Which animals are at risk? Predicting species susceptibility to Covid-19.

In only a few months, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, leaving physicians, scientists, and public health officials racing to understand, treat, and contain this zoonotic disease. SARS-CoV-2 has made the leap from animals to humans, but little is known about variations in species susceptibility that could identify potential reservoir species, animal models, and the risk to pets, wildlife, and livestock. While there is evidence that certain species, such as cats, are susceptible, the vast majority of animal species, including those in close contact with humans, have unknown susceptibility. Hence, methods to predict their infection risk are urgently needed. SARS-CoV-2 spike protein binding to angiotensin converting enzyme 2 (ACE2) is critical for viral cell entry and infection. Here we identified key ACE2 residues that distinguish susceptible from resistant species using in-depth sequence and structural analyses of ACE2 and its binding to SARS-CoV-2. Our findings have important implications for identification of ACE2 and SARS-CoV-2 residues for therapeutic targeting and identification of animal species with increased susceptibility for infection on which to focus research and protection measures for environmental and public health.

Engineered three-dimensional microfluidic device for interrogating cell-cell interactions in the tumor microenvironment.

Stromal cells in the tumor microenvironment play a key role in the metastatic properties of a tumor. It is recognized that cancer-associated fibroblasts (CAFs) and endothelial cells secrete factors capable of influencing tumor cell migration into the blood or lymphatic vessels. We developed a microfluidic device that can be used to image the interactions between stromal cells and tumor cell spheroids in a three dimensional (3D) microenvironment while enabling external control of interstitial flow at an interface, which supports endothelial cells. The apparatus couples a 200-µm channel with a semicircular well to mimic the interface of a blood vessel with the stroma, and the design allows for visualization of the interactions of interstitial flow, endothelial cells, leukocytes, and fibroblasts with the tumor cells. We observed that normal tissue-associated fibroblasts (NAFs) contribute to the "single file" pattern of migration of tumor cells from the spheroid in the 3D microenvironment. In contrast, CAFs induce a rapid dispersion of tumor cells out of the spheroid with migration into the 3D matrix. Moreover, treatment of tumor spheroid cultures with the chemokine CXCL12 mimics the effect of the CAFs, resulting in similar patterns of dispersal of the tumor cells from the spheroid. Conversely, addition of CXCL12 to co-cultures of NAFs with tumor spheroids did not mimic the effects observed with CAF co-cultures, suggesting that NAFs produce factors that stabilize the tumor spheroids to reduce their migration in response to CXCL12.

Mechanistic analysis of challenge-response experiments.

We present an application of mechanistic modeling and nonlinear longitudinal regression in the context of biomedical response-to-challenge experiments, a field where these methods are underutilized. In this type of experiment, a system is studied by imposing an experimental challenge, and then observing its response. The combination of mechanistic modeling and nonlinear longitudinal regression has brought new insight, and revealed an unexpected opportunity for optimal design. Specifically, the mechanistic aspect of our approach enables the optimal design of experimental challenge characteristics (e.g., intensity, duration). This article lays some groundwork for this approach. We consider a series of experiments wherein an isolated rabbit heart is challenged with intermittent anoxia. The heart responds to the challenge onset, and recovers when the challenge ends. The mean response is modeled by a system of differential equations that describe a candidate mechanism for cardiac response to anoxia challenge. The cardiac system behaves more variably when challenged than when at rest. Hence, observations arising from this experiment exhibit complex heteroscedasticity and sharp changes in central tendency. We present evidence that an asymptotic statistical inference strategy may fail to adequately account for statistical uncertainty. Two alternative methods are critiqued qualitatively (i.e., for utility in the current context), and quantitatively using an innovative Monte-Carlo method. We conclude with a discussion of the exciting opportunities in optimal design of response-to-challenge experiments.

Towards monitoring real-time cellular response using an integrated microfluidics-matrix assisted laser desorption ionisation/nanoelectrospray ionisation-ion mobility-mass spectrometry platform.

The combination of microfluidic cell trapping devices with ion mobility-mass spectrometry offers the potential for elucidating in real time the dynamic responses of small populations of cells to paracrine signals, changes in metabolite levels and delivery of drugs and toxins. Preliminary experiments examining peptides in methanol and recording the interactions of yeast and Jurkat cells with their superfusate have identified instrumental set-up and control parameters and online desalting procedures. Numerous initial experiments demonstrate and validate this new instrumental platform. Future outlooks and potential applications are addressed, specifically how this instrumentation may be used for fully automated systems biology studies of the significantly interdependent, dynamic internal workings of cellular metabolic and signalling pathways.

Increased cell migration and plasticity in Nrf2-deficient cancer cell lines.

Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) expression is deregulated in many cancers. Genetic and biochemical approaches coupled with functional assays in cultured cells were used to explore the consequences of Nrf2 repression. Nrf2 suppression by Keap1-directed ubiquitylation or the expression of independent short hairpin RNA (shRNA)/siRNA sequences enhanced cellular levels of reactive oxygen species, Smad-dependent tumor cell motility and growth in soft agar. Loss of Nrf2 was accompanied by concomitant Smad linker region/C-terminus phosphorylation, induction of the E-cadherin transcriptional repressor Slug and suppression of the cell-cell adhesion protein E-cadherin. Ectopic expression of the wildtype but not dominant-negative Nrf2 suppressed the activity of a synthetic transforming growth factor-beta1-responsive CAGA-directed luciferase reporter. shRNA knock-down of Nrf2 enhanced the activity of the synthetic CAGA reporter, as well as the expression of the endogenous Smad target gene plasminogen activator inhibitor-1. Finally, we found that Nrf2/Smad3/Smad4 formed an immunoprecipitable nuclear complex. Thus, loss of Nrf2 increased R-Smad phosphorylation and R-Smad signaling, supporting the hypothesis that loss of Nrf2 in an oncogenic context-dependent manner can enhance cellular plasticity and motility, in part by using transforming growth factor-beta/Smad signaling.

Mirrored pyramidal wells for simultaneous multiple vantage point microscopy.

We report a novel method for obtaining simultaneous images from multiple vantage points of a microscopic specimen using size-matched microscopic mirrors created from anisotropically etched silicon. The resulting pyramidal wells enable bright-field and fluorescent side-view images, and when combined with z-sectioning, provide additional information for 3D reconstructions of the specimen. We have demonstrated the 3D localization and tracking over time of the centrosome of a live Dictyostelium discoideum. The simultaneous acquisition of images from multiple perspectives also provides a five-fold increase in the theoretical collection efficiency of emitted photons, a property which may be useful for low-light imaging modalities such as bioluminescence, or low abundance surface-marker labelling.

3'-phosphoinositides regulate the coordination of speed and accuracy during chemotaxis.

The PI3K/PTEN pathway, as the regulator of 3'-phosphoinositide (3'-PI) dynamics, has emerged as a key regulator of chemoattractant gradient sensing during chemotaxis in Dictyostelium and other cell types. Previous results have shown 3'-PIs to be important for regulating basal cell motility and sensing the direction and strength of the chemoattractant gradient. We examined the chemotaxis of wild-type cells and cells lacking PTEN or PI3K1 and 2 using analytical methods that allowed us to quantitatively discern differences between the genotype's ability to sense and efficiently respond to changes in gradient steepness during chemotaxis. We found that cells are capable of increasing their chemotactic accuracy and speed as they approach a micropipette in a manner that is dependent on the increasing strength of the concentration gradient and 3'-PI signaling. Further, our data show that 3'-PI signaling affects a cell's ability to coordinate speed and direction to increase chemotactic efficiency. Using to our knowledge a new measurement of chemotactic efficiency that reveals the degree of coordination between speed and accuracy, we found that cells also have the capacity to increase their chemotactic efficiency as they approach the micropipette. Like directional accuracy and speed, the increase in chemotactic efficiency of cells with increased gradient strength is sensitive to 3'-PI dysregulation. Our evidence suggests that receptor-driven 3'-PI signaling regulates the ability of a cell to capitalize on stronger directional inputs and minimize the effects of inaccurate turns to increase chemotactic efficiency.

Polarity reversal lowers activation time during diastolic field stimulation of the rabbit ventricles: insights into mechanisms.

To fully characterize the mechanisms of defibrillation, it is necessary to understand the response, within the three-dimensional (3D) volume of the ventricles, to shocks given in diastole. Studies that have examined diastolic responses conducted measurements on the epicardium or on a transmural surface of the left ventricular (LV) wall only. The goal of this study was to use optical imaging experiments and 3D bidomain simulations, including a model of optical mapping, to ascertain the shock-induced virtual electrode and activation patterns throughout the rabbit ventricles following diastolic shocks. We tested the hypothesis that the locations of shock-induced regions of hyperpolarization govern the different diastolic activation patterns for shocks of reversed polarity. In model and experiment, uniform-field monophasic shocks of reversed polarities (cathode over the right ventricle is RV-, reverse polarity is LV-) were applied to the ventricles in diastole. Experiments and simulations revealed that RV- shocks resulted in longer activation times compared with LV- shocks of the same strength. 3D simulations demonstrated that RV- shocks induced a greater volume of hyperpolarization at shock end compared with LV- shocks; most of these hyperpolarized regions were located in the LV. The results of this study indicate that ventricular geometry plays an important role in both the location and size of the shock-induced virtual anodes that determine activation delay during the shock and subsequently affect shock-induced propagation. If regions of hyperpolarization that develop during the shock are sufficiently large, activation delay may persist until shock end.

Engineering challenges of BioNEMS: the integration of microfluidics, micro- and nanodevices, models and external control for systems biology.

Systems biology, i.e. quantitative, postgenomic, postproteomic, dynamic, multiscale physiology, addresses in an integrative, quantitative manner the shockwave of genetic and proteomic information using computer models that may eventually have 10(6) dynamic variables with non-linear interactions. Historically, single biological measurements are made over minutes, suggesting the challenge of specifying 10(6) model parameters. Except for fluorescence and micro-electrode recordings, most cellular measurements have inadequate bandwidth to discern the time course of critical intracellular biochemical events. Micro-array expression profiles of thousands of genes cannot determine quantitative dynamic cellular signalling and metabolic variables. Major gaps must be bridged between the computational vision and experimental reality. The analysis of cellular signalling dynamics and control requires, first, micro- and nano-instruments that measure simultaneously multiple extracellular and intracellular variables with sufficient bandwidth; secondly, the ability to open existing internal control and signalling loops; thirdly, external BioMEMS micro-actuators that provide high bandwidth feedback and externally addressable intracellular nano-actuators; and, fourthly, real-time, closed-loop, single-cell control algorithms. The unravelling of the nested and coupled nature of cellular control loops requires simultaneous recording of multiple single-cell signatures. Externally controlled nano-actuators, needed to effect changes in the biochemical, mechanical and electrical environment both outside and inside the cell, will provide a major impetus for nanoscience.

Vector projection of biomagnetic fields.

Biomagnetic measurements are increasingly popular as functional imaging techniques for the non-invasive assessment of electrically active tissue. Although most currently available magnetometers utilise only one component of the vector magnetic field, some studies have suggested the possibility of obtaining additional information from recordings of the full magnetic field vector. Three projection techniques were applied to different biomagnetic signals for analysis of the three orthogonal components of the vector magnetic field. Vector magnetic fields obtained from fetal cardiac activity were projected into evenly spaced directions around a unit sphere. The vector magnetic field recorded from multiple intestinal current sources with independent temporal frequencies was then projected. Finally, an external reference signal from an invasive electrode was used to project the recorded vector magnetic fields due to gastric electrical activity. In each case, it was found that the information obtained by examination of the projected magnetic field vectors gave superior clinical insight to that obtained by analysis of any single magnetic field component.

Biomagnetic detection of gastric electrical activity in normal and vagotomized rabbits.

We recorded the vector magnetogastrogram (MGG) due to gastric electrical activity (GEA) in normal rabbits using a Superconducting QUantum Interference Device (SQUID) magnetometer and measured the degree of correlation of the MGG with 24 channels of serosal electrodes. The vector magnetometer allows us to non-invasively record three orthogonal magnetic field components and project the recorded magnetic field vector into arbitrary directions. We optimized the magnetic field vector direction to obtain the highest possible correlation with each serosal electrode recording. We performed a vagotomy and examined spatial and temporal changes in the serosal potential and in the transabdominal magnetic field. We obtained spatial information by mapping the recorded signals to the electrode positions in the gastric musculature. Temporal evidence of uncoupling was observed in spectral analyses of both serosal electrode and SQUID magnetometer recordings. We conclude that non-invasive recordings of the vector magnetogastrogram reflect underlying serosal potentials as well as pathophysiological changes following vagotomy.

Histopathologic changes during mesenteric ischaemia and reperfusion.

The basic electrical rhythm (BER) of the intestine is known to decrease during mesenteric ischaemia. Some studies have reported the relationship between the BER and the pathologic changes that occur in the bowel during vascular injury. However, these changes have not been completely elucidated. This study describes the histopathologic pattern when the rabbit small intestine was subjected to ischaemia of varying time lengths (30-150 minutes) and subsequent reperfusion for six hours. Intestinal biopsies were taken at baseline, at the end of ischaemia, and at hourly intervals during reperfusion. Microscopic examination of the biopsies revealed evidence of progressive infarction of the mucosa during ischaemia. There was an acute worsening of the pathology during reperfusion, the severity being greater when reperfusion was preceded by longer periods of ischaemia. These changes were statistically significant. The observed pattern in this study shows clearly that reperfusion injury is reflected in the histopathologic response and that this is worse in severity than the response to ischaemia. Studies of longer duration should further clarify the picture during recovery in ischaemia/reperfusion injuries of the bowel.

Experimental and theoretical analysis of phase singularity dynamics in cardiac tissue.

INTRODUCTION: Quantitative analysis of complex self-excitatory wave patterns, such as cardiac fibrillation and other high-order reentry, requires the development of new tools for identifying and tracking the most important features of the activation, such as phase singularities. METHODS AND RESULTS: Image processing operations can be used to detect the phase singularity at the tip of a spiral wave. The phase space behavior of a spatiotemporal sequence of data may be reconstructed using time-series analysis. The phase singularities then are localized efficiently by computing the topologic charge density as the curl of the spatial phase gradient. We analyzed the singularity interaction dynamics of both experimentally observed and numerically simulated instances of quatrefoil reentry and found that the singularity behavior in the experimental preparations can be classified into three categories on the basis of how their separation changes with time. CONCLUSION: Topologic charge densities can be calculated easily and efficiently to reveal phase singularity behavior. However, the differences between theoretical and experimental observations of singularity separation distances indicate the need for more sophisticated numerical models.

Spatial filter approach for evaluation of the surface Laplacian of the electroencephalogram and magnetoencephalogram.

The surface Laplacian is a technique that has been utilized to improve the spatial resolution of the electroencephalogram (EEG) and the magnetoencephalogram (MEG). We investigate the amount of improvement to the spatial resolution afforded by the surface Laplacian by examining the spatial filters that describe the relationship between cortical current sources and the surface Laplacian. The surface Laplacian spatial filters extend into higher spatial frequencies than do raw signal spatial filters, particularly for EEG Laplacian spatial filters, indicating that substantial improvement in spatial resolution is possible. However, the response of the surface Laplacian operation to the nature and amount of noise in the raw EEG and MEG signals is of paramount importance. Spatially correlated noise, coupled with uncorrelated noise, requires additional regularization of inverse spatial filters resulting in a decrease in spatial resolution. Substantial improvements in spatial resolution may be obtained using the surface Laplacian techniques as long as correlated noise levels are small and raw signals have relatively high signal-to-noise ratios.

Spatial filter approach for comparison of the forward and inverse problems of electroencephalography and magnetoencephalography.

We present an analysis of the relative information content of cortical current source reconstructions from electroencephalogram (EEG) and magnetoencephalogram (MEG) forward calculations by examining the spatial filters that relate the internal sources with the externally measured electric potentials and magnetic fields. The forward spatial filters are seen to be low-pass functions of spatial frequency and spatial resolution degrades in external measurements. Inverse spatial filters may be used to reconstruct cortical sources from external data, but since they are high-pass functions of spatial frequency, they must be regularized to avoid instabilities caused by noise at higher spatial frequencies. The regularization process limits the spatial resolution of source reconstructions. EEG forward spatial filters fall off at lower spatial frequencies than MEG filters; hence, there is less information available in higher spatial frequencies resulting in lower spatial resolution in inverse reconstructions. The tangential component of the magnetic field provides even higher spatial resolution than can be obtained using the radial component. An accompanying article examines the surface Laplacian for both the EEG and the MEG.

The effects of tubulin-binding agents on stretch-induced ventricular arrhythmias.

Stretch-activated ion channels have been identified as transducers of mechanoelectric coupling in the heart, where they may play a role in arrhythmogenesis. The role of the cytoskeleton in ion channel control has been a topic of recent study and the transmission of mechanical stresses to stretch-activated channels by cytoskeletal attachment has been hypothesized. We studied the arrhythmogenic effects of stretch in 16 Langendorff-perfused rabbit hearts in which we pharmacologically manipulated the microtubular network of the cardiac myocytes. Group 1 (n=5) was treated with colchicine, which depolymerizes microtubules, and Group 2 (n=6) was treated with taxol, which polymerizes microtubules. Stretch-induced arrhythmias were produced by transiently increasing the volume of a fluid-filled left ventricular balloon with a volume pump driven by a computer-controlled stepper motor. Electrical events were recorded by a contact electrode which provided high-fidelity recordings of monophasic action potentials and stretch-induced depolarizations. The probability of eliciting a stretch-induced arrhythmia increased (0.22+/-0.11 to 0.62+/-0.19, p=0.001) in hearts treated with taxol (5 microM), whereas hearts treated with colchicine (100 microM) showed no statistically significant change. We conclude that proliferation of microtubules increased the arrhythmogenic effect of transient left ventricle diastolic stretch. This result indicates a possible mode of arrhythmogenesis in chemotherapeutic patients and patients exhibiting uncompensated ventricular hypertrophy. The data would indicate that the cytoskeleton represents a possible target for antiarrhythmic therapies.

Volume conductor effects on the spatial resolution of magnetic fields and electric potentials from gastrointestinal electrical activity.

An analysis of the relative capabilities of methods for magnetic and electric detection of gastrointestinal electrical activity is presented. The model employed is the first volume conductor model for magnetic fields from GEA to appear in the literature. A mathematical model is introduced for the electric potential and magnetic field from intestinal electrical activity in terms of the spatial filters that relate the bioelectric sources with the external magnetic fields and potentials. The forward spatial filters are low-pass functions of spatial frequency, so more superficial external fields and potentials contain less spatial information than fields and potentials near the source. Inverse spatial filters, which are reciprocals of the forward filters, are high-pass functions and must be regularised by windowing. Because of the conductivity discontinuities introduced by low-conductivity fat layers in the abdomen, the electric potentials recorded outside these layers required more regularisation than the magnetic fields, and thus, the spatial resolution of the magnetic fields from intestinal electrical activity is higher than the spatial resolution of the external potentials. In this study, two smooth muscle sources separated by 5cm were adequately resolved magnetically, but not resolved electrically. Thus, sources are more accurately localized and imaged using magnetic measurements than using measurements of electric potential.

Three-dimensional surface reconstruction and fluorescent visualization of cardiac activation.

Optical imaging of transmembrane potentials in cardiac tissue is a rapidly growing technique in cardiac electrophysiology. Traditional studies typically use a monocular imaging setup, thus limiting investigation to a restricted region of tissue. However, studies of large-scale wavefront dynamics, especially those during fibrillation and defibrillation, would benefit from visualization of the entire epicardial surface. To solve this problem, a panoramic cardiac visualization algorithm was developed which performs the two tasks of reconstruction of the surface geometry of the heart, and representation of the panoramic fluorescence information as a texture mapping onto the geometry that was previously created. This system permits measurement of epicardial electrodynamics over a geometrically realistic representation of the actual heart being studied. To verify the accuracy of the algorithm, the procedure was applied to synthetic images of a patterned ball; further verification was provided by application of the algorithm to a model heart placed in the experimental setup. Both sets of images produced mean registration image errors on the order of 2 pixels, corresponding to roughly 3 mm on the geometry. We demonstrate the algorithm by visualizing epicardial wavefronts on an isolated, perfused rabbit heart.

A low temperature transfer of ALH84001 from Mars to Earth.

The ejection of material from Mars is thought to be caused by large impacts that would heat much of the ejecta to high temperatures. Images of the magnetic field of martian meteorite ALH84001 reveal a spatially heterogeneous pattern of magnetization associated with fractures and rock fragments. Heating the meteorite to 40 degrees C reduces the intensity of some magnetic features, indicating that the interior of the rock has not been above this temperature since before its ejection from the surface of Mars. Because this temperature cannot sterilize most bacteria or eukarya, these data support the hypothesis that meteorites could transfer life between planets in the solar system.

A simple nonlinear model of electrical activity in the intestine.

We have simulated electrical activity of the intestine in a computer model that describes the coupled layers of longitudinal muscle (LM) and interstitial cells of Cajal (ICC). The model suggests that pacemaker activity is due to the ICC layer, while the pulse propagation involves the LM layer that is in the excitatory state. The model describes well the experimentally observed phenomena: frequency change along the intestine, synchronization along short distances and desynchronization for long distances, and the decrease of propagation distance and propagation time along the intestine. We have observed the occurrence of phase interruptions or breaks, which are responsible for the limited values of propagation distance and time.