bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competitive Inhibition of Cortisol by Prostaglandins at the Ligand Binding Domain of Glucocorticoid Receptors
Authors: Schaper Charles D. 
Published: November 2019

AbstractCortisol is a steroid hormone that binds to the glucocorticoid receptor with a diverse range of functions including metabolic, neurologic and immune responses. Prostglandins are lipid autacoids that participate in a wide range of functions including the inflammatory response and the vasoactivity of blood vessels and smooth muscle. Previously, a direct interaction between the two classes of biomolecules has not been studied, and here it is shown for the first time that there is competitive inhibition of cortisol and prostaglandins at the critical ligand binding domain of glucocorticoid receptors, which are found in nearly every cell and tissue in the human body. To assess molecular similarity that would enable competitive inhibition, it is first noted that cortisol (CORT, C21H30O5) and prostaglandin E2 (PGE2, C20H32O5) are of nearly the same molecular weight, and have nearly the same number of carbon, hydrogen and oxygen elements. The carbon-carbon double bonds on each of the two branches of PGE2, combined with the five-carbon cyclic centering structure, enable a conformational isomer of PGE2 to position the five oxygen-based functional groups at similar spatial positions as the corresponding five oxygen-based functional groups of CORT. Within the gene-regulating ligand binding domain (LBD) of the glucocorticoid receptor (GR), the average inter-molecular spacing of hydrogen bonding to the corresponding identical five functional groups is 1.778 Å for CORT versus 1.746 Å for PGE2. The conformational isomer of PGE2 within the LBD is at a lower energy state than CORT by 54.9%, indicating preference in stability. Both PGE2 and CORT exhibit a hydrophobic core within the LBD of GR, which is compatible with hydrophobic regions of the LBD. With the incorporation of two calcium ions into both PGE2 and CORT, the energy is further reduced by 58.9% and 113% respectively. PGE2 with calcium ion stabilization is lower by 15.5% in comparison to the equivalent arrangement of CORT. Because of the steroid ring structure of CORT, the spacing of the calcium ions is larger at 16.2Å, whereas PGE2, with just a single ring, collapses to 12.3Å. Analysis of experimental data associated with the adrenal response to an injection of lipopolysaccharide (LPS) is presented to indicate competitive inhibition of PGE2 is responsible for an observed lack of phosphorylation of the GR despite the presence of CORT. Competitive inhibition preventing normative cellular processing of cortisol, a stress hormone, by prostaglandins, which are associated with the inflammatory response, may be the causative source of certain signs and symptoms of disease, and thus is of significant medical importance.
Naturally occurring fluorescence protects the eutardigrade Paramacrobiotus sp. from ultraviolet radiation
Authors: Suma Harikumar R , Prakash Swathi , Giri Debasish , Mugesh Govindasamy , Eswarappa Sandeep M. 
Published: November 2019

AbstractNaturally occurring fluorescence has been observed in multiple species ranging from bacteria to birds. In macroscopic animals such as birds and fishes, fluorescence provides a visual communication signal. However, the functional significance of this phenomenon is not known in most cases. Though photoprotection is attributed to fluorescence under ultraviolet (UV) light in some organisms, it lacks direct experimental evidence. Here, we have identified a new species of eutardigrade belonging to the genus Paramacrobiotus, which exhibits fluorescence under UV light. Using a natural variant of the same species that lacks fluorescence, we show that the fluorescence confers tolerance to lethal UV radiation. Remarkably, we could transfer this property to UV-sensitive Hypsibius exemplaris, another eutardigrade, and also to C. elegans, a nematode. Using high performance liquid chromatography (HPLC) we isolated the fluorescent compound from Paramacrobiotus sp. This compound has excitation maxima (λex) at 370 nm and emission maxima (λem) at 420-430 nm. We propose that Paramacrobiotus sp. uses a fluorescent shield that absorbs harmful UV radiation, and emits harmless blue light, thereby protecting itself from the lethal effects of UV radiation.Summary statementTardigrades are well known for their tolerance to extreme environmental conditions. In this study, we have identified a new tardigrade species that employs a fluorescent shield to protect itself from the germicidal ultra violet radiation.
Single-cell immuno-mechanics: rapid viscoelastic changes are a hall-mark of early leukocyte activation
Authors: Zak Alexandra , Cortés Sara Violeta Merino , Sadoun Anaïs , Babataheri Avin , Dogniaux Stéphanie , Dupré-Crochet Sophie , Hudik Elodie , He Hai-Tao , Barakat Abdul I , Carrasco Yolanda R , Hamon Yannick , Puech Pierre-Henri , Hivroz Claire , Nüsse Oliver , Husson Julien 
Published: November 2019

AbstractTo accomplish their critical task of removing infected cells and fighting pathogens, leukocytes activate by forming specialized interfaces with other cells. Using an innovative micropipette rheometer, we show in three different cell types that when stimulated by microbeads mimicking target cells, leukocytes become up to ten times stiffer and more viscous. These mechanical changes initiate within seconds after contact and evolve rapidly over minutes. Remarkably, leukocyte elastic and viscous properties evolve in parallel, preserving a well-defined ratio that constitutes a mechanical signature specific to each cell type. The current results indicate that simultaneously tracking both elastic and viscous properties during an active cell process provides a new way to investigate cell mechanical processes. Our findings also suggest that dynamic immuno-mechanical measurements provide an identifier of leukocyte type and an indicator of the cell’s state of activation.
A multiscale framework for disentangling the roles of evenness, density and aggregation on diversity gradients
Authors: McGlinn Daniel J. , Engel Thore , Blowes Shane A. , Gotelli Nicholas J. , Knight Tiffany M. , McGill Brian J. , Sanders Nathan , Chase Jonathan M. 
Published: November 2019

AbstractDisentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes changes in species diversity into three components of community structure: the species abundance distribution (SAD), the total community abundance, and the within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that ant species richness decreased along the elevational gradient because of changes in the SAD and in spatial aggregation, but not because of changes in the number of individuals. Specifically, with increasing elevation, species evenness was lower and species were less aggregated. These results do not support the more-individuals hypothesis; alternative hypotheses are required to explain why evenness and aggregation decrease with elevation. Our extension of MoB has the potential to elucidate the drivers of diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients.
Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit
Authors: Hewitt Seanna , Hendrickson Christopher A. , Dhingra Amit 
Published: November 2019

AbstractEuropean pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed established cold temperature conditioning treatments for ripening of two pear cultivars, ‘D’Anjou’ and ‘Bartlett’. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four different developmental stages during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.
Time-of-day-dependent responses of cyanobacterial cellular viability against oxidative stress
Authors: Tanaka Kenya , Shimakawa Ginga , Nakanishi Shuji 
Published: November 2019

AbstractAs an adaptation to periodic fluctuations of environmental light, photosynthetic organisms have evolved a circadian clock. Control by the circadian clock of many cellular physiological functions, including antioxidant enzymes, metabolism and the cell cycle, has attracted attention in the context of oxidative stress tolerance. However, since each physiological function works in an integrated manner to deal with oxidative stress, whether or not cell responses to oxidative stress are under circadian control remains an open question. In fact, circadian rhythms of oxidative stress tolerance have not yet been experimentally demonstrated. In the present work, we applied an assay using methyl viologen (MV), which generates reactive oxygen species (ROS) under light irradiation, and experimentally verified the circadian rhythms of oxidative stress tolerance in photosynthetic cells of the cyanobacterium Synechococcus elongatus PCC7942, a standard model species for investigation of the circadian clock. Here, we report that ROS generated by MV treatment causes damage to stroma components and not to the photosynthetic electron transportation chain, leading to reduced cell viability. The degree of decrease in cell viability was dependent on the subjective time at which oxidative stress was applied. Thus, oxidative stress tolerance was shown to exhibit circadian rhythms. In addition, the rhythmic pattern of oxidative stress tolerance disappeared in mutant cells lacking the essential clock genes. Notably, ROS levels changed periodically, independent of the MV treatment. Thus, we demonstrate for the first time that in cyanobacterial cells, oxidative stress tolerance shows circadian oscillation.
Synergistic cues from diverse bacteria enhance multicellular development in a choanoflagellate
Authors: Ireland Ella V. , Woznica Arielle , King Nicole 
Published: November 2019

AbstractBacteria regulate the life histories of diverse eukaryotes, but relatively little is known about how eukaryotes interpret and respond to multiple bacterial cues encountered simultaneously. To explore how a eukaryote might respond to a combination of bioactive molecules from multiple bacteria, we treated the choanoflagellate Salpingoeca rosetta with two sets of bacterial cues, one that induces mating and the other that induces multicellular development. We found that simultaneous exposure to both sets of cues enhanced multicellular development in S. rosetta, eliciting both larger multicellular colonies and an increase in the number of colonies. Thus, rather than conveying conflicting sets of information, these distinct bacterial cues synergize to augment multicellular development. This study demonstrates how a eukaryote can integrate and modulate its response to cues from diverse bacteria, underscoring the potential impact of complex microbial communities on eukaryotic life histories.ImportanceEukaryotic biology is profoundly influenced by interactions with diverse environmental and host-associated bacteria. However, it is not well understood how eukaryotes interpret multiple bacterial cues encountered simultaneously. This question has been challenging to address because of the complexity of many eukaryotic model systems and their associated bacterial communities. Here, we studied a close relative of animals, the choanoflagellate Salpingoeca rosetta, to explore how eukaryotes respond to diverse bacterial cues. We found that a bacterial chondroitinase that induces mating on its own can also synergize with bacterial lipids that induce multicellular “rosette” development. When encountered together, these cues enhance rosette development, resulting in the formation of more rosettes, each containing more cells than rosettes that form in the absence of the chondroitinase. These findings highlight how synergistic interactions among bacterial cues can influence the biology of eukaryotes.
Novel determination on root-knot nematodes; microspace, mineral profile and transduction of metabolic signals in tomato
Authors: García-Gaytán Víctor , Sánchez-Rodríguez Esteban , Ordaz-Ortiz José J. , Montero-Vargas Josaphat M. , Alonso-Pérez Olimpia , Rojas-Abarca Luis , Gómez-Cabrera Elena , Negrete-Guerrero Juan L. 
Published: November 2019

AbstractGlobally, nematodes are parasites that destroy many crops, however, their presence also serves as an indicator of the state of soil health. Tomato is a very studied, cultivated vegetable. In the micro-space of the knots we determine its pathogenesis. The macronutrients, micronutrients and beneficial elements present on root-knot nematodes were C>O> N (54.73, 37.57, and 3.55%), phosphorus (0.133%), Na>Ca>Mg>K cations (1.13, 1,032, 0.094, and 0.048%), S (0.247%), micronutrients Fe>Cl (0.163, 0.027%), and beneficial elements Si>Al (0.354, 0.985%). Progenesis of the chromatograms (ES+/ES-), 202 compounds were detected in the first polarity, in which 195 have at least one possible identification candidate, the second were 42 compounds, and 41 match with at least one compound. Putative compounds with the highest scores are reported in this research: kukoamina (57.6), furmecyclox (51.1), feruloylputrescina (55.3), N1-transferuloylagmatine (53.9), dehydrotomatin (49.8, 50.8, 52.3, 52.6), jurubine (54.8,51.6), etnangien (50.2), dehydromelilotoside (41.5), tomatine (55), minutissamide (51.7). Nematodes in state (J2), six nematodes within the knots with an average length of 1.16 mm, were found and their interaction with other microorganisms is possible. With the high concentrations of Na+ in the root, the concentration of the cation Mg2+ and K+ decreases; while the N does not present any change.
Do Muscle Synergies Improve Optimization Prediction of Muscle Activations During Gait?
Authors: Michaud Florian , Shourijeh Mohammad S. , Fregly Benjamin J. , Cuadrado Javier 
Published: November 2019

AbstractDetermination of muscle forces during motion can help to understand motor control, assess pathological movement, diagnose neuromuscular disorders, or estimate joint loads. Difficulty of in vivo measurement made computational analysis become a common alternative in which, as several muscles serve each degree of freedom, the muscle redundancy problem must be solved. Unlike static optimization (SO), synergy optimization (SynO) couples muscle activations across all time frames, thereby altering estimated muscle co-contraction. This study explores whether the use of a muscle synergy structure within a static optimization framework improves prediction of muscle activations during walking. A motion/force/EMG gait analysis was performed on five healthy subjects. A musculoskeletal model of the right leg actuated by 43 Hill-type muscles was scaled to each subject and used to calculate joint moments, muscle-tendon kinematics and moment arms. Muscle activations were then estimated using SynO with two to six synergies and traditional SO, and these estimates were compared with EMG measurements. SynO neither improved SO prediction of experimental activation patterns nor provided SO exact matching of joint moments. Finally, synergy analysis was performed on SO estimated activations, being found that the reconstructed activations produced poor matching of experimental activations and joint moments. As conclusion, it can be said that, although SynO did not improve prediction of muscle activations during gait, its reduced dimensional control space could be beneficial for applications such as functional electrical stimulation (FES) or motion control and prediction.
Early-life environmental enrichment generates persistent individualized behavior in mice
Authors: Zocher Sara , Schilling Susan , Grzyb Anna N. , Adusumilli Vijay S. , Lopes Jadna Bogado , Günther Sandra , Overall Rupert W. , Kempermann Gerd 
Published: November 2019

AbstractIndividuals differ in their response to environmental stimuli, but the stability of individualized behaviors and their associated changes in brain plasticity are poorly understood. We developed a novel model of enriched environment to longitudinally monitor 40 inbred mice exploring 35 connected cages over periods of three to six months. We show that behavioral individuality that emerged during the first three months of environmental enrichment persisted when mice were withdrawn from the enriched environment for three additional months. Behavioral trajectories were associated with stable inter-individual differences in adult hippocampal neurogenesis and persistent epigenetic effects on neuronal plasticity genes in the hippocampus. Using genome-wide DNA methylation sequencing, we show that one third of the DNA methylation changes were maintained after withdrawal from the enriched environment. Our results suggest that, even under the most constraint conditions controlling genes and environment, early-life experiences result in lasting individualized changes in behavior and brain plasticity.
A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea
Authors: Kirubakaran Tina Graceline , Andersen Øivind , Moser Michel , Arnyasi Mariann , McGinnity Philip , Lien Sigbjørn , Kent Matthew 
Published: November 2019

ABSTRACTCurrently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed using DNA from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the cold Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. Structurally, the genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig size of 686 Mb with a N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize in detail large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod.
Neural adaptation to accented speech: prefrontal cortex aids attunement in auditory cortices
Authors: Blanco-Elorrieta Esti , Gwilliams Laura , Marantz Alec , Pylkkänen Liina 
Published: November 2019

ABSTRACTSpeech is a complex and ambiguous acoustic signal that varies significantly within and across speakers. A prevalent and ubiquitous example of such variation is accented speech, to which humans adapt extremely rapidly. The goal of this study is to uncover the neurobiological bases of the attunement process that enables such fluent comprehension. Twenty-four native English participants listened to words spoken by an unaccented “canonical” American talker and two “accented” talkers, and performed a word-picture matching task, while magnetoencephalography (MEG) was recorded. Accented speech was created by including systematic phonological substitutions within the word (e.g. [s] → [sh]). Activity in the auditory cortex (superior temporal gyrus) was greater for accented speech, but, critically, this was not attenuated by exposure. By contrast, prefrontal regions showed an interaction between the presence of an accent and amount of exposure: while activity decreased for canonical speech over time, responses to accented speech remained consistently elevated. Grainger causality analyses further revealed that prefrontal responses serve to modulate activity in auditory regions, suggesting the recruitment of top-down processing to decode accented signal. In sum, our results show that accented speech does not elicit the same prefrontal reduction in amplitude over time that unaccented speech does, and points to a dynamic exchange of information between the prefrontal and auditory cortices in order to recalculate phonetic classification and subsequent identification of lexical items.Significance statementHuman ability to adapt to different people’s idiosyncratic pronunciations is a hallmark of speech comprehension. This study aims to address whether adaptation to speakers’ accents manifests itself at the perceptual level (i.e. through adaptation of low-level neural responses in the auditory cortex) or at the post-perceptual level (i.e. higher-order regions correcting the sensory signal received from auditory cortex). Our results support the post-perceptual hypothesis: we found that responses in auditory cortex emitted an error-like signal that was invariant to exposure; whereas responses in the prefrontal cortex were modulated by exposure. These findings provide initial insight into accent adaptation, and illuminate the computational stages supporting speech comprehension more generally.