bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequestration of the exocytic SNARE Psy1 into multiprotein nodes reinforces polarized morphogenesis in fission yeast
Authors: Miller Kristi E. , Magliozzi Joseph O. , Picard Noelle A. , Moseley James B.
Published: May 2020

Polarized morphogenesis is achieved by targeting or inhibiting growth at distinct regions. Rod-shaped fission yeast cells grow exclusively at their ends by restricting exocytosis and secretion to these sites. This growth pattern implies the existence of mechanisms that prevent exocytosis and growth along non-growing cell sides. We previously identified a set of 50-100 megadalton-sized node structures along the sides of fission yeast cells that contain the interacting proteins Skb1 and Slf1. Here, we show that Skb1-Slf1 nodes contain the syntaxin-like SNARE Psy1, which mediates exocytosis in fission yeast. Psy1 localizes in a diffuse pattern at cell tips where it likely promotes exocytosis and growth, but Psy1 is sequestered in Skb1-Slf1 nodes at cell sides where growth does not occur. Mutations that prevent node assembly or inhibit Psy1 localization to nodes lead to aberrant exocytosis at cell sides and increased cell width. Genetic results indicate that this Psy1 node mechanism acts in parallel to actin cables and Cdc42 regulation. Our work suggests that sequestration of syntaxin-like Psy1 at non-growing regions of the cell cortex reinforces cell morphology by restricting exocytosis to proper sites of polarized growth.
Virtual Mouse Brain Histology from Multi-contrast MRI via Deep Learning
Authors: Liang Zifei , Lee Choong H. , Arefin Tanzil. M. , Dong Zijun. , Walczak Piotr , Shi Song-Hai , Knoll Florian , Ge Yulin , Ying Leslie , Zhang Jiangyang
Published: May 2020

1H MRI maps brain structure and function non-invasively through versatile contrasts that exploit inhomogeneity in tissue micro-environments. Inferring histopathological information from MRI findings, however, remains challenging due to absence of direct links between MRI signals and cellular structures. Here, we show that deep convolutional neural networks, developed using co-registered multi-contrast MRI and histological data of the mouse brain, can estimate histological staining intensity directly from MRI signals at each pixel. The results provide three-dimensional maps of axons and myelin with tissue contrasts that closely mimics target histology and enhanced sensitivity and specificity compared to conventional MRI markers. Furthermore, the relative contribution of each MRI contrast within the networks can be used to optimize multi-contrast MRI acquisition. We anticipate our method to be a starting point for translation of MRI results into easy-to-understand virtual histology for neurobiologists and provide resources for validating novel MRI techniques.
Plasticity, repeatability, and phenotypic correlations of aerobic metabolic traits in a small estuarine fish
Authors: Reemeyer Jessica E , Rees Bernard B.
Published: May 2020

Standard metabolic rate (SMR), maximum metabolic rate (MMR), absolute aerobic scope (AAS), and critical oxygen tension (Pcrit) were determined for the Gulf killifish,Fundulus grandis, an ecologically dominant estuarine fish, acclimated to lowered salinity, elevated temperature, and lowered oxygen concentration. Acclimation to low salinity resulted in a small, but significant, elevation of Pcrit; acclimation to elevated temperature increased SMR, MMR, AAS, and Pcrit; acclimation to low oxygen led to a small increase in SMR, but substantial decreases in MMR, AAS, and Pcrit. Variation in these metabolic traits among individuals was consistent and repeatable when measured during multiple control exposures over seven months. Trait repeatability was unaffected by acclimation condition suggesting that repeatability of these traits is not context dependent. There were significant phenotypic correlations between specific metabolic traits: SMR was positively correlated with MMR and Pcrit; MMR was positively correlated with AAS; and AAS was negatively correlated with Pcrit. In general, within-individual variation contributed more than among-individual variation to these phenotypic correlations. The effects of acclimation on these traits demonstrate that aerobic metabolism is plastic and influenced by the conditions experienced by these fish in the dynamic habitats in which they occur; however, the repeatability of these traits and the correlations among them suggest that these traits change in ways that maintains the rank order of performance among individuals across a range of environmental variation.
The M1/M4 agonist xanomeline modulates functional connectivity and NMDAR antagonist-induced changes in the mouse brain
Authors: Montani Caterina , Canella Carola , Schwarz Adam J. , Li Jennifer , Gilmour Gary , Galbusera Alberto , Wafford Keith , McCarthy Andrew , Shaw David , Knitowski Karen , McKinzie David , Gozzi Alessandro , Felder Christian
Published: May 2020

Cholinergic drugs acting at M1/M4 muscarinic receptors hold promise for the treatment of symptoms associated with brain disorders characterized by cognitive impairment, mood disturbances or psychosis, such as Alzheimer’s disease or schizophrenia. However, the brain-wide functional substrates engaged by muscarinic agonists remain poorly understood. Here we used a combination of pharmacological fMRI (phMRI), resting-state fMRI (rsfMRI) and resting-state quantitative EEG (qEEG) to investigate the effects of a behaviorally-active dose of M1/M4 agonist xanomeline on brain functional activity in the rodent brain. We investigated both the effects of xanomelineper seand its modulatory effects on signals elicited by the NMDA-receptor antagonists phencyclidine (PCP) and ketamine. We found that xanomeline induces robust and widespread BOLD signal phMRI amplitude increases and decreased high frequency qEEG spectral activity. rsfMRI mapping in the mouse revealed that xanomeline robustly decreased neocortical and striatal connectivity but induces focal increases in functional connectivity within the nucleus accumbens and basal forebrain. Notably, xanomeline pre-administration robustly attenuated both the cortico-limbic phMRI response and the fronto-hippocampal hyper-connectivity induced by PCP, enhanced PCP-modulated functional connectivity locally within the nucleus accumbens and basal forebrain, and reversed the gamma and high frequency qEEG power increases induced by ketamine. Collectively, these results show that xanomeline robustly induces both cholinergic-like neocortical activation and desynchronization of functional networks in the mammalian brain. These effects could serve as a translatable biomarker for future clinical investigations of muscarinic agents, and bear mechanistic relevance for the putative therapeutic effect of these class of compounds in brain disorders.
Distinct Microcircuit Response to Comparable Input from a Full and Partial Projection Neuron Population
Authors: Colton Gabriel F. , Cook Aaron P. , Nusbaum Michael P.
Published: May 2020

Neuronal inputs to microcircuits are often present as multiple copies of apparently equivalent neurons. Thus far, however, little is known regarding the relative influence on microcircuit output of activating all or only some copies of such an input. We are examining this issue in the crab (Cancer borealis) stomatogastric ganglion, where the gastric mill (chewing) microcircuit is activated by MCN1, a paired modulatory projection neuron. Both MCN1s contain the same cotransmitters, influence the same gastric mill circuit neurons, can drive the biphasic gastric mill rhythm, and are co-activated by all identified MCN1-activating pathways. Here, we determine whether the gastric mill circuit response is equivalent when stimulating one or both MCN1s under conditions where the pair are matched to collectively fire at the same overall rate and pattern as single MCN1 stimulation. The dual MCN1 stimulations elicited more consistently coordinated rhythms, and these rhythms exhibited longer phases and cycle periods. These different outcomes from single and dual MCN1 stimulation may have resulted from the relatively modest, and equivalent, firing rate of the gastric mill neuron LG during each matched set of stimulations. The LG neuron-mediated, ionotropic inhibition of the MCN1 axon terminals is the trigger for the transition from the retraction to protraction phase. This LG neuron influence on MCN1 was more effective during the dual stimulations, where each MCN1 firing rate was half that occurring during the matched single stimulations. Thus, equivalent individual- and co-activation of a class of modulatory projection neurons will not necessarily drive equivalent microcircuit output.

Summary Statement

Co-stimulating both copies of an identified modulatory projection neuron at the same collective firing rate used for single copy stimulation results in distinct microcircuit output.
The importomer is a peroxisomal membrane protein translocase
Authors: Martenson James S , Tam Hanson , McQuown Alexander J , Reif Dvir , Zhou Jing , Denic Vladimir
Published: May 2020

Three sites of membrane protein biogenesis (the endoplasmic reticulum, mitochondria and chloroplasts) receive unfolded substrates from organelle-specific protein targeting factors, then integrate them using separate translocation channels. Peroxisomes also receive membrane proteins from known targeting factors, but whether a separate translocase is needed for integration remains unknown. Here, using a novel genetic screening strategy, we reveal that the importomer–known for matrix protein import–integrates the peroxisomal membrane protein Pex14. In importomer mutants, Pex14 is arrested in a pre-integrated state on the peroxisome surface. To undergo integration, a Pex14 translocation signal binds the importomer’s substrate receptor Pex5 at a distinct site from matrix proteins. En bloc translocation of an engineered protein complex with Pex14’s luminal region argues that integration occurs without substrate unfolding. Our work shows that the handling of membrane protein targeting and integration by discrete machineries is a fundamental principle shared by diverse membrane protein biogenesis pathways.
Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6)
Authors: Yu Alvin , Lee Elizabeth M.Y. , Jin Jaehyeok , Voth Gregory A.
Published: May 2020

Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of the human immunodeficiency virus (HIV). These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6increases the stable life times of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6. We find that capsid hexamers and pentamers have differential binding modes for IP6. Ligand density calculations show three sites of interaction with IP6including at a known capsid-inhibitor binding pocket. Free energy calculations demonstrate that IP6preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6in stabilizing and assembling the retroviral capsid.
ATP driven diffusiophoresis: active cargo transport without motor proteins
Authors: Ramm Beatrice , Goychuk Andriy , Khmelinskaia Alena , Blumhardt Philipp , Ganzinger Kristina A. , Frey Erwin , Schwille Petra
Published: May 2020

Morphogenesis and homeostasis of biological systems are intricately linked to gradient formation through energy dissipation. Such spatial organization may be achieved via reaction-diffusion or directional cargo transport, as prominently executed by motor proteins. In contrast to these processes that rely on specific protein interactions, active transport based on a non-specific, purely physical mechanism remains poorly explored. Here, by a joint experimental and theoretical approach, we describe a hidden function of the MinDE protein system fromE. coli:Besides forming dynamic patterns, this system accomplishes the active transport of large, functionally unrelated cargo on membranesin vitro. Remarkably, this mechanism allows to sort diffusive objects according to their effective size, as evidenced using modular DNA origami–streptavidin nanostructures. We show that the diffusive fluxes of MinDE and cargo couple via density-dependent friction. This non-specific process constitutes a Maxwell-Stefan diffusiophoresis, so far undescribed in a biologically relevant setting. Such nonlinear coupling between diffusive fluxes could represent a generic physical mechanism for the intracellular organization of biomolecules.
Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM
Authors: Farrell Daniel P. , Anishchenko Ivan , Shakeel Shabih , Lauko Anna , Passmore Lori A. , Baker David , DiMaio Frank
Published: May 2020

Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4-8 Å), with visible secondary structure elements but poorly resolved loops, making model-building challenging. In the absence of high-resolution structures of homologues, only coarse-grained structural features are typically inferred from these maps, and it is often impossible to assign specific regions of density to individual protein subunits. This paper describes a new method for overcoming these difficulties that integrates predicted residue distance distributions from a deep-learned convolutional neural network, computational protein folding using Rosetta, and automated EM-map-guided complex assembly. We apply this method to a 4.6 Å resolution cryoEM map of Fanconi Anemia core complex (FAcc), an E3 ubiquitin ligase required for DNA interstrand crosslink repair, which was previously challenging to interpret as it is comprised of 6557 residues, only 1897 of which are covered by homology models. In the published structure built from this map, only 387 residues could be assigned to specific subunits. By building and placing into density 42 deep-learning guided models containing 4795 residues not included in the previously published structure, we are able to determine an almost-complete atomic model of FAcc, in which 5182 of the 6557 residues were placed. The resulting model is consistent with previously published biochemical data, and facilitates interpretation of disease related mutational data. We anticipate that our approach will be broadly useful for cryoEM structure determination of large complexes containing many subunits for which there are no homologues of known structure.
Velcro-like mannose and slime-like sialic acid interactions guide self-adhesion and aggregation of virus N-glycan shields
Authors: Ogharandukun Eric , Tewolde Wintana , Damtae Elbethel , Wang Songping , Ivanov Andrey , Kumari Namita , Nekhai Sergei , Chandran Preethi L.
Published: May 2020

The surfaces of cells and pathogens are covered with short polymers of sugars known as glycans. Complex N-glycans have a core of three mannose sugars, with distal repeats of N-acetylglucosamine and galactose sugars terminating with sialic acid (SA). Long-range slime-like and short-range Velcro-like self-adhesions were observed between SA and mannose residues, respectively, in ill-defined monolayers. We investigated if and how these adhesions translate when SA and mannose residues are presented in complex N-glycan shields on two pseudo-typed viruses brought together in force spectroscopy (FS). Slime-like adhesions were observed between the shields at higher ramp rates, whereas Velcro-like adhesions were observed at lower rates. The complex glycan shield appears penetrable at the lower ramp rates allowing the adhesion from the mannose core to be accessed; whereas the whole virus appears compressed at higher rates permitting only surface SA adhesions to be sampled. The slime-like and velcro-like adhesions were lost when SA and mannose, respectively, were cleaved with glycosidases. While virus self-adhesion in FS was modulated by glycan penetrability, virus self-aggregation in solution was only determined by the surface sugar. Mannose-terminal viruses self-aggregated in solution, while SA-terminal ones required Ca2+ions to self-aggregate. Viruses with galactose or N-acetylglucosamine surfaces did not self-aggregate, irrespective of whether or not a mannose core was present below the N-acetylglucosamine surface. Well-defined rules appear to govern the self-adhesion and -aggregation of N-glycosylated surfaces, regardless of whether the sugars are presented in ill-defined monolayer, or N-glycan, or even polymer architecture.
Shared safety abolishes the recovery of learned threat
Authors: Pan Yafeng , Olsson Andreas , Golkar Armita
Published: May 2020

Social learning offers an efficient route to transmit information about threat and safety. To better isolate the processes that contribute to the efficacy of social safety learning, we developed a novel dyadic model of associative threat and extinction learning. In three separate social groups, we manipulated whether safety information during extinction was acquired via direct exposure to the conditioned stimulus (CS) in the presence of another individual (Direct exposure), via observation of other’s safety behavior (Vicarious exposure), or via the combination of both (Shared exposure). These groups were contrasted against a fourth group receiving direct CS exposure alone (Asocial exposure). Based on skin conductance responses, we observed that all social groups outperformed asocial learning ininhibitingthe recovery of threat, but only Shared exposureabolishedthreat recovery. These results suggest that social safety learning is optimized by a combination of direct exposure and vicariously transmitted safety signals.

Statement of relevance

Humans, like other social animals, learn about threats and safety in the environment through social cues. Yet, the processes that contribute to the efficacy of social safety learning during threat transmission remain unknown. Here, we used a two-person approach to analyze skin conductance responses as participants engaged in a standard fear conditioning procedure (acquisition, extinction, and reinstatement). We found that during extinction, both (i) direct (conditioned stimulus) exposure in the presence of another individual and (ii) vicarious safety signals alone is sufficient to inhibit subsequent threat recovery, but that abolishing the recovery of conditioned threat responses requires a combination of both. This study has relevance for understanding how social information can optimize standard, asocial safety learning procedures to augment the effects of exposure on previously acquired fears. Thus, our work might help identify psychological and social strategies that can be used to counteract maladaptive fears in humans.
Less Is More: A Mutation in the Chemical Defense Pathway ofErysimum cheiranthoides(Brassicaceae) Reduces Total Cardenolide Abundance but Increases Resistance to Insect Herbivores
Authors: Mirzaei Mahdieh , Züst Tobias , Hastings Amy P. , Agrawal Anurag A. , Jander Georg
Published: May 2020

Many plants produce structurally related defensive metabolites with the same target sites in insect herbivores. Two possible drivers of this chemical diversity are: (i) interacting effects of structurally related compounds increase resistance against individual herbivores, and (ii) variants of the same chemical structures differentially affect diverse herbivore species or feeding guilds.Erysimum cheiranthoidesL (Brassicaceae; wormseed wallflower) produces abundant and diverse cardenolide toxins, which are derived from digitoxigenin, cannogenol, and strophanthidin, all of which inhibit Na+/K+-ATPases in animal cells. Here we describe anE. cheiranthoidesmutant with 66% lower cardenolide content, resulting from greatly decreased cannogenol- and strophanthidin-derived cardenolides, partially compensated for by increases in digitoxigenin-derived cardenolides. This compositional change created a more even cardenolide distribution, decreased the average cardenolide polarity, but did not impact glucosinolates, a different class of chemical defenses. Growth of generalist herbivores from two feeding guilds,Myzus persicaeSulzer (Hemiptera: Aphididae; green peach aphid) andTrichoplusia niHübner (Lepidoptera: Noctuidae; cabbage looper), was decreased on the mutant line compared to wildtype. Both herbivores accumulated cardenolides in proportion to plant content, withT. niaccumulating higher total concentrations thanM. persicae.Helveticoside, an abundant cardenolide inE. cheiranthoides, was absent inM. persicae, suggesting that this compound is not present in the phloem. Our results support the hypothesis that cardenolide diversity protects plants against different herbivores, with digitoxigenin-derived compounds providing better protection against insects likeM. persicaeandT. ni, whereas cannogenol and strophanthidin provide better protection against other herbivores ofE. cheiranthoides.

Funding

This research was funded by US National Science Foundation awards 1907491 to AAA and 1645256 to GJ and AAA, Swiss National Science Foundation grant PZ00P3-161472 to TZ, and a Triad Foundation grant to GJ.
Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding
Authors: Newberry Robert W. , Arhar Taylor , Costello Jean , Hartoularos George C. , Maxwell Alison M. , Naing Zun Zar Chi , Pittman Maureen , Reddy Nishith R. , Schwarz Daniel M. C. , Wassarman Douglas R. , Wu Taia S. , Barrero Daniel , Caggiano Christa , Catching Adam , Cavazos Taylor B. , Estes Laurel S. , Faust Bryan , Fink Elissa A. , Goldman Miriam A. , Gomez Yessica K. , Gordon M. Grace , Gunsalus Laura M. , Hoppe Nick , Jaime-Garza Maru , Johnson Matthew C. , Jones Matthew G. , Kung Andrew F. , Lopez Kyle E. , Lumpe Jared , Martyn Calla , McCarthy Elizabeth E. , Miller-Vedam Lakshmi E. , Navarro Erik J. , Palar Aji , Pellegrino Jenna , Saylor Wren , Stephens Christina A. , Strickland Jack , Torosyan Hayarpi , Wankowicz Stephanie A. , Wong Daniel R. , Wong Garrett , Redding Sy , Chow Eric D. , DeGrado William F. , Kampmann Martin
Published: May 2020

Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteinsin vivoremains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of α-synuclein, a dynamic protein linked to Parkinson’s disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of α-synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to α-synuclein biology and pathobiology. We found that the conformation of α-synuclein previously shown to drive yeast toxicity—an extended, membrane-bound helix—is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress α-synuclein toxicity. Moreover, we find that sequence determinants of α-synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that α-synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.
Regulation of dopamine-dependent transcription and cocaine action byGadd45b
Authors: Zipperly Morgan E. , Sultan Faraz A. , Graham Guan-En , Brane Andrew C. , Simpkins Natalie A. , Ianov Lara , Day Jeremy J.
Published: May 2020

Exposure to drugs of abuse produces robust transcriptional and epigenetic reorganization within brain reward circuits that outlives the direct effects of the drug and may contribute to addiction. DNA methylation is a covalent epigenetic modification that is altered following stimulant exposure and is critical for behavioral and physiological adaptations to drugs of abuse. Although activity-related loss of DNA methylation requires theGadd45(Growth arrest and DNA-damage-inducible) gene family, very little is known about how this family regulates the activity of brain reward circuits or behavioral responses to drugs of abuse. Here, we combined genome-wide transcriptional profiling, pharmacological manipulations, electrophysiological measurements, and CRISPR tools with traditional knockout and behavioral approaches in rodent model systems to dissect the role ofGadd45bin dopamine-dependent epigenetic regulation and cocaine reward. We show that acute cocaine administration induces rapid upregulation ofGadd45bmRNA in the rat nucleus accumbens, and that knockout or site-specific CRISPR/Cas9 gene knockdown ofGadd45bblocks cocaine conditioned place preference.In vitro, dopamine treatment in primary striatal neurons increasesGadd45bmRNA expression through a dopamine receptor type 1 (DRD1)-dependent mechanism. Moreover, shRNA-inducedGadd45bknockdown decreases expression of genes involved in psychostimulant addiction, blocks induction of immediate early genes by DRD1 stimulation, and prevents DRD1-mediated changes in DNA methylation. Finally, we demonstrate thatGadd45bknockdown decreases striatal neuron action potential burst durationin vitro, without altering other electrophysiological characteristics. These results suggest that striatalGadd45bfunctions as a dopamine-induced gene that is necessary for cocaine reward memory and DRD1-mediated transcriptional activity.
Artistoo: build, share, and explore simulations of cells and tissues in the web browser
Authors: Wortel Inge M. N. , Textor Johannes
Published: May 2020

The Cellular Potts Model (CPM) is a powerfulin silicomethod for simulating diverse biological processes at tissue scale. Because of its inherently graphical nature, this model should in theory be accessible to a large audience of biologists – without requiring extensive mathematical expertise. But in practice, CPMs are mostly implemented in specialized frameworks that users need to master before they can run and modify the simulation. We here present Artistoo (Artificial Tissue Toolbox), a JavaScript library for building “explorable” CPM simulations where users can change model parameters and see their effects in real time. Artistoo simulations run directly in the web browser and do not require any third-party software, plugins, or back-end servers. Although implemented in JavaScript, Artistoo does not suffer from a major performance loss compared to frameworks written in C++; it remains sufficiently fast to let users interact with simulations in real time. Artistoo provides an opportunity to unlock CPM models for a broader audience: interactive simulations can be shared through a simple URL in azero-installsetting. We discuss how such model sharing may benefit modelling research, science dissemination, open science, and education.

Availability and Implementation

Artistoo is an open-source library released under the MIT license, and is freely available on GitHub athttps://github.com/ingewortel/artistoo.

Contact

Johannes.Textor@radboudumc.nl
Neuronal AMPK coordinates mitochondrial energy sensing and hypoxia resistance
Authors: Berry Brandon J. , Baldzizhar Aksana , Wojtovich Andrew P.
Published: May 2020

Organisms adapt to their environment through coordinated changes in mitochondrial function and metabolism. The mitochondrial protonmotive force (PMF) is an electrochemical gradient that powers ATP synthesis and adjusts metabolism to energetic demands via cellular signaling. It is unknown how or where transient PMF changes are sensed and signaled due to lack of precise spatiotemporal controlin vivo.We addressed this by expressing a light-activated proton pump in mitochondria to spatiotemporally “turn off” mitochondrial function through PMF dissipation in tissues with light. We applied our construct – mitochondria-OFF (mtOFF) – to understand how metabolic status impacts hypoxia resistance, a response that relies on mitochondrial function. mtOFF activation induced starvation-like behavior mediated by AMP-activated protein kinase (AMPK). We found prophylactic mtOFF activation increased survival following hypoxia, and that protection relied on neuronal AMPK. Our study links spatiotemporal control of mitochondrial PMF to cellular metabolic changes that mediate behavior and stress resistance.
Preterm birth impedes structural and functional development of cerebellar Purkinje cells in the developing baboon cerebellum
Authors: Barron Tara , Kim Jun Hee
Published: May 2020

Human cerebellar development occurs late in gestation and is hindered by preterm birth. The fetal development of Purkinje cells, the primary output cells of the cerebellar cortex, is crucial for the structure and function of the cerebellum. However, morphological and electrophysiological features in Purkinje cells at different gestational ages, and the effects of neonatal intensive care unit (NICU) experience on cerebellar development are unexplored. Utilizing non-human primate baboon cerebellum, we investigated Purkinje cell development during the last trimester of pregnancy and the effect of NICU experience following premature birth on developmental features of Purkinje cells. Immunostaining and whole-cell patch clamp recordings of Purkinje cells in the baboon cerebellum at different gestational ages revealed that molecular layer width, driven by Purkinje dendrite extension, drastically increased and refinement of action potential waveform properties occurred throughout the last trimester of pregnancy. Preterm birth followed by NICU experience for 2 weeks impeded development of Purkinje cells, including action potential waveform properties, synaptic input, and dendrite extension compared with age-matched controls. In addition, these alterations impact Purkinje cell output, reducing the spontaneous firing frequency in deep cerebellar nucleus (DCN) neurons. Taken together, primate cerebellum undergoes developmental refinements during late gestation, and NICU experience following preterm birth alters morphological and physiological features in the cerebellum that can lead to functional deficits.

Summary Statement

Baboon cerebellum undergoes developmental refinements during late gestation, and NICU experience following preterm birth impacts cellular development in the cerebellum that can lead to functional deficits.
Higher-order thalamic implication in the processing of bilateral sensory events
Authors: Castejon Carlos , Nuñez Angel
Published: May 2020

In the rodent whisker system, it is well assumed that VPM and POm encode stimulations of the contralateral whisker pad. However, during tactile exploration whiskers are usually stimulated bilaterally. Accordingly, the integration of tactile information from the two sides of the body seems to be fundamental in the processing of these events. Here, to investigate whether POm could be able to codify these bilateral dynamics, whisker-evoked responses in this thalamic nucleus were examined byin vivoextracellular recordings in anesthetized rats using contralateral and ipsilateral stimuli. Strikingly, we found that POm is also able to respond to tactile stimulation of ipsilateral whiskers. Our findings reveal the implication of POm in the representation of bilateral tactile events by integrating simultaneous signals arising from both whisker pads and demonstrate the implication of the higher-order sensory thalamus in the encoding of bilateral sensory events. This can have important implications in bilateral perceptual function.
Fast and accurate approximation of the joint site frequency spectrum of multiple populations
Authors: Jewett Ethan M.
Published: May 2020

Abstract

The site frequency spectrum (SFS) is a statistic that summarizes the distribution of derived allele frequencies in a sample of DNA sequences. The SFS provides useful information about genetic variation within and among populations and it can used to make population genetic inferences. Methods for computing the SFS based on the diffusion approximation are computationally efficient when computing all terms of the SFS simultaneously and they can handle complicated demographic scenarios. However, in practice it is sometimes only necessary to compute a subset of terms of the SFS, in which case coalescent-based methods can achieve greater computational efficiency. Here, we present simple and accurate approximate formulas for the expected joint SFS for multiple populations connected by migration. Compared with existing exact approaches, our approximate formulas greatly reduce the complexity of computing each entry of the SFS and have simple forms. The computational complexity of our method depends on the index of the entry to be computed, rather than on the sample size, and the accuracy of our approximation improves as the sample size increases.
Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem
Authors: Northrop Amanda C. , Avalone Vanessa , Ellison Aaron M. , Ballif Bryan A. , Gotelli Nicholas J.
Published: May 2020

Incremental increases in a driver variable, such as nutrients or detritus, can trigger abrupt shifts in aquatic ecosys-tems. Once these ecosystems change state, a simple reduction in the driver variable may not return them to their original state. Because of the long time scales involved, we still have a poor understanding of the dynamics of ecosys-tem recovery after a state change. A model system for understanding ecosystem recovery is the aquatic microecosystem that inhabits the cup-shaped leaves of the pitcher plantSarracenia purpurea. With enrichment of organic matter, this system flips within 1 to 3 days from an oxygen-rich state to an oxygen-poor (hypoxic) state. In a replicated green-house experiment, we enriched pitcher plant leaves at different rates with bovine serum albumin (BSA), a molecular substitute for detritus. Changes in dissolved oxygen ([O2]) and undigested BSA concentration were monitored during enrichment and recovery phases. At low enrichment rates, ecosystems showed a substantial lag in the recovery of [O2] (clockwise hysteresis). At intermediate enrichment rates, [O2] tracked the levels of undigested BSA with the same profile during the enrichment and recovery phases (no hysteresis). At high enrichment rates, we observed a novel response: changes in [O2] were proportionally larger during the recovery phase than during the enrichment phase (counter-clockwise hysteresis). These experiments demonstrate that detrital enrichment rate can modulate a diversity of hysteretic responses in a single aquatic ecosystem. With counter-clockwise hysteresis, rapid reduction of a driver variable following high enrichment rates may be a viable restoration strategy.
SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?
Authors: Zhan Shing Hei , Deverman Benjamin E. , Chan Yujia Alina
Published: May 2020

In a side-by-side comparison of evolutionary dynamics between the 2019/2020 SARS-CoV-2 and the 2003 SARS-CoV, we were surprised to find that SARS-CoV-2 resembles SARS-CoV in the late phase of the 2003 epidemic after SARS-CoV had developed several advantageous adaptations for human transmission. Our observations suggest that by the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV. However, no precursors or branches of evolution stemming from a less human-adapted SARS-CoV-2-like virus have been detected. The sudden appearance of a highly infectious SARS-CoV-2 presents a major cause for concern that should motivate stronger international efforts to identify the source and prevent near future re-emergence. Any existing pools of SARS-CoV-2 progenitors would be particularly dangerous if similarly well adapted for human transmission. To look for clues regarding intermediate hosts, we analyze recent key findings relating to how SARS-CoV-2 could have evolved and adapted for human transmission, and examine the environmental samples from the Wuhan Huanan seafood market. Importantly, the market samples are genetically identical to human SARS-CoV-2 isolates and were therefore most likely from human sources. We conclude by describing and advocating for measured and effective approaches implemented in the 2002-2004 SARS outbreaks to identify lingering population(s) of progenitor virus.
RootNet: A Convolutional Neural Networks for Complex Plant Root Phenotyping from High-Definition Datasets
Authors: Yasrab Robail , Pound Michael P , French Andrew P , Pridmore Tony P
Published: May 2020

Plant phenotyping using machine learning and computer vision approaches is a challenging task. Deep learning-based systems for plant phenotyping is more efficient for measuring different plant traits for diverse genetic discoveries compared to the traditional image-based phenotyping approaches. Plant biologists have recently demanded more reliable and accurate image-based phenotyping systems for assessing various features of plants and crops. The core of these image-based phenotyping systems is structural classification and features segmentation. Deep learning-based systems, however, have shown outstanding results in extracting very complicated features and structures of above-ground plants. Nevertheless, the below-ground part of the plant is usually more complicated to analyze due to its complex arrangement and distorted appearance. We proposed a deep convolutional neural networks (CNN) model named “RootNet” that detects and pixel-wise segments plant roots features. The feature of the proposed method is detection and segmentation of very thin (1-3 pixels wide roots). The proposed approach segment high definition images without significantly sacrificing pixel density, it leads to more accurate root type detection and segmentation results. It is hard to train CNNs with high definition images due to GPU memory limitations. The proposed patch-based CNN training setup makes use of the entire image (with maximum pixel desisity) to recognize and segment give root system efficiently. We have used wheat (Triticum aestivum L.) seedlings dataset, which consists of wheat roots grown in visible pouches. The proposed system segments are given root systems and save it to the Root System Markup Language (RSML) for future analysis. RootNet trained on the dataset mentioned above along with popular semantic segmentation architectures, and it achieved a benchmark accuracy.
Impact of sustained TGFβ receptor inhibition on chromatin accessibility and gene expression in cultured human endometrial MSC
Authors: Lucciola Raffaella , Vrljicak Pavle , Filby Caitlin , Darzi Saeedeh , Gurung Shanti , Muter Joanne , Ott Sascha , Brosens Jan J , Gargett Caroline E
Published: May 2020

Endometrial mesenchymal stem cells (eMSC) drive the extraordinary regenerative capacity of the human endometrium. Clinical application of eMSC for therapeutic purposes is hampered by spontaneous differentiation and cellular senescence upon large-scale expansionin vitro. A83-01, a selective transforming growth factor-β receptor (TGFβ-R) inhibitor, promotes pharmacological expansion of eMSC in culture by blocking differentiation and senescence, but the underlying mechanisms are incompletely understood. In this study, we combined RNA-seq and ATAC-seq to study the impact of sustained TGFβ-R inhibition on gene expression and chromatin architecture of eMSC. Treatment of primary eMSC with A83-01 for 5 weeks resulted in differential expression of 1,463 genes. Gene ontology analysis showed enrichment of genes implicated in cell growth whereas extracellular matrix genes and genes involved in cell fate commitment were downregulated. ATAC-seq analysis demonstrated that sustained TGFβ-R inhibition results in opening and closure of 3,555 and 2,412 chromatin loci, respectively. Motif analysis revealed marked enrichment of retinoic acid receptor (RAR) binding sites, which was paralleled by the induction ofRARB, encoding retinoic acid receptor beta (RARβ). Selective RARβ inhibition attenuated proliferation and clonogenicity of A83-01 treated eMSC. Taken together, our study provides new insights into the gene networks and genome-wide chromatin changes that underpin maintenance of an undifferentiated phenotype of eMSC in prolonged culture.

Significance statement

Cycling human endometrium is a rich source of adult stem/progenitor cells that could be exploited for clinical purposes. Small molecules, such as A83-01, that modulate cell identity may open new avenues to maintain the functional properties of eMSC upon expansion in culture. By integrating complementary genome-wide profiling techniques, we mapped the dynamic changes in chromatin landscape and gene expression in response to prolonged A83-01 treatment of eMSC. Our findings provide new insights into the mechanisms of action of TGFβ-R inhibition that may lead to the development of more targeted pharmacological approaches for MSC expansion.
MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R
Authors: Rhodes John A. , Baños Hector , Mitchell Jonathan D. , Allman Elizabeth S.
Published: May 2020

MSCquartetsis an R package for species tree hypothesis testing, inference of species trees, and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package includes the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model.
Computational verification of large logical models – application to the prediction of T cell response to checkpoint inhibitors
Authors: Hernandez Céline , Thomas-Chollier Morgane , Naldi Aurélien , Thieffry Denis
Published: May 2020

At the crossroad between biology and mathematical modelling, computational systems biology can contribute to a mechanistic understanding of high-level biological phenomenon. But as knowledge accumulates, the size and complexity of mathematical models increase, calling for the development of efficient dynamical analysis methods. Here, we propose the use of two approaches for the development and analysis of complex cellular network models.

A first approach, called “model verification” and inspired by unitary testing in software development, enables the formalisation and automated verification of validation criteria for whole models or selected sub-parts. When combined with efficient analysis methods, this approach is suitable for continuous testing, thereby greatly facilitating model development.

A second approach, called “value propagation”, enables efficient analytical computation of the impact of specific environmental or genetic conditions on the dynamical behaviour of some models.

We apply these two approaches to the delineation and the analysis of a comprehensive model for T cell activation, taking into account CTLA4 and PD-1 checkpoint inhibitory pathways. While model verification greatly eases the delineation of logical rules complying with a set of dynamical specifications, propagation provides interesting insights into the different potential of CTLA4 and PD-1 immunotherapies.

Both methods are implemented and made available in the all-inclusive CoLoMoTo Docker image, while the different steps of the model analysis are fully reported in two companion interactive jupyter notebooks, thereby ensuring the reproduction of our results.
PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity
Authors: He Sijia , Waheed Abdul A. , Hetrick Brian , Dabbagh Deemah , Akhrymuk Ivan V. , Kehn-Hall Kylene , Freed Eric O. , Wu Yuntao
Published: May 2020

P-selectin glycoprotein ligand-1 (PSGL-1) is a cell surface glycoprotein that binds to P-, E-, and L-selectins to mediate the tethering and rolling of immune cells on the surface of the endothelium for cell migration into inflamed tissues. PSGL-1 has been identified as an interferon-γ (INF-γ)-regulated factor that restricts HIV-1 infectivity, and has recently been found to possess broad-spectrum antiviral activities. Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks virus attachment and infection of target cells. These findings suggest that PSGL-1 may potentially inhibit coronavirus replication in PSGL-1+cells.
FR-Match: Robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test
Authors: Zhang Yun , Aevermann Brian D. , Bakken Trygve E. , Miller Jeremy A. , Hodge Rebecca D. , Lein Ed S. , Scheuermann Richard H.
Published: May 2020

Single cell/nucleus RNA sequencing (scRNAseq) is emerging as an essential tool to unravel the phenotypic heterogeneity of cells in complex biological systems. While computational methods for scRNAseq cell type clustering have advanced, the ability to integrate datasets to identify common and novel cell types across experiments remains a challenge. Here, we introduce a cluster-to-cluster cell type matching method – FR-Match – that utilizes supervised feature selection for dimensionality reduction and incorporates shared information among cells to determine whether two cell type clusters share the same underlying multivariate gene expression distribution. FR-Match is benchmarked with existing cell-to-cell and cell-to-cluster cell type matching methods using both simulated and real scRNAseq data. FR-Match proved to be a stringent method that produced fewer erroneous matches of distinct cell subtypes and had the unique ability to identify novel cell phenotypes in new datasets.In silicovalidation demonstrated that the proposed workflow is the only self-contained algorithm that was robust to increasing numbers of true negatives (i.e. non-represented cell types). FR-Match was applied to two human brain scRNAseq datasets sampled from cortical layer 1 and full thickness middle temporal gyrus. When mapping cell types identified in specimens isolated from these overlapping human brain regions, FR-Match precisely recapitulated the laminar characteristics of matched cell type clusters, reflecting their distinct neuroanatomical distributions. An R package and Shiny application are provided athttps://github.com/JCVenterInstitute/FRmatchfor users to interactively explore and match scRNAseq cell type clusters with complementary visualization tools.
A novelhemAmutation is responsible for small colony variant phenotype inEscherichia coli
Authors: Hubbard Alasdair T. M. , Roberts Adam P.
Published: May 2020

We identified a small colony variant (SCV) of a clinical isolate ofEscherichia colifrom Malawi following sequentialin vitroselection in sub-inhibitory concentrations of amoxicillin-clavulanic acid and gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) inhemA, which encodes a glutamyl-tRNA reductase responsible for the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed this phenotype was stable over multiple generations and the SNP inhemAresulted in a significant fitness cost to the isolate which persisted even in the presence of hemin. AshemAis not found in mammalian cells, and disruption of the gene results in impaired biofilm formation and a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by biofilm-producingE. coli.