bluuebunny/crossref_metadata_2025_split huggingface dataset:
Femtosecond laser microdissection isolating regeneratingC. elegansneurons for single cell RNA sequencing
Authors: Zhao Peisen , Martin Chris , Ma Ke-Yue , Jiang Ning , Ben-Yakar Adela 
Published: January 2021

AbstractOur understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single neuron resolution in small model organisms such asCaenorhabditis elegans. Existing cell isolation techniques cannot isolate regenerating neurons from the nematode. We present femtosecond laser microdissection (fs-LM), a new single cell isolation method that dissects intact cells directly from living tissue by leveraging the micron-scale precision of fs-laser ablation. We show that fs-LM facilitated sensitive and specific gene expression profiling by single cell RNA-sequencing, while mitigating the stress related transcriptional artifacts induced by tissue dissociation. Single cell RNA-sequencing of fs-LM isolated regeneratingC. elegansneurons revealed transcriptional program leading to successful regeneration in wild-type animals or regeneration failure in animals lacking DLK-1/p38 kinase. The ability of fs-LM to isolate specific neurons based on phenotype of interest allowed us to study the molecular basis of regeneration heterogeneity displayed by neurons of the same type. We identified gene modules whose expression patterns were correlated with axon regrowth rate at a single neuron level. Our results establish fs-LM as a highly specific single cell isolation method ideal for precision and phenotype-driven studies.
Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation
Authors: Cholico Giovan N. , Fling Russ R. , Zacharewski Nicholas A. , Fader Kelly A. , Nault Rance , Zacharewski Tim 
Published: January 2021

ABSTRACT2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a persistent environmental contaminant, induces steatosis by increasing hepatic uptake of dietary and mobilized peripheral fats, inhibiting lipoprotein export, and repressing β-oxidation. In this study, the mechanism of β-oxidation inhibition was investigated by testing the hypothesis that TCDD dose-dependently repressed straight-chain fatty acid oxidation gene expression in mice following oral gavage every 4 days for 28 days. Untargeted metabolomic analysis revealed a dose-dependent decrease in hepatic acyl-CoA levels, while octenoyl-CoA and dicarboxylic acid levels increased. TCDD also dose-dependently repressed the hepatic gene expression associated with triacylglycerol and cholesterol ester hydrolysis, fatty acid binding proteins, fatty acid activation, and 3-ketoacyl-CoA thiolysis while inducing acyl-CoA hydrolysis. Moreover, octenoyl-CoA blocked the hydration of crotonyl-CoA suggesting short chain enoyl-CoA hydratase (ECHS1) activity was inhibited. Collectively, the integration of metabolomics and RNA-seq data suggested TCDD induced a futile cycle of fatty acid activation and acyl-CoA hydrolysis resulting in incomplete β-oxidation, and the accumulation octenoyl-CoA levels that inhibited the activity of short chain enoyl-CoA hydratase (ECHS1).
Species ecology explains the various spatial components of genetic diversity in tropical reef fishes
Authors: Donati Giulia Francesca Azzurra , Zemp Niklaus , Manel Stéphanie , Poirier Maude , Claverie Thomas , Ferraton Franck , Gaboriau Théo , Govinden Rodney , Hagen Oskar , Ibrahim Shameel , Mouillot David , Leblond Julien , Julius Pagu , Velez Laure , Zareer Irthisham , Ziyad Adam , Leprieur Fabien , Albouy Camille , Pellissier Loïc 
Published: January 2021

ABSTRACTIntraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between theα, βandγcomponents of genetic diversity, which we subsequently link to six ecological traits. In contrast to what is expected by the neutral theory of molecular evolution, we find that theαandγcomponents of genetic diversity are negatively associated with species abundance, which can be explained by larger variance in reproductive success in large populations and/or higher introgression in less frequent species. Pelagic larval duration, an important dispersal trait in marine fishes, is found to be negatively related to geneticβdiversity, as expected by theory. We conclude that the neutral theory of molecular evolution may not be sufficient to explain genetic diversity in tropical reef fishes and that additional processes influence those relationships.
1-Deoxysphingolipids Tempt Autophagy Resulting in Lysosomal Lipid Substrate Accumulation: Tracing the Impact of 1-Deoxysphingolipids on Ultra-Structural Level using a Novel Click-Chemistry Detection
Authors: Lamberz Christian , Hesse Marina , Kirfel Gregor 
Published: January 2021

SUMMARYSphingolipids (SLs) are pivotal components of biological membranes essentially contributing to their physiological functions. 1-deoxysphingolipids (deoxySLs), an atypical cytotoxic acting sub-class of SLs, is relevant for cellular energy homeostasis and is known to be connected to neurodegenerative disorders including diabetic neuropathy and hereditary sensory neuropathy type 1 (HSAN1). High levels of deoxySLs affect lipid membrane integrity in artificial liposomes. Accordingly, recent reports questioned the impact of deoxySLs on physiological lipid membrane and organelle functions leading to impaired cellular energy homeostasis.However, DeoxySL-related structural effects on cell membranes resulting in organelle dysfunction are still obscure. To illuminate disease-relevant sub-cellular targets of deoxySLs, we traced alkyne-containing 1-deoxysphinganine (alkyne-DOXSA) and resulting metabolites on ultra-structural level using a new labeling approach for electron microscopy (EM) termed “Golden-Click-Method” (GCM). To complement high-resolution analysis with membrane dynamics, selected intracellular compartments were traced using fluorescent live dyes.Our results conclusively linked accumulating cytotoxic deoxySLs with mitochondria and endoplasmic reticulum (ER) damage triggering Autophagy of mitochondria and membrane cisterna of the ER. The induced autophagic flux ultimately leads to accumulating deoxySL containing intra-lysosomal lipid crystals. Lysosomal lipid substrate accumulation impaired physiological lysosome functions and caused cellular starvation. Lysosomal exocytosis appeared as a mechanism for cellular clearance of cytotoxic deoxySLs. In sum, our data define new ultra-structural targets of deoxySLs and link membrane damage to autophagy and abnormal lysosomal lipid accumulation. These insights may support new conclusions about diabetes type 2 and HSNA1 related tissue damage.
NKCC1 modulates microglial phenotype, cerebral inflammatory responses and brain injury in a cell-autonomous manner
Authors: Tóth Krisztina , Lénárt Nikolett , Berki Péter , Fekete Rebeka , Szabadits Eszter , Pósfai Balázs , Cserép Csaba , Alatshan Ahmad , Benkő Szilvia , Kiss Dániel , Hübner Christian A. , Gulyás Attila , Kaila Kai , Környei Zsuzsanna , Dénes Ádám 
Published: January 2021

AbstractThe NKCC1 ion transporter contributes to the pathophysiology of common neurological disorders, but its function in microglia, the main inflammatory cells of the brain, has remained unclear to date. Therefore, we generated a novel transgenic mouse line in which microglial NKCC1 was deleted. We show that microglial NKCC1 shapes both baseline and reactive microglia morphology, process recruitment to the site of injury, and adaptation to osmotic stress in a cell-autonomous manner via regulating membrane potential and chloride fluxes. In addition, microglial NKCC1 deficiency results in increased expression of the D subunit of volume regulated anion channel (VRAC), NLRP3 inflammasome priming and production of interleukin-1β (IL-1β), rendering microglia prone to exaggerated inflammatory responses. In line with this, central (intracortical) administration of the NKCC1 blocker, bumetanide, potentiated intracortical lipopolysaccharide (LPS)-induced cytokine levels, whereas systemic bumetanide application decreased inflammation in the brain. Microglial NKCC1 KO animals exposed to experimental stroke showed significantly increased brain injury, inflammation, cerebral edema and worse neurological outcome. Thus, NKCC1 emerges as an important player in controlling microglial ion homeostasis and inflammatory responses through which microglia modulate brain injury. The contribution of microglia to central NKCC1 actions is likely to be relevant for common neurological disorders.
The effects of long-term exercise training on the neural control of walking
Authors: Yaserifar Morteza , Fallah Mohammadi Ziya , Esmaiel Hosseininejad Sayed , Paeen Afrakoti Iman Esmaili , Meijer Kenneth , Boonstra Tjeerd W. 
Published: January 2021

AbstractHow does long-term training modify the neural control of walking? Here we investigate changes in kinematics and muscle synergies of the lower extremities in 10 soccer players and 10 non-athletes while they walked with eyes open or closed either overground or on a treadmill. Electromyography (EMG) was acquired from eight muscles of the right leg and foot switch data were recorded to extract temporal gait parameters. Muscle synergies were extracted using non-negative matrix factorisation for each participant and condition separately and were then grouped using k-means clustering. We found that both the cycle and stance duration were longer during treadmill walking compared to overground walking, whereas the swing phase was longer during the eyes-open compare to the eyes-closed condition. On average, more synergies were expressed in the athlete compared to the non-athlete group and during treadmill compared to overground walking. We found that synergy 2 involved in ankle plantarflexion was more often activated in athletes than in non-athletes. We did not find statistical group differences for the synergy metrics but several differences were observed between conditions: peak activation of synergy 5 (VM and VL muscles) increased during overground walking compared to treadmill walking. In addition, reduced activation of synergy 3 (TA muscle) and synergy 4 was observed during eyes-closed compared to eyes-open walking. These findings suggest that during walking long-term training results in greater flexibility of muscle coordination by recruiting additional synergies, but we found no evidence that long-term training affects the activation patterns of these synergies.
Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+channels
Authors: Stevens Sharon R. , Longley Colleen M. , Ogawa Yuki , Teliska Lindsay H. , Arumanayagam Anithachristy S. , Nair Supna , Oses-Prieto Juan A. , Burlingame Alma L. , Cykowski Matthew D. , Xue Mingshan , Rasband Matthew N. 
Published: January 2021

ABSTRACTNeuronal ankyrins cluster and link membrane proteins to the actin and spectrin-based cytoskeleton. Among the three vertebrate ankyrins, little is known about neuronal Ankyrin-R (AnkR). We report AnkR is highly enriched in Pv+fast-spiking interneurons in mouse and human. We identify AnkR-associated protein complexes including cytoskeletal proteins, cell adhesion molecules (CAMs), and perineuronal nets (PNNs). We show that loss of AnkR from forebrain interneurons reduces and disrupts PNNs, decreases anxiety-like behaviors, and changes the intrinsic excitability and firing properties of Pv+fast-spiking interneurons. These changes are accompanied by a dramatic reduction in Kv3.1b K+channels. We identify a novel AnkR-binding motif in Kv3.1b, and show that AnkR is both necessary and sufficient for Kv3.1b membrane localization in interneurons and at nodes of Ranvier. Thus, AnkR regulates Pv+fast-spiking interneuron function by organizing ion channels, CAMs, and PNNs, and linking these to the underlyingβ1 spectrin-based cytoskeleton.
Nef dimerization defect abrogates HIV viremia and associated immune dysregulation in the Bone Marrow-Liver-Thymus-Spleen (BLTS) humanized mouse model
Authors: Biradar Shivkumar , Agarwal Yash , Das Antu , Shu Sherry T. , Samal Jasmine , Ho Sara , Beatty Cole , Castronova Isabella , Mailliard Robbie B. , Smithgall Thomas E. , Bility Moses T. 
Published: January 2021

AbstractLoss of function mutations in the human immunodeficiency virus (HIV) negative factor (Nef) gene are associated with reduced viremia, robust T cell immune responses, and delayed acquired immunodeficiency syndrome (AIDS) progression in humans.In vitrostudies have shown that mutations in the Nef dimerization interface significantly attenuate viral replication and impair host defense. However,in vivo, mechanistic studies on the role of Nef dimerization in HIV infection are lacking. Humanized rodents with human immune cells are robust platforms for investigating the interactions between HIV and the human immune system. The bone marrow-liver-thymus-spleen (BLTS) humanized mouse model carries human immune cells and lymphoid tissues that facilitate anti-viral immune responses. Here, we employed the BLTS-humanized mouse model to demonstrate that preventing Nef dimerization abrogates HIV viremia and the associated immune dysregulation. This suggests that Nef dimerization may be a therapeutic target for future HIV cure strategies.
An exploratory study on the role of the stiffness of breast cancer cells in their detachment from spheroids and migration in 3D collagen matrices
Authors: Higgins Ghodeejah , Kim Jessica E. , Ferruzzi Jacopo , Abdalrahman Tamer , Franz Thomas , Zaman Muhammad H. 
Published: January 2021

AbstractBackgroundTumour-cell detachment is a critical early event in the metastatic cascade. However, the role of the cell’s mechanical properties in detachment and migration is not well understood. This exploratory study aimed to assess how intracellular stiffness changes these processes.MethodsMDA-MB-231 cells were embedded as 10,000-cell spheroids in 2 and 4 mg/ml collagen matrices. Intracellular stiffness was assessed with mitochondria tracking microrheology of cells that migrated distances equivalent to four and six times the cell diameter (dC) from the spheroid and compared to cells at the spheroid surface (0dC), representing medium, high and no migration, respectively.Results and discussionThe mitochondrial mean square displacement and intracellular stiffness decreased during detachment and migration for both collagen concentrations (i.e. rigidities). The mean square displacement of 4dCand 6dCcells was similar, whereas cell stiffness was lower for 4dCthan for 6dCcells. With increasing matrix rigidity, the intracellular stiffness decreased for 0dCcells and did not change for 4dCand 6dCcells. It is proposed that decreased cell stiffness drives detachment and migration and increased matrix rigidity physically hinders migration, and cells need to become softer or remodel the environment to migrate. The independence of the stiffness of migrated cells from matrix rigidity suggests that cells remodel their environment through matrix proteins cleavage to migrate.ConclusionsThe study revealed the collective effects of enhanced migratory conditions and increased matrix rigidity on the mechanical properties of the cells. The expression of matrix metalloproteinases and transforming growth factor β and the role of cell volume on detachment and migration in matrices with varying pore sizes are proposed targets for further studies on metastatic cancer cells.
Development and validation of a predictive model for critical illness in adult patients requiring hospitalization for COVID-19
Authors: Paranjape Neha , Staples Lauren L , Stradwick Christina Y , Ray Herman Gene , Saldanha Ian J. 
Published: January 2021

ABSTRACTBackgroundIdentifying factors that can predict severe disease in patients needing hospitalization for COVID-19 is crucial for early recognition of patients at greatest risk.Objective1) Identify factors predicting intensive care unit (ICU) transfer and (2) develop a simple calculator for clinicians managing patients hospitalized with COVID-19.MethodsA total of 2,685 patients with laboratory-confirmed COVID-19 admitted to a large metropolitan health system in Georgia, USA between March and July 2020 were included in the study. Seventy-five percent of patients were included in the training dataset (admitted March 1 to July 10). Through multivariable logistic regression, we developed a prediction model (probability score) for ICU transfer. Then, we validated the model by estimating its performance accuracy (area under the curve [AUC]) using data from the remaining 25% of patients (admitted July 11 to July 31).ResultsWe included 2,014 and 671 patients in the training and validation datasets, respectively. Diabetes mellitus, coronary artery disease, chronic kidney disease, serum C-reactive protein, and serum lactate dehydrogenase were identified as significant risk factors for ICU transfer, and a prediction model was developed. The AUC was 0.752 for the training dataset and 0.769 for the validation dataset. We developed a free, web-based calculator to facilitate use of the prediction model (https://icucovid19.shinyapps.io/ICUCOVID19/).ConclusionOur validated, simple, and accessible prediction model and web-based calculator for ICU transfer may be useful in assisting healthcare providers in identifying hospitalized patients with COVID-19, who are at high risk for clinical deterioration.Triage of such patients for early aggressive treatment can impact clinical outcomes for this potentially deadly disease.
Eagle fatalities are reduced by automated curtailment of wind turbines
Authors: McClure Christopher J. W. , Rolek Brian W. , Dunn Leah , McCabe Jennifer D. , Martinson Luke , Katzner Todd 
Published: January 2021

Abstract

Collision‐caused fatalities of animals at wind power facilities create a ‘green versus green’ conflict between wildlife conservation and renewable energy. These fatalities can be mitigated via informed curtailment whereby turbines are slowed or stopped when wildlife are considered at increased risk of collision. Automated monitoring systems could improve efficacy of informed curtailment, yet such technology is undertested.

We test the efficacy of an automated curtailment system—a camera system that detects flying objects, classifies them and decides whether to curtail individual turbines to avoid potential collision—in reducing counts of fatalities of eagles, at Top of the World Windpower Facility (hereafter, the treatment site) in Wyoming, USA. We perform a before–after–control–impact study, comparing the number of eagle fatalities observed at the treatment site with those at a nearby (15 km) control site without automated curtailment, both before and after the implementation of automated curtailment at the treatment site.

After correcting for carcass detection probability and scaling fatality estimates to turbine‐years, we estimate that the number of fatalities at the treatment site declined by 63% (95% CI = 59%–66%) between before and after periods while increasing at the control site by 113% (51%–218%). In total, there was an 82% (75%–89%) reduction in the fatality rate at the treatment site relative to the control site.

Synthesis and applications. Automated curtailment of wind turbine operation substantially reduced eagle fatalities. This technology therefore has the potential to lessen the conflict between wind energy and raptor conservation. Although automated curtailment reduced fatalities, they were not fully eliminated. Therefore, automated curtailment, as implemented here, is not a panacea and its efficacy could be improved if considered in conjunction with other mitigation actions.
Effect of papaverine on developmental hyperserotonemia induced autism spectrum disorder related behavioural phenotypes by altering markers of neuronal function, inflammation, and oxidative stress in rats
Authors: Luhach Kanishk , Kulkarni Giriraj T. , Singh Vijay P. , Sharma Bhupesh 
Published: January 2021

AbstractHyperserotonemia, in the early developmental phase, generates a variety of behavioural and biochemical phenotypes associated with autism spectrum disorder (ASD) in rats. Papaverine is known to provide benefits in various brain conditions. We investigated the role of a selective phosphodiesterase‐10A (PDE10A) inhibitor, papaverine on ASD related behavioural phenotypes (social behaviour deficits, repetitive behaviour, anxiety and hyperlocomotion) in developmental hyperserotonemia (DHS) rat model. Also, effects on important biochemical markers related with neuronal function (brain‐derived neurotrophic factor (BDNF)‐neuronal survival and phosphorylated‐cAMP response element binding protein (pCREB)‐neuronal transcription factor), brain inflammation (interleukin (IL)‐6, IL‐10 and tumour necrosis factor (TNF)‐α) and brain oxidative stress (TBARS and GSH) were studied in important brain areas (frontal cortex, cerebellum, hippocampus and striatum). Administration of a non‐selective serotonin receptor agonist, such as 5‐methoxytryptamine (5‐MT) to rats prenatally (gestational day 12 – day of parturition) and during early stages (postnatal day (PND) 0 –PND20) of development, resulted in impaired behaviour and brain biochemistry. Administration of papaverine (15/30 mg/kg ip) to 5‐MT administered rats from PND21 to PND48, resulted in improvement of behavioural deficits. Also, papaverine administration significantly increased the levels of BDNF, pCREB/CREB, IL‐10, GSH and significantly decreased TNF‐α, IL‐6 and TBARS levels in different brain areas. Papaverine, in both doses rectified important behavioural phenotypes related with ASD, the higher dose (30 mg/kg ip) showed significantly greater improvement than 15 mg/kg ip, possibly by improving neuronal function, brain inflammation and brain oxidative stress. Thus, PDE10A could be a probable target for pharmacological interventions and furthering our understanding of ASD pathogenesis.
Shotgun metagenomic analysis of kombucha mutualistic community exposed to Mars‐like environment outside the International Space Station
Authors: Góes‐Neto Aristóteles , Kukharenko Olga , Orlovska Iryna , Podolich Olga , Imchen Madangchanok , Kumavath Ranjith , Kato Rodrigo Bentes , de Carvalho Daniel Santana , Tiwari Sandeep , Brenig Bertram , Azevedo Vasco , Reva Oleg , de Vera Jean‐Pierre P. , Kozyrovska Natalia , Barh Debmalya 
Published: January 2021

SummaryKombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acid‐tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts' health and an efficient source of bacterial nanocellulose. In this study, we compared KMC structure and functions before and after samples were exposed to the space/Mars‐like environment outside the International Space Station in order to investigate the changes related to their re‐adaptation to Earth‐like conditions by shotgun metagenomics, using both diversity and functional analyses of Community Ecology and Complex Networks approach. Our study revealed that the long‐term exposure to space/Mars‐like conditions on low Earth orbit may disorganize the KMC to such extent that it will not restore the initial community structure; however, KMC core microorganisms of the community were maintained. Nonetheless, there were no significant differences in the community functions, meaning that the KMC communities are ecologically resilient. Therefore, despite the extremely harsh conditions, key KMC species revived and provided the community with the genetic background needed to survive long periods of time under extraterrestrial conditions.