showed a severe thymus atrophy. This was caused by an early developmental arrest of thymocytes at the double negative (DN) stage. Importantly, even though DN thymocytes expressed the TCRβ chain intracellularly, they completely lacked TCRβ surface expression...
July 9, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29985914/cholinergic-mediated-coordination-of-rhythmic-sympathetic-and-motor-activities-in-the-newborn-rat-spinal-cord
#6
Mélissa Sourioux, Sandrine S Bertrand, Jean-René Cazalets
Here, we investigated intrinsic spinal cord mechanisms underlying the physiological requirement for autonomic and somatic motor system coupling. Using an in vitro spinal cord preparation from newborn rat, we demonstrate that the specific activation of muscarinic cholinergic receptors (mAchRs) (with oxotremorine) triggers a slow burst rhythm in thoracic spinal segments, thereby revealing a rhythmogenic capability in this cord region. Whereas axial motoneurons (MNs) were rhythmically activated during both locomotor activity and oxotremorine-induced bursting, intermediolateral sympathetic preganglionic neurons (IML SPNs) exhibited rhythmicity solely in the presence of oxotremorine...
July 9, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29979672/p38%C3%AE-blocks-brown-adipose-tissue-thermogenesis-through-p38%C3%AE-inhibition
#7
Nuria Matesanz, Ivana Nikolic, Magdalena Leiva, Marta Pulgarín-Alfaro, Ayelén M Santamans, Edgar Bernardo, Alfonso Mora, Leticia Herrera-Melle, Elena Rodríguez, Daniel Beiroa, Ainoa Caballero, Elena Martín-García, Rebeca Acín-Pérez, Lourdes Hernández-Cosido, Luis Leiva-Vega, Jorge L Torres, Francisco Centeno, Angel R Nebreda, José Antonio Enríquez, Rubén Nogueiras, Miguel Marcos, Guadalupe Sabio
Adipose tissue has emerged as an important regulator of whole-body metabolism, and its capacity to dissipate energy in the form of heat has acquired a special relevance in recent years as potential treatment for obesity. In this context, the p38MAPK pathway has arisen as a key player in the thermogenic program because it is required for the activation of brown adipose tissue (BAT) thermogenesis and participates also in the transformation of white adipose tissue (WAT) into BAT-like depot called beige/brite tissue...
July 6, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29975680/drosophila-melanogaster-establishes-a-species-specific-mutualistic-interaction-with-stable-gut-colonizing-bacteria
#8
Inês S Pais, Rita S Valente, Marta Sporniak, Luis Teixeira
Animals live together with diverse bacteria that can impact their biology. In Drosophila melanogaster, gut-associated bacterial communities are relatively simple in composition but also have a strong impact on host development and physiology. It is generally assumed that gut bacteria in D. melanogaster are transient and their constant ingestion with food is required to maintain their presence in the gut. Here, we identify bacterial species from wild-caught D. melanogaster that stably associate with the host independently of continuous inoculation...
July 5, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29969459/a-revised-understanding-of-tribolium-morphogenesis-further-reconciles-short-and-long-germ-development
#9
Matthew A Benton
In Drosophila melanogaster, the germband forms directly on the egg surface and solely consists of embryonic tissue. In contrast, most insect embryos undergo a complicated set of tissue rearrangements to generate a condensed, multilayered germband. The ventral side of the germband is embryonic, while the dorsal side is thought to be an extraembryonic tissue called the amnion. While this tissue organisation has been accepted for decades and has been widely reported in insects, its accuracy has not been directly tested in any species...
July 3, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29965966/nonmonotonic-recruitment-of-ventromedial-prefrontal-cortex-during-remote-memory-recall
#10
Daniel N Barry, Martin J Chadwick, Eleanor A Maguire
Systems-level consolidation refers to the time-dependent reorganisation of memory traces in the neocortex, a process in which the ventromedial prefrontal cortex (vmPFC) has been implicated. Capturing the precise temporal evolution of this crucial process in humans has long proved elusive. Here, we used multivariate methods and a longitudinal functional magnetic resonance imaging (fMRI) design to detect, with high granularity, the extent to which autobiographical memories of different ages were represented in vmPFC and how this changed over time...
July 2, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29965965/brain-computer-interface-use-is-a-skill-that-user-and-system-acquire-together
#11
Dennis J McFarland, Jon R Wolpaw
A brain-computer interface (BCI) is a computer-based system that acquires, analyzes, and translates brain signals into output commands in real time. Perdikis and colleagues demonstrate superior performance in a Cybathlon BCI race using a system based on "three pillars": machine learning, user training, and application. These results highlight the fact that BCI use is a learned skill and not simply a matter of "mind reading."
July 2, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29965960/strength-in-numbers-collaborative-science-for-new-experimental-model-systems
#12
Ross F Waller, Phillip A Cleves, Maria Rubio-Brotons, April Woods, Sara J Bender, Virginia Edgcomb, Eric R Gann, Adam C Jones, Leonid Teytelman, Peter von Dassow, Steven W Wilhelm, Jackie L Collier
Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models...
July 2, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29953453/a-speed-fidelity-trade-off-determines-the-mutation-rate-and-virulence-of-an-rna-virus
#13
William J Fitzsimmons, Robert J Woods, John T McCrone, Andrew Woodman, Jamie J Arnold, Madhumita Yennawar, Richard Evans, Craig E Cameron, Adam S Lauring
Mutation rates can evolve through genetic drift, indirect selection due to genetic hitchhiking, or direct selection on the physicochemical cost of high fidelity. However, for many systems, it has been difficult to disentangle the relative impact of these forces empirically. In RNA viruses, an observed correlation between mutation rate and virulence has led many to argue that their extremely high mutation rates are advantageous because they may allow for increased adaptability. This argument has profound implications because it suggests that pathogenesis in many viral infections depends on rare or de novo mutations...
June 28, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29949573/intracellular-attenuation-of-bmp-signaling-via-ckip-1-smurf1-is-essential-during-neural-crest-induction
#14
Michael L Piacentino, Marianne E Bronner
The neural crest is induced at the neural plate border during gastrulation by combined bone morphogenetic protein (BMP), fibroblast growth factor (FGF), and Wnt signaling. While intermediate BMP levels are critical for this induction, secreted BMP inhibitors are largely absent from the neural plate border. Here, we propose a morphogen model in which intracellular attenuation of BMP signaling sets the required intermediate levels to maintain neural crest induction. We show that the scaffold protein casein kinase interacting protein 1 (CKIP-1) and ubiquitin ligase Smad ubiquitin regulatory factor 1 (Smurf1) are coexpressed with BMP4 at the chick neural plate border...
June 27, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29949571/condensin-atpase-motifs-contribute-differentially-to-the-maintenance-of-chromosome-morphology-and-genome-stability
#15
Roger Palou, Thillaivillalan Dhanaraman, Rim Marrakchi, Mirela Pascariu, Mike Tyers, Damien D'Amours
Effective transfer of genetic information during cell division requires a major reorganization of chromosome structure. This process is triggered by condensin, a conserved pentameric ATPase essential for chromosome condensation. How condensin harnesses the energy of ATP hydrolysis to promote chromatin reorganization is unknown. To address this issue, we performed a genetic screen specifically focused on the ATPase domain of Smc4, a core subunit of condensin. Our screen identified mutational hotspots that impair condensin's ability to condense chromosomes to various degrees...
June 27, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29940019/haploid-selection-sex-ratio-bias-and-transitions-between-sex-determining-systems
#16
Michael Francis Scott, Matthew Miles Osmond, Sarah Perin Otto
Sex determination is remarkably dynamic; many taxa display shifts in the location of sex-determining loci or the evolution of entirely new sex-determining systems. Predominant theories for why we observe such transitions generally conclude that novel sex-determining systems are favoured by selection if they equalise the sex ratio or increase linkage with a locus that experiences different selection in males versus females. We use population genetic models to extend these theories in two ways: (1) We consider the dynamics of loci very tightly linked to the ancestral sex-determining loci, e...
June 25, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29939998/coding-of-self-motion-induced-and-self-independent-visual-motion-in-the-rat-dorsomedial-striatum
#17
Anett J Nagy, Yuichi Takeuchi, Antal Berényi
Evolutionary development of vision has provided us with the capacity to detect moving objects. Concordant shifts of visual features suggest movements of the observer, whereas discordant changes are more likely to be indicating independently moving objects, such as predators or prey. Such distinction helps us to focus attention, adapt our behavior, and adjust our motor patterns to meet behavioral challenges. However, the neural basis of distinguishing self-induced and self-independent visual motions is not clarified in unrestrained animals yet...
June 25, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29939986/visual-attention-is-not-deployed-at-the-endpoint-of-averaging-saccades
#18
Luca Wollenberg, Heiner Deubel, Martin Szinte
The premotor theory of attention postulates that spatial attention arises from the activation of saccade areas and that the deployment of attention is the consequence of motor programming. Yet attentional and oculomotor processes have been shown to be dissociable at the neuronal level in covert attention tasks. To investigate a potential dissociation at the behavioral level, we instructed human participants to move their eyes (saccade) towards 1 of 2 nearby, competing saccade targets. The spatial distribution of visual attention was determined using oriented visual stimuli presented either at the target locations, between them, or at several other equidistant locations...
June 25, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29939982/descending-pathways-generate-perception-of-and-neural-responses-to-weak-sensory-input
#19
Michael G Metzen, Chengjie G Huang, Maurice J Chacron
Natural sensory stimuli frequently consist of a fast time-varying waveform whose amplitude or contrast varies more slowly. While changes in contrast carry behaviorally relevant information necessary for sensory perception, their processing by the brain remains poorly understood to this day. Here, we investigated the mechanisms that enable neural responses to and perception of low-contrast stimuli in the electrosensory system of the weakly electric fish Apteronotus leptorhynchus. We found that fish reliably detected such stimuli via robust behavioral responses...
June 25, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29939981/the-role-of-inferior-frontal-junction-in-controlling-the-spatially-global-effect-of-feature-based-attention-in-human-visual-areas
#20
Xilin Zhang, Nicole Mlynaryk, Sara Ahmed, Shruti Japee, Leslie G Ungerleider
Feature-based attention has a spatially global effect, i.e., responses to stimuli that share features with an attended stimulus are enhanced not only at the attended location but throughout the visual field. However, how feature-based attention modulates cortical neural responses at unattended locations remains unclear. Here we used functional magnetic resonance imaging (fMRI) to examine this issue as human participants performed motion- (Experiment 1) and color- (Experiment 2) based attention tasks. Results indicated that, in both experiments, the respective visual processing areas (middle temporal area [MT+] for motion and V4 for color) as well as early visual, parietal, and prefrontal areas all showed the classic feature-based attention effect, with neural responses to the unattended stimulus significantly elevated when it shared the same feature with the attended stimulus...
June 25, 2018: PLoS Biology
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