bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of ventral subiculum neuronal ensembles in incubation of oxycodone craving after electric barrier-induced voluntary abstinence
Authors: Fredriksson Ida , Shekara Aniruddha , Applebey Sarah V. , Minier-Toribio Angelica , Altidor Lindsay , Cifani Carlo , Hope Bruce T. , Bossert Jennifer M. , Shaham Yavin
Published: March 2021

We recently developed a rat model of incubation of oxycodone craving where opioid seeking progressively increases after voluntary suppression of drug self-administration by adverse consequences of drug seeking. Here, we studied the role of ventral subiculum (vSub) neuronal ensembles in this incubation, using the activity marker Fos, muscimol-baclofen (GABAergic agonists) inactivation, and Daun02 chemogenetic inactivation.

We trained Sprague-Dawley orFos-lacZtransgenic male and female rats to self-administer oxycodone (0.1 mg/kg/infusion, 6-h/d) for 14 days. The rats were then exposed for 14 days to an electric barrier of increasing intensity (0.1 to 0.4 mA) near the drug-paired lever that caused voluntary abstinence or were exposed to 14 days of forced abstinence. We tested Sprague-Dawley rats for relapse to oxycodone seeking without shock and drug on abstinence day 15 and extracted their brains for Fos-immunohistochemistry, or tested them after vSub vehicle or muscimol-baclofen injections on abstinence days 1 and 15. We performed Daun02 inactivation of relapse-activated vSub Fos neurons in Fos-lacZ transgenic rats on abstinence day 15 and then tested them for relapse on abstinence day 18.

Relapse after electric barrier-induced abstinence increased Fos expression in vSub. Muscimol-baclofen inactivation or Daun02 selective inactivation of vSub Fos-expressing neuronal ensembles decreased “incubated” oxycodone seeking after voluntary abstinence. Muscimol-baclofen vSub inactivation had no effect on non-incubated opioid seeking on abstinence day 1 or incubation after forced abstinence.

Our results demonstrate a selective role of vSub neuronal ensembles in incubation of opioid craving after cessation of drug self-administration by adverse consequences of drug seeking.

Significance statement

High relapse rate is a cardinal feature of opioid addiction and a major impediment for successful treatment. In humans, abstinence is often self-imposed, and relapse typically involves a conflict situation between the desire to experience the drug’s rewarding effects and negative consequences of drug seeking. To mimic this human condition, we recently introduced a rat model of incubation of oxycodone craving after electric barrier-induced voluntary abstinence. Here, we used the activity marker Fos, muscimol-baclofen (GABAergic agonists) inactivation, and Daun02 chemogenetic inactivation to demonstrate a selective role of vSub neuronal ensembles in incubation of oxycodone craving after electric barrier-induced voluntary abstinence, but not in incubation of opioid craving after forced abstinence or non-incubated opioid seeking during early abstinence.
Extracellular Matrix Hydrogels Promote Expression of Muscle-Tendon Junction Proteins
Authors: Gaffney Lewis S. , Davis Zachary G. , Mora-Navarro Camilo , Fisher Matthew B. , Freytes Donald O.
Published: March 2021

Muscle and tendon injuries are prevalent and range from minor sprains and strains to traumatic, debilitating injuries. However, the interactions between these tissues during injury and recovery remain unclear. Three-dimensional tissue models that incorporate both tissues and a physiologically relevant junction between muscle and tendon may help understand how the two tissues interact. Here, we use tissue specific extracellular matrix (ECM) derived from muscle and tendon to determine how cells of each tissue interact with the microenvironment of the opposite tissue resulting in junction specific features. ECM materials were derived from the Achilles tendon and gastrocnemius muscle, decellularized, and processed to form tissue specific pre-hydrogel digests. ECM materials were unique in respect to protein composition and included many types of ECM proteins, not just collagens. After digestion and gelation, ECM hydrogels had similar complex viscosities which were less than type I collagen hydrogels at the same concentration. C2C12 myoblasts and tendon fibroblasts were cultured in tissuespecific ECM conditioned media or encapsulated in tissue-specific ECM hydrogels to determine cell-matrix interactions and the effects on a muscle-tendon junction marker, paxillin. ECM conditioned media had only a minor effect on upregulation of paxillin in cells cultured in monolayer. However, cells cultured within ECM hydrogels had 50-70% higher paxillin expression than cells cultured in type I collagen hydrogels. Contraction of the ECM hydrogels varied by the type of ECM used. Subsequent experiments with varying density of type I collagen (and thus contraction) showed no correlation between paxillin expression and the amount of gel contraction, suggesting that a constituent of the ECM was the driver of paxillin expression in the ECM hydrogels. In addition, the extracellular matrix protein type XXII collagen had similar expression patterns as paxillin, with smaller effect sizes. Using tissue specific ECM allowed for the de-construction of the cell-matrix interactions similar to muscletendon junctions to study the expression of MTJ specific proteins.

Impact Statement

The muscle-tendon junction is an important feature of muscle-tendon units; however, despite crosstalk between the two tissue types, it is overlooked in current research. Deconstructing the cell-matrix interactions will provide the opportunity to study significant junction specific features and markers that should be included in tissue models of the muscletendon unit, while gaining a deeper understanding of the natural junction. This research aims to inform future methods to engineer a more relevant multi-tissue platform to study the muscletendon unit.
Stress is basic: ABA alkalinizes both the xylem sap and the cytosol of Arabidopsis vascular bundle sheath cells by inhibiting their P-type H+-ATPase and stimulating their V-type H+-ATPase
Authors: Torne Tanmayee , Grunwald Yael , Dalal Ahan , Yaaran Adi , Moshelion Menachem , Moran Nava
Published: March 2021

BACKGROUND AND HYPOTHESIS

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Under water deprivation, in many perennial species, the stress hormone, ABA, appears in the xylem sap in the shoot (including leaf) veins and the xylem sap pH (pHEXT) increases. This study aimed to test the hypothesis that ABA is the signal for an altered proton balance of the leaf-vein-enwrapping bundle sheath cells (BSCs).

METHODS

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Plant Material.We used a fewArabidopsis thaliana(L.) Heynh. genotypes: wildtype (WT) of two accessions, Landsbergerecta(Ler) and Columbia (Col), and a few mutants and transformants in these backgrounds.

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H+-Pumps activities.We monitored ABA effects on the H+-pump activities in the BSCs cytosol-delimiting membranes (plasma membrane and tonoplast) by monitoring the cytosol and the xylem pH, and the membrane potential (EM), by imaging the fluorescence of pH- and membrane potential (EM)-reporting probes: (a) the BSCs’ pHEXT– with the ratiometric fluorescent dye FITC-dextran petiole-fed into detached leaves in unbuffered xylem perfusion solution (XPS), (b) the BSCs’ pHCYT– with the ratiometric dye SNARF1 loaded into BSCs isolated protoplasts, and (c) the BSCs’ EM– with the ratiometric dye di- 8-ANEPPS.

RESULTS

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ABA increased the pHEXT; this response was abolished in anabi1-1mutant with impaired signaling via a PP2C (ABI1) and in anaha2-4mutant with knocked-down AHA2;

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ABA depolarized the WT BSCs;

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ABA increased pHCYTirrespective of AHA2 activity (i.e., whether or not AHA was inhibited by vanadate, or in theaha2-4mutant);

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The ABA-induced cytosol alkalinization was abolished in the absence of VHA activity (i.e., when VHA was inhibited by bafilomycin A1, or in thevha-a2 vha-a3double mutant with inactive VHA);

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All these results resemble the ABA effect on GCs;

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In contrast to GCs, AHA2 and not AHA1 is the ABA major target in BSCs;

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Blue light (BL) enabled the response of the BSCs’ VHA to ABA;

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The ABA- and BL-signaling pathways acting on both BSCs’ pumps, AHA2 and VHA, are likely to be BSCs autonomous, based on (a) the presence in the BSCs of many genes of the ABA- and BL-signaling pathways and (b) ABA responses (depolarization and pHCYTelevation) demonstrated under BL in isolated protoplasts.

SIGNIFICANCE STATEMENT

We reveal here an alkalinizing effect of the plant drought-stress hormone ABA on the pH on both sides of the plasmalemma of the vein-enwrapping bundle sheath cells (BSCs), due to ABA inhibition of the BSCs’ AHA2, the plasmalemma H+- ATPase and stimulation of VHA, their vacuolar H+-ATPase. Since pH affects the BSCs’ selective regulation of solute and water fluxes into the leaf, these H+- pumps may be attractive targets for manipulations aiming to improve plant drought response.
Negative effects of agricultural intensification on the food provisioning rate of a declining aerial insectivore
Authors: Garrett Daniel R. , Pelletier Fanie , Garant Dany , Bélisle Marc
Published: March 2021

The historical rise of intensive agricultural practices is hypothesized to be related to declines of grassland and aerial insectivorous birds. Drivers of declines may also influence the overall abundance and spatial distribution of insects within agricultural landscapes. Subsequently, the food provisioning rate of birds breeding within more agro-intensive landscapes may be impacted. Lower provisioning rates in agro-intensive landscapes may lead to reduced growth rate, body condition or fledging success of nestlings but also to diminished body condition of food provisioning adults. Results from a previous study supported this hypothesis as the fledging success and proxies of nestling body condition were lowest for an aerial insectivore breeding in more agro intensive landscapes. Of the multiple hypotheses put forward to explain these correlations, one mechanism may act through variation in food provisioning rates. In this study, we expounded on this hypothesis using data derived from the aforementioned study system and assessed if provisioning rates to nestlings and food provisioning behavior of adults varied across a gradient of agricultural intensification in a declining aerial insectivore, the Tree Swallow (Tachycineta bicolor). We found that the hourly provisioning rate was lower in agro-intensive landscapes, and yet travel distances were longest within less agro-intensive landscapes. Our results highlight that, in order to maximize long term average gain rates, Tree Swallows breeding within agro-intensive landscapes must forage with greater intensity, perhaps at a cost to themselves, or else costs will transfer to growing broods. Our work provides further evidence that agricultural intensification on the breeding grounds can contribute to the declines of aerial insectivores in part through a trophic pathway.
Interhemispheric Connectivity Supports Load-Dependent Working Memory Maintenance for Complex Visual Stimuli
Authors: Plaska Chelsea Reichert , Ortega Jefferson , Gomes Bernard A. , Ellmore Timothy M.
Published: March 2021

A critical manipulation used to study the neural basis of working memory (WM) is to vary the information load at encoding followed by measurements of activity and connectivity during maintenance in the subsequent delay period. The hallmark finding is that delay period activity and connectivity increases between frontal and parietal brain regions as load is increased. Most WM studies, however, employ simple stimuli (e.g., simple shapes or letters) during encoding and utilize unfilled intervals (e.g., a blank screen or fixation cross) during the delays. In the present study, we asked how delay period activity and connectivity change during low and high load maintenance of complex stimuli. Twenty-two participants completed a modified Sternberg WM task with two or five naturalistic scenes as stimuli while scalp EEG was recorded. In each trial, the delay interval was filled with phase scrambled scenes to provide a visual perceptual control with color and spatial frequency similar to the non-scrambled scenes presented during encoding. The results showed that theta and alpha delay activity amplitude was reduced during high compared to low WM load across frontal, central, and parietal sources. Functional connectivity during the delay was assessed by phase-locking value (PLV) and revealed a network with higher connectivity during low WM load consisting of increased PLV between 1) left frontal and right posterior temporal sources in the theta and alpha bands, 2) right anterior temporal and left central sources in the alpha and lower beta bands, and 3) left anterior temporal and posterior temporal sources in the theta, alpha, and lower beta bands. These findings demonstrate a role for interhemispheric connectivity during WM maintenance of complex stimuli. We discuss significance with respect to allocation of limited attentional resources and the filtering of interference.
A folder mechanism ensures size uniformity amongC. elegansindividuals by coupling growth and development
Authors: Towbin Benjamin D. , Grosshans Helge
Published: March 2021

Animals increase by orders of magnitude in their volume during development. Hence, even small differences in the growth rates between individuals could generate large differences in their adult body size. Yet, such volume divergence among individuals is usually not observed in nature.

We combined theory and experiment to understand the mechanisms of body size uniformity. Using live imaging, we measured the volume growth of hundreds of individuals ofC. elegansover the entire span of their postembryonic development. We find thatC. elegansgrows exponentially in volume with a coefficient of variation of the growth rate of ∼7%, but that individuals diverge much less in volume than expected from this heterogeneity. The mechanism counteracting size divergence does not involve size thresholds for developmental milestones. Instead, an inverse coupling of the growth rate and the duration of development produces a constant volume fold change per larval stage.

The duration of larval stages ofC. elegansis determined by the period of a developmental oscillator. Using mathematical modelling, we show that an anti-correlation between the growth rate and the oscillatory period emerges as an intrinsic property of a genetic oscillator. We propose that the robustness of body volume fold change is a hard-wired characteristic of the oscillatory circuit and does not require elaborate mechanisms of size control by cellular signalling. Indeed, the coupling of growth and development was unaltered by mutation of canonical pathways of growth control. This novel concept of size homeostasis may broadly apply to other multicellular systems controlled by genetic oscillators.
minicore: Fast scRNA-seq clustering with various distances
Authors: Baker Daniel N. , Dyjack Nathan , Braverman Vladimir , Hicks Stephanie C. , Langmead Ben
Published: March 2021

Single-cell RNA-sequencing (scRNA-seq) analyses typically begin by clustering a gene-by-cell expression matrix to empirically define groups of cells with similar expression profiles. We describe new methods and a new open source library,minicore, for efficientk-means++ center finding andk-means clustering of scRNA-seq data.Minicoreworks with sparse count data, as it emerges from typical scRNA-seq experiments, as well as with dense data from after dimensionality reduction.Minicore’s novel vectorized weighted reservoir sampling algorithm allows it to find initialk-means++ centers for a 4-million cell dataset in 1.5 minutes using 20 threads.Minicorecan cluster using Euclidean distance, but also supports a wider class of measures like Jensen-Shannon Divergence, Kullback-Leibler Divergence, and the Bhattacharyya distance, which can be directly applied to count data and probability distributions.

Further,minicoreproduces lower-cost centerings more efficiently than scikit-learn for scRNA-seq datasets with millions of cells. With careful handling of priors,minicoreimplements these distance measures with only minor (<2-fold) speed differences among all distances. We show that aminicorepipeline consisting ofk-means++, localsearch++ and minibatchk-means can cluster a 4-million cell dataset in minutes, using less than 10GiB of RAM. This memory-efficiency enables atlas-scale clustering on laptops and other commodity hardware. Finally, we report findings on which distance measures give clusterings that are most consistent with known cell type labels.

Availability

The open source library is athttps://github.com/dnbaker/minicore. Code used for experiments is athttps://github.com/dnbaker/minicore-experiments.
A viral toolbox for conditional and transneuronal gene expression in zebrafish
Authors: Satou Chie , Neve Rachael L. , Oyibo Hassana K. , Zmarz Pawel , Huang Kuo-Hua , Bouldoires Estelle Arn , Mori Takuma , Higashijima Shin-ichi , Keller Georg B. , Friedrich Rainer W.
Published: March 2021

The zebrafish is an important model in systems neuroscience but a key limitation is the lack of viral tools to dissect the structure and function of neuronal circuitry. We developed methods for efficient gene transfer and retrograde tracing in adult and larval zebrafish by herpes simplex viruses (HSV1). HSV1 can be combined with the Gal4/UAS system to target cell types with high spatial, temporal and molecular specificity. We also established methods for efficient transneuronal tracing by modified rabies viruses in zebrafish. We demonstrate that HSV1 and rabies viruses can be used to visualize and manipulate genetically or anatomically identified neurons within and across different brain areas of adult and larval zebrafish. An expandable library of viruses is provided to express fluorescent proteins, calcium indicators, optogenetic probes, toxins and other molecular tools. This toolbox creates new opportunities to interrogate neuronal circuits in zebrafish through combinations of genetic and viral approaches.
Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket ofBurkholderia pseudomalleiDsbA
Authors: Petit Guillaume A. , Mohanty Biswarajan , McMahon Róisín M. , Nebl Stefan , Hilko David H. , Wilde Karyn L. , Scanlon Martin J. , Martin Jennifer L. , Halili Maria A.
Published: March 2021

DiSulfideBond forming proteins (DSB) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide bond protein A (DsbA) catalyzes the formation of disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, we identified two fragments -1(bromophenoxy propanamide) and2(4-methoxy-N-phenylbenzenesulfonamide), that bind to the DsbA from the pathogenic bacteriumBurkholderia pseudomallei, the causative agent of melioidosis. Crystal structures of the oxidizedB. pseudomalleiDsbA (termed BpsDsbA) co-crystallized with1or2suggests that both fragments bind to a hydrophobic pocket that is formed by a change in the side chain orientation of tyrosine 110. This conformational change opens a “cryptic” pocket that is not evident in theapo-protein structure. This binding location was supported by 2D-NMR studies which identified a chemical shift perturbation of the tyrosine 110 backbone amide resonance of more than 0.05 ppm upon addition of 2 mM of fragment1and over 0.04 ppm upon addition of 1 mM of fragment2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (KD) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the modelled crystal structures which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as1and2are not expected to have high binding affinity due to their size and the relatively small surface area that can be involved in intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. Identification of the binding sites of1and2to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.

Synopsis

Describes the binding properties of two drug-like fragments to a conformationally dynamic site in the disulfide-bond forming protein A fromBurkholderia pseudomallei.
Pseudohydrosme bognerisp. nov. (Araceae), a spectacular Critically Endangered (Possibly Extinct) species from Gabon, long confused withAnchomanes nigritianus
Authors: Moxon-Holt Lois , Cheek Martin
Published: March 2021

A Gabonese taxon cultivated for decades in the botanic gardens of Europe asAnchomanes nigritianusis shown to be a new species to science, and on current evidence, is best placed as the fourth species of the Gabonese-centred, poorly known genusPseudohydrosme. Data on the morphological separation betweenAnchomanesandPseudohydrosmeare reviewed. Although phylogenomic studies may show in future that the two genera need to be merged, for the moment their separation is reinforced on morphological grounds.Anchomaneslacks the spathe tube, ovoid-globose, 2 – 4 locular pistil and thick, lobed stigma on a symmetric, stout style that we show to characterise the redelimitedPseudohydrosme. (Anchomaneshas oblong, polygonal, 1-locular pistils, stigmas asymmetric, sessile, thin and disc-like or on asymmetrical conical styles and are pointed or brush-like). In addition,Pseudohydrosme(where known) has stipitate (versus sessile) fruits and on current evidence lacks the lacticifers recorded fromAnchomanes. We test the hypothesis that the taxon is a new species to science, naming it asPseudohydrosme bogneri, and conclude that it is Critically Endangered (Possibly Extinct) using the IUCN 2012 standard.Pseudohydrosme bogneriappears to be the tenth documented probable global extinction of a plant species that has occurred among the narrowly endemic plant species of the Libreville area, Gabon.
Effects of stochasticity on the length and behaviour of ecological transients
Authors: Hastings Alan , Abbott Karen C. , Cuddington Kim , Francis Tessa , Lai Ying-Cheng , Morozov Andrew , Petrovskii Sergei , Zeeman Mary Lou
Published: March 2021

There is a growing recognition that ecological systems can spend extended periods of time far away from an asymptotic state, and that ecological understanding will therefore require a deeper appreciation for how long ecological transients arise. Recent work has defined classes of deterministic mechanisms that can lead to long transients. Given the ubiquity of stochasticity in ecological systems, a similar systematic treatment of transients that includes the influence of stochasticity is important. Stochasticity can of course promote the appearance of transient dynamics by preventing systems from settling permanently near their asymptotic state, but stochasticity also interacts with deterministic features to create qualitatively new dynamics. As such, stochasticity may shorten, extend, or fundamentally change a system’s transient dynamics. Here, we describe a general framework that is developing for understanding the range of possible outcomes when random processes impact the dynamics of ecological systems over realistic time scales. We emphasize that we can understand the ways in which stochasticity can either extend or reduce the lifetime of transients by studying the interactions between the stochastic and deterministic processes present, and we summarize both the current state of knowledge and avenues for future advances.
Exploring Integrated Environmental Viral Surveillance of Indoor Environments: A comparison of surface and bioaerosol environmental sampling in hospital rooms with COVID-19 patients
Authors: Dietz Leslie , Constant David A. , Fretz Mark , Horve Patrick F. , Olsen-Martinez Andreas , Stenson Jason , Wilkes Andrew , Martindale Robert G. , Messer William B. , Van Den Wymelenberg Kevin G.
Published: March 2021

The outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has dramatically transformed policies and practices surrounding public health. One such shift is the expanded emphasis on environmental surveillance for pathogens. Environmental surveillance methods have primarily relied upon wastewater and indoor surface testing, and despite substantial evidence that SARS-CoV-2 commonly travels through space in aerosols, there has been limited indoor air surveillance. This study investigated the effectiveness of integrated surveillance including an active air sampler, surface swabs and passive settling plates to detect SARS-CoV-2 in hospital rooms with COVID-19 patients and compared detection efficacy among sampling methods. The AerosolSense active air sampler was found to detect SARS-CoV-2 in 53.8% of all samples collected compared to 12.1% detection by passive air sampling and 14.8% detection by surface swabs. Approximately 69% of sampled rooms (22/32) returned a positive environmental sample of any type. Among positive rooms, ~32% had only active air samples that returned positive, while ~27% and ~9% had only one or more surface swabs or passive settling plates that returned a positive respectively, and ~32% had more than one sample type that returned a positive result. This study demonstrates the potential for the AerosolSense to detect SARS-CoV-2 RNA in real-world healthcare environments and suggests that integrated sampling that includes active air sampling is an important addition to environmental pathogen surveillance in support of public health.
What multiple Mendelian randomization approaches reveal about obesity and gout
Authors: Adams Charleen D. , Boutwell Brian B.
Published: March 2021

Background/Objectives

Gout is a painful arthritic disease. A robust canon of observational literature suggests strong relationships between obesity, high urate levels, and gout. But findings from observational studies can be fraught with confounding and reverse causation. They can conflict with findings from Mendelian randomization (MR), designed to tackle these biases. We aimed to determine whether the relationships between obesity, higher urate levels, and gout were causal using multiple MR approaches, including an investigation of how other closely related traits, LDL, HDL cholesterol, and triglyceride levels fit into the picture.

Subjects/Methods

Summary results from genome-wide association studies of the five above-mentioned traits were extracted and used to perform two-sample (univariable, multivariable, and two-step) MR and MR mediation analysis.

Results

Obesity increased urate (beta=0.127; 95% CI=0.098, 0.157; P-value=1.2E-17) and triglyceride levels (beta=0.082; 95% CI=0.065, 0.099; P-value=1.2E-21) and decreased HDL cholesterol levels (beta=-0.083; 95% CI=-0.101, −0.065; P-value=2.5E-19). Higher triglyceride levels increased urate levels (beta=0.198; 95% CI=0.146, 0.251; P-value=8.9E-14) and higher HDL levels decreased them (beta=-0.109; 95% CI=-0.148, −0.071; P-value=2.7E-08). Higher urate levels (OR=1.030; 95% CI=1.028, 1.032; P-value=1.1E-130) and obesity caused gout (OR=1.003; 95% CI=1.001, 1.004; P-value=1.3E-04). The mediation MR of obesity on gout with urate levels as a mediator revealed, however, that essentially all of the effect of obesity on gout is mediated through urate. The impact of obesity on LDL cholesterol was null (beta=-0.011; 95% CI=-0.030, 0.008; P-value=2.6E-01), thus it was not included in the multivariable MR. The multivariable MR of obesity, HDL cholesterol, and triglycerides on urate levels revealed that obesity has an effect on urate levels even when accounting for HDL cholesterol and triglyceride levels.

Conclusions

Obesity impacts gout indirectly by influencing urate levels and possibly other traits, such as triglycerides, that increase urate levels. Obesity’s impact on urate is exacerbated by its apparent ability to decrease HDL cholesterol.
Your pleasure is mine; when people share a musical emotional experience during a live music performance in a concert hall
Authors: Chabin Thibault , Gabriel Damien , Comte Alexandre , Haffen Emmanuel , Moulin Thierry , Pazart Lionel
Published: March 2021

Over the years, several publications have proposed that musical sound could be an ancestral emotional way of communication, thus positing an ancestral biological function for music. Understanding how musical emotions, and the pleasure derived from music regardless of the musical valence, can be shared between individuals is a fascinating question, and investigating it can shed light on the function of musical reward. Is the pleasure felt at the individual level transmitted on a collective level? And if so, how? We investigated these questions in a natural setting during an international competition for orchestra conductors. Participants (n=15) used a dedicated smartphone app to report their subjective emotional experiences in real time during a concert. We recorded participant’s electrodermal activity (EDA) and cerebral activity with electroencephalography (EEG). The overall behavioral real time ratings suggest a possible social influence on the reported and felt pleasure. The physically closer the participants, the more similar their reported pleasure. We estimated the inter-individual cerebral coherence, which indicates the degree of mutual cerebral information between pairs of participants in the frequency domain. The results show that when people simultaneously reported either high or low pleasure, their cerebral activities were closer than for simultaneous neutral pleasure reports. Participants’ skin conductance levels were also more coupled when reporting higher emotional degrees simultaneously. More importantly, the participants who were physically closer had higher cerebral coherence, but only when they simultaneously reported intense pleasure. We propose that mechanisms of emotional contagion and/or emotional resonance could explain why a form of ‘emotional connecting force’ could arise between people.
Aberrant glycosylation of anti-SARS-CoV-2 IgG is a pro-thrombotic stimulus for platelets
Authors: Bye Alexander P , Hoepel Willianne , Mitchell Joanne L , Jégouic Sophie , Loureiro Silvia , Sage Tanya , de Taeye Steven , van Gils Marit , Kriek Neline , Cooper Nichola , Jones Ian , den Dunnen Jeroen , Gibbins Jonathan M
Published: March 2021

A subset of patients with COVID-19 become critically ill, suffering from severe respiratory problems and also increased rates of thrombosis. The causes of thrombosis in severely ill COVID-19 patients are still emerging, but the coincidence of critical illness with the timing of the onset of adaptive immunity could implicate an excessive immune response. We hypothesised that platelets might be susceptible to activation by anti-SARS-CoV-2 antibodies and contribute to thrombosis. We found that immune complexes containing recombinant SARS-CoV-2 spike protein and anti-spike IgG enhanced platelet-mediated thrombosis on von Willebrand Factor in vitro, but only when the glycosylation state of the Fc domain was modified to correspond with the aberrant glycosylation previously identified in patients with severe COVID-19. Furthermore, we found that activation was dependent on FcyRIIA and we provide in vitro evidence that this pathogenic platelet activation can be counteracted by therapeutic small molecules R406 (fostamatinib) and ibrutinib that inhibit tyrosine kinases syk and btk respectively or by the P2Y12 antagonist cangrelor.
Improved architectures for flexible DNA production using retrons across kingdoms of life
Authors: Lopez Santiago C. , Crawford Kate D. , Bhattarai-Kline Santi , Shipman Seth L.
Published: March 2021

Exogenous DNA is a critical molecular tool for biology. This is particularly true for gene editing, where exogenous DNA can be used as a template to introduce precise changes to the sequence of a cell’s genome. This DNA is typically synthesized or assembledin vitroand then delivered to target cells. However, delivery can be inefficient, and low abundance of template DNA may be one reason that precise editing typically occurs at a low rate. It has recently been shown that producing DNA inside cells can using reverse transcriptases can increase the efficiency of genome editing. One tool to produce that DNA is a retron, a bacterial retroelement that has an endogenous role in phage defense. However, little effort has been directed at optimizing the retron for production of designed sequences when used as a component of biotechnology. Here, we identify modifications to the retron non-coding RNA that result in more abundant reverse transcribed DNA. We also test architectures of the retron operon that enable efficient reverse transcription across kingdoms of life from bacteria, to yeast, to cultured human cells. We find that gains in DNA production using modified retrons are portable from prokaryotic to eukaryotic cells. Finally, we demonstrate that increased production of RT-DNA results in more efficient genome editing in both prokaryotic and eukaryotic cells. These experiments provide a general framework for production of DNA using a retron for biotechnological applications.
Apparent sunk cost effect in rational agents
Authors: Ott Torben , Masset Paul , Gouvêa Thiago S. , Kepecs Adam
Published: March 2021

Rational decision makers aim to maximize their gains, but humans and other animals often fail to do so, exhibiting biases and distortions in their choice behavior. In a recent study of economic decisions, humans, mice, and rats have been reported to succumb to the sunk cost fallacy, making decisions based on irrecoverable past investments in detriment of expected future returns. We challenge this interpretation because it is subject to a statistical fallacy, a form of attrition bias, and the observed behavior can be explained without invoking a sunk cost-dependent mechanism. Using a computational model, we illustrate how a rational decision maker with a reward-maximizing decision strategy reproduces the reported behavioral pattern and propose an improved task design to dissociate sunk costs from fluctuations in decision valuation. Similar statistical confounds may be common in analyses of cognitive behaviors, highlighting the need to use causal statistical inference and generative models for interpretation.
Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts
Authors: Suda Kojiro , Moriyama Yohsuke , Masukagami Yumiko , Razali Nurhanani Binti , Chiu Yatzu , Nishimura Koutarou , Barbee Hunter , Takase Hiroshi , Sugiyama Shinju , Sato Yoshikatsu , Higashiyama Tetsuya , Johmura Yoshikazu , Nakanishi Makoto , Kono Keiko
Published: March 2021

Plasma membrane damage (PMD) occurs in all cell types due to environmental perturbation and cell-autonomous activities. However, cellular outcomes of PMD remain largely unknown except for recovery or death. Here, using budding yeast and normal human fibroblasts, we show that cellular senescence, irreversible cell cycle arrest contributing to organismal aging, is the long-term outcome of PMD. To identify the genes essential for PMD response, we developed a simple PMD-damaging assay using a detergent and performed a systematic yeast genome-wide screen. The screen identified 48 genes. The top hits in the screen are the endosomal sorting complexes required for transport (ESCRT) genes, encoding the well-described plasma membrane repair proteins in eukaryotes. Unexpectedly, the replicative lifespan regulator genes are enriched in our 48 hits. This finding suggests a close genetic association between the PMD response and the replicative lifespan regulations. Indeed, we show that PMD limits the replicative lifespan in budding yeast; the ESCRT activator AAA-ATPaseVPS4-overexpression extends it. These results suggest that PMD limits replicative lifespan in budding yeast. Moreover, in normal human fibroblasts, we find that PMD induces premature senescence via the Ca2+-p53 axis but not the major senescence pathway, ATM/ATR pathway. Consistent with the results in yeast, transient overexpression of ESCRT-III, CHMP4B, suppressed the PMD-dependent senescence in normal human fibroblasts. Our study proposes that PMD limits cellular lifespan in two different eukaryotic cell types and highlights an underappreciated but ubiquitous senescent cell subtype, namely PMD-dependent senescent cells.
Cross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics
Authors: Ihling Christian H. , Piersimoni Lolita , Kipping Marc , Sinz Andrea
Published: March 2021

The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) Bovine serum albumin, (ii)E. coliribosome, and (iii) HEK293T cell nuclear lysates. We identified a total of 508 unique cross-linking sites for BSA, 868 for theE. coliribosome, and 1,623 unique cross-links for nuclear lysates, corresponding to 1,088 intra- and 535 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving 3D-structures of single proteins, but also for performing system-wide protein interaction studies.

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The anthropometric and physical qualities of women’s rugby league Super League and international players; identifying differences in playing position and standard
Authors: Scantlebury Sean , McCormack Sam , Sawczuk Thomas , Emmonds Stacey , Collins Neil , Beech Jake , Ramirez Carlos , Owen Cameron , Jones Ben
Published: March 2021

Participation in women’s rugby league has been growing since the foundation of the English women’s rugby league Super League in 2017. However, the evidence base to inform women’s rugby league remains sparse. This study provides the largest quantification of anthropometric and physical qualities of women’s rugby league players to date, identifying differences between positions (forwards & backs) and playing standard (Women’s Super League [WSL] vs. International). The height, weight, body composition, lower body strength, jump height, speed and aerobic capacity of 207 players were quantified during the pre-season period. Linear mixed models and effects sizes were used to determine differences between positions and standards. Forwards were significantly (p < 0.05) heavier (forwards: 82.5 ± 14.8kg; backs: 67.7 ± 9.2kg) and have a greater body fat % (forwards: 37.7 ± 6.9%; backs: 30.4 ± 6.3%) than backs. Backs had significantly greater lower body power measured via jump height (forwards: 23.5 ± 4.4cm; backs: 27.6 ± 4.9cm), speed over 10m (forwards: 2.12 ± 0.14s; backs: 1.98 ± 0.11s), 20m (forwards: 3.71 ± 0.27s; backs: 3.46 ± 0.20s), 30m (forwards: 5.29 ± 0.41s; backs: 4.90 ± 0.33s), 40m (forwards: 6.91 ± 0.61s; backs: 6.33 ± 0.46s) and aerobic capacity (forwards: 453.4 ± 258.8m; backs: 665.0 ± 298.2m) than forwards. Additionally, international players were found to have greater anthropometric and physical qualities in comparison to their WSL counterparts. This study adds to the limited evidence base surrounding the anthropometric and physical qualities of elite women’s rugby league players. Comparative values for anthropometric and physical qualities are provided which practitioners may use to evaluate the strengths and weaknesses of players, informing training programs to prepare players for the demands of women’s rugby league.
STRESS, an automated geometrical characterization of deformable particles forin vivomeasurements of cell and tissue mechanical stresses
Authors: Gross Ben , Shelton Elijah , Gomez Carlos , Campàs Otger
Published: March 2021

From cellular mechanotransduction to the formation of embryonic tissues and organs, mechanics has been shown to play an important role in the control of cell behavior and embryonic development. Most of our existing knowledge of how mechanics affects cell behavior comes fromin vitrostudies, mainly because measuring cell and tissue mechanics in 3D multicellular systems, and especiallyin vivo, remains challenging. Oil microdroplet sensors, and more recently gel microbeads, use surface deformations to directly quantify mechanical stresses within developing tissues,in vivoandin situ, as well as in 3Din vitrosystems like organoids or multicellular spheroids. However, an automated analysis software able to quantify the spatiotemporal evolution of stresses and their characteristics from particle deformations is lacking. Here we develop STRESS (Surface Topography Reconstruction for Evaluation of Spatiotemporal Stresses), an analysis software to quantify the geometry of deformable particles of spherical topology, such as microdroplets or gel microbeads, that enables the automatic quantification of the temporal evolution of stresses in the system and the spatiotemporal features of stress inhomogeneities in the tissue. As a test case, we apply these new code to measure the temporal evolution of mechanical stresses using oil microdroplets in developing zebrafish tissues. Starting from a 3D timelapse of a droplet, the software automatically calculates the statistics of local anisotropic stresses, decouples the deformation modes associated with tissue- and cell-scale stresses, obtains their spatial features on the droplet surface and analyzes their spatiotemporal variations using spatial and temporal stress autocorrelations. The automated nature of the analysis will help users obtain quantitative information about mechanical stresses in a wide range of 3D multicellular systems, from developing embryos or tissue explants to organoids.

Author summary

The measurement of mechanical stresses in 3D multicellular systems, such as living tissues, has been very challenging because of a lack in technologies for this purpose. Novel microdroplet techniques enable direct, quantitativein situmeasurements of mechanical stresses in these systems. However, computational tools to obtain mechanical stresses from 3D images of microdroplets in an automated and accurate manner are lacking. Here we develop STRESS, an automated analysis software to analyze the spatiotemporal characteristics of mechanical stresses from microdroplet deformations in a wide range of systems, from living embryonic tissues and tissue explants to organoids and multicellular spheroids.
Low-cost drug discovery with engineeredE. colireveals an anti-mycobacterial activity of benazepril
Authors: Bongaerts Nadine , Edoo Zainab , Abukar Ayan A. , Song Xiaohu , Sosa Carrillo Sebastián , Lindner Ariel B. , Wintermute Edwin H.
Published: March 2021

Whole-cell screening forMycobacterium tuberculosis(Mtb) inhibitors is complicated by the pathogen’s slow growth and biocontainment requirements. Here we present a synthetic biology framework for assayingMtbdrug targets in engineeredE. coli. We construct Target Essential SurrogateE. coli(TESEC) in which an essential metabolic enzyme is deleted and replaced with anMtb-derived functional analog, linking bacterial growth to the activity of the target enzyme. High throughput screening of a TESEC model forMtbalanine racemase (ALR) revealed benazepril as a targeted inhibitor. In vitro biochemical assays indicated a noncompetitive mechanism unlike that of clinical ALR inhibitors. This is the first report of an antimicrobial activity in an approved Angiotensin Converting Enzyme (ACE) inhibitor and may explain clinical data associating use of ACE inhibitors with reducedMtbinfection risk. We establish the scalability of TESEC for drug discovery by characterizing TESEC strains for four additional targets.

SIGNIFICANCE STATEMENT

The challenge of discovering new antibiotics is both scientific and economic. No simple test can determine if a given molecule will be safe and effective in real human patients. Many drug candidates must therefore be advanced for each new antibiotic that reaches the market - a risky and expensive process.

In this work we use synthetic biology to engineer the common laboratory model bacteriumE. colias a tool for early stage antibiotic discovery. As a proof of concept we expressed a known tuberculosis drug target and found a novel inhibitor: benazepril.

Many other drug targets could be screened similarly using the system that we describe. BecauseE. colican be grown safely and cheaply, this approach may help to reduce costs and make drug discovery more accessible.
RNA chaperones Hfq and ProQ play a key role in the virulence of the plant pathogenic bacteriumDickeya dadantii
Authors: Leonard Simon , Villard Camille , Nasser William , Reverchon Sylvie , Hommais Florence
Published: March 2021

Dickeya dadantiiis an important pathogenic bacterium that infects a number of crops including potato and chicory. While extensive works have been carried out on the control of the transcription of its genes encoding the main virulence functions, little information is available on the post-transcriptional regulation of these functions. We investigated the involvement of the RNA chaperones Hfq and ProQ in the production of the mainD. dadantiivirulence functions. Phenotypic assays on thehfqandproQmutants showed that inactivation ofhfqresulted in a growth defect, a modified capacity for biofilm formation and strongly reduced motility, and in the production of degradative extracellular enzymes (proteases, cellulase and pectate lyases). Accordingly, thehfqmutant failed to cause soft rot on chicory leaves. TheproQmutant had reduced resistance to osmotic stress, reduced extracellular pectate lyase activity compared to the wild-type strain, and reduced virulence on chicory leaves. Most of the phenotypes of thehfqandproQmutants were related to the low amounts of mRNA of the corresponding virulence factors. Complementation of the double mutanthfq-proQby each individual protein and cross-complementation of each chaperone suggested that they might exert their effects via partially overlapping but different sets of targets. Overall, it clearly appeared that the two Hfq and ProQ RNA chaperones are important regulators of pathogenicity inD. dadantii. This underscores that virulence genes are regulated post transcriptionally by non-coding RNAs.
Differential viral RNA methylation contributes to pathogen blocking inWolbachia-colonized arthropods
Authors: Bhattacharya Tamanash , Yan Liewei , Zaher Hani , Newton Irene L.G. , Hardy Richard W.
Published: March 2021

Arthropod endosymbiontWolbachia pipientisis part of a global biocontrol strategy to reduce the replication of mosquito-borne RNA viruses such as alphaviruses. We previously demonstrated the importance of a host cytosine methyltransferase, DNMT2, inDrosophilaand viral RNA as a cellular target during pathogen-blocking. Here we report on the role of DNMT2 inWolbachia-induced alphavirus inhibition inAedesspecies. Expression of DNMT2 in mosquito tissues, including the salivary glands, is elevated upon virus infection. Notably, this is suppressed inWolbachia-colonizedanimals, coincident with reduced virus replication and decreased infectivity of progeny virus. Ectopic expression of DNMT2 in culturedAedescells is proviral, increasing progeny virus infectivity, and this effect of DNMT2 on virus replication and infectivity is dependent on its methyltransferase activity. Finally, examining the effects ofWolbachiaon modifications of viral RNA by LC-MS show a decrease in the amount of 5-methylcytosine modification consistent with the down-regulation of DNMT2 inWolbachiacolonized mosquito cells and animals. Collectively, our findings support the conclusion that disruption of 5-methylcytosine modification of viral RNA is a vital mechanism operative in pathogen blocking. These data also emphasize the essential role of epitranscriptomic modifications in regulating fundamental alphavirus replication and transmission processes.