Temporal coordination of the transcription factor response to H2O2 stress.

Oxidative stress from excess H2O2 activates transcription factors that restore redox balance and repair oxidative damage. Although many transcription factors are activated by H2O2, it is unclear whether they are activated at the same H2O2 concentration, or time. Dose-dependent activation is likely as oxidative stress is not a singular state and exhibits dose-dependent outcomes including cell-cycle arrest and cell death. Here, we show that transcription factor activation is both dose-dependent and coordinated over time. Low levels of H2O2 activate p53, NRF2 and JUN. Yet under high H2O2, these transcription factors are repressed, and FOXO1, NF-κB, and NFAT1 are activated. Time-lapse imaging revealed that the order in which these two groups of transcription factors are activated depends on whether H2O2 is administered acutely by bolus addition, or continuously through the glucose oxidase enzyme. Finally, we provide evidence that 2-Cys peroxiredoxins control which group of transcription factors are activated.

Lateralized Neural Entropy modulates with Grip Force during Precision Grasping.

When holding a coffee mug filled to the brim, we strive to avoid spilling the coffee. This ability relies on the neural processes underlying the control of finger forces on a moment-to-moment basis. The brain activity lateralized to the contralateral hemisphere averaged over a trial and across the trials is known to be associated with the magnitude of grip force applied on an object. However, the mechanistic involvement of the variability in neural signals during grip force control remains unclear. In this study, we examined the dependence of neural variability over the frontal, central, and parietal regions assessed using noninvasive electroencephalography (EEG) on grip force magnitude during an isometric force control task. We hypothesized laterally specific modulation in EEG variability with higher magnitude of the grip force exerted during grip force control. We utilized an existing EEG dataset (64 channel) comprised of healthy young adults, who performed an isometric force control task while receiving visual feedback of the force applied. The force magnitude to be exerted on the instrumented object was cued to participants during the task, and varied pseudorandomly among 5, 10, and 15% of their maximum voluntary contraction (MVC) across the trials. We quantified neural variability via sample entropy (sequence-dependent measure) and standard deviation (sequence-independent measure) of the temporal EEG signal over the frontal, central, and parietal electrodes. The EEG sample entropy over the central electrodes showed lateralized, nonlinear, localized, modulation with force magnitude. Similar modulation was not observed over frontal or parietal EEG activity, nor for standard deviation in the EEG activity. Our findings highlight specificity in neural control of grip forces by demonstrating the modulation in sequence-dependent but not sequence-independent component of EEG variability. This modulation appeared to be lateralized, spatially constrained, and functionally dependent on the grip force magnitude. We discuss the relevance of these findings in scenarios where a finer precision is essential to enable grasp application, such as prosthesis and associated neural signal integration, and propose directions for future studies investigating the mechanistic role of neural entropy in grip force control.

Temporal Coordination of the Transcription Factor Response to H2O2 stress.

Oxidative stress from excess H2O2 activates transcription factors (TFs) that restore redox balance and repair oxidative damage. Though many TFs are activated by H2O2, it is unknown whether they are activated at the same H2O2 concentration or time after H2O2 stress. We found TF activation is tightly coordinated over time and dose dependent. We first focused on p53 and FOXO1 and found that in response to low H2O2, p53 is activated rapidly while FOXO1 remains inactive. In contrast, cells respond to high H2O2 in two temporal phases. In the first phase FOXO1 rapidly shuttles to the nucleus while p53 remains inactive. In the second phase FOXO1 shuts off and p53 levels rise. Other TFs are activated in the first phase with FOXO1 (NF-κB, NFAT1), or the second phase with p53 (NRF2, JUN), but not both. The two phases result in large differences in gene expression. Finally, we provide evidence that 2-Cys peroxiredoxins control which TF are activated and the timing of TF activation.

Temporal Coordination of the Transcription Factor Response to H2O2 stress.

The p53 and FOXO transcription factors (TFs) share many similarities despite their distinct evolutionary origins. Both TFs are activated by a variety of cellular stresses and upregulate genes in similar pathways including cell-cycle arrest and apoptosis. Oxidative stress from excess H2O2 activates both FOXO1 and p53, yet whether they are activated at the same time is unclear. Here we found that cells respond to high H2O2 levels in two temporal phases. In the first phase FOXO1 rapidly shuttles to the nucleus while p53 levels remain low. In the second phase FOXO1 exits the nucleus and p53 levels rise. We found that other oxidative stress induced TFs are activated in the first phase with FOXO1 (NF-κB, NFAT1), or the second phase with p53 (NRF2, JUN) but not both following H2O2 stress. The two TF phases result in large differences in gene expression patterns. Finally, we provide evidence that 2-Cys peroxiredoxins control the timing of the TF phases in response to H2O2.

FOXO nuclear shuttling dynamics are stimulus-dependent and correspond with cell fate.

FOXO transcription factors are regulators of cellular homeostasis linked to increased lifespan and tumor suppression. FOXOs are activated by diverse cell stresses including serum starvation and oxidative stress. FOXO activity is regulated through posttranslational modifications that control shuttling of FOXO proteins to the nucleus. In the nucleus, FOXOs up-regulate genes in multiple, often conflicting pathways, including cell-cycle arrest and apoptosis. How cells control FOXO activity to ensure the proper response for a given stress is an open question. Using quantitative immunofluorescence and live-cell imaging, we found that the dynamics of FOXO nuclear shuttling is stimulus-dependent and corresponds with cell fate. H2O2 treatment leads to an all-or-none response where some cells show no nuclear FOXO accumulation, while other cells show a strong nuclear FOXO signal. The time that FOXO remains in the nucleus increases with the dose and is linked with cell death. In contrast, serum starvation causes low-amplitude pulses of nuclear FOXO and predominantly results in cell-cycle arrest. The accumulation of FOXO in the nucleus is linked with low AKT activity for both H2O2 and serum starvation. Our findings suggest the dynamics of FOXO nuclear shuttling is one way in which the FOXO pathway dictates different cellular outcomes.

Feedback in the ß-catenin destruction complex imparts bistability and cellular memory.

Wnt ligands are considered classical morphogens, for which the strength of the cellular response is proportional to the concentration of the ligand. Herein, we show an emergent property of bistability arising from feedback among the Wnt destruction complex proteins that target the key transcriptional co-activator ß-catenin for degradation. Using biochemical reconstitution, we identified positive feedback between the scaffold protein Axin and the kinase glycogen synthase kinase 3 (GSK3). Theoretical modeling of this feedback between Axin and GSK3 suggested that the activity of the destruction complex exhibits bistable behavior. We experimentally confirmed these predictions by demonstrating that cellular cytoplasmic ß-catenin concentrations exhibit an "all-or-none" response with sustained memory (hysteresis) of the signaling input. This bistable behavior was transformed into a graded response and memory was lost through inhibition of GSK3. These findings provide a mechanism for establishing decisive, switch-like cellular response and memory upon Wnt pathway stimulation.

Live-cell imaging in human colonic monolayers reveals ERK waves limit the stem cell compartment to maintain epithelial homeostasis.

The establishment and maintenance of different cellular compartments in tissues is a universal requirement across all metazoans. Maintaining the correct ratio of cell types in time and space allows tissues to form patterned compartments and perform complex functions. Patterning is especially evident in the human colon, where tissue homeostasis is maintained by stem cells in crypt structures that balance proliferation and differentiation. Here, we developed a human 2D patient derived organoid screening platform to study tissue patterning and kinase pathway dynamics in single cells. Using this system, we discovered that waves of ERK signaling induced by apoptotic cells play a critical role in maintaining tissue patterning and homeostasis. If ERK is activated acutely across all cells instead of in wave-like patterns, then tissue patterning and stem cells are lost. Conversely, if ERK activity is inhibited, then stem cells become unrestricted and expand dramatically. This work demonstrates that the colonic epithelium requires coordinated ERK signaling dynamics to maintain patterning and tissue homeostasis. Our work reveals how ERK can antagonize stem cells while supporting cell replacement and the function of the gut.

A Roadmap Towards Standards for Neurally Controlled End Effectors.

The control and manipulation of various types of end effectors such as powered exoskeletons, prostheses, and 'neural' cursors by brain-machine interface (BMI) systems has been the target of many research projects. A seamless "plug and play" interface between any BMI and end effector is desired, wherein similar user's intent cause similar end effectors to behave identically. This report is based on the outcomes of an IEEE Standards Association Industry Connections working group on End Effectors for Brain-Machine Interfacing that convened to identify and address gaps in the existing standards for BMI-based solutions with a focus on the end-effector component. A roadmap towards standardization of end effectors for BMI systems is discussed by identifying current device standards that are applicable for end effectors. While current standards address basic electrical and mechanical safety, and to some extent, performance requirements, several gaps exist pertaining to unified terminologies, data communication protocols, patient safety and risk mitigation.

Concerns in the Blurred Divisions between Medical and Consumer Neurotechnology.

Neurotechnology has traditionally been central to the diagnosis and treatment of neurological disorders. While these devices have initially been utilized in clinical and research settings, recent advancements in neurotechnology have yielded devices that are more portable, user-friendly, and less expensive. These improvements allow laypeople to monitor their brain waves and interface their brains with external devices. Such improvements have led to the rise of wearable neurotechnology that is marketed to the consumer. While many of the consumer devices are marketed for innocuous applications, such as use in video games, there is potential for them to be repurposed for medical use. How do we manage neurotechnologies that skirt the line between medical and consumer applications and what can be done to ensure consumer safety? Here, we characterize neurotechnology based on medical and consumer applications and summarize currently marketed uses of consumer-grade wearable headsets. We lay out concerns that may arise due to the similar claims associated with both medical and consumer devices, the possibility of consumer devices being repurposed for medical uses, and the potential for medical uses of neurotechnology to influence commercial markets related to employment and self-enhancement.

Towards a Portable Magnetoencephalography Based Brain Computer Interface with Optically-Pumped Magnetometers.

Brain Computer Interfaces (BCIs) allow individuals to control devices, machines and prostheses with their thoughts. Most feasibility studies with BCIs have utilized scalp electroencephalography (EEG), due to it being accessible, noninvasive, and portable. While BCIs have been studied with magnetoencephalography (MEG), the modality has limited applications due to the large immobile hardware. Here we propose that room-temperature, optically-pumped magnetometers (OPMs) can potentially serve a portable modality that can be used for BCIs. OPMs have the added advantage that low-frequency neuromagnetic fields are not affected by volume conduction, which is known to distort EEG signals. In this feasibility study, we tested an OPM system with a real-time BCI where able bodied participants controlled a cursor to reach two targets. This BCI system used alpha and beta-band power modulations associated with hand movements. Our preliminary results show significant alpha and beta-band desynchronization due to movement, as found in previous literature.

Regression-based reconstruction of human grip force trajectories with noninvasive scalp electroencephalography.

OBJECTIVE: Robotic devices show promise in restoring motor abilities to individuals with upper limb paresis or amputations. However, these systems are still limited in obtaining reliable signals from the human body to effectively control them. We propose that these robotic devices can be controlled through scalp electroencephalography (EEG), a neuroimaging technique that can capture motor commands through brain rhythms. In this work, we studied if EEG can be used to predict an individual's grip forces produced by the hand. APPROACH: Brain rhythms and grip forces were recorded from able-bodied human subjects while they performed an isometric force production task and a grasp-and-lift task. Grip force trajectories were reconstructed with a linear model that incorporated delta band (0.1-1 Hz) voltage potentials and spectral power in the theta (4-8 Hz), alpha (8-13 Hz), beta (13-30 Hz), low gamma (30-50 Hz), mid gamma (70-110 Hz), and high gamma (130-200 Hz) bands. Trajectory reconstruction models were trained and tested through 10-fold cross validation. MAIN RESULTS: Modest accuracies were attained in reconstructing grip forces during isometric force production (median r = 0.42), and the grasp-and-lift task (median r = 0.51). Predicted trajectories were also analyzed further to assess the linear models' performance based on task requirements. For the isometric force production task, we found that predicted grip trajectories did not yield static grip forces that were distinguishable in magnitude across three task conditions. For the grasp-and-lift task, we estimate there would be an approximate 25% error in distinguishing when a user wants to hold or release an object. SIGNIFICANCE: These findings indicate that EEG, a noninvasive neuroimaging modality, has predictive information in neural features associated with finger force control and can potentially contribute to the development of brain machine interfaces (BMI) for performing activities of daily living.

Designing combination therapies with modeling chaperoned machine learning.

Chemotherapy resistance is a major challenge to the effective treatment of cancer. Thus, a systematic pipeline for the efficient identification of effective combination treatments could bring huge biomedical benefit. In order to facilitate rational design of combination therapies, we developed a comprehensive computational model that incorporates the available biological knowledge and relevant experimental data on the life-and-death response of individual cancer cells to cisplatin or cisplatin combined with the TNF-related apoptosis-inducing ligand (TRAIL). The model's predictions, that a combination treatment of cisplatin and TRAIL would enhance cancer cell death and exhibit a "two-wave killing" temporal pattern, was validated by measuring the dynamics of p53 accumulation, cell fate, and cell death in single cells. The validated model was then subjected to a systematic analysis with an ensemble of diverse machine learning methods. Though each method is characterized by a different algorithm, they collectively identified several molecular players that can sensitize tumor cells to cisplatin-induced apoptosis (sensitizers). The identified sensitizers are consistent with previous experimental observations. Overall, we have illustrated that machine learning analysis of an experimentally validated mechanistic model can convert our available knowledge into the identity of biologically meaningful sensitizers. This knowledge can then be leveraged to design treatment strategies that could improve the efficacy of chemotherapy.

Assaying neural activity of children during video game play in public spaces: a deep learning approach.

OBJECTIVE: Understanding neural activity patterns in the developing brain remains one of the grand challenges in neuroscience. Developing neural networks are likely to be endowed with functionally important variability associated with the environmental context, age, gender, and other variables. Therefore, we conducted experiments with typically developing children in a stimulating museum setting and tested the feasibility of using deep learning techniques to help identify patterns of brain activity associated with different conditions. APPROACH: A four-channel dry EEG-based Mobile brain-body imaging data of children at rest and during videogame play (VGP) was acquired at the Children's Museum of Houston. A data-driven approach based on convolutional neural networks (CNN) was used to describe underlying feature representations in the EEG and their ability to discern task and gender. The variability of the spectral features of EEG during the rest condition as a function of age was also analyzed. MAIN RESULTS: Alpha power (7-13 Hz) was higher during rest whereas theta power (4-7 Hz) was higher during VGP. Beta (13-18 Hz) power was the most significant feature, higher in females, when differentiating between males and females. Using data from both temporoparietal channels to classify between VGP and rest condition, leave-one-subject-out cross-validation accuracy of 67% was obtained. Age-related changes in EEG spectral content during rest were consistent with previous developmental studies conducted in laboratory settings showing an inverse relationship between age and EEG power. SIGNIFICANCE: These findings are the first to acquire, quantify and explain brain patterns observed during VGP and rest in freely behaving children in a museum setting using a deep learning framework. The study shows how deep learning can be used as a data driven approach to identify patterns in the data and explores the issues and the potential of conducting experiments involving children in a natural and engaging environment.

Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages.

The origin of lineage correlations among single cells and the extent of heterogeneity in their intermitotic times (IMT) and apoptosis times (AT) remain incompletely understood. Here we developed single cell lineage-tracking experiments and computational algorithms to uncover correlations and heterogeneity in the IMT and AT of a colon cancer cell line before and during cisplatin treatment. These correlations could not be explained using simple protein production/degradation models. Sister cell fates were similar regardless of whether they divided before or after cisplatin administration and did not arise from proximity-related factors, suggesting fate determination early in a cell's lifetime. Based on these findings, we developed a theoretical model explaining how the observed correlation structure can arise from oscillatory mechanisms underlying cell fate control. Our model recapitulated the data only with very specific oscillation periods that fit measured circadian rhythms, thereby suggesting an important role of the circadian clock in controlling cellular fates.

Drug-induced aneuploidy and polyploidy is a mechanism of disease relapse in MYC/BCL2-addicted diffuse large B-cell lymphoma.

Double-hit (DH) or double-expresser (DE) lymphomas are high-grade diffuse large B-cell lymphomas (DLBCL) that are mostly incurable with standard chemo-immunotherapy due to treatment resistance. The generation of drug-induced aneuploid/polyploid (DIAP) cells is a common effect of anti-DLBCL therapies (e.g. vincristine, doxorubicin). DIAP cells are thought to be responsible for treatment resistance, as they are capable of re-entering the cell cycle during off-therapy periods. Previously we have shown that combination of alisertib plus ibrutinib plus rituximab can partially abrogate DIAP cells and induce cell death. Here, we provide evidence that DIAP cells can re-enter the cell cycle and escape cell death during anti-DLBCL treatment. We also discuss MYC/BCL2 mediated molecular mechanism that underlie treatment resistance. We isolated aneuploid/polyploid populations of DH/DE-DLBCL cells after treatment with the aurora kinase (AK) inhibitor alisertib. Time-lapse microscopy of single polyploid cells revealed that following drug removal, a subset of these DIAP cells divide and proliferate by reductive cell divisions, including multipolar mitosis, meiosis-like nuclear fission and budding. Genomic, proteomic, and kinomic profiling demonstrated that alisertib-induced aneuploid/polyploid cells up-regulate DNA damage, DNA replication and immune evasion pathways. In addition, we identified amplified receptor tyrosine kinase and T-cell receptor signaling, as well as MYC-mediated dysregulation of the spindle assembly checkpoints RanGAP1, TPX2 and KPNA2. We infer that these factors contribute to treatment resistance of DIAP cells. These findings provide opportunities to develop novel DH/DE-DLBCL therapies, specifically targeting DIAP cells. KEY POINTS: ● MYC mediated upregulation of TPX2, KPNA2 and RanGAP1 dysregulate the spindle assembly checkpoint in drug-induced polyploid cells.● Drug-induced polyploid cells re-enter the cell cycle via multipolar mitosis, fission or budding, a mechanism of disease relapse.

A dynamical framework for complex fractional killing.

When chemotherapy drugs are applied to tumor cells with the same or similar genotypes, some cells are killed, while others survive. This fractional killing contributes to drug resistance in cancer. Through an incoherent feedforward loop, chemotherapy drugs not only activate p53 to induce cell death, but also promote the expression of apoptosis inhibitors which inhibit cell death. Consequently, cells in which p53 is activated early undergo apoptosis while cells in which p53 is activated late survive. The incoherent feedforward loop and the essential role of p53 activation timing makes fractional killing a complex dynamical challenge, which is hard to understand with intuition alone. To better understand this process, we have constructed a representative model by integrating the control of apoptosis with the relevant signaling pathways. After the model was trained to recapture the observed properties of fractional killing, it was analyzed with nonlinear dynamical tools. The analysis suggested a simple dynamical framework for fractional killing, which predicts that cell fate can be altered in three possible ways: alteration of bifurcation geometry, alteration of cell trajectories, or both. These predicted categories can explain existing strategies known to combat fractional killing and facilitate the design of novel strategies.

Cell-to-Cell Variation in p53 Dynamics Leads to Fractional Killing.

Many chemotherapeutic drugs kill only a fraction of cancer cells, limiting their efficacy. We used live-cell imaging to investigate the role of p53 dynamics in fractional killing of colon cancer cells in response to chemotherapy. We found that both surviving and dying cells reach similar levels of p53, indicating that cell death is not determined by a fixed p53 threshold. Instead, a cell's probability of death depends on the time and levels of p53. Cells must reach a threshold level of p53 to execute apoptosis, and this threshold increases with time. The increase in p53 apoptotic threshold is due to drug-dependent induction of anti-apoptotic genes, predominantly in the inhibitors of apoptosis (IAP) family. Our study underlines the importance of measuring the dynamics of key players in response to chemotherapy to determine mechanisms of resistance and optimize the timing of combination therapy.

An exploration of grip force regulation with a low-impedance myoelectric prosthesis featuring referred haptic feedback.

BACKGROUND: Haptic display technologies are well suited to relay proprioceptive, force, and contact cues from a prosthetic terminal device back to the residual limb and thereby reduce reliance on visual feedback. The ease with which an amputee interprets these haptic cues, however, likely depends on whether their dynamic signal behavior corresponds to expected behaviors-behaviors consonant with a natural limb coupled to the environment. A highly geared motor in a terminal device along with the associated high back-drive impedance influences dynamic interactions with the environment, creating effects not encountered with a natural limb. Here we explore grasp and lift performance with a backdrivable (low backdrive impedance) terminal device placed under proportional myoelectric position control that features referred haptic feedback. METHODS: We fabricated a back-drivable terminal device that could be used by amputees and non-amputees alike and drove aperture (or grip force, when a stiff object was in its grasp) in proportion to a myoelectric signal drawn from a single muscle site in the forearm. In randomly ordered trials, we assessed the performance of N=10 participants (7 non-amputee, 3 amputee) attempting to grasp and lift an object using the terminal device under three feedback conditions (no feedback, vibrotactile feedback, and joint torque feedback), and two object weights that were indiscernible by vision. RESULTS: Both non-amputee and amputee participants scaled their grip force according to the object weight. Our results showed only minor differences in grip force, grip/load force coordination, and slip as a function of sensory feedback condition, though the grip force at the point of lift-off for the heavier object was significantly greater for amputee participants in the presence of joint torque feedback. An examination of grip/load force phase plots revealed that our amputee participants used larger safety margins and demonstrated less coordination than our non-amputee participants. CONCLUSIONS: Our results suggest that a backdrivable terminal device may hold advantages over non-backdrivable devices by allowing grip/load force coordination consistent with behaviors observed in the natural limb. Likewise, the inconclusive effect of referred haptic feedback on grasp and lift performance suggests the need for additional testing that includes adequate training for participants.

Draft Genome Sequence of the Ale-Fermenting Saccharomyces cerevisiae Strain GSY2239.

Saccharomyces cerevisiae strain GSY2239 is derived from an industrial yeast strain used to ferment ale-style beer. We present here the 11.5-Mb draft genome sequence for this organism.

Global cortical activity predicts shape of hand during grasping.

Recent studies show that the amplitude of cortical field potentials is modulated in the time domain by grasping kinematics. However, it is unknown if these low frequency modulations persist and contain enough information to decode grasp kinematics in macro-scale activity measured at the scalp via electroencephalography (EEG). Further, it is unclear as to whether joint angle velocities or movement synergies are the optimal kinematics spaces to decode. In this offline decoding study, we infer from human EEG, hand joint angular velocities as well as synergistic trajectories as subjects perform natural reach-to-grasp movements. Decoding accuracy, measured as the correlation coefficient (r) between the predicted and actual movement kinematics, was r = 0.49 ± 0.02 across 15 hand joints. Across the first three kinematic synergies, decoding accuracies were r = 0.59 ± 0.04, 0.47 ± 0.06, and 0.32 ± 0.05. The spatial-temporal pattern of EEG channel recruitment showed early involvement of contralateral frontal-central scalp areas followed by later activation of central electrodes over primary sensorimotor cortical areas. Information content in EEG about the grasp type peaked at 250 ms after movement onset. The high decoding accuracies in this study are significant not only as evidence for time-domain modulation in macro-scale brain activity, but for the field of brain-machine interfaces as well. Our decoding strategy, which harnesses the neural "symphony" as opposed to local members of the neural ensemble (as in intracranial approaches), may provide a means of extracting information about motor intent for grasping without the need for penetrating electrodes and suggests that it may be soon possible to develop non-invasive neural interfaces for the control of prosthetic limbs.