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Optimal reproductive phenology under size‐dependent cannibalism
Get PDFIntra-cohort cannibalism is an example of a size-mediated priority effect. If early life stages cannibalize slightly smaller individuals, then parents face a trade-off between breeding at the best time for larval growth or development and predation risk from offspring born earlier. This game-theoretic situation among parents may drive adaptive reproductive phenology toward earlier breeding. However, it is not straightforward to quantify how cannibalism affects seasonal egg fitness or to distinguish emergent breeding phenology from alternative adaptive drivers. Here, we devise an age-structured game-theoretic mathematical model to find evolutionary stable breeding phenologies. We predict how size-dependent cannibalism acting on eggs, larvae, or both changes emergent breeding phenology and find that breeding under inter-cohort cannibalism occurs earlier than the optimal match to environmental conditions. We show that emergent breeding phenology patterns at the level of the population are sensitive to the ontogeny of cannibalism, that is, which life stage is subject to cannibalism. This suggests that the nature of cannibalism among early life stages is a potential driver of the diversity of reproductive phenologies seen across taxa and may be a contributing factor in situations where breeding occurs earlier than expected from environmental conditions.journal articl
Polarization and consensus by opposing external sources
Get PDFWe introduce a socially motivated extension of the voter model in which individual voters are also influenced by two opposing, fixed-opinion news sources. These sources forestall consensus and instead drive the population to a politically polarized state, with roughly half the population in each opinion state. Two types of social networks for the voters are studied: (a) the complete graph of N voters and, more realistically, (b) the two-clique graph with N voters in each clique. For the complete graph, many dynamical properties are soluble within an annealed-link approximation, in which a link between a news source and a voter is replaced by an average link density. In this approximation, we show that the average consensus time grows as [Formula: see text]. Here p is the probability that a voter consults a news source rather than a neighboring voter, and is the link density between a news source and voters, so that can be greater than 1. The polarization time, namely, the time to reach a politically polarized state from an initial strong majority state, is typically much less than the consensus time. For voters on the two-clique graph, either reducing the density of interclique links or enhancing the influence of news sources again promotes polarization.journal articl
Paired high‐throughput, in situ imaging and high‐throughput sequencing illuminate acantharian abundance and vertical distribution
Get PDFAcantharians (supergroup Rhizaria) can be important contributors to surface primary production and to carbon flux to the deep sea, but are often underestimated because their delicate structures are destroyed by plankton nets or dissolved by chemical fixatives. As they are also uncultured, relatively little is known about acantharian biology, especially regarding their life cycles. Here, we take a paired approach, bringing together high-throughput, in situ imaging and metabarcode sequencing, to investigate acantharian abundance, vertical distribution, and life history in the western North Pacific. Concentrations of imaged acantharian cells correlated well with relative abundances of 18S rRNA gene sequences from acantharians with known, recognizable morphologies, but not to sequences corresponding to acantharians with unknown morphology. These results suggest that morphologically undescribed clades may lack the characteristic star-shaped acantharian skeleton or are much smaller than described acantharians. The smaller size of acantharians imaged at depth supports current hypotheses regarding nonsymbiotic acantharian life cycles: cysts or vegetative cells release reproductive swarmer cells in deep water and juvenile cells grow as they ascend toward the surface. Moreover, sequencing data present the possibility that some photosymbiotic acantharians may also reproduce at depth, like their nonsymbiotic, encysting relatives, which is counter to previous hypotheses. Finally, in situ imaging captured a new acantharian behavior that may be a previously undescribed predation strategyjournal articl
A high-coverage Neandertal genome from Chagyrskaya Cave
Get PDFWe sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prufer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prufer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.journal articl
Voltage-gated ion channels mediate the electrotaxis of glioblastoma cells in a hybrid PMMA/PDMS microdevice
Get PDFTransformed astrocytes in the most aggressive form cause glioblastoma, the most common cancer in the central nervous system with high mortality. The physiological electric field by neuronal local field potentials and tissue polarity may guide the infiltration of glioblastoma cells through the electrotaxis process. However, microenvironments with multiplex gradients are difficult to create. In this work, we have developed a hybrid microfluidic platform to study glioblastoma electrotaxis in controlled microenvironments with high throughput quantitative analysis by machine learning-powered single cell tracking software. By equalizing the hydrostatic pressure difference between inlets and outlets of the microchannel, uniform single cells can be seeded reliably inside the microdevice. The electrotaxis of two glioblastoma models, T98G and U-251MG, requires an optimal laminin-containing extracellular matrix and exhibits opposite directional and electro-alignment tendencies. Calcium signaling is a key contributor in glioblastoma pathophysiology but its role in glioblastoma electrotaxis is still an open question. Anodal T98G electrotaxis and cathodal U-251MG electrotaxis require the presence of extracellular calcium cations. U-251MG electrotaxis is dependent on the P/Q-type voltage-gated calcium channel (VGCC) and T98G is dependent on the R-type VGCC. U-251MG electrotaxis and T98G electrotaxis are also mediated by A-type (rapidly inactivating) voltage-gated potassium channels and acid-sensing sodium channels. The involvement of multiple ion channels suggests that the glioblastoma electrotaxis is complex and patient-specific ion channel expression can be critical to develop personalized therapeutics to fight against cancer metastasis. The hybrid microfluidic design and machine learning-powered single cell analysis provide a simple and flexible platform for quantitative investigation of complicated biological systems.journal articl
Rydberg Excitation and Other Multiphoton Processes in Cold Rubidium Atoms Near an Optical Nanofibre
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOptical nanofibres (ONF) are used to confine light in subwavelength dimensions. In ONFs, a large evanescent field component extends beyond the fibre surface into the urroundings. In this thesis, we propose and explore the possibility of exciting neutral rubidium Rydberg atoms near an ONF and thereby exploring new aspects of Rydberg physics heretofore experimentally inaccessible. Rydberg atoms exhibits many unique properties which makes them attractive. In this dissertation, optical methods to detect and manipulate Rydberg atoms such as multiphoton excitation and electromagnetically induced transparency (EIT) are investigated. The primary results of this dissertation shows that the Rydberg atoms have been generated no more than a few hundred nm from the ONF surface, through an atom loss method and advances in realising Rydberg EIT in an ONF-cold atom system is discussed. The single-frequency, twophoton excitation at 993 nm addressing the 5S1/2 → 6S1/2 transition in ground state rubidium atoms mediated via the ONF is explored. The single-frequency, two-photon excitation serves as an alternative to two-photon excitation to Rydberg levels and could be crucial for developments in the neutral Rydberg atom-ONF interface, where we can avoid the possibility of ionisation. This thesis research forms the groundwork for future ONF-Rydberg atom studies of this nature.doctoral thesi
Fermionic order by disorder in a van der Waals antiferromagnet
Get PDFCeTe₃ is a unique platform to investigate the itinerant magnetism in a van der Waals (vdW) coupled metal. Despite chemical pressure being a promising route to boost quantum fluctuation in this system, a systematic study on the chemical pressure effect on Ce³⁺(4f¹) states is absent. Here, we report on the successful growth of a series of Se doped single crystals of CeTe₃. We found a fluctuation driven exotic magnetic rotation from the usual easy-axis ordering to an unusual hard-axis ordering. Unlike in localized magnetic systems, near-critical magnetism can increase itinerancy hand-in-hand with enhancing fluctuation of magnetism. Thus, seemingly unstable hard-axis ordering emerges through kinetic energy gain, with the self-consistent observation of enhanced magnetic fluctuation (disorder). As far as we recognize, this order-by-disorder process in fermionic system is observed for the first time within vdW materials. Our finding opens a unique experimental platform for direct visualization of the rich quasiparticle Fermi surface deformation associated with the Fermionic order-by-disorder process. Also, the search for emergent exotic phases by further tuning of quantum fluctuation is suggested as a promising future challenge.journal articl
Extreme storms cause rapid but short‐lived shifts in nearshore subtropical bacterial communities
Get PDFClimate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run‐off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early‐ and late‐season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment – locally known as red soil pollution – and caused moderate increases of macronutrients, especially SiO2 and PO43−, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run‐off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short‐lived and bacterial communities quickly recovered following both storm events. The early‐ and late‐season storms caused different physicochemical and bacterial community changes, demonstrating the context‐dependency of extreme storm responses in a subtropical coastal ecosystem.journal articl
Unmapped RNA Virus Diversity in Termites and Their Symbionts
Get PDFDespite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel RNA viruses, characterized their genomes, quantified their abundance and inferred their evolutionary history. These viruses were found within or similar to those from the Togaviridae, Iflaviridae, Polycipiviridae, Flaviviridae, Leviviridae, Narnaviridae, Mitoviridae, Lispivirdae, Phasmaviridae, Picobirnaviridae and Partitiviridae. However, all viruses identified were novel and divergent, exhibiting only 20% to 45% amino acid identity to previously identified viruses. Our analysis suggested that 17 of the viruses identified were termite-infecting, with the remainder likely associated with the termite microbiome or diet. Unclassified sobemo-like and bunya-like viruses dominated termite viromes, while most of the phylogenetic diversity was provided by the picobirna- and mitovirus-like viruses. Of note was the identification of a novel flavi-like virus most closely related to those found in marine vertebrates and invertebrates. Notably, the sampling procedure had the strongest association with virome composition, with greater RNA virome diversity in libraries prepared from whole termite bodies than those that only sampled heads.journal articl
Flavor moonshine
Get PDFThe flavor moonshine hypothesis is formulated to suppose that all particle masses (leptons, quarks, Higgs, and gauge particles—more precisely, their mass ratios) are expressed as coefficients in the Fourier expansion of some modular forms just as, in mathematics, dimensions of representations of a certain group are expressed as coefficients in the Fourier expansion of some modular forms. The mysterious hierarchical structure of the quark and lepton masses is thus attributed to that of the Fourier coefficient matrices of certain modular forms. Our intention here is not to prove this hypothesis starting from some physical assumptions but rather to demonstrate that this hypothesis is experimentally verified and, assuming that the string theory correctly describes the natural law, to calculate the geometry (Kähler potential and the metric) of the moduli space of the Calabi–Yau manifold, thus providing a way to calculate the metric of the Calabi–Yau manifold itself directly from the experimental data.journal articl