HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence.

The expansion of fluorescence bioimaging toward more complex systems and geometries requires analytical tools capable of spanning widely varying timescales and length scales, cleanly separating multiple fluorescent labels and distinguishing these labels from background autofluorescence. Here we meet these challenging objectives for multispectral fluorescence microscopy, combining hyperspectral phasors and linear unmixing to create Hybrid Unmixing (HyU). HyU is efficient and robust, capable of quantitative signal separation even at low illumination levels. In dynamic imaging of developing zebrafish embryos and in mouse tissue, HyU was able to cleanly and efficiently unmix multiple fluorescent labels, even in demanding volumetric timelapse imaging settings. HyU permits high dynamic range imaging, allowing simultaneous imaging of bright exogenous labels and dim endogenous labels. This enables coincident studies of tagged components, cellular behaviors and cellular metabolism within the same specimen, providing more accurate insights into the orchestrated complexity of biological systems.

FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish.

Visualizing cell shapes and interactions of differentiating cells is instrumental for understanding organ development and repair. Across species, strategies for stochastic multicolour labelling have greatly facilitated in vivo cell tracking and mapping neuronal connectivity. Yet integrating multi-fluorophore information into the context of developing zebrafish tissues is challenging given their cytoplasmic localization and spectral incompatibility with common fluorescent markers. Inspired by Drosophila Raeppli, we developed FRaeppli (Fish-Raeppli) by expressing bright membrane- or nuclear-targeted fluorescent proteins for efficient cell shape analysis and tracking. High spatiotemporal activation flexibility is provided by the Gal4/UAS system together with Cre/lox and/or PhiC31 integrase. The distinct spectra of the FRaeppli fluorescent proteins allow simultaneous imaging with GFP and infrared subcellular reporters or tissue landmarks. We demonstrate the suitability of FRaeppli for live imaging of complex internal organs, such as the liver, and have tailored hyperspectral protocols for time-efficient acquisition. Combining FRaeppli with polarity markers revealed previously unknown canalicular topologies between differentiating hepatocytes, reminiscent of the mammalian liver, suggesting common developmental mechanisms. The multispectral FRaeppli toolbox thus enables the comprehensive analysis of intricate cellular morphologies, topologies and lineages at single-cell resolution in zebrafish.

Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection.

Mycobacterium tuberculosis infection in humans triggers formation of granulomas, which are tightly organized immune cell aggregates that are the central structure of tuberculosis. Infected and uninfected macrophages interdigitate, assuming an altered, flattened appearance. Although pathologists have described these changes for over a century, the molecular and cellular programs underlying this transition are unclear. Here, using the zebrafish-Mycobacterium marinum model, we found that mycobacterial granuloma formation is accompanied by macrophage induction of canonical epithelial molecules and structures. We identified fundamental macrophage reprogramming events that parallel E-cadherin-dependent mesenchymal-epithelial transitions. Macrophage-specific disruption of E-cadherin function resulted in disordered granuloma formation, enhanced immune cell access, decreased bacterial burden, and increased host survival, suggesting that the granuloma can also serve a bacteria-protective role. Granuloma macrophages in humans with tuberculosis were similarly transformed. Thus, during mycobacterial infection, granuloma macrophages are broadly reprogrammed by epithelial modules, and this reprogramming alters the trajectory of infection and the associated immune response.

Increased COVID-19 mortality among immigrants compared with US-born individuals: a cross-sectional analysis of 2020 mortality data.

OBJECTIVE: Multiple studies have shown that racially minoritized groups had disproportionate COVID-19 mortality relative to non-Hispanic White individuals. However, there is little known regarding mortality by immigrant status nationally in the United States, despite being another vulnerable population. STUDY DESIGN: This was an observational cross-sectional study using mortality vital statistics system data to calculate proportionate mortality ratios (PMRs) and mortality rates due to COVID-19 as the underlying cause. METHODS: Rates were compared by decedents' identified race, ethnicity (Hispanic vs non-Hispanic), and immigrant (immigrants vs US born) status. Asian race was further disaggregated into "Asian Indian," "Chinese," "Filipino," "Japanese," "Korean," and "Vietnamese." RESULTS: Of the over 3.4 million people who died in 2020, 10.4% of all deaths were attributed to COVID-19 as the underlying cause (n = 351,530). More than double (18.9%, n = 81,815) the percentage of immigrants who died of COVID-19 compared with US-born decedents (9.1%, n = 269,715). PMRs due to COVID-19 were higher among immigrants compared with US-born individuals for non-Hispanic White, non-Hispanic Black, Hispanic, and most disaggregated Asian groups. Among disaggregated Asian immigrants, age- and sex-adjusted PMR due to COVID-19 ranged from 1.58 times greater mortality among Filipino immigrants (95% confidence interval [CI]: 1.53, 1.64) to 0.77 times greater mortality among Japanese immigrants (95% CI: 0.68, 0.86). Age-adjusted mortality rates were also higher among immigrant individuals compared with US-born people. CONCLUSIONS: Immigrant individuals experienced greater mortality due to COVID-19 compared with their US-born counterparts. As COVID-19 becomes more endemic, greater clinical and public health efforts are needed to reduce disparities in mortality among immigrants compared with their US-born counterparts.

River Basin Export Reduction Optimization Support Tool; a tool to screen options for reducing nutrient loads while minimizing cost.

Excess loading of nitrogen and phosphorus to river networks causes environmental harm, but reducing loads from large river basins is difficult and expensive. We develop a new tool, the River Basin Export Reduction Optimization Support Tool (RBEROST) to identify least-cost combinations of management practices that will reduce nutrient loading to target levels in downstream and mid-network waterbodies. We demonstrate the utility of the tool in a case study in the Upper Connecticut River basin in New England, USA. The total project cost of optimized lowest-cost plans ranged from $18.0 million to $41.0 million per year over 15 years depending on user specifications. Plans include both point source and non-point source management practices, and most costs are associated with urban stormwater practices. Adding a 2% margin of safety to loading targets improved estimated probability of success from 37.5% to 99%. The large spatial scale of RBEROST, and the consideration of both point and non-point source contributions of nutrients, makes it well suited as an initial screening tool in watershed planning.

Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging.

Time-lapse imaging of multiple labels is challenging for biological imaging as noise, photobleaching and phototoxicity compromise signal quality, while throughput can be limited by processing time. Here, we report software called Hyper-Spectral Phasors (HySP) for denoising and unmixing multiple spectrally overlapping fluorophores in a low signal-to-noise regime with fast analysis. We show that HySP enables unmixing of seven signals in time-lapse imaging of living zebrafish embryos.

An E3-ligase-based method for ablating inhibitory synapses.

Although neuronal activity can be modulated using a variety of techniques, there are currently few methods for controlling neuronal connectivity. We introduce a tool (GFE3) that mediates the fast, specific and reversible elimination of inhibitory synaptic inputs onto genetically determined neurons. GFE3 is a fusion between an E3 ligase, which mediates the ubiquitination and rapid degradation of proteins, and a recombinant, antibody-like protein (FingR) that binds to gephyrin. Expression of GFE3 leads to a strong and specific reduction of gephyrin in culture or in vivo and to a substantial decrease in phasic inhibition onto cells that express GFE3. By temporarily expressing GFE3 we showed that inhibitory synapses regrow following ablation. Thus, we have created a simple, reversible method for modulating inhibitory synaptic input onto genetically determined cells.

Effects of the Alpha-1 Antagonist Prazosin on KOR Agonist-Induced Reinstatement of Alcohol Seeking.

BACKGROUND: Stress is associated with relapse to alcohol seeking during abstinence, but the processes underlying this relationship are poorly understood. Noradrenaline is a key transmitter in stress responses and in stress-induced drug seeking. The alpha-1 adrenoceptor antagonist prazosin has been investigated as a treatment for alcoholism and for chronic stress disorders that are frequently comorbid with alcoholism. In rats, we previously showed that prazosin blocks reinstatement of alcohol seeking induced by footshock and yohimbine stressors and reduces yohimbine-induced brain activation. The role of alpha-1 adrenoceptors in reinstatement induced by other stressors is not known. Our most recent work is on the role of kappa opioid receptors in stress-induced reinstatement of alcohol seeking and have reported that the selective kappa opioid receptor agonist U50,488 induces reinstatement and neuronal activation in stress- and relapse-related brain regions. Here we determine the involvement of alpha-1 receptors in reinstatement and brain activation induced by U50,488. METHODS: We trained male Long-Evans rats to self-administer alcohol (12% w/v), extinguished alcohol-reinforced responding, and then determined the effects of prazosin (1 mg/kg) on U50,488 (2.5 mg/kg)-induced reinstatement and regional Fos expression. RESULTS: Prazosin blocked U50,488-induced reinstatement and decreased U50,488-induced Fos expression in the orbitofrontal cortex, nucleus accumbens core, ventral bed nucleus of the stria terminalis, central and basolateral amygdalar nuclei and ventral tegmental area. CONCLUSIONS: These findings suggest that prazosin may reduce U50,488-induced relapse by inhibiting activity in 1 or more of these brain areas.

Pressure Tensor Elements Breaking the Frozen-In Law During Reconnection in Earth's Magnetotail.

Aided by fully kinetic simulations, spacecraft observations of magnetic reconnection in Earth's magnetotail are analyzed. The structure of the electron diffusion region is in quantitative agreement with the numerical model. Of special interest, the spacecraft data reveal how reconnection is mediated by off-diagonal stress in the electron pressure tensor breaking the frozen-in law of the electron fluid.

Observations of Multiple Nuclear Reaction Histories and Fuel-Ion Species Dynamics in Shock-Driven Inertial Confinement Fusion Implosions.

Fuel-ion species dynamics in hydrodynamiclike shock-driven DT^{3}He-filled inertial confinement fusion implosion is quantitatively assessed for the first time using simultaneously measured D^{3}He and DT reaction histories. These reaction histories are measured with the particle x-ray temporal diagnostic, which captures the relative timing between different nuclear burns with unprecedented precision (∼10 ps). The observed 50±10 ps earlier D^{3}He reaction history timing (relative to DT) cannot be explained by average-ion hydrodynamic simulations and is attributed to fuel-ion species separation between the D, T, and ^{3}He ions during shock convergence and rebound. At the onset of the shock burn, inferred ^{3}He/T fuel ratio in the burn region using the measured reaction histories is much higher as compared to the initial gas-filled ratio. As T and ^{3}He have the same mass but different charge, these results indicate that the charge-to-mass ratio plays an important role in driving fuel-ion species separation during strong shock propagation even for these hydrodynamiclike plasmas.

Treating a novel plasticity defect rescues episodic memory in Fragile X model mice.

Episodic memory, a fundamental component of human cognition, is significantly impaired in autism. We believe we report the first evidence for this problem in the Fmr1-knockout (KO) mouse model of Fragile X syndrome and describe potentially treatable underlying causes. The hippocampus is critical for the formation and use of episodes, with semantic (cue identity) information relayed to the structure via the lateral perforant path (LPP). The unusual form of synaptic plasticity expressed by the LPP (lppLTP) was profoundly impaired in Fmr1-KOs relative to wild-type mice. Two factors contributed to this defect: (i) reduced GluN1 subunit levels in synaptic NMDA receptors and related currents, and (ii) impaired retrograde synaptic signaling by the endocannabinoid 2-arachidonoylglycerol (2-AG). Studies using a novel serial cue paradigm showed that episodic encoding is dependent on both the LPP and the endocannabinoid receptor CB1, and is strikingly impaired in Fmr1-KOs. Enhancing 2-AG signaling rescued both lppLTP and learning in the mutants. Thus, two consequences of the Fragile-X mutation converge on plasticity at one site in hippocampus to prevent encoding of a basic element of cognitive memory. Collectively, the results suggest a clinically plausible approach to treatment.

Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish.

Interrogation of gene regulatory circuits in complex organisms requires precise and robust methods to label cell-types for profiling of target proteins in a tissue-specific fashion as well as data analysis to understand interconnections within the circuits. There are several strategies for obtaining cell-type and subcellular specific genome-wide data. We have developed a methodology, termed "biotagging" that uses tissue-specific, genetically encoded components to biotinylate target proteins, enabling in depth genome-wide profiling in zebrafish. We have refined protocols to use the biotagging approach that led to enhanced isolation of coding and non-coding RNAs from ribosomes and nuclei of genetically defined cell-types. The ability to study both the actively translated and transcribed transcriptome in the same cell population, coupled to genomic accessibility assays has enabled the study of cell-type specific gene regulatory circuits in zebrafish due to the high signal-to-noise achieved via its stringent purification protocol. Here, we provide detailed methods to isolate, profile and analyze cell-type specific polyribosome and nuclear transcriptome in zebrafish.

Time-resolved imaging of bound and dissociating nuclear wave packets in strong-field ionized iodomethane.

We report the results of a time-resolved coincident ion momentum imaging experiment probing nuclear wave packet dynamics in the strong-field ionization and dissociation of iodomethane (CH3I), a prototypical polyatomic system for photochemistry and ultrafast laser science. By measuring yields, kinetic energies, and angular distributions of CH3+ + I+ and CH3+ + I++ ion pairs as a function of the delay between two 25 fs, 790 nm pump and probe pulses, we map both, bound and dissociating nuclear wave packets in intermediate cationic states, thereby tracking different ionization and dissociation pathways. In both channels, we find oscillatory features with a 130 fs periodicity resulting from vibrational motion (C-I symmetric stretch mode) in the first electronically excited state of CH3I+. This vibrational wave packet dephases within 1 ps, in good agreement with a simple wave packet propagation model. Our results indicate that the first excited cationic state plays a key role in the dissociative ionization of CH3I and that it represents an important intermediate in the sequential double and multiple ionization at moderate intensities.

A versatile gene trap to visualize and interrogate the function of the vertebrate proteome.

We report a multifunctional gene-trapping approach, which generates full-length Citrine fusions with endogenous proteins and conditional mutants from a single integration event of the FlipTrap vector. We identified 170 FlipTrap zebrafish lines with diverse tissue-specific expression patterns and distinct subcellular localizations of fusion proteins generated by the integration of an internal citrine exon. Cre-mediated conditional mutagenesis is enabled by heterotypic lox sites that delete Citrine and "flip" in its place mCherry with a polyadenylation signal, resulting in a truncated fusion protein. Inducing recombination with Cerulean-Cre results in fusion proteins that often mislocalize, exhibit mutant phenotypes, and dramatically knock down wild-type transcript levels. FRT sites in the vector enable targeted genetic manipulation of the trapped loci in the presence of Flp recombinase. Thus, the FlipTrap captures the functional proteome, enabling the visualization of full-length fluorescent fusion proteins and interrogation of function by conditional mutagenesis and targeted genetic manipulation.

Oral Rehabilitation of Patients Sustaining Orofacial Injuries: The UPenn Initiative.

Tissue injuries in the oral and maxillofacial structures secondary to trauma, warfare, ablative cancer, and benign tumor surgery result in significant losses of speech, masticatory and swallowing functions, aesthetic deformities, and overall psychological stressors and compromise. Optimal oral rehabilitation remains a formidable challenge and an unmet clinical need due to the influence of multiple factors related to the physiologic limitations of tissue repair, the lack of site and function-specific donor tissues and constructs, and an integrated team of multidisciplinary professionals. The advancements in stem cell biology, biomaterial science, and tissue engineering technologies, particularly the 3-dimensional bioprinting technology, together with digital imaging and computer-aided design and manufacturing technologies, have paved the path for personalized/precision regenerative medicine. At the University of Pennsylvania, we have launched the initiative to integrate multidisciplinary health professionals and translational/clinical scientists in medicine, dentistry, stem cell biology, tissue engineering, and regenerative medicine to develop a comprehensive, patient-centered approach for precision and personalized reconstruction, as well as oral rehabilitation of patients sustaining orofacial tissue injuries and defects, especially oral cancer patients.

New LC-MS/MS method with single-step pretreatment analyzes fat-soluble vitamins in plasma and amniotic fluid.

Fat-soluble vitamins (FSVs), A, D, and E, are components of prenatal vitamin care. Previously, limited evidence existed to explain on a molecular level how maternal FSV supplementation affects the fetus during pregnancy. We developed a simplified LC-MS/MS method to simultaneously detect FSVs in maternal plasma (MP) and amniotic fluid (AF); we used this approach to investigate the correlation between FSV levels in these two matrices. With this method, we circumvented frequently used liquid-liquid extraction or solid-phase extraction methods and, instead, used simple protein precipitation with acetonitrile for sample preparation. This method displayed satisfactory linearity, intra- and inter-day imprecision, and accuracy. We validated the consistency with standard reference material 972a and 968f certification. In analysis of MP and AF samples from 50 pregnant women in the second trimester, concentrations of retinol, 25-hydroxyvitamin D3 [25(OH)D3], and α-tocopherol (reflecting vitamins A, D, and E, respectively) were lower in AF than in MP. Significant positive correlations existed between MP and AF for 25(OH)D3 (r = 0.667; P < 0.001) and retinol (r = 0.393; P = 0.005), but not for α-tocopherol (r = 0.145, P > 0.05). This novel LC-MS/MS method shows prominent applicability for FSV detection and the observed correlations contribute to research on fetal development.

Spacecraft Observations of Oblique Electron Beams Breaking the Frozen-In Law During Asymmetric Reconnection.

Fully kinetic simulations of asymmetric magnetic reconnection reveal the presence of magnetic-field-aligned beams of electrons flowing toward the topological magnetic x line. Within the ∼6d_{e} electron-diffusion region, the beams become oblique to the local magnetic field, providing a unique signature of the electron-diffusion region where the electron frozen-in law is broken. The numerical predictions are confirmed by in situ Magnetospheric Multiscale spacecraft observations during asymmetric reconnection at Earth's dayside magnetopause.

Electron Bulk Acceleration and Thermalization at Earth's Quasiperpendicular Bow Shock.

Electron heating at Earth's quasiperpendicular bow shock has been surmised to be due to the combined effects of a quasistatic electric potential and scattering through wave-particle interaction. Here we report the observation of electron distribution functions indicating a new electron heating process occurring at the leading edge of the shock front. Incident solar wind electrons are accelerated parallel to the magnetic field toward downstream, reaching an electron-ion relative drift speed exceeding the electron thermal speed. The bulk acceleration is associated with an electric field pulse embedded in a whistler-mode wave. The high electron-ion relative drift is relaxed primarily through a nonlinear current-driven instability. The relaxed distributions contain a beam traveling toward the shock as a remnant of the accelerated electrons. Similar distribution functions prevail throughout the shock transition layer, suggesting that the observed acceleration and thermalization is essential to the cross-shock electron heating.

Zebrafish Model for Functional Screening of Flow-Responsive Genes.

OBJECTIVE: Atherosclerosis is initiated at branches and bends of arteries exposed to disturbed blood flow that generates low shear stress. This mechanical environment promotes lesions by inducing endothelial cell (EC) apoptosis and dysfunction via mechanisms that are incompletely understood. Although transcriptome-based studies have identified multiple shear-responsive genes, most of them have an unknown function. To address this, we investigated whether zebrafish embryos can be used for functional screening of mechanosensitive genes that regulate EC apoptosis in mammalian arteries. APPROACH AND RESULTS: First, we demonstrated that flow regulates EC apoptosis in developing zebrafish vasculature. Specifically, suppression of blood flow in zebrafish embryos (by targeting cardiac troponin) enhanced that rate of EC apoptosis (≈10%) compared with controls exposed to flow (≈1%). A panel of candidate regulators of apoptosis were identified by transcriptome profiling of ECs from high and low shear stress regions of the porcine aorta. Genes that displayed the greatest differential expression and possessed 1 to 2 zebrafish orthologues were screened for the regulation of apoptosis in zebrafish vasculature exposed to flow or no-flow conditions using a knockdown approach. A phenotypic change was observed in 4 genes; p53-related protein (PERP) and programmed cell death 2-like protein functioned as positive regulators of apoptosis, whereas angiopoietin-like 4 and cadherin 13 were negative regulators. The regulation of perp, cdh13, angptl4, and pdcd2l by shear stress and the effects of perp and cdh13 on EC apoptosis were confirmed by studies of cultured EC exposed to flow. CONCLUSIONS: We conclude that a zebrafish model of flow manipulation coupled to gene knockdown can be used for functional screening of mechanosensitive genes in vascular ECs, thus providing potential therapeutic targets to prevent or treat endothelial injury at atheroprone sites.