title: Heat stress leads to rapid lipid remodelling and transcriptional adaptations in Nicotiana tabacum pollen tubes

abstract:
After reaching the stigma, pollen grains germinate and form a pollen tube that transports the sperm cells to the ovule. Due to selection pressure between pollen tubes, they likely evolved mechanisms to quickly adapt to temperature changes to sustain an elongation at the highest possible rate. We investigated these adaptions in Nicotiana tabacum pollen tubes grown in vitro under 22 {degrees}C and 37 {degrees}C by a multi-omic approach including lipidomic, metabolomic and transcriptomic analysis. Both glycerophospholipids and galactoglycerolipids increased in saturated acyl chains under heat stress while triacylglycerols changed less in respect to desaturation but showed higher levels. Free sterol composition was altered, and sterol ester levels decreased. The levels of sterylglycosides and several sphingolipid classes and species were augmented. Most amino acids increased during heat stress, including the non-codogenic amino acids {gamma}-amino butyrate and pipecolate. Furthermore, the sugars sedoheptulose and sucrose showed higher levels. Also the transcriptome underwent pronounced changes with 1,570 of 24,013 genes being differentially up- and 813 being downregulated. Transcripts coding for heat shock proteins and many transcriptional regulators were most strongly upregulated, but also transcripts that have so far not been linked to heat stress. Transcripts involved in triacylglycerol synthesis were increased, while the modulation of acyl chain desaturation seemed not to be transcriptionally controlled indicating other means of regulation.

One sentence summaryNicotiana tabacum pollen tubes react to heat stress with metabolomic adaptations, transcriptional adjustments, and a rapid and reversible lipid remodelling.


title: Self-organization of in vitro neuronal assemblies drives to complex network topology

abstract: Activity-dependent self-organization plays an important role in the formation of specific and stereotyped connectivity patterns in neural circuits. By combining neuronal cultures, tools with approaches from network neuroscience and information theory, we can study how complex network topology emerges from local neuronal interactions. We constructed effective connectivity networks using a transfer entropy analysis of electrophysiological signals recorded from rat embryo dissociated hippocampal neuron cultures between 6 and 35 days in vitro to investigate how the neuronal network topology evolves during maturation. The methodology for constructing the networks considered the synapse delay and addressed the influence of firing rate and population bursts as well as spurious effects on the inference of connections. We found that the number of links in the networks grew over the course of development, shifting from a segregated to a more integrated architecture. As part of this progression, three significant aspects of complex network topology emerged. In agreement with previous in silico and in vitro studies, a small-world architecture was detected, largely due to strong clustering among neurons. Additionally, the networks developed in a modular community topology, with most modules comprising nearby neurons. Finally, highly active neurons acquired topological characteristics that made them important nodes to the network and integrators of communities. These findings leverage new insights into how neuronal effective network topology relates to neuronal assembly self-organization mechanisms.

category: neuroscience


title: PDFGRα+ Stromal Cells Promote Salivary Gland Proacinar Differentiation Through FGF2-dependent BMP7 Signaling.

abstract:
3.0Stromal cells can direct epithelial differentiation during organ development; however, these pathways remain poorly defined. FGF signaling is essential for submandibular salivary gland development, and FGF2 can regulate proacinar cell differentiation in organoids through autocrine signaling in stromal cells. We performed scRNA Seq and identified stromal cell subsets expressing Fgf2 and Fgf10 that also express Pdgfr. When combined with epithelial cells in organoids, MACS-sorted PDGFR+ cells sufficiently promoted proacinar differentiation. Gene expression analysis revealed FGF2 activates the gene Bmp7 in the stroma. BMP7 could replace stromalsignaling and stimulate epithelial acinar differentiation but not branching. However, in the absence of FGF2, pathway analysis revealed that the stromal cells differentiated into myofibroblasts. Myofibroblast differentiation was induced when we treated organoids with TGF{beta}1, which also prevented proacinar differentiation. Conversely, FGF2 reversed TGF{beta}s effects. Dissecting pathways driving acinar differentiation will facilitate development of regenerative therapies.

2.0 Summary StatementEmbryonic salivary glands contain multiple stromal cell populations. FGF2 maintains the stromal Pdgfr+ population in-vitro. The PDGFR+ stromal cells drive early epithelial secretory cell differentiation using BMP7.

category: developmental biology


title: Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1 (EAAT1)

abstract: Excitatory amino acid transporters (EAATs) are glutamate transporters that belong to the solute carrier 1A (SLC1A) family. They couple glutamate transport to the co-transport of three sodium (Na+) ions and one proton (H+) and the counter-transport of one potassium (K+) ion. In addition to this coupled transport, binding of substrate and Na+ ions to EAATs activates a thermodynamically uncoupled chloride (Cl-) conductance. Structures of SLC1A family members have revealed that these transporters use a twisting elevator mechanism of transport, where a mobile transport domain carries substrate and coupled ions across the membrane, while a static scaffold domain anchors the transporter in the membrane. We have recently demonstrated that the uncoupled Cl- conductance is activated by the formation of an aqueous pore at the domain interface during the transport cycle in archaeal GltPh. However, a pathway for the uncoupled Cl- conductance has not been reported for the EAATs and it is unclear if such a pathway is conserved. Here, we employ all-atom molecular dynamics (MD) simulations combined with enhanced sampling, free-energy calculations, and experimental mutagenesis to approximate large-scale conformational changes during the transport process and identified a Cl- conducting conformation in human EAAT1. We were able to extensively sample the large-scale structural transitions, allowing us to capture an intermediate conformation formed during the transport cycle with a continuous aqueous pore at the domain interface. The free-energy calculations performed for the conduction of Cl- and Na+ ions through the captured conformation, highlight the presence of two hydrophobic gates which control the selective movement of Cl- through the aqueous pathway. Overall, our findings provide insights into the mechanism by which a human glutamate transporter can support the dual functions of active transport and passive Cl- permeation and confirming the commonality of this mechanism in different members of the SLC1A family.

category: biophysics


title: The effect of external stimulation on functional networks in the aging healthy human brain

abstract: Understanding the brain changes occurring during aging can provide new insights for developing treatments that alleviate or reverse cognitive decline. Neurostimulation techniques have emerged as potential treatments for brain disorders and to improve cognitive functions. Nevertheless, given the ethical restrictions of neurostimulation approaches, in silico perturbation protocols based on causal whole-brain models are fundamental to gaining a mechanistic understanding of brain dynamics. Furthermore, this strategy could serve as a more specific biomarker relating local activity with global brain dynamics. Here, we used a large resting-state fMRI dataset divided into middle-aged (N=310, aged < 65 years) and older adults (N=310, aged[≥] 65) to characterize brain states in each group as a probabilistic metastable substate (PMS) space, each with a probabilistic occurrence and frequency. Then, we fitted the PMS to a whole-brain model and applied in silico stimulations with different intensities in each node to force transitions from the brain states of the older group to the middle-age group. We found that the precuneus, a brain area belonging to the default mode network and the rich club, was the best stimulation target. These findings might have important implications for designing neurostimulation interventions to revert the effects of aging on whole-brain dynamics.


title: Transcriptome and fatty-acid signatures of adipocyte hypertrophy and its non-invasive MR-based characterization in human adipose tissue

abstract: Adipose tissue is an organ with great plasticity and its hypertrophic expansion is associated with adipocyte dysfunction. How changes in adipocyte morphology are linked to gene expression and which cellular functions are affected remains elusive. We show that adipocyte hypertrophy is associated with transcriptomic changes using RNA-Seq data obtained from adipose tissue and size-separated adipocytes. Genes involved in oxidative phosphorylation, protein biosynthesis and fatty acid metabolism were down-regulated in large adipocytes while genes involved in inflammation were upregulated. For mitochondrial function, a reduction in the expression of thermogenesis related genes and estimated brown/beige adipocyte content was observed in individuals with large adipocytes. As a novel finding the total adipose tissue fatty acid composition was dependent on cell size and depot. MR spectroscopy methods for clinical scanning were developed to characterize adipocyte size and fatty acid composition in a fast and non-invasive manner. Together, the present data provides mechanistic insights on how adipocyte hypertrophy contributes to the manifestation of metabolic disease at the molecular and cellular level. MR spectroscopy was identified as a promising technique for an in-parallel assessment of adipose morphology and fatty acid composition allowing to translate our findings into an improved, non-invasive phenotyping of adipose tissue.

category: cell biology


title: Doppler Slicing for Ultrasound Super-Resolution Without Contrast Agents

abstract: Much of the information needed for diagnosis and treatment monitoring of diseases like cancer and cardiovascular disease is found at scales below the resolution limit of classic ultrasound imaging. Recently introduced vascular super-localization methods provide more than a ten-fold improvement in spatial resolution by precisely estimating the positions of microbubble contrast agents. However, most vascular ultrasound scans are currently performed without contrast agents due to the associated cost, training, and post-scan monitoring. Here we show that super-resolution ultrasound imaging of dense vascular structures can be achieved using the natural contrast of flowing blood cells. Instead of relying on separable targets, we used Fourier-based decomposition to separate signals arising from the different scales of vascular structures while removing speckle noise using multi-ensemble processing. This approach enabled the use of compressed sensing for super-resolution imaging of the underlying vascular structures, improving resolution by a factor of four. Reconstruction of ultrafast mouse brain scans revealed details that could not be resolved in regular Doppler images, agreeing closely with bubble-based super-localization microscopy of the same fields of view. By combining multi-ensemble Doppler acquisitions with narrowband Fourier decomposition and computational super-resolution imaging, this approach opens new opportunities for affordable and scalable super-resolution ultrasound imaging.

category: bioengineering


title: Assessment of temporal complexity in functional MRI between rest and task conditions

abstract: Dynamic models of cortical activity, as measured by functional magnetic resonance imaging (fMRI), have recently brought out important insights into the organization of brain function. In terms of temporal complexity, these hemodynamic signals have been shown to exhibit critical behaviour at the edge between order and disorder. In this study, we aimed to revisit the properties and spatial distribution of temporal complexity in resting state and task fMRI of 100 unrelated subjects from the Human Connectome Project (HCP). First, we compared two common choices of complexity measures (i.e., Hurst exponent versus multiscale entropy) and reported high similarity between them. Second, we investigated the influence of experimental paradigms and found high task-specific complexity. We considered four mental tasks in the HCP database for the analysis: Emotion, Working memory, Social, and Language. Third, we tailored a recently-proposed statistical framework that incorporates the structural connectome, to assess the spatial distribution of complexity measures. These results highlight brain regions including parts of the default mode network and cingulate cortex with significantly stronger complex behaviour than the rest of the brain, irrespective of task. In sum, temporal complexity measures of fMRI are reliable markers of the cognitive status.


title: Disruption Of Proprioceptive Information During Electrical Stimulation Of The Cutaneous Afferents

abstract: Restoration of proprioception with neurotechnology is critical to improve effectiveness of robotic neuro-prostheses. Unfortunately, after initial enthusiasm clinical results showed that unlike touch, proprioception could not be reliably induced. Here we show that concurrent activation of multiple sensory modalities may trigger unwanted sensory regulation mechanisms that disrupt proprioception. We recorded intra-spinal neural activity induced by stimulation of proprioceptive afferents from the radial nerve in three monkeys. Then, we superimposed stimulation of the radial nerve cutaneous branch and quantified its impact on spinal neural activity via population analysis. Proprioceptive pulses produced robust neural trajectories in the neural manifold that were disrupted by concurrent stimulation of cutaneous afferents. This disruption correlated with a reduction of afferent volleys and multi-unit activity both in the spinal cord and somatosensory cortex. Our results suggest that limited specificity not only impacts localization of artificial percepts, but also their nature to an extent that was never considered.


title: Theta activity during encoding interacts with NREM sleep oscillations to predict memory generalization

abstract: Relatively little is known regarding the interaction between encoding-related neural activity and sleep-based memory consolidation. One suggestion is that a function of encoding-related theta power may be to  tag memories for subsequent processing during sleep. This study aimed to extend previous work on the relationships between sleep spindles, slow oscillation-spindle coupling and task-related theta activity with a combined Deese-Roediger-McDermott (DRM) and nap paradigm. This allowed us to examine the influence of task- and sleep-related oscillatory activity on the recognition of both encoded list words and associative theme words. Thirty-three participants (29 females, mean age = 23.2 years) learned and recognised DRM lists separated by either a 2hr wake or sleep period. Mixed-effects modelling revealed the sleep condition endorsed more associative theme words and fewer list words in comparison to the wake group. Encoding-related theta power was also found to influence sleep spindle density, and this interaction was predictive of memory outcomes. The influence of encoding-related theta was specific to sleep spindle density, and did not appear to influence the strength of slow oscillation-spindle coupling as it relates to memory outcomes. The finding of interactions between wakeful and sleep oscillatory-related activity in promoting memory and learning has important implications for theoretical models of sleep-based memory consolidation.


title: Beyond gradients: Noise correlations control Hebbian plasticity to shape credit assignment

abstract: Two key problems that span biological and industrial neural network research are how networks can be trained to generalize well and to minimize destructive interference between tasks. Both hinge on credit assignment, the targeting of specific network weights for change. In artificial networks, credit assignment is typically governed by gradient descent. Biological learning is thus often analyzed as a means to approximate gradients. We take the complementary perspective that biological learning rules likely confer advantages when they arent gradient approximations. Further, we hypothesized that noise correlations, often considered detrimental, could usefully shape this learning. Indeed, we show that noise and three-factor plasticity interact to compute directional derivatives of reward, which can improve generalization, robustness to interference, and multi-task learning. This interaction also provides a method for routing learning quasi-independently of activity and connectivity, and demonstrates how biologically inspired inductive biases can be fruitfully embedded in learning algorithms.


title: Putting the theory into 'burstlet theory': A biophysical model of bursts and burstlets in the respiratory preBötzinger complex

abstract: Inspiratory breathing rhythms arise from synchronized neuronal activity in a bilaterally distributed brainstem structure known as the preBotzinger complex (preBotC). In in vitro slice preparations containing the preBotC, extracellular potassium must be elevated above physiological levels (to 7 - 9 mM) to observe regular rhythmic respiratory motor output in the hypoglossal nerve to which the preBotC projects. Reexamination of how extracellular K+ affects preBotC neuronal activity has revealed that low amplitude oscillations persist at physiological levels. These oscillatory events are sub-threshold from the standpoint of transmission to motor output and are dubbed burstlets. Burstlets arise from synchronized neural activity in a rhythmogenic neuronal subpopulation within the preBotC that in some instances may fail to recruit the larger network events, or bursts, required to generate motor output. The fraction of subthreshold preBotC oscillatory events (burstlet fraction) decreases sigmoidally with increasing extracellular potassium. These observations underlie the burstlet theory of respiratory rhythm generation. Experimental and computational studies have suggested that recruitment of the non-rhythmogenic component of the preBotC population requires intracellular Ca2+ dynamics and activation of a calcium-activated non-selective cationic current. In this computational study, we show how intracellular calcium dynamics driven by synaptically triggered Ca2+ influx as well as Ca2+ release/uptake by the endoplasmic reticulum in conjunction with a calcium-activated non-selective cationic current can explain all of the key observations underlying the burstlet theory of respiratory rhythm generation. Thus, we provide a mechanistic basis to unify the experimental findings on rhythm generation and motor output recruitment in the preBotC.


title: Non-invasive visualization of amyloid-beta deposits in Alzheimer amyloidosis mice using magnetic resonance imaging and fluorescence molecular tomography

abstract: Abnormal cerebral accumulation of amyloid-beta peptide (A{beta}) is a major hallmark of Alzheimers disease. Non-invasive monitoring of A{beta} deposits enables assessing the disease burden in patients and animal models mimicking aspects of the human disease as well as evaluating the efficacy of A{beta}-modulating therapies. Previous in vivo assessments of plaque load in mouse models of cerebral amyloidosis have been predominantly based on two-dimensional diffuse fluorescence reflectance imaging (2D-FRI) and two-photon microscopy (2PM) using A{beta}-specific imaging agents. However, 2D-FRI lacks depth resolution, whereas 2PM is restricted by the limited field of view preventing coverage of large brain regions. Here, we utilized a magnetic resonance imaging (MRI) and fluorescence molecular tomography (FMT) pipeline with the curcumin derivative fluorescent probe CRANAD-2 to achieve full 3D brain coverage for detecting A{beta} accumulation in the arcA{beta} mouse model of cerebral amyloidosis. A homebuilt FMT system was used for data acquisition in combination with a customized software platform enabling the integration of anatomical information derived from MRI as prior information for FMT image reconstruction. The results obtained from the FMT-MRI study were compared to data obtained from conventional 2D-FRI recorded under similar physiological conditions. The two methods yielded comparable time courses of the fluorescence intensity following intravenous injection of CRANAD-2 in a region of interest comprising the mouse brain. The depth resolution inherent to FMT allowed separation of signal contributions from the scalp and different brain regions, indicating preferential accumulation of the fluorescent tracer in the cerebral cortex, a region characterized by significant plaque deposition in arc A{beta} mice. In conclusion, we have demonstrated the feasibility of visualizing A{beta} deposition in 3D using a multimodal FMT-MRI method. This hybrid imaging method provides complementary anatomical, physiological and molecular information, thereby enabling the detailed characterization of the disease status in mouse models of cerebral amyloidosis, which is also important for monitoring the efficacy of putative treatments targeting A{beta}.


title: Oxygenated hemoglobin signal provides greater predictive performance of experimental condition than de-oxygenated

abstract: Continuous-wave functional near-infrared spectroscopy (fNIRS) neuroimaging provides an estimate of relative changes in oxygenated and de-oxygenated hemoglobin content, from which regional neural activity is inferred. The relation between both signals is governed by neurovascular coupling mechanisms. However, the magnitude of concentration changes and the contribution of noise sources to each chromophore is unique. Subsequently, it is not apparent if either chromophore signal practically provides greater information about the underlying neural state and relation to an experimental condition. To assess this question objectively, we applied a machine-learning approach to four datasets and evaluated which hemoglobin signal best differentiated between experimental conditions. To further ensure the objective nature of the analysis, the algorithm utilized all samples from the epoched data rather than pre-selected features. Regardless of experimental task, brain region, or stimulus, the oxygenated hemoglobin signal was better able to differentiate between conditions than the de-oxygenated signal. Incorporating both signals into the analysis provided no additional improvement over oxygenated hemoglobin alone. These results indicate that oxyhemoglobin is the most informative fNIRS signal in relation to experimental condition.


title: Glutamate-Weighted Magnetic Resonance Imaging (GluCEST) Detects Effects of Transcranial Magnetic Stimulation to the Motor Cortex

abstract:
Transcranial magnetic stimulation (TMS) is used in several FDA-approved treatments and, increasingly, to treat neurological disorders in off-label uses. However, the mechanism by which TMS causes physiological change is unclear, as are the origins of response variability in the general population. Ideally, objective in vivo biomarkers could shed light on these unknowns and eventually inform personalized interventions. Continuous theta burst stimulation (cTBS) is a form of TMS which has been observed to reduce motor evoked potentials (MEPs) for 60 minutes or longer post-stimulation, although the consistency of this effect and its mechanism continue to be under debate. Here, we use glutamate-weighted chemical exchange saturation transfer (gluCEST) magnetic resonance imaging (MRI) at ultra-high magnetic field (7T) to measure changes in glutamate concentration at the site of cTBS. We find that gluCEST signal in the ipsilateral hemisphere of the brain generally decreases in response to cTBS, whereas consistent changes were not detected in the contralateral or in subjects receiving a sham stimulation.

One Sentence SummaryWe used glutamate-weighted Chemical Exchange Saturation Transfer (GluCEST) imaging to detect changes in glutamate contrast in the brains of young, healthy adults undergoing transcranial magnetic stimulation (TMS) to the motor cortex.


title: Frontal but not parietal cortex is required for decisions under risk

abstract: Neurons in frontal and parietal cortex encode task variables during decision-making, but causal manipulations of the two regions produce strikingly different results. For example, silencing the posterior parietal cortex (PPC) in rats and monkeys produces minimal effects in perceptual decisions requiring integration of sensory evidence, but silencing frontal cortex profoundly impairs the same decisions. Here, we tested, for the first time, the causal roles of the rat frontal orienting field (FOF) and PPC in economic choice under risk. On each trial, rats chose between a lottery and a small but guaranteed surebet. The magnitude of the lottery was independently varied across trials and was indicated to the rat by the pitch of an auditory cue. As in perceptual decisions, both unilateral and bilateral PPC muscimol inactivations produced minimal effects. FOF inactivations produced substantial changes in behavior even though our task had no working memory component. We quantified control and bilateral inactivation behavior with a multi-agent model consisting of a mixture of a  rational utility-maximizing agent (U = V{rho}) with two  habitual agents that either choose surebet or lottery. Silencing PPC produced no significant shifts in any parameters relative to controls. Effects of FOF silencing were best explained by a decrease in{rho} , the exponent of the utility function. This effect was parsimoniously explained by a dynamical model where the FOF is part of network that performs sensory-to-value transformations.


title: Reset Networks: Emergent Topography in Networks of Convolutional Neural Networks

abstract: We introduce the Reset model, a composition of neural networks - typically several levels of convolutional neural networks - whose outputs at one level are gathered and reshaped into a spatial input for the next level. We show that units in Reset networks self-organize into clusters when trained on MNIST, Fashion MNIST, CIFAR-10 and CIFAR-100. We then show that a stronger type of self-organization, reminiscent of the topography found for numbers in parietal cortex, arises when number images are mapped onto developmentally realistic number codes. We outline the implications of this model for theories of the cortex and developmental neuroscience.


title: Reset Networks: Emergent Topography by Composition of Convolutional Neural Networks


title: The P600, but not N400, is modulated by sustained attention

abstract: The functional significance of the two prominent language-related ERP components N400 and P600 is still under debate. It has recently been suggested that one important dimension along which the two vary, is in terms of automaticity versus attentional control, with N400 amplitudes reflecting more automatic and P600 amplitudes reflecting more controlled aspects of sentence comprehension. The availability of executive resources necessary for controlled processes depends on sustained attention, which fluctuates over time. Here, we thus tested whether P600 and N400 amplitudes depend on the level of sustained attention. We re-analyzed EEG and behavioral data from a sentence processing task by Sassenhagen & Bornkessel-Schlesewsky (2015, Cortex), which included sentences with morphosyntactic and semantic violations. Participants read sentences phrase by phrase and indicated whether a sentence contained any type of anomaly as soon as they had the relevant information. To quantify periods of high versus low sustained attention, we extracted a moving reaction time coefficient of variation over the entire course of the task. We found that the P600 amplitude was significantly larger during periods of low reaction time variability (high sustained attention) than in periods of high reaction time variability (low sustained attention). In contrast, the amplitude of the N400 was not affected by reaction time variability. These results thus suggest that the P600 component is sensitive to sustained attention while the N400 component is not, which provides independent evidence for accounts suggesting that P600 amplitudes reflect more controlled and N400 amplitudes more automatic aspects of sentence comprehension.


title: Designing and comparing cleaning pipelines for TMS-EEG data: a theoretical overview and practical example

abstract:
Combining transcranial magnetic stimulation (TMS) with electroencephalography (EEG) is growing in popularity as a method for probing the reactivity and connectivity of neural circuits in basic and clinical research. However, using EEG to measure the neural responses to TMS is challenging due to the unique artifacts introduced by combining the two techniques. In this paper, we overview the artifacts present in TMS-EEG data and the offline cleaning methods used to suppress these unwanted signals. We then describe how open science practices, including the development of open-source toolboxes designed for TMS-EEG analysis (e.g., TESA - the TMS-EEG signal analyser), have improved the availability and reproducibility of TMS-EEG cleaning methods. We provide theoretical and practical considerations for designing TMS-EEG cleaning pipelines and then give an example of how to compare different pipelines using TESA. We show that changing even a single step in a pipeline designed to suppress decay artifacts results in TMS-evoked potentials (TEPs) with small differences in amplitude and spatial topography. The variability in TEPs resulting from the choice of cleaning pipeline has important implications for comparing TMS-EEG findings between research groups which use different online and offline approaches. Finally, we discuss the challenges of validating cleaning pipelines and recommend that researchers compare outcomes from TMS-EEG experiments using multiple pipelines to ensure findings are not related to the choice of cleaning methods. We conclude that the continued improvement, availability, and validation of cleaning pipelines is essential to ensure TMS-EEG reaches its full potential as a method for studying human neurophysiology.

HighlightsO_LIConcurrent TMS-EEG is challenging due to artifacts in the recorded signals.
C_LIO_LIWe overview offline methods for cleaning TEPs and provide tips on pipeline design.
C_LIO_LIWe use TESA to compare pipelines and show changing a single step alters TEPs.
C_LIO_LIWe discuss the challenges in validating pipelines for TMS-EEG analysis.
C_LIO_LIWe suggest using multiple pipelines to minimise the impact of method choice on TEPs.
C_LI


title: Oscillatory population-level activity of dorsal raphe serotonergic neurons sculpts sleep structure

abstract:
Dorsal raphe (DR) 5-HT neurons are involved in regulating sleep-wake transitions. Previous studies demonstrated that single-unit activity of DR 5-HT neurons is high during wakefulness, decreases during non-rapid eye movement (NREM) sleep, and ceases during rapid eye movement (REM) sleep. However, characteristics of the population-level activity of DR 5-HT neurons, which can influence the entire brain, are largely unknown. Here we measured population activities of 5-HT neurons in male and female mouse DR across the sleep-wake cycle by a ratiometric fiber photometry system. We found a slow oscillatory activity of compound intracellular Ca2+ signals during NREM sleep. The trough of concave 5-HT activity increased along with sleep progression, but the 5-HT activity level always returned to that seen in wake periods. When the trough reached the minimum level and remained there, REM sleep initiated. We also found a unique coupling of the oscillatory 5-HT activity and EEG power fluctuation, suggesting that EEG fluctuation is a proxy for 5-HT activity. Optogenetic activation of 5-HT neurons during NREM sleep triggered a high EMG power and induced wakefulness. Optogenetic inhibition induced REM sleep or sustained NREM with an EEG power increase and EEG fluctuation. These manipulations demonstrated a causal role of DR 5-HT neurons in sculpting sleep-wake structure. We also observed EEG fluctuations in human males during NREM sleep, implicating the existence of 5- HT oscillatory activity in humans. We propose that NREM sleep is not a monotonous state, but that it is dynamically regulated by the oscillatory population activity of DR 5- HT neurons.

Significant statementPrevious studies have demonstrated single-cell 5-HT neuronal activity across sleep- wake conditions; however, population-level activities of these neurons are largely unknown. We monitored dorsal raphe (DR) 5-HT population activity using a fiber photometry system in mice and demonstrated that activity was highest during wakefulness, and lowest during rapid eye movement (REM) sleep. Surprisingly, during non-REM (NREM) sleep, the 5-HT population activity decreased with an oscillatory pattern, coinciding with EEG fluctuations. We examined the causal role of these 5-HT neuron activities by optogenetics and found that DR 5-HT neurons sculpted sleep-wake conditions by influencing EEG and EMG patterns. We found similar EEG fluctuations in a human sleep EEG study, suggesting the presence of oscillatory 5-HT neuron activity during NREM across species.


title: Listeria spp. Isolated from Soil Samples Collected in the Great Smoky Mountains

abstract:
Listeria monocytogenes, a foodborne pathogen, and other Listeria spp. are present in natural environments. Isolating and characterizing strains from natural reservoirs can provide insight into the prevalence and diversity of Listeria spp. in these environments, elucidate their contribution to contamination of agricultural and food processing environments and food products, and lead to the discovery of novel species. In this study, we evaluated the diversity of Listeria spp. isolated from soil samples in a small region of the Great Smoky Mountains National Park (GSMNP), which is the most biodiverse national park in the United States National Park system. Of the 17 Listeria isolates that were recovered, whole-genome sequencing revealed that 14 were unique strains. The unique strains were shown to represent a diversity of Listeria spp., including L. monocytogenes (n=9), L. cossartiae subsp. cossartiae (n=1), L. marthii (n=1), L. booriae (n=1), and a novel Listeria sp. (n=2). The Listeria isolated in this study were collected from high elevation sites near a creek that drains into a series of rivers ultimately leading to the Mississippi River; thus, the Listeria present in this natural environment could potentially travel downstream to a large region that includes portions of nine southeastern and midwestern states in the U.S. The Listeria spp. isolated and described in this study provide insight into the diversity of Listeria spp. found in the Great Smoky Mountains and indicate that this environment is a reservoir of novel Listeria spp.

IMPORTANCEListeria monocytogenes is a foodborne pathogen that can cause serious systemic illness that, although rare, usually results in hospitalization and has a relatively high mortality rate compared to other foodborne pathogens. Identification of novel and diverse Listeria spp. provides insight into the genomic evolution, ecology, and evolution and variance of pathogenicity of this genus, especially in natural environments. Comparing L. monocytogenes and Listeria spp. isolates from natural environments, such as those recovered in this study, to contamination and/or outbreak strains may provide more information about the original natural sources of these strains and the pathways and mechanisms that lead to contamination of food products and agricultural or food processing environments.

category: microbiology


title: A large scale, multiple genome comparison of acidophilic Archaea (pH <= 5.0) extends our understanding of oxidative stress responses in polyextreme environments

abstract: Acidophilic Archaea thrive in anaerobic and aerobic low pH environments (<pH 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (*OH) and superoxide (O2 *-). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic Archaea with sequenced genomes. These organisms can be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what can this tell us about the evolution of these mechanisms in acidophilic Archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic Archaea and between acidophilic Archaea and acidophilic Bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in Archaea and possible Horizontal Gene Transfer (HGT) events.


title: Circadian regulation of lung repair and regeneration

abstract: Optimal lung repair and regeneration is essential for recovery from viral infections such as that induced by influenza A virus (IAV). We have previously demonstrated that lung inflammation induced by IAV is under circadian control. However, it is not known if the circadian clock exerts its influence on lung repair and regenerative processes independent of acute inflammation from IAV. Here, we demonstrate for the first time that lung organoids have a functional clock as they mature and that the absence of an intact circadian clock impairs regenerative capacity. Using several models of circadian disruption, we show that with the absence of an intact clock lung proliferation is disrupted. Further, we find that the circadian clock acts through direct control of the Wnt/{beta}-catenin pathway. We speculate, that adding the circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes. Finally, we use data from UK Biobank to demonstrate at the population level, the role of poor circadian rhythms in mediating negative outcomes following lung infection.


title: Host exposure to symbionts and ecological drift generate divergence in parasite community assembly

abstract:
The initial colonization of a host by symbionts, ranging from parasites to mutualists, can generate priority effects that alter within-host interactions and the trajectory of parasite community assembly. At the same time, variation in parasite communities among hosts can also stem from stochastic processes. Community ecology theory posits that multiple processes (e.g. dispersal, selection and drift) interact to generate variation in community structure, but these processes are rarely considered simultaneously during community assembly. To test the role of these processes in a parasite community, we experimentally simulated dispersal of three symbionts by factorially inoculating individual plants of tall fescue with two foliar fungal parasites, Colletotrichum cereale and Rhizoctonia solani, and a hypothesized mutualist endophyte, Epichloe coenophiala. We then tracked parasite infections longitudinally in the field. After the initial inoculations, hosts were exposed to a common pool of parasites in the field, which we expected to cause parasite communities to converge towards a similar community state. To test for convergence, we analyzed individual hosts parasite community trajectories in multivariate space. In contrast to our expectation, there was no signal of convergence. Instead, parasite community trajectories generally diverged over time between treatment groups and the magnitude of divergence depended on the symbiont species inoculated. Parasite communities of hosts that were inoculated with only the mutualist, Epichloe, showed significant trends of divergence relative to all other symbiont inoculation treatments. In contrast, hosts inoculated with only Rhizoctonia did not exhibit clear trends of divergence when compared to other parasite inoculations. Further, co-inoculation with both parasite species resulted in faster rates of divergence and greater temporal change in parasite communities relative to hosts inoculated with only the parasite Colletotrichum. As predicted by existing theory, parasite communities showed evidence of drift during the beginning of the experiment, which contributed to among-host divergence in parasite community structure. Overall, these data provide evidence that initial dispersal of symbionts produced persistent changes in parasite community structure via ecological selection, that drift was important during the early stages of parasite community assembly, and together, dispersal, selection and drift resulted in parasite community divergence.

Open Research statementThe data and code that support the findings of this study are available through Zenodo at https://doi.org/10.5281/zenodo.5714452

category: ecology


title: Strict adherence to Mendel's First Law across a large sample of human sperm genomes

abstract: Mendels Law of Segregation states that the offspring of a diploid, heterozygous parent will inherit either allele with equal probability. While the vast majority of loci adhere to this rule, research in model and non-model organisms has uncovered numerous exceptions whereby "selfish" alleles are disproportionately transmitted to the next generation. Evidence of such "transmission distortion" (TD) in humans remains equivocal in part because scans of human pedigrees have been under-powered to detect small effects. Recently published single-cell sequencing data from individual human sperm (n = 41,189; 969-3,377 cells from each of 25 donors) offer an opportunity to revisit this question with unprecedented statistical power, but require new methods tailored to extremely low-coverage data ([~]0.01 x per cell). To this end, we developed a method, named rhapsodi, that leverages sparse gamete genotype data to phase the diploid genomes of the donor individuals, impute missing gamete genotypes, and discover meiotic recombination breakpoints, benchmarking its performance across a wide range of study designs. After applying rhapsodi to the sperm sequencing data, we then scanned the gametes for evidence of TD. Our results exhibited close concordance with binomial expectations under balanced transmission, in contrast to tenuous signals of TD that were previously reported in pedigree-based studies. Together, our work excludes the existence of even weak TD in this sample, while offering a powerful quantitative framework for testing this and related hypotheses in other cohorts and study systems.

category: genomics


title: A Method for Computationally Constructing Eukaryotic Synthetic Signal Peptide Sequences

abstract: We developed a computational method for constructing synthetic signal peptides from a base set of signal peptides (SPs) and non-SP sequences. A large number of structured "building blocks", represented as m-step ordered pairs of amino acids, are extracted from the base. Using a straightforward procedure, the building blocks enable the construction of a diverse set of synthetic SPs that could be utilized for industrial and therapeutic purposes. We have validated the proposed methodology using existing sequence prediction platforms such as Signal-BLAST and MULocDeep. In one experiment, 9,555 protein sequences were generated from a large randomly selected set of "building blocks". Signal-BLAST identified 8,444 (88%) of the sequences as signal peptides. In addition, the Signal-BLAST tool predicted that the generated synthetic sequences belonged to 854 distinct eukaryotic organisms. Here, we provide detailed descriptions and results from various experiments illustrating the potential usefulness of the methodology in generating signal peptide protein sequences.

category: bioinformatics


title: Systematic in silico discovery of novel solute carrier-like proteins from proteomes

abstract: Solute carrier (SLC) proteins represent the largest superfamily of transmembrane transporters. While many of them play key biological roles, their systematic analysis has been hampered by their functional and structural heterogeneity. Based on available nomenclature systems, we hypothesized that many as yet unidentified SLC transporters exist in the human genome, which await further systematic analysis. Here, we present criteria for defining "SLC-likeness" to curate a set of "SLC-like" protein families from the Transporter Classification Database (TCDB) and Protein families (Pfam) databases. Computational sequence similarity searches surprisingly identified [~]130 more proteins in human with potential SLC-like properties compared to previous annotations. Interestingly, several of these have documented transport activity in the scientific literature. To complete the overview of the "SLC-ome", we present an algorithm to classify SLC-like proteins into protein families, investigating their known functions and evolutionary relationships to similar proteins from 6 other clinically relevant experimental organisms, and pinpoint structural orphans. We envision that our work will serve as a stepping stone for future studies of the biological function and the identification of the natural substrates of the many under-explored SLC transporters, as well as for the development of new therapeutic applications, including strategies for personalized medicine and drug delivery.


title: Substrate dependent homeostatic control of c-di-AMP synthase (MsDisA) and hydrolase (MsPDE) from Mycobacterium smegmatis

abstract: In bacteria, cyclic-di-nucleotide based second messengers regulate various physiological processes including the stress response. For the past few decades, cyclic diadenosine monophosphate (c-di-AMP) is emerging as a crucial second messenger in bacterial world. It is an essential molecule and has been implicated in fatty acid metabolism, antibiotic resistance, biofilm formation, virulence and activates the cytosolic pathway of innate immunity in host cell. The level of c-di-AMP is maintained within the cell by the action of two opposing enzymes, namely diadenylate cyclases and phosphodiesterases. However, such kind of c-di-AMP modulation remains to be explored in Mycobacterium smegmatis. Here, we systematically investigate the c-di-AMP synthase (MsDisA) and a hydrolase (MsPDE) from M. smegmatis at different pHs and osmolytic conditions. Our biochemical assays showed that the MsDisA activity is enhanced during the alkaline stress and c-di-AMP is readily produced without any intermediates. At pH 9.4, the MsDisA promoter activity increases significantly, further strengthening this observation. However, under physiological conditions, the activity of MsDisA is moderate with the formation of intermediates. We also observe that the size of MsDisA is significantly increased upon incubation with substrate. To further get deep insights into the structural characteristics, we report a 3.8 [A] cryo-EM structure of the MsDisA protein, distinct from the earlier reported structure of DisA from Thermotoga maritima. The domain mutant experiments prove that the N-terminal minimal region can form a functional octamer. Thus, our results reveal how mycobacterial c-di-AMP is biochemically and structurally regulated in response to different environment.


title: The annotation and analysis of complex 3D plant organs using 3DCoordX

abstract: A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. It enables rapid spatial annotation of cells even in highly curved biological shapes. With the help of 3DCoordX we obtained new insight by analyzing cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis thaliana. Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia polymorpha and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia gibba. Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

category: plant biology


title: A ROS-Ca2+ signalling pathway identified from a chemical screen for modifiers of sugar-activated circadian gene expression.

abstract: Sugars are essential metabolites for energy and anabolism that can also act as signals to regulate plant physiology and development. Experimental tools to disrupt major sugar signalling pathways are limited. We have performed a chemical screen for modifiers of activation of circadian gene expression by sugars to discover pharmacological tools to investigate and manipulate plant sugar signalling. Using a library of commercially available bioactive compounds, we identified 75 confident hits that modified the response of a circadian luciferase reporter to sucrose in dark-adapted seedlings. We validated the transcriptional effect on a subset of the hits and measured their effects on a range of sugar-dependent phenotypes for 13 of these chemicals. Chemicals were identified that appear to influence known and unknown sugar signalling pathways. Pentamidine isethionate (PI) was identified as a modifier of a sugar-activated Ca2+ signal that acts downstream of superoxide in a metabolic signalling pathway affecting circadian rhythms, primary metabolism and plant growth. Our data provide a resource of new experimental tools to manipulate plant sugar signalling and identify novel components of these pathways.


title: Balancing selection and the crossing of fitness valleys in structured populations: diversification in the gametophytic self-incompatibility system

abstract: The self-incompatibility locus (S-locus) of flowering plants displays a striking allelic diversity. How such a diversity has emerged remains unclear. In this paper, we performed numerical simulations in a finite island population genetics model to investigate how population subdivision affects the diversification process at a S-locus, given that the two-genes architecture typical of S-loci involves the crossing of a fitness valley. We show that population structure increases the number of self-incompatibility haplotypes (S-haplotypes) maintained in the whole metapopulation, but at the same time also slightly reduces the parameter range allowing for their diversification. This increase is partly due to a reinforcement of the diversification and replacement dynamics of S-haplotypes within and among demes. We also show that the two-genes architecture leads to a higher diversity compared with a simpler genetic architecture where new S-haplotypes appear in a single mutation step. We conclude that population structure helps explain the large allelic diversity at the self-incompatibility locus. Overall, our results suggest that population subdivision can act in two opposite directions: it makes easier S-haplotypes diversification but increases the risk that the SI system is lost.

category: evolutionary biology


title: A Comparison Study between Autism Spectrum Disorder and Typically Control in Graph Frequency Bands Using Graph and Triadic Interaction Metrics

abstract:
Many researchers using many different approaches have attempted to find features discriminating between autism spectrum disorder (ASD) and typically control (TC) subjects. In this study, this attempt has been continued by analyzing global metrics of functional graphs and metrics of functional triadic interactions of the brain in the low, middle, and high-frequency bands (LFB, MFB, and HFB) of the structural graph. The graph signal processing (GSP) provided the combinatorial usage of the functional graph of resting-state fMRI and structural graph of DTI. In comparison to TCs, ASDs had significantly higher clustering coefficients in the MFB, higher efficiencies and strengths in the MFB and HFB, and lower small-world propensity in the HFB. These results show over-connectivity, more global integration, and probably decreased local specialization in ASDs compared to TCs. Triadic analysis showed that the numbers of unbalanced triads were significantly lower for ASDs in the MFB. This finding may show the reason for restricted and repetitive behavior in ASDs. Also, in the MFB and HFB, the numbers of balanced triads and the energies of triadic interactions were significantly higher and lower for ASDs, respectively. These findings may reflect the disruption of the optimum balance between functional integration and specialization. All of these results demonstrated that the significant differences between ASDs and TCs existed in the MFB and HFB of the structural graph when analyzing the global metrics of the functional graph and triadic interaction metrics. In conclusion, the results demonstrate the promising perspective of GSP for attaining discriminative features and new knowledge, especially in the case of ASD.

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title: Constructing threat probability, fear behaviour, and aversive prediction error in the brainstem.

abstract: When faced with potential threat we must estimate its probability, respond advantageously, and leverage experience to update future estimates. Threat estimates are the proposed domain of the forebrain, while behaviour is elicited by the brainstem. Yet, the brainstem is also a source of prediction error, a learning signal to acquire and update threat estimates. Neuropixels probes allowed us to record single-unit activity across a 21-region brainstem axis during probabilistic fear discrimination. Against a backdrop of widespread threat probability and behaviour signaling, a dorsally-based brainstem network rapidly signaled threat probability. Remapping of neuronal function following shock outcome gave rise to brainstem networks signaling prediction error on multiple times-cales. The results reveal construction of threat probability, behaviour, and prediction error along a single brainstem axis.


title: Distinct neurocognitive bases for social trait judgments of faces in autism spectrum disorder

abstract: Autism spectrum disorder (ASD) is characterized by difficulties in social processes, interactions, and communication. Yet, the neurocognitive bases underlying these difficulties are unclear. Here, we triangulated the  trans-diagnostic approach to personality, social trait judgments of faces, and neurophysiology to investigate (1) the relative position of autistic traits in a comprehensive social-affective personality space and (2) the distinct associations between the social-affective personality dimensions and social trait judgment from faces in individuals with ASD and neurotypical individuals. We collected personality and facial judgment data from a large sample of online participants (N = 89 self-identified ASD; N = 308 neurotypical controls). Factor analysis with 33 sub-scales of 10 social-affective personality questionnaires identified a 4-dimensional personality space. This analysis revealed that ASD and control participants did not differ significantly along the personality dimensions of empathy and prosociality, antisociality, or social agreeableness. However, the associations between these dimensions and judgments of facial trustworthiness and warmth differed across groups. Neurophysiological data also indicated that ASD and control participants might rely on distinct neuronal representations for judging trustworthiness and warmth from faces. These results suggest that the atypical association between social-affective personality and social trait judgment from faces may contribute to the social and affective difficulties associated with ASD.


title: Heat activation and inactivation of bacterial spores. Is there an overlap?

abstract: Heat activation at a sublethal temperature is widely applied to promote Bacillus species spore germination. This treatment also has potential to be employed in food processing to eliminate undesired bacterial spores by enhancing their germination, and then inactivating the less heat resistant germinated spores at a milder temperature. However, incorrect heat treatment could also generate heat damage in spores, and lead to more heterogeneous spore germination. Here, the heat activation and heat damage profile of Bacillus subtilis spores was determined by testing spore germination and outgrowth at both population and single spore levels. The heat treatments used were 40-80{degrees}C, and for 0-300 min. The results were as follows. 1) Heat activation at 40-70{degrees}C promoted L-valine and L-asparagine-glucose-fructose-potassium (AGFK) induced germination in a time dependent manner. 2) The optimal heat activation temperatures for AGFK and L-valine germination via the GerB plus GerK or GerA germinant receptors were 65 and 50-65{degrees}C, respectively. 3) Heat inactivation of dormant spores appeared at 70{degrees}C, and the heat damage of molecules essential for germination and growth began at 70 and 65{degrees}C, respectively. 4) Heat treatment at 75{degrees}C resulted in both activation of germination and damage to the germination apparatus, and 80{degrees}C treatment caused more pronounced heat damage. 5) For the spores that should withstand adverse environmental temperatures in nature, heat activation seems functional for a subsequent optimal germination process, while heat damage affected both germination and outgrowth.


title: cNap1 bridges centriole contact sites to maintain centrosome cohesion

abstract: Centrioles are non-membrane bound organelles that participate in fundamental cellular processes through their ability to form physical contacts with other structures. During interphase, two mature centrioles can associate to form a single centrosome - a phenomenon known as centrosome cohesion. Centrosome cohesion is important for processes such as cell migration, and yet how it is maintained is unclear. Current models indicate that pericentriolar fibres termed rootlets, also known as the centrosome linker, entangle to maintain centriole proximity. Here, I uncover a new centriole-centriole contact site and mechanism of centrosome cohesion, based on coalescence of the proximal centriole component cNap1. Using live-cell imaging of endogenously tagged cNap1, I show that proximal centrioles form dynamic contacts in response to physical force from the cytoskeleton. Expansion microscopy reveals that cNap1 bridges between these contact sites, physically linking proximal centrioles on the nanoscale. When ectopically tethered to organelles such as lysosomes, cNap1 forms viscous and cohesive condensates that promote organelle spatial proximity. Conversely, cNap1 mutants with reduced viscosity are unable to maintain centrosome cohesion. These results define a previously unrecognised mechanism of centrosome cohesion by cNap1 assemblies at the proximal centriole and illustrate how a non-membrane bound organelle forms dynamic organelle contact sites.


title: Fast DNA-PAINT imaging using a deep neural network

abstract: DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a super-resolution technique with relatively easy-to-implement multi-target imaging. However, image acquisition is slow as sufficient statistical data has to be generated from spatio-temporally isolated single emitters. Here, we trained the neural network (NN) DeepSTORM to predict fluorophore positions from high emitter density DNA-PAINT data. This achieves image acquisition in one minute. We demonstrate multi-color super-resolution imaging of structure-conserved semi-thin neuronal tissue and imaging of large samples. This improvement can be integrated into any single-molecule microscope and enables fast single-molecule super-resolution microscopy.


title: Active Segregation Dynamics in the Living Cell

abstract: In this paper, we bring together our efforts in identifying and understanding nonequilibrium phase segregation driven by active processes in the living cell, with special focus on the segregation of cell membrane components driven by active contractile stresses arising from cortical actomyosin. This also has implications for active segregation dynamics in membraneless regions within the cytoplasm and nucleus (3d). We formulate an active version of the Flory-Huggins theory that incorporates a contribution from fluctuating active stresses. Apart from knitting together some of our past theoretical work in a comprehensive narrative, we highlight some new results, and establish a correspondence with recent studies on Active Model B/B+. We point to the many unusual aspects of the dynamics of active phase segregation, such as (i) anomalous growth dynamics, (ii) coarsening accompanied by propulsion and coalescence of domains that exhibit nonreciprocal effects, (iii) segregation into mesoscale domains, (iv) emergence of a nonequilibrium phase segregated steady state characterised by strong macroscopic fluctuations (fluctuation dominated phase ordering (FDPO)), and (v) mesoscale segregation even above the equilibrium Tc. Apart from its implications for actively driven segregation of binary fluids, these ideas are at the heart of an Active Emulsion description of the lateral organisation of molecules on the plasma membrane of living cells, whose full molecular elaboration appears elsewhere.


title: A multiscale X-ray phase-contrast tomography dataset of whole human left lung

abstract: Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows to decouple sample size and resolution, while maintaining high sensitivity to the microstructure of soft, partially dehydrated tissues. The recently developed imaging technique, hierarchical phase-contrast tomography, is a comprehensive approach to address the challenge of organ-scale (up to tens of centimeters) soft tissue imaging with resolution and sensitivity down to the cellular level. Using this technique, we imaged ex vivo an entire human left lung at an isotropic voxel size of 25.08 m along with local zooms down to 6.05 - 6.5 m and 2.45 - 2.5 m in voxel size. The high tissue contrast offered by the fourth-generation synchrotron source at the European Synchrotron Radiation Facility reveals complex multiscale anatomical constitution of the human lung from the macroscopic (centimeter) down to the microscopic (micrometer) scale. The dataset provides complete organ-scale 3D information of the secondary pulmonary lobules and delineates the microstructure of lung nodules with unprecedented detail.

category: physiology


title: The Contributions of Eye Gaze Fixations and Target-Lure Similarity to Behavioral and fMRI Indices of Pattern Separation and Pattern Completion

abstract: Pattern separation and pattern completion are generally studied in humans using mnemonic discrimination tasks such as the Mnemonic Similarity Task (MST) where participants identify similar lures and repeated items from a series of images. Failures to correctly discriminate lures are thought to reflect a failure of pattern separation and a propensity toward pattern completion. Recent research has challenged this perspective, suggesting that poor encoding rather than pattern completion accounts for the occurrence of false alarm responses to similar lures. In two experiments, participants completed a continuous recognition task version of the MST while eye movement (Experiments 1 and 2) and fMRI data (Experiment 2) were collected. In Experiment 1, we replicated the result that fixation counts at study predicted accuracy on lure trials (consistent with poor encoding predicting mnemonic discrimination performance), but this effect was not observed in our fMRI task. In both experiments we found that target-lure similarity was a strong predictor of accuracy on lure trials. Further, we found that fMRI activation changes in the hippocampus were significantly correlated with the number of fixations at study for correct but not incorrect mnemonic discrimination judgments when controlling for target-lure similarity. Our findings indicate that while eye movements during encoding predict subsequent hippocampal activation changes for correct mnemonic discriminations, the predictive power of eye movements for activation changes for incorrect mnemonic discrimination trials was modest at best.


title: Multi-timescale biological learning algorithms train spiking neuronal network motor control

abstract: Biological learning operates at multiple interlocking timescales, from long evolutionary stretches down to the relatively short timespan of an individuals life. While each process has been simulated individually as a learning algorithm in spiking neuronal networks (SNNs), the integration of the two is limited. In this study, we first train SNNs separately using individual model learning using spike-timing dependent reinforcement learning (STDP-RL) and evolutionary (EVOL) learning algorithms to solve the CartPole reinforcement learning (RL) control problem. We then develop an interleaved algorithm inspired by biological evolution that combines the EVOL and STDP-RL learning in sequence (EVOL+STDP-RL). This sequential algorithm implements the Baldwin Effect, by allowing learning during a models lifetime to indirectly influence future model generations produced by EVOL. We evaluate performance of each algorithm after training and through the creation of sensory/motor action maps that delineate the networks transformation of sensory inputs into higher-order representations and motor decisions. Compared to STDP-RL and EVOL algorithms operating on their own, our EVOL+STDP-RL interleaved training paradigm enhanced performance robustness and shortened the required training to reach optimal performance. The different model strategies were revealed through analysis of sensory/motor mappings. Our modeling opens up new capabilities for SNNs in RL and could serve as a testbed for neurobiologists aiming to understand multi-timescale learning mechanisms and dynamics in neuronal circuits.


title: Epigenetic changes in autoimmune monocytes contribute to disease and can be targeted by JAKinhibition

abstract: How the local inflammatory environment regulates epigenetic changes in the context of autoimmune diseases remains unclear. Here we assessed the transcriptional and active enhancer profile of monocytes derived from the inflamed joints of Juvenile Idiopathic Arthritis (JIA) patients, a model well-suited for studying autoimmune diseases. RNA-sequencing analysis demonstrated that synovial-derived monocytes display an activated phenotype, characterized by increased expression of surface activation markers and multiple chemokines and cytokines. This increased expression is regulated on the epigenetic level, as ChIP-sequencing indicated increased H3K27 acetylation of genes upregulated in synovial monocytes. IFN signaling-associated genes are increased and epigenetically altered in synovial monocytes, suggesting a role for IFN in establishing the inflammatory phenotype. Treatment of human synovial monocytes with the Janus-associated kinase (JAK) inhibitor Ruxolitinib, which inhibits IFN signaling, transformed the activated enhancer landscape and reduced disease-associated gene expression, thereby inhibiting the inflammatory phenotype. Taken together, these data provide novel insight into epigenetic regulation of autoimmune disease-patient derived monocytes and suggest that altering the epigenetic profile can be a therapeutic approach for the treatment of autoimmune diseases.

category: immunology


title: Organization and dynamics of the SpoVAEa protein, and its surrounding inner membrane lipids upon germination of Bacillus subtilis spores

abstract: The SpoVA proteins make up a channel in the inner membrane (IM) of B. subtilis spore. This channel responds to signals from activated germinant receptors (GRs), and allows release of Ca2+-DPA from the spore core during germination. In the current work, we studied the location and dynamics of SpoVAEa in dormant spores. Notably, the SpoVAEa-SGFP2 proteins were present in a single spot in spores, similar to the complex formed by all GRs. However, while the GRs spot remains in one location, the SpoVAEa-SGFP2 spot in the IM moved randomly with high frequency. The dynamics of the SpoVAEa-SGFP2 and its surrounding IM region as stained by fluorescent dyes were also tracked during spore germination, as the dormant spore IM appeared to have an immobile germination related functional microdomain. This microdomain disappeared around the time of appearance of a germinated spore, the loss of fluorescence of the IM by fluorescent dyes, as well as the appearance of SpoVAEa-SGFP2 peak fluorescent intensity occurred in parallel. These observed events were highly related to the rapid phase darkening, which is considered as the Ca2+DPA rapid release. We also tested the response of SpoVAEa and the IM to thermal treatments at 40-80{degrees}C. Heat treatment triggered an increase of green autofluorescence, which is speculated to be due to coat protein denaturation, and 80{degrees}C treatments induce the appearance of phase-grey-like spores. These spores presumably have a similar intracellular physical state as the phase grey spores detected in the germination but lack the functional proteins for further germination events.


title: A glycerol shunt functions as a glucose excess security valve in pancreatic β-cells

abstract: The recently identified glycerol-3-phosphate (Gro3P) phosphatase (G3PP) in mammalian cells, encoded by the PGP gene, was shown to regulate intermediary metabolism by hydrolyzing Gro3P and to control glucose-stimulated insulin secretion (GSIS) in {beta}-cells, in vitro. We now examined in inducible {beta}-cell specific G3PP-KO (BKO) mice, the role of G3PP in the control of insulin secretion in vivo, {beta}-cell function and glucotoxicity. BKO mice, compared to MCre controls, showed increased body weight, adiposity, fed insulinemia, GSIS, reduced plasma triglycerides and mildly altered glucose tolerance. Isolated BKO mouse islets at high (16.7 mM) but not low or intermediate glucose (3-8 mM) showed elevated GSIS, Gro3P, metabolites reflecting {beta}-cell activation, O2 consumption, ATP production and reduced glycerol release. BKO islets chronically exposed to elevated glucose showed increased apoptosis, reduced insulin content and expression of Pdx-1, MafA and Ins-2 genes. As G3PP channels glucose carbons towards glycerol formation and release, the results demonstrate that {beta}-cell are endowed with a "glycerol shunt" acting as a glucose excess security valve. We propose that the glycerol shunt plays a role in glucodetoxification, the prevention of insulin hypersecretion, acts as a defense against excess body weight gain and contributes to {beta}-cell mass preservation in the face of hyperglycemia.

category: biochemistry


title: Single-Channel Permeability from Markovian Milestoning, Umbrella Sampling, and Voltage Simulations

abstract: Various all-atom molecular dynamics (MD) simulation methods have been developed to compute free energies and crossing rates of ions and small molecules through ion channels. However, a systemic comparison across different methods is scarce. Using a carbon nanotube as a model of small conductance ion channel, we computed the single-channel permeability for potassium ion using umbrella sampling, Markovian milestoning, and steady-state flux under applied voltage. We show that a slightly modified inhomogeneous solubility-diffusion equation yields a single-channel permeability consistent with the mean first passage time (MFPT)-based method. For milestoning, applying cylindrical and spherical bulk boundary conditions yield consistent MFPT if factoring in the effective bulk concentration. The sensitivity of the MFPT to the output frequency of collective variables is highlighted using the convergence and symmetricity of the inward and outward MFPT profiles. The consistent transport kinetic results from all three methods demonstrated the robustness of MD-based methods in computing ion channel permeation. The advantages and disadvantages of each technique are discussed, focusing on the future applications of milestoning in more complex systems.


title: Unifying Single-Channel Permeability from Rare-Event Sampling and Steady-State Flux


title: Conformational Changes in the Negative Arm of the Circadian Clock Correlate with Dynamic Interactomes Involved in Post-transcriptionally Regulated Processes

abstract: The circadian clock employs a transcriptional/translational negative feedback loop (TTFL) to anticipate environmental changes due to the Earths diurnal cycle, with regulation of organismal physiology believed to stem from temporal transcriptional activation by the positive arm. However, up to 80% of oscillating proteins do not have rhythmic mRNA, establishing circadian post-transcriptional regulation through unknown mechanisms. Given the pervasive conservation of the intrinsically disordered nature of negative-arm clock proteins, we hypothesized that post-transcriptional regulation may stem from conformational shifts in negative-arm proteins that time vacillations in the constituents of negative-arm macromolecular complexes to time cellular physiology. Our investigation of the negative arm clock protein in Neurospora crassa, FREQUENCY (FRQ), demonstrated temporal conformational fluidity correlated with daily changes in physiologically diverse macromolecular complex components. A parallel investigation of the macromolecular complexes centered around Drosophila melanogaster PERIOD (dPER) and human PERIOD (hPER2) found a similar number and physiological diversity of interacting partners in higher eukaryotes. Short linear motifs (SLiMs) associated with the interactors localized to disordered and phosphorylated regions on the PERs and FRQ, with disordered interactors oscillating in the macromolecular complexes over circadian time. This oscillation correlated with oscillations in post-transcriptionally regulated proteins, suggesting the negative arm may tune cellular physiology and proteostasis post-transcriptionally via vacillations in the circadian negative-arm macromolecular protein complexes.

category: molecular biology


title: Cohesion in male singing behavior predicts group reproductive output in a social songbird

abstract: All social groups require organization to function optimally. Group organization is often shaped by social  rules, which function to manage conflict, discourage cheating, or promote cooperation1-5. If social rules promote effective social living, then the ability to learn and follow these rules may be expected to influence individual and group-level fitness. However, such links can rarely be tested, due to the complexity of the factors mediating social systems and the difficulty of gathering data across multiple groups. Songbirds offer an opportunity to investigate the link between social rules and reproductive output because most of their social interactions are mediated by song, a well-studied and readily quantifiable behavior6,7. Using observations from 19 groups of brown-headed cowbirds (Molothrus ater) studied across 15 years, we find evidence for a previously undocumented social rule: cohesive group transitions between dominance- and courtship-related singing. Comparing across groups, the degree of cohesion in male singing behavior predicts the reproductive output of their group. Experimental manipulation of group structure via the introduction of juvenile males to captive flocks reduced group cohesion and adult male reproductive success. Taken together, these results demonstrate that cohesion in group behavioral states can affect both individual and group-level reproductive success, suggesting that selection can act not only on individual-level traits, but also on an individuals ability and opportunity to participate effectively in organized social interactions. Social cohesion could therefore be an unappreciated force affecting social evolution in many diverse systems.


title: RNA-Seq analysis identifies novel roles for the primary cilia gene SPAG17 and the SOX9 locus non-coding RNAs in systemic sclerosis

abstract: Systemic sclerosis (SSc) is characterized by immune activation, vasculopathy, and unresolving fibrosis in the skin, lungs, and other organs. We performed RNA-Seq analysis on skin biopsies and peripheral blood mononuclear cells (PBMCs) from SSc patients and controls to better understand SSc pathogenesis. We analyzed these data to 1) test for case-control differences, and 2) identify genes whose expression levels correlate with SSc severity as measured by local skin score, modified Rodnan skin score (MRSS), forced vital capacity (FVC), or diffusion capacity for carbon monoxide (DLCO). We found that PBMCs from SSc patients showed a strong type 1 interferon signature. This signal replicated in the skin, with additional signals for increased extracellular matrix (ECM) genes, classical complement pathway activation, and the presence of B cells. Notably, we observed a marked decrease in the expression of SPAG17, a cilia component, in SSc skin. We identified genes that correlated with MRSS, DLCO, and FVC in SSc PBMCs and skin using weighted gene co-expression analysis (WGCNA). These genes were largely distinct from the case/control differentially expressed genes. In PBMCs, type 1 interferon signatures negatively correlated with DLCO. In SSc skin, ECM gene expression positively correlated with MRSS. Network analysis of SSc skin genes correlated with clinical features identified the non-coding RNAs SOX9-AS1 and ROCR, both near the SOX9 locus, as highly connected, "hub-like" genes in the network. These results identify non-coding RNAs and SPAG17 as novel factors potentially implicated in SSc pathogenesis.


title: A novel mutation (E83Q) unlocks the pathogenicity of human alpha-synuclein fibrils and recapitulates its pathological diversity

abstract:
A novel mutation (E83Q), the first in the NAC domain of alpha-synuclein (aSyn), was recently identified in a patient with dementia with Lewy bodies. We investigated the effects of this mutation on the aggregation of aSyn monomers and the structure, morphology, dynamic, and seeding activity of the aSyn fibrils in neurons. We found that it dramatically accelerates aSyn fibrillization and results in the formation of fibrils with distinct structural and dynamic properties. In cells, this mutation is associated with higher levels of aSyn, accumulation of pS129, and increased toxicity. In a neuronal seeding model of Lewy bodies (LB) formation, the E83Q mutation significantly enhances the internalization of fibrils into neurons, induce higher seeding activity and results in the formation of diverse aSyn pathologies, including the formation of LB-like inclusions that recapitulate the immunohistochemical and morphological features of brainstem LBs observed in PD patient brains.

TeaserA novel mutation (E83Q) exacerbates alpha-synuclein aggregation and toxicity and reproduces PD pathological diversity.


title: Individual Stability of Pain- and Touch-Related Neuronal Gamma Oscillations

abstract:
BackgroundThe processing of brief pain and touch stimuli has been associated with an increase of neuronal oscillations in the gamma range (40-90 Hz). However, some studies report divergent gamma effects across single participants.

MethodsIn two repeated sessions we recorded gamma responses to pain and touch stimuli using EEG. Individual gamma responses were extracted from EEG channels and from ICA components that contain a strong gamma amplitude.

ResultsWe observed gamma responses in the majority of the participants. If present, gamma synchronisation was always bound to a component that contained a laser-evoked response. We found a broad variety of individual cortical processing: some participants showed a clear gamma effect, others did not exhibit any gamma. For both modalities, the effect was reproducible between sessions. In addition, participants with a strong gamma response showed a similar time-frequency pattern across sessions.

ConclusionsOur results indicate that current measures of reproducibility of research results do not reflect the complex reality of the diverse individual processing pattern of applied pain and touch. The present findings raise the question of whether we would find similar quantitatively different processing patterns in other domains in neuroscience: group results would be replicable but the overall effect is driven by a subgroup of the participants.


title: Re-evaluating the actin-dependence of spectraplakin functions during axon growth and maintenance

abstract: Axons are the long and slender processes of neurons constituting the biological cables that wire the nervous system. The growth and maintenance of axons require bundles of microtubules that extend through their entire length. Understanding microtubule regulation is therefore an essential aspect of axon biology. Key regulators of neuronal microtubules are the spectraplakins, a well-conserved family of cytoskeletal cross-linkers that underlie neuropathies in mouse and humans. Spectraplakin deficiency in mouse or Drosophila causes severe decay of microtubule bundles and axon growth inhibition. The underlying mechanisms are best understood for Drosophila Short stop (Shot) and believed to involve cytoskeletal cross-linkage: the N-terminal calponin homology (CH) domains bind to F-actin, and the C-terminus to microtubules and Eb1. Here we have gained new understanding by showing that the F-actin interaction must be finely balanced: altering the properties of F-actin networks or deleting/exchanging Shots CH domains induces changes in Shot function - with a Lifeact-containing Shot variant causing remarkable remodelling of neuronal microtubules. In addition to actin-MT cross-linkage, we find strong indications that Shot executes redundant MT bundle-promoting roles that are F-actin-independent. We argue that these likely involve the neuronal Shot-PH isoform, which is characterised by a large, unexplored central plakin repeat region (PRR). Work on PRRs might therefore pave the way towards important new mechanisms of axon biology and architecture that might similarly apply to central PRRs in mammalian spectraplakins.


title: Regnase-1 deficiency restrains Klebsiella pneumoniae infection by regulation of a Type I interferon response

abstract:
Excessive inflammatory responses can cause collateral tissue damage or autoimmune inflammation, sometimes with severe morbidity or mortality. During host defense responses, numerous negative feedback mechanisms are established to prevent excessive unchecked inflammation. However, this restraint can sometimes come at the cost of suboptimal infection control, and we do not fully understand how this balance is maintained during different infection settings. The endoribonuclease Regnase-1 (Reg1, Zc3h12a, MCPIP1) is an RNA binding protein (RBP) that binds and degrades many target mRNA transcripts. Reg1 is a potent feedback regulator of IL-17 and LPS signal transduction, among other stimuli. Consequently, Reg1 deficiency exacerbates autoimmune inflammation in multiple mouse models, but on the other hand, reduced Reg1 improves immunity to fungal infection. To date, the role of Reg1 in bacterial immunity is poorly defined. Here, we show that mice deficient in Reg1 are more resistant to pulmonary Klebsiella pneumoniae (KP) infection. Unexpectedly, effects of Reg1 deficiency were not due to accelerated eradication of bacteria or increased pro-inflammatory cytokine expression. Rather, alveolar macrophages from Reg1-deficient mice showed enrichment of Type I IFN-related genes upon KP infection, accompanied by increased Ifnb1 expression. Surprisingly, the stability of Ifnb1 mRNA was not altered by Reg1-deficiency; rather, mRNA encoding its upstream regulator IRF7 appeared to be a more prominent target. Blockade of IFNR during KP infection reversed disease improvement. Thus, impaired Reg1 induces Type I IFN and enhances resistance to KP, raising the possibility that Reg1 could be a potential clinical target in acute bacterial infections.

Graphical abstract

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title: Respiratory Syncytial virus NS1 protein targets the transactivator binding domain of MED25

abstract:
Respiratory syncytial virus has evolved a unique strategy to evade host immune response by coding for two non-structural proteins NS1 and NS2. Recently it was shown that in infected cells, nuclear NS1 could be involved in transcription regulation of host genes linked to innate immune response, via an interaction with chromatin and the Mediator complex. Here we identified the MED25 Mediator subunit as an NS1 interactor in a yeast two-hybrid screen. We demonstrate that NS1 directly interacts with MED25 in vitro and in cellula, and that this interaction involves the C-terminal 3 helix of NS1 and the MED25 ACID domain. More specifically we showed by NMR that the NS1 3 sequence primarily binds to the MED25 ACID H2 face, which is a transactivation domain (TAD) binding site for transcription regulators such as ATF6, a master regulator of ER stress response activated upon viral infection. Moreover, we found out that the NS1 3 helix could compete with ATF6 TAD binding to MED25. This finding points to a mechanism of NS1 interfering with innate immune response by impairing recruitment by cellular TADs of the Mediator via MED25 and hence transcription of specific genes by RNA polymerase II.

ImportanceHuman RSV is the leading cause of infantile bronchiolitis in the world and one of the major causes of childhood deaths in resource-poor settings. It is a major unmet target for vaccines and anti-viral drugs. RSV non-structural protein NS1 is known to antagonize the cellular immune response and was recently shown to be involved in transcription regulation of infected cells. However, the exact mechanism of this regulation is not well defined. Here we show that nuclear NS1 interacts directly with the Mediator subunit MED25 and is able to compete with a cellular transcription activator, which is activated during viral infection. We hypothesize that this interaction may underlie regulation of the expression of genes involved in the innate immune response.


title: Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

abstract:
BackgroundUnderstanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species, in which sexual selection may play an important role by generating and maintaining sexual dimorphism. The mechanism of how sexual selection operated in speciation with gene flow remains an open question and the subject of many research. Two species in genus Chrysolophus, Golden pheasant (C. pictus) and Lady Amhersts pheasant (C. amherstiae), which both exhibit significant plumage dichromatism, are currently parapatric in the southwest China with several hybrid recordings in field.

MethodsIn this research, we estimated the pattern of gene flow during the speciation of two pheasants using the Approximate Bayesian Computation (ABC) method based on the multiple genes data. With a new assembled de novo genome of Lady Amhersts pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by pairwise sequentially Markovian coalescent (PSMC).

ResultsThe results provide clear evidence that the gene flow between the two pheasants were consistent with the prediction of isolation with migration model for allopatric populations, indicating that there was long-term gene flow after the initially divergence (ca. 2.2 million years ago), and further support the secondary contact when included the parapatric populations since around 30 ka ongoing gene flow to now, which might be induced by the population expansion of the Golden pheasant in late Pleistocene.

ConclusionsThe results of the study support the scenario of speciation between Golden pheasant (C. pictus) and Lady Amhersts pheasant (C. amherstiae) with cycles of mixing-isolation-mixing due to the dynamics of natural selection and sexual selection in late Pleistocene that provide a good research system as evolutionary model to test reinforcement selection in speciation.


title: Transcriptomic Analysis of 3D Vasculature-On-A-Chip Reveals Paracrine Factors Affecting Vasculature Growth and Maturation

abstract: In vitro models of vasculature are of great importance for modelling vascular physiology and pathology. However, there is usually a lack of proper spatial patterning of interacting heterotypic cells in conventional vasculature dish models, which might confound results between contact and non-contact interactions. We use a microfluidic platform with structurally defined separation between human microvasculature and fibroblasts to probe their dynamic, paracrine interactions. We also develop a novel, versatile technique to retrieve cells embedded in extracellular matrix from the microfluidic device for downstream transcriptomic analysis, and uncover growth factor and cytokine expression profiles associated with improved vasculature growth. Paired receptor-ligand analysis further reveals paracrine signaling molecules that could be supplemented into the medium for vasculatures models where fibroblast co-culture is undesirable or infeasible. These findings also provide deeper insights into the molecular cues for more physiologically relevant vascular mimicry and vascularized organoid model for clinical applications such as drug screening and disease modeling.


title: Unsupervised cell functional annotation for single-cell RNA-Seq

abstract:
One of the first steps in the analysis of single cell RNA-Sequencing data (scRNA-Seq) is the assignment of cell types. While a number of supervised methods have been developed for this, in most cases such assignment is performed by first clustering cells in low-dimensional space and then assigning cell types to different clusters. To overcome noise and to improve cell type assignments we developed UNIFAN, a neural network method that simultaneously clusters and annotates cells using known gene sets. UNIFAN combines both, low-dimensional representation for all genes and cell specific gene set activity scores to determine the clustering. We applied UNIFAN to human and mouse scRNA-Seq datasets from several different organs. As we show, by using knowledge on gene sets, UNIFAN greatly outperforms prior methods developed for clustering scRNA-Seq data. The gene sets assigned by UNIFAN to different clusters provide strong evidence for the cell type that is represented by this cluster making annotations easier.

Softwarehttps://github.com/doraadong/UNIFAN


title: Systematic Interrogation of Protein Refolding Under Cellular-Like Conditions

abstract: The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chains intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting proteins safe passage to their native states; however, the complexity of this medium has generally precluded biophysical techniques from interrogating protein folding under cellular-like conditions for single proteins, let alone entire proteomes. Here, we develop a limited-proteolysis mass spectrometry approach paired with an isotope-labeling strategy to globally monitor the structures of refolding E. coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data, and is particularly important for restoring acidic proteins and proteins with three to five domains, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than indirect measures like binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones both unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. The data support a model in which chaperone-nonrefolders have evolved to fold efficiently once and only once, co-translationally, and remain kinetically trapped in their native conformations.


title: A Proteome-Wide Map of Chaperone-Assisted Protein Refolding in the Cytosol


title: Artificial Intelligence uncovers carcinogenic human metabolites

abstract: The genome of a eukaryotic cell is often vulnerable to both intrinsic and extrinsic threats due to its constant exposure to a myriad of heterogeneous compounds. Despite the availability of innate DNA damage response pathways, some genomic lesions trigger cells for malignant transformation. Accurate prediction of carcinogens is an ever-challenging task due to the limited information about bona fide (non)carcinogens. We developed Metabokiller, an ensemble classifier that accurately recognizes carcinogens by quantitatively assessing their electrophilicity as well as their potential to induce proliferation, oxidative stress, genomic instability, alterations in the epigenome, and anti-apoptotic response. Concomitant with the carcinogenicity prediction, Metabokiller is fully interpretable since it reveals the contribution of the aforementioned biochemical properties in imparting carcinogenicity. Metabokiller outperforms existing best-practice methods for carcinogenicity prediction. We used Metabokiller to unravel cells endogenous metabolic threats by screening a large pool of human metabolites and predicted a subset of these metabolites that could potentially trigger malignancy in normal cells. To cross-validate Metabokiller predictions, we performed a range of functional assays using Saccharomyces cerevisiae and human cells with two Metabokiller-flagged human metabolites namely 4-Nitrocatechol and 3,4-Dihydroxyphenylacetic acid and observed high synergy between Metabokiller predictions and experimental validations.


title: Transient inhibition to light explains stronger V1 responses to dark stimuli

abstract: Neurons in the primary visual cortex (V1) receive excitation and inhibition from two different pathways processing lightness (ON) and darkness (OFF). V1 neurons overall respond more strongly to dark than light stimuli (Yeh, Xing and Shapley, 2010; Kremkow et al., 2014), consistent with a preponderance of darker regions in natural images (Ratliff et al., 2010), as well as human psychophysics (Buchner & Baumgartner, 2007). However, it has been unclear whether this "dark-dominance" is due to more excitation from the OFF pathway (Jin et al., 2008) or more inhibition from the ON pathway (Taylor et al., 2018). To understand the mechanisms behind dark-dominance, we record electrophysiological responses of individual simple-type V1 neurons to natural image stimuli and then train biologically inspired convolutional neural networks to predict the neurons responses. Analyzing a sample of 74 neurons (in anesthetized, paralyzed cats) has revealed their responses to be more driven by dark than light stimuli, consistent with previous investigations (Yeh et al., 2010; Kremkow et al., 2013). We show this asymmetry to be predominantly due to slower inhibition to dark stimuli rather than by stronger excitation from the thalamocortical OFF pathway. Consistent with dark-dominant neurons having faster responses than light-dominant neurons (Komban et al., 2014), we find dark-dominance to solely occur in the early latencies of neurons responses. Neurons that are strongly dark-dominated also tend to be less orientation selective. This novel approach gives us new insight into the dark-dominance phenomenon and provides an avenue to address new questions about excitatory and inhibitory integration in cortical neurons.