bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of SUR1 subtype KATPchannels alters antinociception and locomotor activity after opioid administration
Authors: Sakamaki Gerald , Johnson Kayla , Mensinger Megan , Hmu Eindray , Klein Amanda H. 
Published: December 2020

AbstractBackgroundOpioid signaling can occur through several downstream mediators and influence analgesia as well as reward mechanisms in the nervous system. KATPchannels are downstream targets of the μ opioid receptor and contribute to morphine-induced antinociception.AimsThe aim of the present work was to assess the role of SUR1-subtype KATPchannels in antinocicpetion and hyperlocomotion of synthetic and semi-synthetic opioids.MethodsAdult male and female mice wild-type (WT) and SUR1 deficient (KO) mice were assessed for mechanical and thermal antinociception after administration of either buprenorphine, fentanyl, or DAMGO. Potassium flux was assessed in the dorsal root ganglia and superficial dorsal horn cells in WT and KO mice. Hyperlocomotion was also assessed in WT and KO animals after buprenorphine, fentanyl, or DAMGO administration.ResultsSUR1 KO mice had attenuated mechanical antinociception after systemic administration of buprenorphine, fentanyl, and DAMGO. Potassium flux was also attenuated in the dorsal root ganglia and spinal cord cells after acute administration of buprenorphine and fentanyl. Hyperlocomotion after administration of morphine and buprenorphine was potentiated in SUR1 KO mice, but was not seen after administration of fentanyl or DAMGO.ConclusionsThese results suggest SUR1-subtype KATPchannels mediate the antinociceptive response of several classes of opioids (alkaloid and synthetic/semi-synthetic), but may not contribute to the “drug-seeking” behaviors of all classes of opioids.
Learning differentially shapes prefrontal and hippocampal activity during classical conditioning
Authors: Klee Jan L. , Souza Bryan C. , Battaglia Francesco P. 
Published: December 2020

AbstractThe ability to use sensory cues to inform goal directed actions is a critical component of intelligent behavior. To study how sound cues are translated into anticipatory licking during classical appetitive conditioning, we employed high-density electrophysiological recordings from the hippocampal CA1 area and the prefrontal cortex (PFC). CA1 and PFC neurons undergo distinct learning dependent changes at the single cell level and maintain representations of cue identity during anticipatory behavior at the population level. In addition, reactivation of task-related neuronal assemblies during hippocampal awake Sharp-Wave Ripples (aSWR) changed within individual sessions in CA1 and over the course of multiple sessions in PFC. Despite both areas being highly engaged and synchronized during the task, we found no evidence for coordinated single cell or assembly activity during conditioning trials or aSWR.
Summary Visualisations of Gene Ontology Terms with GO-Figure!
Authors: Reijnders Maarten JMF , Waterhouse Robert M 
Published: December 2020

AbstractThe Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis of biological data from large- scale assays. Key to this success is how the GO can be used to support hypotheses or conclusions about the biology or evolution of a study system by identifying annotated functions that are overrepresented in subsets of genes of interest. Graphical visualisations of such GO term enrichment results are critical to aid interpretation and avoid biases by presenting researchers with intuitive visual data summaries. Amongst current visualisation tools and resources there is a lack of standalone open-source software solutions that facilitate systematic comparisons of multiple lists of GO terms. To address this we developed GO-Figure!, an open-source Python software for producing user-customisable semantic similarity scatterplots of redundancy-reduced GO term lists. The lists are simplified by grouping together GO terms with similar functions using their quantified information contents and semantic similarities, with user-control over grouping thresholds. Representatives are then selected for plotting in two-dimensional semantic space where similar GO terms are placed closer to each other on the scatterplot, with an array of user-customisable graphical attributes. GO-Figure! offers a simple solution for command-line plotting of informative summary visualisations of lists of GO terms, designed to support exploratory data analyses and multiple dataset comparisons.
Local and distributed cortical markers of effort expenditure during sustained goal pursuit
Authors: Patrick Lauren M. , Anderson Kevin M. , Holmes Avram J. 
Published: December 2020

AbstractThe adaptive adjustment of behavior in pursuit of desired goals is critical for survival. To accomplish this complex feat, individuals must weigh the potential benefits of a given course of action against time, energy, and resource costs. Prior research in this domain has greatly advanced understanding of the cortico-striatal circuits that support the anticipation and receipt of desired outcomes, characterizing core aspects of subjective valuation at discrete points in time. However, motivated goal pursuit is not a static or cost neutral process and the brain mechanisms that underlie individual differences in the dynamic updating of effort expenditure across time remain unclear. Here, 38 healthy right-handed participants underwent functional MRI (fMRI) while completing a novel paradigm to examine their willingness to exert physical effort over a prolonged trial, either to obtain monetary rewards or avoid punishments. During sustained goal pursuit, medial prefrontal cortex (mPFC) response scaled with trial-to-trial differences in effort expenditure as a function of both monetary condition and eventual task earnings. Multivariate pattern analysis (MVPA) searchlights were used to examine relations linking prior trial-level effort expenditure to subsequent brain responses to feedback. At reward feedback, whole-brain searchlights identified signals reflecting past effort expenditure in dorsal and ventral mPFC, encompassing broad swaths of frontoparietal and dorsal attention networks. These results suggest a core role for mPFC in scaling effort expenditure during sustained goal pursuit, with the subsequent tracking of effort costs following successful goal attainment extending to incorporate distributed brain networks that support executive functioning and externally oriented attention.Significance StatementHistorically, much of the research on subjective valuation has focused on discrete points in time. Here, we examine brain responses associated with willingness to exert physical effort during the sustained pursuit of desired goals. Our analyses reveal a distributed pattern of brain activity encompassing aspects of ventral mPFC that tracks with trial-level variability in effort expenditure. Indicating that the brain represents echoes of effort at the point of feedback, searchlight analyses revealed signals associated with past effort expenditure in broad swaths of dorsal and medial PFC. These data have important implications for the study of how the brain’s valuation mechanisms contend with the complexity of real-world dynamic environments with relevance for the study of behavior across health and disease.
Characterising pre-clinical sub-phenotypic models of Acute Respiratory Distress Syndrome: an experimental ovine study
Authors: Millar Jonathan E , Wildi Karin , Bartnikowski Nicole , Bouquet Mahe , Hyslop Kieran , Passmore Margaret R , Ki Katrina K , See Hoe Louise E , Obonyo Nchafatso G , Neyton Lucile , Pedersen Sanne , Rozencwajg Sacha , Baillie J Kenneth , Bassi Gianluigi Li , Suen Jacky Y , McAuley Daniel F , Fraser John F 
Published: December 2020

AbstractThe Acute Respiratory Distress Syndrome (ARDS) describes a heterogenous population of patients with acute severe respiratory failure. However, contemporary advances have begun to identify distinct sub-phenotypes that exist within its broader envelope. These sub-phenotypes have varied outcomes and respond differently to several previously studied interventions. A more precise understanding of their pathobiology and an ability to prospectively identify them, may allow for the development of precision therapies in ARDS. Historically, animal models have played a key role in translational research, although few studies have so far assessed either the ability of animal models to replicate these sub-phenotypes or investigated the presence of sub-phenotypes within animal models. Here, in three ovine models of ARDS, using combinations of oleic acid and intravenous, or intratracheal lipopolysaccharide, we demonstrate the presence of sub-phenotypes which qualitatively resemble those found in clinical cohorts. Principal Components Analysis and partitional clustering reveal two clusters, differentiated by markers of shock, inflammation, and lung injury. This study provides the first preliminary evidence of ARDS phenotypes in pre-clinical models and develops a methodology for investigating this phenomenon in future studies.
DNA transduction inSodalisspecies: implications for the genetic modification of uncultured endosymbionts of insects
Authors: Keller Chelsea M. , Kendra Christopher G. , Bruna Roberto E. , Craft David , Pontes Mauricio H. 
Published: December 2020

AbstractBacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation ofEscherichia coliand a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing and promoting transduction in members of the bacterial genusSodalis, including the maternally inherited insect endosymbiontSodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.SummaryA large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherit nature of these associations, insect endosymbionts cannot be usually isolated in pure culture nor genetically manipulated. Here we use a broad-host range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad host range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.
The nucleotide messenger (p)ppGpp is a co-repressor of the purine synthesis transcription regulator PurR in Firmicutes
Authors: Anderson Brent W. , Schumacher Maria A. , Yang Jin , Turdiev Asan , Turdiev Husan , He Qixiang , Lee Vincent T. , Brennan Richard G. , Wang Jue D. 
Published: December 2020

ABSTRACTThe nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Yet despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria. Here we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes from soil bacteria to pathogens: (p)ppGpp serves as a co-repressor of the transcription factor PurR to downregulate purine biosynthesis. We identified PurR as a receptor of (p)ppGpp inBacillus anthracisand revealed that (p)ppGpp strongly enhances PurR binding to its regulon in theBacillus subtilisgenome. A co-structure reveals that (p)ppGpp binds to a PurR pocket reminiscent of the active site of PRT enzymes that has been repurposed to serve a purely regulatory role, where the effectors (p)ppGpp and PRPP compete to allosterically control transcription. PRPP inhibits PurR DNA binding to induce transcription of purine synthesis genes, whereas (p)ppGpp antagonizes PRPP to enhance PurR DNA binding and repress transcription. A (p)ppGpp-refractorypurRmutant fails to downregulate purine synthesis genes upon starvation. Our work establishes precedent of (p)ppGpp as a classical transcription co-repressor and reveals the key function of (p)ppGpp in regulating nucleotide synthesis through gene regulation, from the human intestinal tract to host-pathogen interfaces.
Efficacy of Biofilm Disrupters AgainstCandida aurisand OtherCandidaspecies
Authors: Cox Claudia A , Vazquez Jose A , Wakade Sushama , Bogacz Marek , Myntti Matthew , Manavathu Elias K 
Published: December 2020

ABSTRACTBackgroundC. aurishas become a globally emerging fungal pathogen, frequently reported to be multi-drug resistant, commonly found withStaphylococcus aureusin polymicrobial nosocomial infections. Although chlorhexidine (CHD) has been shown to be effective, it is associated with serious anaphylaxis reactions. Biofilm disrupters (BDs) are novel agents with a broad spectrum of antimicrobial activity. BDs have been used in the management of chronic wounds and to sterilize environmental surfaces. The goal of this study was to evaluate BDs against polymicrobial biofilms compared to CHD.MethodologyWe evaluated various BDs (BlastX, Torrent, NSSD) and CHD againstCandida sppandS. aureuspolymicrobial biofilms by zone of inhibition, biofilm, and time-kill assays. Effectiveness was based on the inhibition zone and the reduction of CFU, respectively, compared to the drug-free control.ResultsAll BDs and CHD inhibitedC. aurisgrowth effectively in a concentration-dependent manner. Additionally, CHD and the BDs all showed excellent antimicrobial activity against polymicrobial biofilms. BDs were all highly effective against bothC. aurisisolates, whereas CHD was only moderately effective againstC. auris0386, suggesting resistance/tolerance. A comparative analysis of the BDs and CHD againstC. auris and C. albicansby biofilm kill-curves showed at least 99.999% killing.ConclusionsAll three BDs and CHD have excellent activity against differentCandidaspecies, includingC. auris. However, certain isolates ofC. aurisshowed resistance/tolerance to CHD, but not to the BDs. The fungicidal activity of these novel agents will be valuable in eradicating surface colonization ofCandida spp, includingC. auris.
Potentiating CD8+T cell antitumor activity by targeting the PCSK9/LDLR axis
Authors: Yuan Juanjuan , Cai Ting , Zheng Xiaojun , Ren Yangzi , Qi Jinwen , Lu Xiaofei , Chen Huihui , Lin Huizhen , Chen Zijie , Liu Mengnan , He Shangwen , Chen Qijun , Feng Siyang , Wu Yinjun , Zhang Zhenhai , Ding Yanqing , Yang Wei 
Published: December 2020

ABSTRACTMetabolic regulation has proven to play a critical role in T cell antitumor immunity. Cholesterol metabolism is a key component of this response but remains largely unexplored. Herein, we found that the LDL receptor (LDLR), which has been previously identified as a transporter for cholesterol and fatty acids, plays a pivotal role in regulating CD8+T cell antitumor activity, with the genetic ablation of LDLR significantly attenuating CD8+T cell activation and clonal expansion. Additionally, we found that LDLR interacts with the T-cell receptor (TCR) signalosome and regulates TCR signaling, facilitating CD8+T cell activation and effector function. Furthermore, we found that the tumor microenvironment downregulates CD8+T cell LDLR levels and TCR signaling via tumor cell-derived PCSK9, which binds and prevents the recycling of LDLR and TCR into the plasma membrane. Our findings indicate that genetic deletion or pharmacological inhibition of PCSK9 in tumor cells can enhance the antitumor activity of CD8+T cells by alleviating the tumor microenvironment’s suppressive effect on CD8+T cells and consequently inhibit tumor progression. While previously established as a hyperlipidemia target, this study highlights PCSK9 as a potential target for cancer immunotherapy as well.
Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice
Authors: Schukken Klaske M. , Zhu Yinan , Bakker Petra L. , Harkema Liesbeth , Youssef Sameh A. , de Bruin Alain , Foijer Floris 
Published: December 2020

AbstractChromosomal instability (CIN) is a hallmark of cancer, leading to aneuploid cells. To study the role that CIN plays in tumor evolution, several mouse models have been engineered over the last two decades. These studies have unequivocally shown that systemic high-grade CIN is embryonic lethal. We and others have previously shown that embryonic lethality can be circumvented by provoking CIN in a tissue-specific fashion. In this study, we provoke systemic high-grade CIN in adult mice as an alternative to circumvent embryonic lethality. For this, we disrupt the spindle assembly checkpoint (SAC) by alleviating Mad2 or truncating Mps1, both essential genes for SAC functioning, with or without p53 inactivation. We find that disruption of the SAC leads to rapid villous atrophy, atypia and apoptosis of intestinal epithelia, substantial weight loss, and death within 10 days after the start of the CIN insult. Despite this severe intestinal phenotype, most other tissues are unaffected, except for minor abnormalities in spleen, presumably due to the low proliferation rate in these tissues. We conclude that high-grade CINin vivoin adult mice is most toxic to intestinal epithelia, presumably due to the high cell turnover in this tissue.
High-fidelity, efficient, and reversible labeling of endogenous proteins using CRISPR-based designer exon insertion
Authors: Zhong Haining , Massengill Crystian I. , Muniak Michael A. , Ma Lei , Qin Maozhen , Petrie Stefanie Kaech , Mao Tianyi 
Published: December 2020

ABSTRACTPrecise and efficient insertion of large DNA fragments into somatic cells using gene editing technologies to label or modify endogenous proteins remains challenging. Non-specific insertions/deletions (INDELs) resulting from the non-homologous end joining pathway make the process error-prone. Further, the insert is not readily removable. Here, we describe a method calledCRISPR-mediated insertion ofexon (CRISPIE) that can precisely and reversibly label endogenous proteins using CRISPR/Cas9-based editing. CRISPIE inserts a designer donor module, which consists of an exon encoding the protein sequence flanked by intron sequences, into an intronic location in the target gene. INDELs at the insertion junction will be spliced out, leaving mRNAs nearly error-free. We used CRISPIE to fluorescently label endogenous proteins in neuronsin vivowith previously unachieved efficiency. We demonstrate that this method is broadly applicable, and that the insert can be readily removed later. CRISPIE permits protein sequence insertion with high fidelity, efficiency, and flexibility.
Transformation of European ash (Fraxinus excelsiorL.) callus as a starting point for understanding the molecular basis of ash dieback
Authors: Hebda Anna , Liszka Aleksandra , Zgłobicki Piotr , Nawrot-Chorabik Katarzyna , Lyczakowski Jan J. 
Published: December 2020

AbstractPlant genetic engineering requires transfer of genetic material into plant cells, a process that is frequently challenging for tree species. Here we report first successful genetic transformation of European ash (Fraxinus excelsior). The protocol relies on the use ofAgrobacterium tumefaciensto transform callus tissue derived from embryos ofF. excelsior. In our experiments, we use the β-glucuronidase (GUS) reporter system to demonstrate transformation of ash callus tissue. Moreover, we describe an antibiotic-resistance based selection process enabling formation of stable transgenic callus lines. Since ash dieback threatens the long-term stability of many nativeF. excelsiorpopulations, we hope that the transformation techniques described in this manuscript will facilitate rapid progress in uncovering the molecular basis of the disease and mechanisms used by trees to resist it.
Identification of low micromolar SARS-CoV-2 Mproinhibitors from hits identified byin silicoscreens
Authors: Rossetti Giacomo G. , Ossorio Marianna , Barriot Samia , Tropia Laurence , Dionellis Vasilis S. , Gorgulla Christoph , Arthanari Haribabu , Mohr Peter , Gamboni Remo , Halazonetis Thanos D. 
Published: December 2020

ABSTRACTMpro, also known as 3CLpro, is the main protease of the SARS-CoV-2 coronavirus and, as such, is essential for the viral life cycle. Two studies have each screened and rankedin silicomore than one billion chemical compounds in an effort to identify putative inhibitors of Mpro. More than five hundred of the seven thousand top-ranking hits were synthesized by an external supplier and examined with respect to their activity in two biochemical assays: a protease activity assay and a thermal shift assay. Two clusters of chemical compounds with Mproinhibitory activity were identified. An additional five hundred molecules, analogues of the compounds in the two clusters described above, were also synthesized and characterizedin vitro. The study of the analogues revealed that the compounds of the first cluster acted by denaturing Mproand might denature other proteins as well. In contrast, the compounds of the second cluster targeted Mprowith much greater specificity and enhanced its melting temperature, consistent with the formation of stable Mpro-inhibitor complexes. The most active compounds of the second cluster exhibited IC50values between 4 and 7 μM and their chemical structure suggests that they could serve as leads for the development of potent Mproinhibitors.
Molecular basis of the logical evolution of the novel coronavirus SARS-CoV-2: A comparative analysis
Authors: Dwivedy Abhisek , Murmu Krushna Chandra , Ahmad Mohammed , Prasad Punit , Biswal Bichitra Kumar , Aich Palok 
Published: December 2020

AbstractA novel disease, COVID-19, is sweeping the world since end of 2019. While in many countries, the first wave is over, but the pandemic is going through its next phase with a significantly higher infectability. COVID-19 is caused by the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that seems to be more infectious than any other previous human coronaviruses. To understand any unique traits of the virus that facilitate its entry into the host, we compared the published structures of the viral spike protein of SARS-CoV-2 with other known coronaviruses to determine the possible evolutionary pathway leading to the higher infectivity. The current report presents unique information regarding the amino acid residues that were a) conserved to maintain the binding with ACE2 (Angiotensin-converting enzyme 2), and b) substituted to confer an enhanced binding affinity and conformational flexibility to the SARS-CoV-2 spike protein. The present study provides novel insights into the evolutionary nature and molecular basis of higher infectability and perhaps the virulence of SARS-CoV-2.