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Studying stochastic systems biology of the cell with single-cell genomics data
No full textRecent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach
Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids
No full textMicrotubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids
Enantio- and Diastereoenriched Enzymatic Synthesis of 1,2,3-Polysubstituted Cyclopropanes from (Z/E)-Trisubstituted Enol Acetates
No full textIn nature and synthetic chemistry, stereoselective [2+1] cyclopropanation is the most prevalent strategy for the synthesis of chiral cyclopropanes, a class of key pharmacophores in pharmaceuticals and bioactive natural products. One of the most extensively studied reactions in the organic chemist’s arsenal, stereoselective [2+1] cyclopropanation, largely relies on the use of stereodefined olefins, which require elaborate laboratory synthesis or tedious separation to ensure high stereoselectivity. Here we report engineered hemoproteins derived from a bacterial cytochrome P450 that catalyze the synthesis of chiral 1,2,3-polysubstituted cyclopropanes, regardless of the stereopurity of the olefin substrates used. Cytochrome P450_(BM3) variant IC-G3 exclusively converts (Z)-enol acetates to enantio- and diastereoenriched cyclopropanes and in our model reaction delivers a leftover (E)-enol acetate with 98% stereopurity, using whole Escherichia coli cells. IC-G3 was further engineered with a single mutation to enable the biotransformation of (E)-enol acetates to α-branched ketones with high levels of enantioselectivity while simultaneously catalyzing the cyclopropanation of (Z)-enol acetates with excellent activities and selectivities. We conducted docking studies and molecular dynamics simulations to understand how active-site residues distinguish between the substrate isomers and enable the enzyme to perform these distinct transformations with such high selectivities. Computational studies suggest the observed enantio- and diastereoselectivities are achieved through a stepwise pathway. These biotransformations streamline the synthesis of chiral 1,2,3-polysubstituted cyclopropanes from readily available mixtures of (Z/E)-olefins, adding a new dimension to classical cyclopropanation methods
Evolution of neuronal cell classes and types in the vertebrate retina
No full textThe basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information
Dominant two-dimensional electron-phonon interactions in the bulk Dirac semimetal Na₃Bi
No full textBulk Dirac semimetals (DSMs) exhibit unconventional transport properties and phase transitions due to their peculiar low-energy band structure. Yet the electronic interactions governing nonequilibrium phenomena in DSMs are not fully understood. Here we show that electron-phonon (e-ph) interactions in a prototypical bulk DSM, Na3Bi, are predominantly two-dimensional (2D). Our first-principles calculations discover a 2D optical phonon with strong e-ph interactions associated with in-plane vibrations of Na atoms. We show that this 2D mode governs e-ph scattering and charge transport in Na₃Bi, and induces a dynamical phase transition to a Weyl semimetal. Our work advances quantitative analysis of electron interactions in topological semimetals and reveals dominant low-dimensional interactions in bulk quantum materials
Phosphate deprivation‐induced changes in tomato are mediated by an interaction between brassinosteroid signaling and zinc
No full textInorganic phosphate (Pi) is a necessary macronutrient for basic biological processes. Plants modulate their root system architecture (RSA) and cellular processes to adapt to Pi deprivation albeit with a growth penalty. Excess application of Pi fertilizer, on the contrary, leads to eutrophication and has a negative environmental impact.
We compared RSA, root hair elongation, acid phosphatase activity, metal ion accumulation, and brassinosteroid hormone levels of Solanum lycopersicum (tomato) and Solanum pennellii, which is a wild relative of tomato, under Pi sufficiency and deficiency conditions to understand the molecular mechanism of Pi deprivation response in tomato.
We showed that S. pennellii is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response, which is dependent on zinc overaccumulation.
Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation
Porosity evolution of mafic crystal mush during reactive flow
No full textThe emergence of the “mush paradigm” has raised several questions for conventional models of magma storage and extraction: how are melts extracted to form eruptible liquid-rich domains? What mechanism controls melt transport in mush-rich systems? Recently, reactive flow has been proposed as a major contributing factor in the formation of high porosity, melt-rich regions. Yet, owing to the absence of accurate geochemical simulations, the influence of reactive flow on the porosity of natural mush systems remains under-constrained. Here, we use a thermodynamically constrained model of melt-mush reaction to simulate the chemical, mineralogical, and physical consequences of reactive flow in a multi-component mush system. Our results demonstrate that reactive flow within troctolitic to gabbroic mushes can drive large changes in mush porosity. For example, primitive magma recharge causes an increase in the system porosity and could trigger melt channelization or mush destabilization, aiding rapid melt transfer through low-porosity mush reservoirs
Bond-selective fluorescence imaging with single-molecule sensitivity
No full textBioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here we report bond-selective fluorescence-detected infrared-excited (BonFIRE) spectro-microscopy. BonFIRE employs two-photon excitation in the mid- and near-infrared to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tunable narrowband picosecond pulses to ensure high sensitivity, biocompatibility and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons and tissues, with promise for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations
The Flux‐Differencing Discontinuous Galerkin Method Applied to an Idealized Fully Compressible Nonhydrostatic Dry Atmosphere
No full textDynamical cores used to study the circulation of the atmosphere employ various numerical methods ranging from finite-volume, spectral element, global spectral, and hybrid methods. In this work, we explore the use of Flux-Differencing Discontinuous Galerkin (FDDG) methods to simulate a fully compressible dry atmosphere at various resolutions. We show that the method offers a judicious compromise between high-order accuracy and stability for large-eddy simulations and simulations of the atmospheric general circulation. In particular, filters, divergence damping, diffusion, hyperdiffusion, or sponge-layers are not required to ensure stability; only the numerical dissipation naturally afforded by FDDG is necessary. We apply the method to the simulation of dry convection in an atmospheric boundary layer and in a global atmospheric dynamical core in the standard benchmark of Held and Suarez (1994, https://doi.org/10.1175/1520-0477(1994)075〈1825:apftio〉2.0.co;2)
Plasma lensing near the eclipses of the Black Widow pulsar B1957+20
No full textRecently, several eclipsing millisecond pulsars have been shown to experience strong and apparent weak lensing from the outflow of their ionized companions. Lensing can be a powerful probe of the ionized plasma, with the strongest lenses potentially resolving emission regions of pulsars. Understanding lensing in the ‘laboratory-like’ conditions of an eclipsing pulsar may be analogously applied to fast radio bursts, many of which reside in dense, magnetized environments. We examined variable dispersion measure (DM), absorption, scattering, and flux density in the original Black Widow pulsar PSR B1957+20 through an eclipse at the Arecibo Observatory at 327 MHz. We discovered clear evidence of the two regimes of lensing, strong, and apparent weak. We show that the flux density variations in the apparently weak lensing regime can be modelled directly from variations of DM, using geometric optics. The mean effective velocities in the ingress, (954 ± 99) km s⁻¹, and egress (604 ± 47) km s⁻¹ cannot be explained by orbital motions alone, but are consistent with significant outflow velocity of material from the companion. We also show that geometric optics can predict when and where the lensing regime-change between weak and strong occurs, and argue that the apparent weak lensing is due to averaging many images. Our framework can be applied in any source with variable electron columns, measuring their relative velocities and distances. In other eclipsing pulsars, this provides a unique opportunity to measure companion outflow velocity, predict regions of weak and strong lensing, and in principle independently constrain orbital inclinations