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Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO
Get PDFTraditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as species-specific information or time calibrations are often displayed in separate figures, making the entire picture difficult for readers to grasp. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, were created to overcome such challenges by allowing interactive displays of complex data sets. The new phylogeny.IO web server (https://phylogeny.io) overcomes this issue by allowing users to easily import, annotate, and share interactive phylogenetic trees. It allows a range of static (e.g. such as shapes and colors) and dynamic (e.g. pop-up text and images) annotations. Annotated trees can be saved on the server for subsequent modification or they may be shared as IFrame HTML objects, easily embeddable in any web page. The principal goal of phylogeny.IO is not to produce publication-ready figures, but rather to provide a simple and intuitive annotation interface that allows easy and rapid sharing of figures in blogs, lecture notes, press releases, etc.journal articl
Proximity proteomics identifies cancer cell membrane cis‐molecular complex as a potential cancer target
Get PDFCancer-specific antigens expressed in the cell membrane have been used as targets for several molecular targeted strategies in the last 20 years with remarkable success. To develop more effective cancer treatments, novel targets and strategies for targeted therapies are needed. Here, we examined the cancer cell membrane-resident "cis-bimolecular complex" as a possible cancer target (cis-bimolecular cancer target: BiCAT) using proximity proteomics, a technique that has attracted attention in the last 10 years. BiCAT were detected using a previously developed method termed the enzyme-mediated activation of radical source (EMARS), to label the components proximal to a given cell membrane molecule. EMARS analysis identified some BiCAT, such as close homolog of L1 (CHL1), fibroblast growth factor 3 (FGFR3) and alpha2 integrin, which are commonly expressed in mouse primary lung cancer cells and human lung squamous cell carcinoma cells. Analysis of cancer specimens from 55 lung cancer patients revealed that CHL1 and alpha2 integrin were highly co-expressed in almost all cancer tissues compared with normal lung tissues. As an example of BiCAT application, in vitro simulation of effective drug combinations used for multiple drug treatment strategies was performed using reagents targeted to BiCAT molecules. The combination treatment based on BiCAT information moderately suppressed cancer cell proliferation compared with single administration, suggesting that the information about BiCAT in cancer cells is useful for the appropriate selection of the combination among molecular targeted reagents. Thus, BiCAT has the potential to contribute to several molecular targeted strategies in future.journal articl
Primer to Voltage Imaging With ANNINE Dyes and Two-Photon Microscopy
Get PDFANNINE-6 and ANNINE-6plus are voltage-sensitive dyes that when combined with two-photon microscopy are ideal for recording of neuronal voltages in vivo, in both bulk loaded tissue and the dendrites of single neurons. Here, we describe in detail but for a broad audience the voltage sensing mechanism of fast voltage-sensitive dyes, with a focus on ANNINE dyes, and how voltage imaging can be optimized with one-photon and two-photon excitation. Under optimized imaging conditions the key strengths of ANNINE dyes are their high sensitivity (0.5%/mV), neglectable bleaching and phototoxicity, a linear response to membrane potential, and a temporal resolution which is faster than the optical imaging devices currently used in neurobiology (order of nanoseconds). ANNINE dyes in combination with two-photon microscopy allow depth-resolved voltage imaging in bulk loaded tissue to study average membrane voltage oscillations and sensory responses. Alternatively, if ANNINE-6plus is applied internally, supra and sub threshold voltage changes can be recorded from dendrites of single neurons in awake animals. Interestingly, in our experience ANNINE-6plus labeling is impressively stable in vivo, such that voltage imaging from single Purkinje neuron dendrites can be performed for 2 weeks after a single electroporation of the neuron. Finally, to maximize their potential for neuroscience studies, voltage imaging with ANNINE dyes and two-photon microscopy can be combined with electrophysiological recording, calcium imaging, and/or pharmacology, even in awake animals.journal articl
Differential Gene Expression Supports a Resource‐Intensive, Defensive Role for Colony Production in the Bloom‐Forming Haptophyte, Phaeocystis globosa
Get PDFPhaeocystis globosa forms dense, monospecific blooms in temperate, northern waters. Blooms are usually dominated by the colonial morphotype—nonflagellated cells embedded in a secreted mucilaginous mass. Colonial Phaeocystis blooms significantly affect food‐web structure and function and negatively impact fisheries and aquaculture, but factors regulating colony formation remain enigmatic. Destructive P. globosa blooms have been reported in tropical and subtropical regions more recently and warm‐water blooms could become more common with continued climate change and coastal eutrophication. We therefore assessed genetic pathways associated with colony formation by investigating differential gene expression between colonial and solitary cells of a warm‐water P. globosa strain. Our results illustrate a transcriptional shift in colonial cells with most of the differentially expressed genes downregulated, supporting a reallocation of resources associated with forming and maintaining colonies. Dimethylsulfide and acrylate production and pathogen interaction pathways were upregulated in colonial cells, suggesting a defensive role for producing colonies. We identify several protein kinase signaling pathways that may influence the transition between morphotypes, providing targets for future research into factors affecting colony formation. This study provides novel insights into genetic mechanisms involved in Phaeocystis colony formation and provides new evidence supporting a defensive role for Phaeocystis colonies.journal articl
Coupling of vortex breakdown and stability in a swirling flow
Get PDFSwirling flows are ubiquitous over a large range of length scales and applications including micron-scale microfluidic devices up to geophysical flows such as tornadoes. As the viscous dissipation, shear, and centrifugal stresses interact, such flows can often exhibit unexpected fluid dynamics. Here, we use microfluidic experiments and numerical simulations to study the flow in a vortex T-mixer: a T-shaped channel with staggered, offset inlets. The vortex T-mixer flow is characterized by a single dominant vortex, the stability of which is closely coupled to the appearance of vortex breakdown. Specifically, at a Reynolds number of Re≈90, a first vortex breakdown region appears in the steady-state solution, rendering the vortex pulsatively unstable. A second vortex breakdown region appears at Re≈120, which restabilizes the vortex. Finally, a third vortex breakdown region appears at Re≈180, which renders the vortex helically unstable. Thus, a counterintuitive flow regime exists for the vortex T-mixer in which increasing the Reynolds number has a stabilizing effect on the steady-state flow. The pulsatively unstable vortex evolves into a periodically pulsating state with a Strouhal number of St≈0.5, and the helically unstable vortex evolves into a helically oscillating state with St≈1.75. These transitions can be explained within the framework of linear hydrodynamic stability. In addition, the vortex T-mixer flow exhibits multistability; multiple flow states are stable over various ranges of Re, including a narrow range of tristability for 160≤Re≤170, in which the steady state, the pulsatile oscillation, and the helical oscillation are all stable. This study provides experimental and numerical evidence of the close coupling between vortex breakdown and flow stability, including the restabilization of the flow with increasing Reynolds number due to the appearance of a vortex breakdown region, which will provide new insights into how vortex breakdown can affect the stability of a swirling flow.journal articl
Geographic Dependence of the Solar Irradiance Spectrum at Intermediate to High Frequencies
Get PDFTemporal fluctuations in the solar irradiance are important for renewable-energy harvesting, as well as for climate and ecological-systems analysis. Environmental studies usually focus on slow fluctuations of the solar irradiance, assuming that fast fluctuations are averaged out, while studies of solar power generation emphasize the role of faster fluctuations, due to their effect on grid stability. Several analyses have reported a power-law dependence of the generated-power spectrum for frequencies ranging from 1/min to 1/year. However, both the origin of this power law and its geographic dependence are not fully understood, an issue of significance when one considers smoothing of solar-photovoltaic-power fluctuations by combining geographically distributed generation sources. Here we show that the power law appears in the global and direct components of the solar radiation and not only in the generated power. We also show that the exponent of the power law has a clear latitudinal dependence. At most locations, the spectral power-law dependence of the intermediate (1/day1/h) frequencies. Using a simple model, we explain the origin of the power-law spectra and the latitudinal dependence. The implications of the power law for photovoltaic power generation and grid stability are discussed. We also suggest that the analysis of solar power generation should consider the power spectrum of the clear-sky irradiance at the location of interest in order to separate atmospheric effects from geographical ones.journal articl
Waveguide-induced dispersion interaction between two two-level atoms with orthogonal in-transverse-plane dipoles
Get PDFWe study the dispersion interaction between two ground-state two-level atoms near a cylindrical vacuum-clad optical waveguide. We focus on the case where the electric-dipole matrix-element vectors of the atoms are perpendicular to each other and to the interatomic axis. When these atoms are in free space, the dispersion interaction between them vanishes. In the presence of a waveguide aligned parallel to the interatomic axis, the energy of the dispersion interaction between the atoms may become nonzero and comparable to the average energy of the dispersion interaction between two atoms with arbitrarily oriented dipoles in free space. This waveguide-induced dispersion interaction is a consequence of the anisotropy of the medium around the atoms.journal articl
Nickel(II) Complexes with Electron-Rich, Sterically Hindered PNP Pincer Ligands Enable Uncommon Modes of Ligand Dearomatization
Get PDFWe report the reactivity and characterization of hydride, methyl, and bromo Ni-II complexes with a new class of electron-rich and sterically hindered PNP pincer ligands, Me₄PNPR (R = Pr-i, Bu-t), in which a classical metal-ligand cooperative mode of reactivity via CH2 arm deprotonation is blocked by methylation. This enables new, uncommon modes of PNP ligand dearomatization that involve reactivity in the para position of the pyridine ring. In particular, the reduction of [(Me₄PNPiPr) (NiMe)-Me-II]B(Ar-F)(4) with KC₈ leads to the formation of a new C-C bond via dimerization of two complexes through the para position. This reactivity stands in sharp contrast to the previously reported bromo or chloro complexes, where stable Ni-I halogen moieties are formed. Computational analysis showed a greater propensity for ligand-centered radical formation for the presumed intermediate one-electron-reduced species. UV-induced homolysis of the Ni-II-Me bond in [(Me₄PNPiPr) (NiMe)-Me-II]B(Ar-F)(4) leads to the formation of a Me radical detected by radical traps and Ni(I )intermediates that can be trapped in the presence of halide ions to give previously characterized, stable Ni-I halogen complexes. In addition, treatment of the bromo complexes [(Me₄PNPR)(NiBr)-Br-II]BPh₄ with a powerful hydride source, LiBEt₃H, leads to the reduction of the pyridine ring and the formation of Ni-II complexes with an anionic amide donor reduced pincer ligand, although aromatic Ni-II hydride complexes could also be obtained with a weaker hydride source. We have observed that steric bulk at the phosphine donors controls the reactivity of the resulting Ni(II)H( )complexes. While t-Bu-substituted [(Me₄PNPtBu) (NiH)-H-II]Y(Y=BPh₄, B(Ar-F)(4)) does not react with O-2, the less sterically hindered Pr-i-substituted [(Me₄PNPiPr)(NiH)-H-II]Y reacts instantaneously to give an unstable superoxide adduct that can be observed by EPR.journal articl
Improved SnO2 Electron Transport Layers Solution-Deposited at Near Room Temperature for Rigid or Flexible Perovskite Solar Cells with High Efficiencies
Get PDFElectron transport layer (ETL) is a functional layer of great significance for boosting the power conversion efficiency (PCE) of perovskite solar cells (PSCs). To date, it is still a challenge to simultaneously reduce the surface defects and improve the crystallinity in ETLs during their low-temperature processing. Here, a novel strategy for the mediation of in situ regrowth of SnO2 nanocrystal ETLs is reported: introduction of controlled trace amounts of surface absorbed water on the fluorinated tin oxide (FTO) or indium-tin oxide (ITO) surfaces of the substrates using ultraviolet ozone (UVO) pretreatment. The optimum amount of adsorbed water plays a key role in balancing the hydrolysis-condensation reactions during the structural evolution of SnO2 thin films. This new approach results in a full-coverage SnO2 ETL with a desirable morphology and crystallinity for superior optical and electrical properties, as compared to the control SnO2 ETL without the UVO pretreatment. Finally, the rigid and flexible PSC devices based on the new SnO2 ETLs yield high PCEs of up to 20.5% and 17.5%, respectively.journal articl
Facile and reversible double dearomatization of pyridines in non-phosphine MnI complexes with N,S-donor pyridinophane ligand
Get PDFSingle and double dearomatization of pyridine rings was observed in Mn(I) complexes with an N2S2 pyridinophane ligand via deprotonation of one or two CH2 arms, respectively. In contrast to other N,S-donor pincer-like systems, the dearomatized (N2S2)Mn species were found to be stable, with the dearomatization being reversible.journal articl