bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is diversity in worker body size important for the performance of bumble bee colonies?
Authors: Holland Jacob G. , Nakayama Shinnosuke , Porfiri Maurizio , Nov Oded , Bloch Guy 
Published: May 2020

ABSTRACTSpecialization and plasticity are important for many forms of collective behavior, but the interplay between these factors is little understood. In insect societies, workers are often predisposed to specialize in different tasks, sometimes with morphological or physiological adaptations, facilitating a division of labor. Workers may also plastically switch between tasks or vary their effort. The degree to which predisposed specialization limits plasticity is not clear and has not been systematically tested in ecologically relevant contexts. We addressed this question in 20 freely-foraging bumble bee (Bombus terrestris) colonies by continually manipulating colonies to contain either a typically diverse or reduced (“homogeneous”) worker body size distribution, over two trials. Pooling both trials, diverse colonies did better in several indices of colony performance. The importance of body size was further demonstrated by the finding that foragers were larger than nurses even in homogeneous colonies with a very narrow body size range. However, the overall effect of size diversity stemmed mostly from one trial. In the other trial, homogeneous and diverse colonies showed comparable performance. By comparing behavioral profiles based on several thousand observations, we found evidence that workers in homogeneous colonies in this trial rescued colony performance by plastically increasing behavioral specialization and/or individual effort, compared to same-sized individuals in diverse colonies. Our results are consistent with a benefit to colonies of predisposed (size-diverse) specialists under certain conditions, but also suggest that plasticity or effort, can compensate for reduced (size-related) specialization. Thus, we suggest that an intricate interplay between specialization and plasticity is functionally adaptive in bumble bee colonies.
Mycena genomes resolve the evolution of fungal bioluminescence
Authors: Ke Huei-Mien , Lee Hsin-Han , Lin Chan-Yi Ivy , Liu Yu-Ching , Lu Min R. , Hsieh Jo-Wei Allison , Chang Chiung-Chih , Wu Pei-Hsuan , Lu Meiyeh Jade , Li Jeng-Yi , Shang Gaus , Lu Rita Jui-Hsien , Nagy László G. , Chen Pao-Yang , Kao Hsiao-Wei , Tsai Isheng Jason 
Published: May 2020

AbstractMushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life, yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies ∼150Mb are amongst the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in most Mycena species, but conserved in the Armillaria lineage. Luciferase cluster members were co-expressed across developmental stages, with highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species.SignificanceWe present the genomes of five new bonnet mushroom Mycena species, formerly the last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in the luciferase cluster across all fungi and additional genes involved in bioluminescence. We show that luciferase clusters were differentially lost in different fungal lineages and in particular a substantial loss was observed in the Mycena lineage. This can be attributed to genome regions of Mycena underwent different evolutionary dynamics. Our findings offer insights into the evolution of how a gene cluster that emerged 160 million years ago and was frequently lost or maintained due to differences in genome plasticity.
Identification of PDE6D as a potential target of sorafenib via PROTAC technology
Authors: Li Yang , Meng Qingshi , Wang Ping , Liu Xiaolei , Fu Qiuyu , Xie Yuting , Zhou Yu , Qi Xiangbing , Huang Niu 
Published: May 2020

AbstractThe identification of unknown target of a multi-kinase inhibitor sorafenib is important to better understand the mechanism of action of this drug in anti-cancer and anti-fibrotic treatments. Here, we report the combination of PROTAC technique with quantitative proteomic analysis to identify the unknown cellular targets of sorafenib. Sorafenib-based PROTAC can strongly degrade a non-kinase target PDEδ in different types of cells. We also confirmed the direct binding interaction of PDEδ with sorafenib by CETSA and SPR assays. Together, our research suggests that PDEδ is a new potential target of sorafenib, and PROTAC technology may be a promising approach for cellular target identification of bioactive compounds of interest.
Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide
Authors: Martin Belinda C. , Middleton Jen A. , Fraser Matthew W. , Marshall Ian P.G. , Scholz Vincent V. , Schmidt Hannes 
Published: May 2020

AbstractSeagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems where lucinids do not occur. Hence, we hypothesised that seagrasses themselves host sulphur-oxidising bacteria that could secure their survival when lucinids are absent. We analysed newly generated and publicly available 16S rRNA gene sequences from seagrass roots and sediments across 14 seagrass species and 10 countries and found that persistent and colonising seagrasses across the world harbour sulphur-oxidisingCa. Thiodiazotropha, regardless of the presence of lucinids. We used fluorescencein situhybridisation to visually confirm the presence ofCa. Thiodiazotropha on roots ofHalophila ovalis, a colonising seagrass species with wide geographical, water depth range, and sedimentary sulphide concentrations. We provide the first evidence thatCa. Thiodiazotropha are commonly present on seagrass roots, providing a mechanism for seagrasses to alleviate sulphide stress globally.
Identification of Lipid Droplets in Gut Microbiota
Authors: Zhang Kai , Zhou Chang , Zhou Ziyun , Li Xuehan , Li Zemin , Zhang Mengwei , Zhang Xuelin , Zhang Congyan , Wei Taotao , Zhang Shuyan , Liu Pingsheng 
Published: May 2020

SummaryRecent research has accumulating evidence to support that gut microbiota can be a newly discovered organ/tissue for humans. Although the functions of gut microbiota have been linked to almost all aspects of human physiological, most findings so far are still either belonged to correlational research or at preliminary stage of causal study due to the complexity of gut microbiota as well as lack of proper tools and methods. Thus, development of new approaches is essential and necessary. Lipid droplet is a cellular organelle governing cell lipid homeostasis that is directly related to human metabolic syndromes. Previously we and other groups found lipid droplets in several bacterial strains. We wonder if gut bacteria have lipid droplets. If so, these bacteria may play key roles to regulate gut lipid content, remove unnecessary lipids and produce useful lipid molecules for host. Here we identified lipid droplet-like structures in freshly isolated bacteria from mouse small and large intestines, as well as mouse and human feces. We also purified and analyzed lipid droplets from a cloned human gut bacteriumStreptomyces thermovulgaris. Together, we demonstrate the existence of lipid droplets in gut microbiota and established an approach to study them.
Neutral sphingomyelinase 2 regulates inflammatory responses in monocytes/macrophages induced by TNF-α
Authors: Al-Rashed Fatema , Ahmad Zunair , Thomas Reeby , Melhem Motasem , Snider Ashley J. , Obeid Lina M. , Al-Mulla Fahd , Hannun Yusuf A. , Ahmad Rasheed 
Published: May 2020

ABSTRACTObesity is associated with elevated levels of TNF-α and proinflammatory CD11c monocytes /macrophages. TNF-α mediated dysregulation in the plasticity of monocytes/macrophages is concomitant with pathogenesis of several inflammatory diseases, including metabolic syndrome, but the underlying mechanisms are incompletely understood. Since neutral sphingomyelinase 2 (nSMase2; product of the sphingomyelin phosphodiesterase 3 gene,SMPD3) is a key enzyme for ceramide production involved in inflammation, we investigated whether nSMase2 contributed to the inflammatory changes in the monocytes/macrophages induced by TNF-α. In this study, we demonstrate that the disruption of nSMase activity in monocytes/macrophages either by chemical inhibitor GW4869 or small interfering RNA (siRNA) against SMPD3 results in defects in the TNF-α mediated expression of CD11c. Furthermore, blockage of nSMase in monocytes/macrophages inhibited the secretion of inflammatory mediators IL-1b and MCP-1. In contrast, inhibition of acid SMase (aSMase) activity did not attenuate CD11c expression or secretion of IL-1b and MCP-1. TNF-α-induced phosphorylation of JNK, p38 and NF-κB was also attenuated by the inhibition of nSMase2. Moreover, NF-kB/AP-1 activity was blocked by the inhibition of nSMase2. SMPD3 was elevated in PBMCs from obese individuals and positively corelated with TNF-α gene expression. These findings indicate that nSMase2 acts, at least in part, as a master switch in the TNF-α mediated inflammatory responses in monocytes/macrophages.
Dectin-1 limits central nervous system autoimmunity through a non-canonical pathway
Authors: Deerhake M. Elizabeth , Danzaki Keiko , Inoue Makoto , Cardakli Emre D. , Nonaka Toshiaki , Aggarwal Nupur , Barclay William E. , Ji Ru Rong , Shinohara Mari L. 
Published: May 2020

ABSTRACTPathologic roles for innate immunity in neurologic disorders are well-described, but protective aspects of the immune response are less understood. Dectin-1, a C-type lectin receptor (CLR), is largely known to induce inflammation. However, we found that Dectin-1 is protective in experimental autoimmune encephalomyelitis (EAE), while its canonical signaling mediator, Card9, promotes the disease. Notably, Dectin-1 does not respond to heat-killedMycobacteria, an adjuvant to induce EAE. Myeloid cells mediate the protective function of Dectin-1 in EAE and upregulate gene expression of neuroprotective molecules, including Oncostatin M (Osm) through a non-canonical Card9-independent pathway, mediated by NFAT. Furthermore, we found that the Osm receptor (OsmR) functions specifically in astrocytes to reduce EAE severity. Our study revealed a new mechanism of protective myeloid-astrocyte crosstalk regulated by a non-canonical Dectin-1 pathway and identifies novel therapeutic targets for CNS autoimmunity.Graphical AbstractDectin-1 is a protective C-type lectin receptor (CLR) in experimental autoimmune encephalomyelitis (EAE)Dectin-1 promotes expression ofOsm, a neuroprotective IL-6 family cytokine, in myeloid cellsOsmR signaling in astrocytes limits EAE progression and promotes remissionNon-canonical Card9-independent signaling drives a distinct Dectin-1-mediated transcriptional program to induce expression ofOsmand other factors with protective or anti-inflammatory functions
A role for tectorial membrane mechanics in activating the cochlear amplifier
Authors: Nankali A. , Wang Y. , Strimbu C. E. , Olson E. S. , Grosh K. 
Published: May 2020

ABSTRACTThe mechanical and electrical responses of the mammalian cochlea to acoustic stimuli are nonlinear and highly tuned in frequency. This is due to the electromechanical properties of cochlear outer hair cells (OHCs). At each location along the cochlear spiral, the OHCs mediate an active process in which the sensory tissue motion is enhanced at frequencies close to the most sensitive frequency (called the characteristic frequency CF). Previous experimental results showing an approximate 0.3 cycle phase shift in the OHC-generated extracellular voltage relative the basilar membrane displacement that is initiated at a frequency approximately one-half octave lower than the CF are repeated in the present paper with similar findings. This shift is significant because it brings the phase of the OHC-derived electromotile force near to that of the basilar membrane velocity at frequencies above the shift, thereby enabling the transfer of electrical to mechanical power at the basilar membrane. In order to seek a candidate physical mechanism for this phenomenon, we used a comprehensive electromechanical mathematical model of the cochlear response to sound. The model predicts the phase shift in the extracellular voltage referenced to the basilar membrane at a frequency approximately one-half octave below CF, in accordance with the experimental data. In the model, this feature arises from a minimum in the radial impedance of the tectorial membrane and its limbal attachment. These experimental and theoretical results are consistent with the hypothesis that a tectorial membrane resonance introduces the correct phasing between mechanical and electrical responses for power generation, effectively turning on the cochlear amplifier.SIGNIFICANCEThe mechanical and electrical responses of the mammalian cochlea are nonlinear exhibiting up to a thousand-fold difference in gain depending on the frequency and level of sound stimulus. Cochlear outer hair cells (OHC) are broadband electro-mechanical energy converters that mediate this nonlinear active process. However, the mechanism by which the OHC electromotile force acquires the appropriate phase to power this nonlinearity remains unknown. By analyzing new and existing experimental data and using a mathematical model, we address this open issue. We present evidence which suggests that a relatively simple feature, the frequency dependence of the radial impedance of the tectorial membrane, provides requisite mechanics to turn on the frequency-specific nonlinear process essential for healthy hearing.
Interceptive capturing in large-billed crows: Velocity-dependent weighing of prediction of future target location and visual feedback of current target location
Authors: Ujihara Yusuke , Matsui Hiroshi , Izawa Ei-Ichi 
Published: May 2020

AbstractInterception of a moving target is a fundamental behaviour of predators and requires tight coupling between the sensory and motor systems. In the literature of foraging studies, feedback mechanisms based on current target position are frequently reported. However, there have also been recent reports of animals employing feedforward mechanisms, in which prediction of future target location plays an important role. In nature, coordination of these two mechanisms may contribute to intercepting evasive prey. However, how animals weigh these two mechanisms remain poorly understood. Here, we conducted a behavioural experiment involving crows (which show flexible sensorimotor coordination in various domains) capturing a moving target. We changed the velocity of the target to examine how the crows utilised prediction of the target location. The analysis of moment-to-moment head movements and computational simulations revealed that the crows used prediction of future target location when the target velocity was high. In contrast, their interception depended on the current momentary position of the target when the target velocity was slow. These results suggest that crows successfully intercept targets by weighing predictive and visual feedback mechanisms, depending on the target velocity.
Spatially clustered resources increase aggregation and mating duration inDrosophila melanogaster
Authors: Churchill Emily R. , Bridle Jon R. , Thom Michael D. F. 
Published: May 2020

ABSTRACTIn environments where females mate multiply, males should adjust their behaviour and physiology in response to the prevailing perceived level of sperm competition. This expectation is well supported by both laboratory and field studies, but we don’t yet know what mechanisms facilitate these plastic responses in natural populations. One way in which males appear to assess sperm competition risk is through encounter rates with conspecific males. Such encounter rates may be driven by the spatial distribution of resources required by male. However, explicit links between resource distribution, male encounter rate, and shifts in behaviour related to sperm competition have not been demonstrated. Here we show that a small increase in the distance of patches of food resources in the laboratory: (a) approximately halves the mean distances between pairs of males; and (b) is associated with an increase in subsequent copulation duration – previously shown to be a reliable indicator of male perception of sperm competition risk – by more than two minutes. Aggregation of resources, operating via increased encounter rate, is a mechanism that can stimulate plastic male sperm competition responses. Because spatial distribution of resources, including those exploited byDrosophila, is variable in nature, this may explain one way in which sperm competition-related plasticity is influenced in wild-living males.
VviMYB41 orthologs contribute to the water deficit induced suberization of grapevine fine roots
Authors: Zhang Li , Merlin Isabelle , Pascal Stéphanie , Bert Pierre-François , Domergue Frédéric , Gambetta Gregory A. 
Published: May 2020

ABSTRACTThe permeability of roots to water and nutrients is controlled through a variety of mechanisms and one of the most conspicuous is the presence of structures such as the Casparian strips and suberin lamellae. Roots actively regulate the creation of these structures developmentally, along the length of the root, and in response to the environment, including abiotic stresses such as drought. In the current study, we characterized the suberin composition along the length of grapevine fine roots during development and in response to water deficit. In parallel samples we quantified changes in expression of suberin biosynthesis- and deposition-related gene families (via RNAseq) allowing the identification of drought-responsive suberin-related genes. Grapevine suberin composition did not differ between primary and lateral roots, and was similar to that of other species. Under water deficit there was a global upregulation of suberin biosynthesis which resulted in an increase of suberin specific monomers, but without changes in their relative abundances, and this upregulation took place across all the developmental stages of fine roots. These changes corresponded to the upregulation of numerous suberin biosynthesis- and deposition-related genes which included orthologs of the previously characterized AtMYB41 transcriptional factor. Functional validation of two grapevine MYB41 orthologs, VviMYB41 and VviMYB41-like, confirmed their ability to globally upregulate suberin biosynthesis and deposition. This study provides a detailed characterization of the developmental and water deficit induced suberization of grapevine fine roots and identifies important orthologs responsible for suberin biosynthesis, deposition, and its regulation in grape.One sentence summaryOur study details the biochemical changes and molecular regulation of how grapevines decrease their root permeability during drought.
DMT alters cortical travelling waves
Authors: Alamia Andrea , Timmermann Christopher , VanRullen Rufin , Carhart-Harris Robin L. 
Published: May 2020

AbstractPsychedelic drugs are potent modulators of conscious states and therefore powerful tools for investigating their neurobiology. N,N, Dimethyltryptamine (DMT) is a particularly interesting serotonergic psychedelic that can rapidly induce an extremely immersive state of consciousness characterized by vivid and elaborate visual imagery. In the present study, we investigated the electrophysiological correlates of the DMT-induced altered state, by recording EEG signals from a pool of participants receiving DMT and (separately) placebo (saline), intravenously, while instructed to keep their eyes closed (i.e. ‘resting state’). Consistent with our prior hypotheses, results revealed a spatio-temporal pattern of cortical activation (i.e., travelling waves) similar to that elicited by visual stimulation. Moreover, the typical top-down alpha-band rhythms of closed-eyes rest (i.e. a backward travelling wave) were significantly decreased, while the bottom-up ‘forward travelling wave’, was significantly increased. These results support a recent model proposing that psychedelics reduce the ‘precision-weighting of priors’, thus altering the balance of top-down versus bottom-up information passing, where properties of backward waves are considered correlates of this precision weighting. The robust hypothesis-confirming nature of the present findings imply the discovery of an important mechanistic principle underpinning psychedelic-induced altered states – i.e. reduced backward and increased forward travelling waves - and lend further support to prior assumptions about the functional significance of cortical travelling waves.
Binding Mechanism of the Matrix Domain of HIV-1 Gag on Lipid Membranes
Authors: Monje-Galvan V. , Voth Gregory A. 
Published: May 2020

AbstractAggregation of the HIV-1 Gag protein onto the plasma membrane (PM) enables viral budding and infection propagation. Gag assembly at the membrane interface is mediated by its matrix domain (MA), the Myristoylated (Myr) N-terminus. MA targets the PM through electrostatic interactions, mainly at its highly-basic-region (HBR). The mechanism of Myr insertion and its role in protein-membrane dynamics remains unclear. Using all-atom molecular dynamics, we examined an MA unit in the vicinity of lipid bilayers that model different characteristics of the PM. Interaction with PIP2and PS lipids is highly favored around the HBR, and is enough to keep the protein bound. Additionally, we simulated three MA units near our bilayers and quantified the collective effects of free monomers vs. formed trimers on Myr insertion events. Micro-second-long trajectories allowed us to observe Myr insertion, propose a mechanism, quantify specific interactions with lipids, and examine the response of the local membrane environment.